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moreo:bayes
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moreo:lequa2024
moreo:kdey2
moreo:retrieval
moreo:census
moreo:accuracy
moreo:benchmark
moreo:ordinal
moreo:kdey
moreo:kdeypriv
moreo:lab
moreo:transduction
moreo:ediscovery
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moreo:crosslingual
moreo:ipacc
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moreo:0.2.1
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moreo:devel
moreo:master
moreo:bayes
moreo:ieee
moreo:lequa2024
moreo:kdey2
moreo:retrieval
moreo:census
moreo:accuracy
moreo:benchmark
moreo:ordinal
moreo:kdey
moreo:kdeypriv
moreo:lab
moreo:transduction
moreo:ediscovery
moreo:classweight
moreo:lequa2022
moreo:tweetsent
moreo:crosslingual
moreo:ipacc
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108
.github/workflows/ci.yml vendored
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@ -1,108 +0,0 @@
name: CI
on:
pull_request:
push:
branches:
- master
- devel
tags:
- "[0-9]+.[0-9]+.[0-9]+"
jobs:
# take out unit tests
test:
name: Unit tests (Python ${{ matrix.python-version }})
runs-on: ubuntu-latest
strategy:
matrix:
python-version:
- "3.11"
env:
QUAPY_TESTS_OMIT_LARGE_DATASETS: True
steps:
- uses: actions/checkout@v4
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Install dependencies
run: |
python -m pip install --upgrade pip setuptools wheel
python -m pip install "qunfold @ git+https://github.com/mirkobunse/qunfold@main"
python -m pip install -e .[bayes,tests]
- name: Test with unittest
run: python -m unittest
# build and push documentation to gh-pages (only if pushed to the master branch)
docs:
name: Documentation
runs-on: ubuntu-latest
if: github.ref == 'refs/heads/master'
steps:
- uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: 3.11
- name: Install dependencies
run: |
python -m pip install --upgrade pip setuptools wheel "jax[cpu]"
python -m pip install "qunfold @ git+https://github.com/mirkobunse/qunfold@main"
python -m pip install -e .[neural,docs]
- name: Build documentation
run: sphinx-build -M html docs/source docs/build
- name: Publish documentation
run: |
git clone ${{ github.server_url }}/${{ github.repository }}.git --branch gh-pages --single-branch __gh-pages/
cp -r docs/build/html/* __gh-pages/
cd __gh-pages/
git config --local user.email "action@github.com"
git config --local user.name "GitHub Action"
git add .
git commit -am "Documentation based on ${{ github.sha }}" || true
- name: Push changes
uses: ad-m/github-push-action@master
with:
branch: gh-pages
directory: __gh-pages/
github_token: ${{ secrets.GITHUB_TOKEN }}
release:
name: Build & Publish Release
runs-on: ubuntu-latest
if: startsWith(github.ref, 'refs/tags/')
steps:
- uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: "3.11"
- name: Install build dependencies
run: |
python -m pip install --upgrade pip build twine
- name: Build package
run: python -m build
- name: Publish to TestPyPI
uses: pypa/gh-action-pypi-publish@release/v1
with:
user: __token__
# use these for TESTs!
# password: ${{ secrets.TEST_PYPI_API_TOKEN }}
# repository_url: https://test.pypi.org/legacy/
password: ${{ secrets.PYPI_API_TOKEN }}
repository_url: https://upload.pypi.org/legacy/
- name: Create GitHub Release
id: create_release
uses: actions/create-release@v1
with:
tag_name: ${{ github.ref_name }}
release_name: Release ${{ github.ref_name }}
body: |
Changes in this release:
- see commit history for details
draft: false
prerelease: false
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

41
.gitignore vendored
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@ -69,12 +69,8 @@ instance/
# Scrapy stuff:
.scrapy
# vscode config:
.vscode/
# Sphinx documentation
docs/_build/doctest
docs/_build/doctrees
docs/_build/
# PyBuilder
target/
@ -89,11 +85,6 @@ ipython_config.py
# pyenv
.python-version
# poetry
poetry.toml
pyproject.toml
poetry.lock
# pipenv
# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
# However, in case of collaboration, if having platform-specific dependencies or dependencies
@ -139,33 +130,3 @@ dmypy.json
.pyre/
*__pycache__*
*.pdf
*.zip
*.png
*.csv
*.pkl
*.dataframe
# other projects
LeQua2022
MultiLabel
NewMethods
Ordinal
Retrieval
eDiscovery
poster-cikm
slides-cikm
slides-short-cikm
quick_experiment
svm_perf_quantification/svm_struct
svm_perf_quantification/svm_light
TweetSentQuant
*.png
.idea

249
CHANGE_LOG.txt
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@ -1,249 +0,0 @@
Change Log 0.2.1
-----------------
- Improved documentation of confidence regions. Added QuaPy logo :')
- Added Bayesian KDEy and Bayesian MAPLS quantifiers.
- Added temperature calibration utilities for Bayesian confidence-aware methods.
- Added compositional CLR and ILR transformations.
- Extended KDEy with Aitchison/ILR kernels, shrinkage, and improved numerical stability.
- Added image-embedding-based datasets including CIFAR10, CIFAR100, CIFAR100coarse, VSHN, FashionMNIST, MNIST.
- Added TemperatureScalingFromLogits for calibrating pretrained logits.
- Added DirichletProtocol for prevalence sampling from Dirichlet priors.
- Added ReadMe method by Daniel Hopkins and Gary King.
- Internal index in LabelledCollection is now "lazy", and is only constructed if required.
- Improved unit testing and separated integration tests.
- Added RLLS (Regularized Learning for Domain Adaptation under Label Shifts) method.
- Added visualization tools for 3-class problems in the simplex, see also the new example no.19
- Deep code revision and improved codebase
- Added EDx/EDy from quantificationlib (thanks to Pablo and Juanjo!)
Change Log 0.2.0
-----------------
- Base code Refactor:
- Removing coupling between LabelledCollection and quantification methods; the fit interface changes:
def fit(data:LabelledCollection): -> def fit(X, y):
- Adding function "predict" (function "quantify" is still present as an alias, for the nostalgic)
- Aggregative methods's behavior in terms of fit_classifier and how to treat the val_split is now
indicated exclusively at construction time, and it is no longer possible to indicate it at fit time.
This is because, in v<=0.1.9, one could create a method (e.g., ACC) and then indicate:
my_acc.fit(tr_data, fit_classifier=False, val_split=val_data)
in which case the first argument is unused, and this was ambiguous with
my_acc.fit(the_data, fit_classifier=False)
in which case the_data is to be used for validation purposes. However, the val_split could be set as a fraction
indicating only part of the_data must be used for validation, and the rest wasted... it was certainly confusing.
- This change imposes a versioning constrain with qunfold, which now must be >= 0.1.6
- EMQ has been modified, so that the representation function "classify" now only provides posterior
probabilities and, if required, these are recalibrated (e.g., by "bcts") during the aggregation function.
- A new parameter "on_calib_error" is passed to the constructor, which informs of the policy to follow
in case the abstention's calibration functions failed (which happens sometimes). Options include:
- 'raise': raises a RuntimeException (default)
- 'backup': reruns by silently avoiding calibration
- Parameter "recalib" has been renamed "calib"
- Added aggregative bootstrap for deriving confidence regions (confidence intervals, ellipses in the simplex, or
ellipses in the CLR space). This method is efficient as it leverages the two-phases of the aggregative quantifiers.
This method applies resampling only to the aggregation phase, thus avoiding to train many quantifiers, or
classify multiple times the instances of a sample. See:
- quapy/method/confidence.py (new)
- the new example no. 16.confidence_regions.py
- BayesianCC moved to confidence.py, where methods having to do with confidence intervals belong.
- Improved documentation of qp.plot module.
Change Log 0.1.9
----------------
- Added LeQua 2024 datasets and normalized match distance to qp.error
- Improved data loaders for UCI binary and UCI multiclass datasets (thanks to Lorenzo Volpi!); these datasets
can be loaded with standardised covariates (default)
- Added a default classifier for aggregative quantifiers, which now can be instantiated without specifying
the classifier. The default classifier can be accessed in qp.environ['DEFAULT_CLS'] and is assigned to
sklearn.linear_model.LogisticRegression(max_iter=3000). If the classifier is not specified, then a clone
of said classifier is returned. E.g.:
> pacc = PACC()
is equivalent to:
> pacc = PACC(classifier=LogisticRegression(max_iter=3000))
- Improved error loging in model selection. In v0.1.8 only Status.INVALID was reported; in v0.1.9 it is
now accompanied by a textual description of the error
- The number of parallel workers can now be set via an environment variable by running, e.g.:
> N_JOBS=10 python3 your_script.py
which has the same effect as writing the following code at the beginning of your_script.py:
> import quapy as qp
> qp.environ["N_JOBS"] = 10
- Some examples have been added to the ./examples/ dir, which now contains numbered examples from basics (0)
to advanced topics (higher numbers)
- Moved the wiki documents to the ./docs/ folder so that they become editable via PR for the community
- Added Composable methods from Mirko Bunse's qunfold library! (thanks to Mirko Bunse!)
- Added Continuous Integration with GitHub Actions (thanks to Mirko Bunse!)
- Added Bayesian CC method (thanks to Pawel Czyz!). The method is described in detail in the paper
Ziegler, Albert, and Paweł Czyż. "Bayesian Quantification with Black-Box Estimators."
arXiv preprint arXiv:2302.09159 (2023).
- Removed binary UCI datasets {acute.a, acute.b, balance.2} from the list qp.data.datasets.UCI_BINARY_DATASETS
(the datasets are still loadable from the fetch_UCIBinaryLabelledCollection and fetch_UCIBinaryDataset
functions, though). The reason is that these datasets tend to yield results (for all methods) that are
one or two orders of magnitude greater than for other datasets, and this has a disproportionate impact in
methods average (I suspect there is something wrong in those datasets).
Change Log 0.1.8
----------------
- Added Kernel Density Estimation methods (KDEyML, KDEyCS, KDEyHD) as proposed in the paper:
Moreo, A., González, P., & del Coz, J. J. Kernel Density Estimation for Multiclass Quantification.
arXiv preprint arXiv:2401.00490, 2024
- Substantial internal refactor: aggregative methods now inherit a pattern by which the fit method consists of:
a) fitting the classifier and returning the representations of the training instances (typically the posterior
probabilities, the label predictions, or the classifier scores, and typically obtained through kFCV).
b) fitting an aggregation function
The function implemented in step a) is inherited from the super class. Each new aggregative method now has to
implement only the "aggregative_fit" of step b).
This pattern was already implemented for the prediction (thus allowing evaluation functions to be performed
very quicky), and is now available also for training. The main benefit is that model selection now can nestle
the training of quantifiers in two levels: one for the classifier, and another for the aggregation function.
As a result, a method with a param grid of 10 combinations for the classifier and 10 combinations for the
quantifier, now implies 10 trainings of the classifier + 10*10 trainings of the aggregation function (this is
typically much faster than the classifier training), whereas in versions <0.1.8 this amounted to training
10*10 (classifiers+aggregations).
- Added different solvers for ACC and PACC quantifiers. In quapy < 0.1.8 these quantifiers try to solve the system
of equations Ax=B exactly (by means of np.linalg.solve). As noted by Mirko Bunse (thanks!), such an exact solution
does sometimes not exist. In cases like this, quapy < 0.1.8 resorted to CC for providing a plausible solution.
ACC and PACC now resorts to an approximated solution in such cases (minimizing the L2-norm of the difference
between Ax-B) as proposed by Mirko Bunse. A quick experiment reveals this heuristic greatly improves the results
of ACC and PACC in T2A@LeQua.
- Fixed ThresholdOptimization methods (X, T50, MAX, MS and MS2). Thanks to Tobias Schumacher and colleagues for pointing
this out in Appendix A of "Schumacher, T., Strohmaier, M., & Lemmerich, F. (2021). A comparative evaluation of
quantification methods. arXiv:2103.03223v3 [cs.LG]"
- Added HDx and DistributionMatchingX to non-aggregative quantifiers (see also the new example "comparing_HDy_HDx.py")
- New UCI multiclass datasets added (thanks to Pablo González). The 5 UCI multiclass datasets are those corresponding
to the following criteria:
- >1000 instances
- >2 classes
- classification datasets
- Python API available
- New IFCB (plankton) dataset added (thanks to Pablo González). See qp.datasets.fetch_IFCB.
- Added new evaluation measures NAE, NRAE (thanks to Andrea Esuli)
- Added new meta method "MedianEstimator"; an ensemble of binary base quantifiers that receives as input a dictionary
of hyperparameters that will explore exhaustively, fitting and generating predictions for each combination of
hyperparameters, and that returns, as the prevalence estimates, the median across all predictions.
- Added "custom_protocol.py" example.
- New API documentation template.
Change Log 0.1.7
----------------
- Protocols are now abstracted as instances of AbstractProtocol. There is a new class extending AbstractProtocol called
AbstractStochasticSeededProtocol, which implements a seeding policy to allow replicate the series of samplings.
There are some examples of protocols, APP, NPP, UPP, DomainMixer (experimental).
The idea is to start the sample generation by simply calling the __call__ method.
This change has a great impact in the framework, since many functions in qp.evaluation, qp.model_selection,
and sampling functions in LabelledCollection relied of the old functions. E.g., the functionality of
qp.evaluation.artificial_prevalence_report or qp.evaluation.natural_prevalence_report is now obtained by means of
qp.evaluation.report which takes a protocol as an argument. I have not maintained compatibility with the old
interfaces because I did not really like them. Check the wiki guide and the examples for more details.
- Exploration of hyperparameters in Model selection can now be run in parallel (there was a n_jobs argument in
QuaPy 0.1.6 but only the evaluation part for one specific hyperparameter was run in parallel).
- The prediction function has been refactored, so it applies the optimization for aggregative quantifiers (that
consists in pre-classifying all instances, and then only invoking aggregate on the samples) only in cases in
which the total number of classifications would be smaller than the number of classifications with the standard
procedure. The user can now specify "force", "auto", True of False, in order to actively decide for applying it
or not.
- examples directory created!
- DyS, Topsoe distance and binary search (thanks to Pablo González)
- Multi-thread reproducibility via seeding (thanks to Pablo González)
- n_jobs is now taken from the environment if set to None
- ACC, PACC, Forman's threshold variants have been parallelized.
- cross_val_predict (for quantification) added to model_selection: would be nice to allow the user specifies a
test protocol maybe, or None for bypassing it?
- Bugfix: adding two labelled collections (with +) now checks for consistency in the classes
- newer versions of numpy raise a warning when accessing types (e.g., np.float). I have replaced all such instances
with the plain python type (e.g., float).
- new dependency "abstention" (to add to the project requirements and setup). Calibration methods from
https://github.com/kundajelab/abstention added.
- the internal classifier of aggregative methods is now called "classifier" instead of "learner"
- when optimizing the hyperparameters of an aggregative quantifier, the classifier's specific hyperparameters
should be marked with a "classifier__" prefix (just like in scikit-learn with estimators), while the quantifier's
specific hyperparameters are named directly. For example, PCC(LogisticRegression()) quantifier has hyperparameters
"classifier__C", "classifier__class_weight", etc., instead of "C" and "class_weight" as in v0.1.6.
- hyperparameters yielding to inconsistent runs raise a ValueError exception, while hyperparameter combinations
yielding to internal errors of surrogate functions are reported and skipped, without stopping the grid search.
- DistributionMatching methods added. This is a general framework for distribution matching methods that caters for
multiclass quantification. That is to say, one could get a multiclass variant of the (originally binary) HDy
method aligned with the Firat's formulation.
- internal method properties "binary", "aggregative", and "probabilistic" have been removed; these conditions are
checked via isinstance
- quantifiers (i.e., classes that inherit from BaseQuantifier) are not forced to implement classes_ or n_classes;
these can be used anyway internally, but the framework will not suppose (nor impose) that a quantifier implements
them
- qp.evaluation.prediction has been optimized so that, if a quantifier is of type aggregative, and if the evaluation
protocol is of type OnLabelledCollection, then the computation is faster. In this specific case, the predictions
are issued only once and for all, and not for each sample. An exception to this (which is implement also), is
when the number of instances across all samples is anyway smaller than the number of instances in the original
labelled collection; in this case the heuristic is of no help, and is therefore not applied.
- the distinction between "classify" and "posterior_probabilities" has been removed in Aggregative quantifiers,
so that probabilistic classifiers return posterior probabilities, while non-probabilistic quantifiers
return crisp decisions.
- OneVsAll fixed. There are now two classes: a generic one OneVsAllGeneric that works with any quantifier (e.g.,
any instance of BaseQuantifier), and a subclass of it called OneVsAllAggregative which implements the
classify / aggregate interface. Both are instances of OneVsAll. There is a method getOneVsAll that returns the
best instance based on the type of quantifier.

35
NewMethods/evaluate_results.py Normal file
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import numpy as np
import quapy as qp
import settings
import os
import pickle
from glob import glob
import itertools
import pathlib
qp.environ['SAMPLE_SIZE'] = settings.SAMPLE_SIZE
resultdir = './results'
methods = ['*']
def evaluate_results(methods, datasets, error_name):
results_str = []
all = []
error = qp.error.from_name(error_name)
for method, dataset in itertools.product(methods, datasets):
for experiment in glob(f'{resultdir}/{dataset}-{method}-{error_name}.pkl'):
true_prevalences, estim_prevalences, tr_prev, te_prev, te_prev_estim, best_params = \
pickle.load(open(experiment, 'rb'))
result = error(true_prevalences, estim_prevalences)
string = f'{pathlib.Path(experiment).name}: {result:.3f}'
results_str.append(string)
all.append(result)
results_str = sorted(results_str)
for r in results_str:
print(r)
print()
print(f'Ave: {np.mean(all):.3f}')
evaluate_results(methods=['epacc*mae1k'], datasets=['*'], error_name='mae')

220
NewMethods/experiments.py Normal file
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from sklearn.linear_model import LogisticRegression
import quapy as qp
from classification.methods import PCALR
from method.meta import QuaNet
from method.non_aggregative import MaximumLikelihoodPrevalenceEstimation
from methods import *
from quapy.method.aggregative import CC, ACC, PCC, PACC, EMQ, OneVsAll, SVMQ, SVMKLD, SVMNKLD, SVMAE, SVMRAE, HDy
from quapy.method.meta import EPACC, EEMQ
import quapy.functional as F
import numpy as np
import os
import pickle
import itertools
from joblib import Parallel, delayed
import settings
import argparse
import torch
import shutil
qp.environ['SAMPLE_SIZE'] = settings.SAMPLE_SIZE
def newLR():
return LogisticRegression(max_iter=1000, solver='lbfgs', n_jobs=-1)
__C_range = np.logspace(-4, 5, 10)
lr_params = {'C': __C_range, 'class_weight': [None, 'balanced']}
svmperf_params = {'C': __C_range}
def experimental_models():
def newLR():
return LogisticRegression(max_iter=1000, solver='lbfgs', n_jobs=-1)
__C_range = np.logspace(-4, 5, 10)
lr_params = {'C': __C_range, 'class_weight': [None, 'balanced']}
svmperf_params = {'C': __C_range}
#yield 'paccsld', PACCSLD(newLR()), lr_params
# yield 'hdysld', OneVsAll(HDySLD(newLR())), lr_params # <-- promising!
yield 'PACC(5)', PACC(newLR(), val_split=5), {}
yield 'PACC(10)', PACC(newLR(), val_split=10), {}
def classic_models():
# methods tested in Gao & Sebastiani 2016
yield 'cc', CC(newLR()), lr_params
yield 'acc', ACC(newLR()), lr_params
yield 'pcc', PCC(newLR()), lr_params
yield 'pacc', PACC(newLR()), lr_params
yield 'sld', EMQ(newLR()), lr_params
yield 'svmq', OneVsAll(SVMQ(args.svmperfpath)), svmperf_params
yield 'svmkld', OneVsAll(SVMKLD(args.svmperfpath)), svmperf_params
yield 'svmnkld', OneVsAll(SVMNKLD(args.svmperfpath)), svmperf_params
# methods added
yield 'svmmae', OneVsAll(SVMAE(args.svmperfpath)), svmperf_params
yield 'svmmrae', OneVsAll(SVMRAE(args.svmperfpath)), svmperf_params
yield 'hdy', OneVsAll(HDy(newLR())), lr_params
def cuda_models():
device = 'cuda' if torch.cuda.is_available() else 'cpu'
print(f'Running QuaNet in {device}')
learner = PCALR(**newLR().get_params())
yield 'quanet', QuaNet(learner, settings.SAMPLE_SIZE, checkpointdir=args.checkpointdir, device=device), lr_params
def ensembles():
param_mod_sel = {
'sample_size': settings.SAMPLE_SIZE,
'n_prevpoints': 21,
'n_repetitions': 5,
'verbose': False
}
common={
'max_sample_size': 1000,
'n_jobs': settings.ENSEMBLE_N_JOBS,
'param_grid': lr_params,
'param_mod_sel': param_mod_sel,
'val_split': 0.4,
'min_pos': 10
}
# hyperparameters will be evaluated within each quantifier of the ensemble, and so the typical model selection
# will be skipped (by setting hyperparameters to None)
hyper_none = None
#yield 'epaccmaeptr', EPACC(newLR(), optim='mae', policy='ptr', **common), hyper_none
yield 'epaccmaemae1k', EPACC(newLR(), optim='mae', policy='mae', **common), hyper_none
# yield 'esldmaeptr', EEMQ(newLR(), optim='mae', policy='ptr', **common), hyper_none
# yield 'esldmaemae', EEMQ(newLR(), optim='mae', policy='mae', **common), hyper_none
#yield 'epaccmraeptr', EPACC(newLR(), optim='mrae', policy='ptr', **common), hyper_none
#yield 'epaccmraemrae', EPACC(newLR(), optim='mrae', policy='mrae', **common), hyper_none
#yield 'esldmraeptr', EEMQ(newLR(), optim='mrae', policy='ptr', **common), hyper_none
#yield 'esldmraemrae', EEMQ(newLR(), optim='mrae', policy='mrae', **common), hyper_none
def evaluate_experiment(true_prevalences, estim_prevalences):
print('\nEvaluation Metrics:\n'+'='*22)
for eval_measure in [qp.error.mae, qp.error.mrae]:
err = eval_measure(true_prevalences, estim_prevalences)
print(f'\t{eval_measure.__name__}={err:.4f}')
print()
def evaluate_method_point_test(true_prev, estim_prev):
print('\nPoint-Test evaluation:\n' + '=' * 22)
print(f'true-prev={F.strprev(true_prev)}, estim-prev={F.strprev(estim_prev)}')
for eval_measure in [qp.error.mae, qp.error.mrae]:
err = eval_measure(true_prev, estim_prev)
print(f'\t{eval_measure.__name__}={err:.4f}')
def result_path(path, dataset_name, model_name, optim_loss):
return os.path.join(path, f'{dataset_name}-{model_name}-{optim_loss}.pkl')
def is_already_computed(dataset_name, model_name, optim_loss):
if dataset_name=='semeval':
check_datasets = ['semeval13', 'semeval14', 'semeval15']
else:
check_datasets = [dataset_name]
return all(os.path.exists(result_path(args.results, name, model_name, optim_loss)) for name in check_datasets)
def save_results(dataset_name, model_name, optim_loss, *results):
rpath = result_path(args.results, dataset_name, model_name, optim_loss)
qp.util.create_parent_dir(rpath)
with open(rpath, 'wb') as foo:
pickle.dump(tuple(results), foo, pickle.HIGHEST_PROTOCOL)
def run(experiment):
optim_loss, dataset_name, (model_name, model, hyperparams) = experiment
if is_already_computed(dataset_name, model_name, optim_loss=optim_loss):
print(f'result for dataset={dataset_name} model={model_name} loss={optim_loss} already computed.')
return
elif (optim_loss == 'mae' and 'mrae' in model_name) or (optim_loss=='mrae' and 'mae' in model_name):
print(f'skipping model={model_name} for optim_loss={optim_loss}')
return
else:
print(f'running dataset={dataset_name} model={model_name} loss={optim_loss}')
benchmark_devel = qp.datasets.fetch_twitter(dataset_name, for_model_selection=True, min_df=5, pickle=True)
benchmark_devel.stats()
# model selection (hyperparameter optimization for a quantification-oriented loss)
if hyperparams is not None:
model_selection = qp.model_selection.GridSearchQ(
model,
param_grid=hyperparams,
sample_size=settings.SAMPLE_SIZE,
n_prevpoints=21,
n_repetitions=5,
error=optim_loss,
refit=False,
timeout=60*60,
verbose=True
)
model_selection.fit(benchmark_devel.training, benchmark_devel.test)
model = model_selection.best_model()
best_params = model_selection.best_params_
else:
best_params = {}
# model evaluation
test_names = [dataset_name] if dataset_name != 'semeval' else ['semeval13', 'semeval14', 'semeval15']
for test_no, test_name in enumerate(test_names):
benchmark_eval = qp.datasets.fetch_twitter(test_name, for_model_selection=False, min_df=5, pickle=True)
if test_no == 0:
print('fitting the selected model')
# fits the model only the first time
model.fit(benchmark_eval.training)
true_prevalences, estim_prevalences = qp.evaluation.artificial_sampling_prediction(
model,
test=benchmark_eval.test,
sample_size=settings.SAMPLE_SIZE,
n_prevpoints=21,
n_repetitions=25,
n_jobs=-1 if isinstance(model, qp.method.meta.Ensemble) else 1
)
test_estim_prevalence = model.quantify(benchmark_eval.test.instances)
test_true_prevalence = benchmark_eval.test.prevalence()
evaluate_experiment(true_prevalences, estim_prevalences)
evaluate_method_point_test(test_true_prevalence, test_estim_prevalence)
save_results(test_name, model_name, optim_loss,
true_prevalences, estim_prevalences,
benchmark_eval.training.prevalence(), test_true_prevalence, test_estim_prevalence,
best_params)
#if isinstance(model, QuaNet):
#model.clean_checkpoint_dir()
if __name__ == '__main__':
parser = argparse.ArgumentParser(description='Run experiments for Tweeter Sentiment Quantification')
parser.add_argument('results', metavar='RESULT_PATH', type=str,
help='path to the directory where to store the results')
parser.add_argument('--svmperfpath', metavar='SVMPERF_PATH', type=str, default='./svm_perf_quantification',
help='path to the directory with svmperf')
parser.add_argument('--checkpointdir', metavar='PATH', type=str, default='./checkpoint',
help='path to the directory where to dump QuaNet checkpoints')
args = parser.parse_args()
print(f'Result folder: {args.results}')
np.random.seed(0)
optim_losses = ['mae', 'mrae']
datasets = qp.datasets.TWITTER_SENTIMENT_DATASETS_TRAIN
qp.util.parallel(run, itertools.product(optim_losses, datasets, experimental_models()), n_jobs=settings.N_JOBS)
# qp.util.parallel(run, itertools.product(optim_losses, datasets, classic_models()), n_jobs=settings.N_JOBS)
# qp.util.parallel(run, itertools.product(optim_losses, datasets, cuda_models()), n_jobs=settings.CUDA_N_JOBS)
# qp.util.parallel(run, itertools.product(optim_losses, datasets, ensembles()), n_jobs=1)

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NewMethods/fgsld/__init__.py Normal file
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import numpy as np
import logging
from collections import namedtuple
from sklearn.metrics import brier_score_loss
from sklearn.preprocessing import MultiLabelBinarizer
from metrics import smoothmacroF1, isometric_brier_decomposition, isomerous_brier_decomposition
History = namedtuple('History', ('posteriors', 'priors', 'y', 'iteration', 'stopping_criterium'))
MeasureSingleHistory = namedtuple('MeasureSingleHistory', (
'soft_acc', 'soft_f1', 'abs_errors', 'test_priors', 'train_priors', 'predict_priors', 'brier',
'isometric_ref_loss', 'isometric_cal_loss', 'isomerous_ref_loss', 'isomerous_cal_loss'
))
def get_measures_single_history(history: History, multi_class) -> MeasureSingleHistory:
y = history.y
y_bin = MultiLabelBinarizer(classes=list(range(history.posteriors.shape[1]))).fit_transform(np.expand_dims(y, 1))
soft_acc = soft_accuracy(y, history.posteriors)
f1 = smoothmacroF1(y_bin, history.posteriors)
if multi_class:
test_priors = np.mean(y_bin, 0)
abs_errors = abs(test_priors - history.priors)
train_priors = history.priors
predict_priors = np.mean(history.posteriors, 0)
brier = 0
else:
test_priors = np.mean(y_bin, 0)[1]
abs_errors = abs(test_priors - history.priors[1])
train_priors = history.priors[1]
predict_priors = np.mean(history.posteriors[:, 1])
brier = brier_score_loss(y, history.posteriors[:, 1])
isometric_cal_loss, isometric_ref_loss = isometric_brier_decomposition(y, history.posteriors)
isomerous_em_cal_loss, isomerous_em_ref_loss = isomerous_brier_decomposition(y, history.posteriors)
return MeasureSingleHistory(
soft_acc, f1, abs_errors, test_priors, train_priors, predict_priors, brier, isometric_ref_loss,
isometric_cal_loss, isomerous_em_ref_loss, isomerous_em_cal_loss
)
def soft_accuracy(y, posteriors):
return sum(posteriors[y == c][:, c].sum() for c in range(posteriors.shape[1])) / posteriors.sum()
def soft_f1(y, posteriors):
cont_matrix = {
'TPM': posteriors[y == 1][:, 1].sum(),
'TNM': posteriors[y == 0][:, 0].sum(),
'FPM': posteriors[y == 0][:, 1].sum(),
'FNM': posteriors[y == 1][:, 0].sum()
}
precision = cont_matrix['TPM'] / (cont_matrix['TPM'] + cont_matrix['FPM'])
recall = cont_matrix['TPM'] / (cont_matrix['TPM'] + cont_matrix['FNM'])
return 2 * (precision * recall / (precision + recall))
def em(y, posteriors_zero, priors_zero, epsilon=1e-6, multi_class=False, return_posteriors_hist=False):
"""
Implements the prior correction method based on EM presented in:
"Adjusting the Outputs of a Classifier to New a Priori Probabilities: A Simple Procedure"
Saerens, Latinne and Decaestecker, 2002
http://www.isys.ucl.ac.be/staff/marco/Publications/Saerens2002a.pdf
:param y: true labels of test items, to measure accuracy, precision and recall.
:param posteriors_zero: posterior probabilities on test items, as returned by a classifier. A 2D-array with shape
Ø(items, classes).
:param priors_zero: prior probabilities measured on training set.
:param epsilon: stopping threshold.
:param multi_class: whether the algorithm is running in a multi-label multi-class context or not.
:param return_posteriors_hist: whether posteriors for each iteration should be returned or not. If true, the returned
posteriors_s will actually be the list of posteriors for every iteration.
:return: posteriors_s, priors_s, history: final adjusted posteriors, final adjusted priors, a list of length s
where each element is a tuple with the step counter, the current priors (as list), the stopping criterium value,
accuracy, precision and recall.
"""
s = 0
priors_s = np.copy(priors_zero)
posteriors_s = np.copy(posteriors_zero)
if return_posteriors_hist:
posteriors_hist = [posteriors_s.copy()]
val = 2 * epsilon
history = list()
history.append(get_measures_single_history(History(posteriors_zero, priors_zero, y, s, 1), multi_class))
while not val < epsilon and s < 999:
# M step
priors_s_minus_one = priors_s.copy()
priors_s = posteriors_s.mean(0)
# E step
ratios = priors_s / priors_zero
denominators = 0
for c in range(priors_zero.shape[0]):
denominators += ratios[c] * posteriors_zero[:, c]
for c in range(priors_zero.shape[0]):
posteriors_s[:, c] = ratios[c] * posteriors_zero[:, c] / denominators
# check for stop
val = 0
for i in range(len(priors_s_minus_one)):
val += abs(priors_s_minus_one[i] - priors_s[i])
logging.debug(f"Em iteration: {s}; Val: {val}")
s += 1
if return_posteriors_hist:
posteriors_hist.append(posteriors_s.copy())
history.append(get_measures_single_history(History(posteriors_s, priors_s, y, s, val), multi_class))
if return_posteriors_hist:
return posteriors_hist, priors_s, history
return posteriors_s, priors_s, history

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from sklearn.calibration import CalibratedClassifierCV
from sklearn.svm import LinearSVC
from fgsld.fgsld_quantifiers import FakeFGLSD
from method.aggregative import EMQ, CC
import quapy as qp
qp.environ['SAMPLE_SIZE'] = 500
dataset = qp.datasets.fetch_reviews('kindle')
qp.data.preprocessing.text2tfidf(dataset, min_df=5, inplace=True)
training = dataset.training
test = dataset.test
cls = CalibratedClassifierCV(LinearSVC())
method_names, true_prevs, estim_prevs, tr_prevs = [], [], [], []
for model, model_name in [
(CC(cls), 'CC'),
# (FakeFGLSD(cls, nbins=5, isomerous=False, recompute_bins=False), 'FGSLD-isometric-stat-5'),
(FakeFGLSD(cls, nbins=5, isomerous=True, recompute_bins=True), 'FGSLD-isometric-dyn-5'),
# (FakeFGLSD(cls, nbins=5, isomerous=True, recompute_bins=False), 'FGSLD-isomerous-stat-5'),
# (FakeFGLSD(cls, nbins=10, isomerous=True, recompute_bins=True), 'FGSLD-isomerous-dyn-10'),
#(FakeFGLSD(cls, nbins=5, isomerous=False), 'FGSLD-5'),
#(FakeFGLSD(cls, nbins=10, isomerous=False), 'FGSLD-10'),
#(FakeFGLSD(cls, nbins=50, isomerous=False), 'FGSLD-50'),
#(FakeFGLSD(cls, nbins=100, isomerous=False), 'FGSLD-100'),
# (FakeFGLSD(cls, nbins=1, isomerous=False), 'FGSLD-1'),
#(FakeFGLSD(cls, nbins=10, isomerous=True), 'FGSLD-10-ISO'),
# (FakeFGLSD(cls, nbins=50, isomerous=False), 'FGSLD-50'),
(EMQ(cls), 'SLD'),
]:
print('running ', model_name)
model.fit(training)
true_prev, estim_prev = qp.evaluation.artificial_sampling_prediction(
model, test, qp.environ['SAMPLE_SIZE'], n_repetitions=5, n_prevpoints=11, n_jobs=-1
)
method_names.append(model_name)
true_prevs.append(true_prev)
estim_prevs.append(estim_prev)
tr_prevs.append(training.prevalence())
qp.plot.binary_diagonal(method_names, true_prevs, estim_prevs, train_prev=tr_prevs[0], savepath='./plot_fglsd.png')

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from sklearn.calibration import CalibratedClassifierCV
from sklearn.svm import LinearSVC
from NewMethods.fgsld.fine_grained_sld import FineGrainedSLD
from quapy.method.aggregative import EMQ, CC, training_helper
from quapy.data import LabelledCollection
from quapy.method.base import BaseQuantifier
import quapy.functional as F
class FakeFGLSD(BaseQuantifier):
def __init__(self, learner, nbins, isomerous, recompute_bins):
self.learner = learner
self.nbins = nbins
self.isomerous = isomerous
self.recompute_bins = recompute_bins
def fit(self, data: LabelledCollection):
self.Xtr, self.ytr = data.Xy
self.learner.fit(self.Xtr, self.ytr)
return self
def quantify(self, instances):
tr_priors = F.prevalence_from_labels(self.ytr, n_classes=2)
fgsld = FineGrainedSLD(self.Xtr, instances, self.ytr, tr_priors, self.learner, n_bins=self.nbins)
priors, posteriors = fgsld.run(self.isomerous, compute_bins_at_every_iter=self.recompute_bins)
return priors
def get_params(self, deep=True):
pass
def set_params(self, **parameters):
pass

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import numpy as np
from metrics import isomerous_bins, isometric_bins
from em import History, get_measures_single_history
from sklearn.model_selection import cross_val_predict
import math
class FineGrainedSLD:
def __init__(self, x_tr, x_te, y_tr, tr_priors, clf, n_bins=10):
self.y_tr = y_tr
self.clf = clf
self.tr_priors = tr_priors
self.te_preds = clf.predict_proba(x_te)
self.tr_preds = cross_val_predict(clf, x_tr, y_tr, method='predict_proba', n_jobs=10)
self.n_bins = n_bins
self.history: [History] = []
self.multi_class = False
def run(self, isomerous_binning, epsilon=1e-6, compute_bins_at_every_iter=True, return_posteriors_hist=False):
"""
Run the FGSLD algorithm.
:param isomerous_binning: whether to use isomerous or isometric binning.
:param epsilon: stopping condition.
:param compute_bins_at_every_iter: whether FGSLD should recompute the posterior bins at every iteration or not.
:param return_posteriors_hist: whether to return posteriors at every iteration or not.
:return: If `return_posteriors_hist` is true, the returned posteriors will be a list of numpy arrays, else a single numpy array with posteriors at last iteration.
"""
smoothing_tr = 1 / (2 * self.tr_preds.shape[0])
smoothing_te = 1 / (2 * self.te_preds.shape[0])
s = 0
tr_bin_priors = np.zeros((self.n_bins, self.tr_preds.shape[1]), dtype=np.float)
te_bin_priors = np.zeros((self.n_bins, self.te_preds.shape[1]), dtype=np.float)
tr_bins = self.__create_bins(training=True, isomerous_binning=isomerous_binning)
te_bins = self.__create_bins(training=False, isomerous_binning=isomerous_binning)
self.__compute_bins_priors(tr_bin_priors, self.tr_preds, tr_bins, smoothing_tr)
val = 2 * epsilon
if return_posteriors_hist:
posteriors_hist = [self.te_preds.copy()]
while not val < epsilon and s < 1000:
assert np.all(np.around(self.te_preds.sum(axis=1), 4) == 1), f"Probabilities do not sum to 1:\ns={s}, " \
f"probs={self.te_preds.sum(axis=1)}"
if compute_bins_at_every_iter:
te_bins = self.__create_bins(training=False, isomerous_binning=isomerous_binning)
if s == 0:
te_bin_priors_prev = tr_bin_priors.copy()
else:
te_bin_priors_prev = te_bin_priors.copy()
self.__compute_bins_priors(te_bin_priors, self.te_preds, te_bins, smoothing_te)
te_preds_cp = self.te_preds.copy()
for label_idx, bins in te_bins.items():
for i, bin_ in enumerate(bins):
if bin_.shape[0] == 0:
continue
te = te_bin_priors[i][label_idx]
tr = tr_bin_priors[i][label_idx]
# local_min = (math.floor(tr * 10) / 10)
# local_max = local_min + .1
# trans = lambda l: min(max((l - local_min) / 1, 0), 1)
trans = lambda l: l
self.te_preds[:, label_idx][bin_] = (te_preds_cp[:, label_idx][bin_]) * \
(trans(te) / trans(tr))
# Normalization step
self.te_preds = (self.te_preds / self.te_preds.sum(axis=1, keepdims=True))
val = 0
for label_idx in range(te_bin_priors.shape[1]):
temp = max(abs((te_bin_priors[:, label_idx] / te_bin_priors_prev[:, label_idx]) - 1))
if temp > val:
val = temp
s += 1
if return_posteriors_hist:
posteriors_hist.append(self.te_preds.copy())
if return_posteriors_hist:
return self.te_preds.mean(axis=0), posteriors_hist
return self.te_preds.mean(axis=0), self.te_preds
def __compute_bins_priors(self, bin_priors_placeholder, posteriors, bins, smoothing):
for label_idx, bins in bins.items():
for i, bin_ in enumerate(bins):
if bin_.shape[0] == 0:
bin_priors_placeholder[i, label_idx] = smoothing
continue
numerator = posteriors[:, label_idx][bin_].mean()
bin_prior = (numerator + smoothing) / (1 + self.n_bins * smoothing) # normalize priors
bin_priors_placeholder[i, label_idx] = bin_prior
def __find_bin_idx(self, label_bins: [np.array], idx: int or list):
if hasattr(idx, '__len__'):
idxs = np.zeros(len(idx), dtype=np.int)
for i, bin_ in enumerate(label_bins):
for j, id_ in enumerate(idx):
if id_ in bin_:
idxs[j] = i
return idxs
else:
for i, bin_ in enumerate(label_bins):
if idx in bin_:
return i
def __create_bins(self, training: bool, isomerous_binning: bool):
bins = {}
preds = self.tr_preds if training else self.te_preds
if isomerous_binning:
for label_idx in range(preds.shape[1]):
bins[label_idx] = isomerous_bins(label_idx, preds, self.n_bins)
else:
intervals = np.linspace(0., 1., num=self.n_bins, endpoint=False)
for label_idx in range(preds.shape[1]):
bins_ = isometric_bins(label_idx, preds, intervals, 0.1)
bins[label_idx] = [bins_[i] for i in intervals]
return bins

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import numpy as np
"""
Scikit learn provides a full set of evaluation metrics, but they treat special cases differently.
I.e., when the number of true positives, false positives, and false negatives ammount to 0, all
affected metrics (precision, recall, and thus f1) output 0 in Scikit learn.
We adhere to the common practice of outputting 1 in this case since the classifier has correctly
classified all examples as negatives.
"""
def isometric_brier_decomposition(true_labels, predicted_labels, bin_intervals=np.arange(0., 1.1, 0.1), step=0.1):
"""
The Isometric Brier decomposition or score is obtained by partitioning U into intervals I_1j,...,I_bj that
have equal length, where U is the total size of our test set (i.e., true_labels.shape[0]). This means that,
if b=10 then I_1j = [0.0,0.1), I_2j = [0.2, 0.3),...,I_bj = [0.9,1.0).
bin_intervals is a numpy.array containing the range of the different intervals. Since it is a single dimensional
array, for every interval I_n we take the posterior probabilities Pr_n(x) such that I_n <= Pr_n(x) < I_n + step.
This variable defaults to np.arange(0., 1.0, 0.1), i.e. an array like [0.1, 0.2, ..., 1.0].
:return: a tuple (calibration score, refinement score)
"""
labels = set(true_labels)
calibration_score, refinement_score = 0.0, 0.0
for i in range(len(labels)):
bins = isometric_bins(i, predicted_labels, bin_intervals, step)
c_score, r_score = brier_decomposition(bins.values(), true_labels, predicted_labels, class_=i)
calibration_score += c_score
refinement_score += r_score
return calibration_score, refinement_score
def isomerous_brier_decomposition(true_labels, predicted_labels, n=10):
"""
The Isomerous Brier decomposition or score is obtained by partitioning U into intervals I_1j,...,I_bj such that
the corresponding bins B_1j,...,B_bj have equal size, where U is our test set. This means that, for every x' in
B_sj and x'' in B_tj with s < t, it holds that Pr(c_j|x') <= Pr(c_j|x'') and |B_sj| == |B_tj|, for any s,t in
{1,...,b}.
The n variable holds the number of bins we want (defaults to 10). Notice that we perform a numpy.array_split on
the predicted_labels, creating l % n sub-arrays of size l//n + 1 and the rest of size l//n, where l is the length
of the array.
:return: a tuple (calibration score, refinement score)
"""
labels = set(true_labels)
calibration_score, refinement_score = 0.0, 0.0
for i in range(len(labels)):
bins = isomerous_bins(i, predicted_labels, n)
c_score, r_score = brier_decomposition(bins, true_labels, predicted_labels, class_=i)
calibration_score += c_score
refinement_score += r_score
return calibration_score, refinement_score
def brier_decomposition(bins, true_labels, predicted_labels, class_=1):
"""
:param bins: must be an array of indices
:return: a tuple (calibration_score, refinement_score)
"""
calibration_score = 0
refinement_score = 0
for bin_ in bins:
if bin_.size <= 0:
continue
v_x = (bin_.shape[0] / true_labels.shape[0])
ro_x = np.mean(true_labels[bin_] == class_)
calibration_score += v_x * (predicted_labels[bin_, class_].mean() - ro_x)**2
refinement_score += (v_x * ro_x) * (1 - ro_x)
labels_len = len(set(true_labels))
return calibration_score / (labels_len * len(bins)), refinement_score / (labels_len * len(bins))
def isometric_bins(label_index, predicted_labels, bin_intervals, step):
predicted_class_label = predicted_labels[:, label_index]
return {interv: np.where(np.logical_and(interv <= predicted_class_label, predicted_class_label < interv + step))[0]
for interv in bin_intervals}
def isomerous_bins(label_index, predicted_labels, n):
sorted_indices = predicted_labels[:, label_index].argsort()
return np.array_split(sorted_indices, n)
# true_labels and predicted_labels are two matrices in sklearn.preprocessing.MultiLabelBinarizer format
def macroF1(true_labels, predicted_labels):
return macro_average(true_labels, predicted_labels, f1)
# true_labels and predicted_labels are two matrices in sklearn.preprocessing.MultiLabelBinarizer format
def microF1(true_labels, predicted_labels):
return micro_average(true_labels, predicted_labels, f1)
# true_labels and predicted_labels are two matrices in sklearn.preprocessing.MultiLabelBinarizer format
def macroK(true_labels, predicted_labels):
return macro_average(true_labels, predicted_labels, K)
# true_labels and predicted_labels are two matrices in sklearn.preprocessing.MultiLabelBinarizer format
def microK(true_labels, predicted_labels):
return micro_average(true_labels, predicted_labels, K)
# true_labels is a matrix in sklearn.preprocessing.MultiLabelBinarizer format and posterior_probabilities is a matrix
# of the same shape containing real values in [0,1]
def smoothmacroF1(true_labels, posterior_probabilities):
return macro_average(true_labels, posterior_probabilities, f1, metric_statistics=soft_single_metric_statistics)
# true_labels is a matrix in sklearn.preprocessing.MultiLabelBinarizer format and posterior_probabilities is a matrix
# of the same shape containing real values in [0,1]
def smoothmicroF1(true_labels, posterior_probabilities):
return micro_average(true_labels, posterior_probabilities, f1, metric_statistics=soft_single_metric_statistics)
# true_labels is a matrix in sklearn.preprocessing.MultiLabelBinarizer format and posterior_probabilities is a matrix
# of the same shape containing real values in [0,1]
def smoothmacroK(true_labels, posterior_probabilities):
return macro_average(true_labels, posterior_probabilities, K, metric_statistics=soft_single_metric_statistics)
# true_labels is a matrix in sklearn.preprocessing.MultiLabelBinarizer format and posterior_probabilities is a matrix
# of the same shape containing real values in [0,1]
def smoothmicroK(true_labels, posterior_probabilities):
return micro_average(true_labels, posterior_probabilities, K, metric_statistics=soft_single_metric_statistics)
class ContTable:
def __init__(self, tp=0, tn=0, fp=0, fn=0):
self.tp = tp
self.tn = tn
self.fp = fp
self.fn = fn
def get_d(self): return self.tp + self.tn + self.fp + self.fn
def get_c(self): return self.tp + self.fn
def get_not_c(self): return self.tn + self.fp
def get_f(self): return self.tp + self.fp
def get_not_f(self): return self.tn + self.fn
def p_c(self): return (1.0 * self.get_c()) / self.get_d()
def p_not_c(self): return 1.0 - self.p_c()
def p_f(self): return (1.0 * self.get_f()) / self.get_d()
def p_not_f(self): return 1.0 - self.p_f()
def p_tp(self): return (1.0 * self.tp) / self.get_d()
def p_tn(self): return (1.0 * self.tn) / self.get_d()
def p_fp(self): return (1.0 * self.fp) / self.get_d()
def p_fn(self): return (1.0 * self.fn) / self.get_d()
def tpr(self):
c = 1.0 * self.get_c()
return self.tp / c if c > 0.0 else 0.0
def fpr(self):
_c = 1.0 * self.get_not_c()
return self.fp / _c if _c > 0.0 else 0.0
def __add__(self, other):
return ContTable(tp=self.tp + other.tp, tn=self.tn + other.tn, fp=self.fp + other.fp, fn=self.fn + other.fn)
def accuracy(cell):
return (cell.tp + cell.tn) * 1.0 / (cell.tp + cell.fp + cell.fn + cell.tn)
def f1(cell):
num = 2.0 * cell.tp
den = 2.0 * cell.tp + cell.fp + cell.fn
if den > 0: return num / den
# we define f1 to be 1 if den==0 since the classifier has correctly classified all instances as negative
return 1.0
def K(cell):
specificity, recall = 0., 0.
AN = cell.tn + cell.fp
if AN != 0:
specificity = cell.tn * 1. / AN
AP = cell.tp + cell.fn
if AP != 0:
recall = cell.tp * 1. / AP
if AP == 0:
return 2. * specificity - 1.
elif AN == 0:
return 2. * recall - 1.
else:
return specificity + recall - 1.
# computes the (hard) counters tp, fp, fn, and tn fron a true and predicted vectors of hard decisions
# true_labels and predicted_labels are two vectors of shape (number_documents,)
def hard_single_metric_statistics(true_labels, predicted_labels):
assert len(true_labels) == len(predicted_labels), "Format not consistent between true and predicted labels."
nd = len(true_labels)
tp = np.sum(predicted_labels[true_labels == 1])
fp = np.sum(predicted_labels[true_labels == 0])
fn = np.sum(true_labels[predicted_labels == 0])
tn = nd - (tp + fp + fn)
return ContTable(tp=tp, tn=tn, fp=fp, fn=fn)
# computes the (soft) contingency table where tp, fp, fn, and tn are the cumulative masses for the posterioir
# probabilitiesfron with respect to the true binary labels
# true_labels and posterior_probabilities are two vectors of shape (number_documents,)
def soft_single_metric_statistics(true_labels, posterior_probabilities):
assert len(true_labels) == len(posterior_probabilities), "Format not consistent between true and predicted labels."
pos_probs = posterior_probabilities[true_labels == 1]
neg_probs = posterior_probabilities[true_labels == 0]
tp = np.sum(pos_probs)
fn = np.sum(1. - pos_probs)
fp = np.sum(neg_probs)
tn = np.sum(1. - neg_probs)
return ContTable(tp=tp, tn=tn, fp=fp, fn=fn)
# if the classifier is single class, then the prediction is a vector of shape=(nD,) which causes issues when compared
# to the true labels (of shape=(nD,1)). This method increases the dimensions of the predictions.
def __check_consistency_and_adapt(true_labels, predictions):
if predictions.ndim == 1:
return __check_consistency_and_adapt(true_labels, np.expand_dims(predictions, axis=1))
if true_labels.ndim == 1:
return __check_consistency_and_adapt(np.expand_dims(true_labels, axis=1), predictions)
if true_labels.shape != predictions.shape:
raise ValueError("True and predicted label matrices shapes are inconsistent %s %s."
% (true_labels.shape, predictions.shape))
_, nC = true_labels.shape
return true_labels, predictions, nC
def macro_average(true_labels, predicted_labels, metric, metric_statistics=hard_single_metric_statistics):
true_labels, predicted_labels, nC = __check_consistency_and_adapt(true_labels, predicted_labels)
return np.mean([metric(metric_statistics(true_labels[:, c], predicted_labels[:, c])) for c in range(nC)])
def micro_average(true_labels, predicted_labels, metric, metric_statistics=hard_single_metric_statistics):
true_labels, predicted_labels, nC = __check_consistency_and_adapt(true_labels, predicted_labels)
accum = ContTable()
for c in range(nC):
other = metric_statistics(true_labels[:, c], predicted_labels[:, c])
accum = accum + other
return metric(accum)

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import quapy as qp
import settings
import os
import pathlib
import pickle
from glob import glob
import sys
from TweetSentQuant.util import nicename
from os.path import join
qp.environ['SAMPLE_SIZE'] = settings.SAMPLE_SIZE
plotext='png'
resultdir = './results'
plotdir = './plots'
os.makedirs(plotdir, exist_ok=True)
def gather_results(methods, error_name):
method_names, true_prevs, estim_prevs, tr_prevs = [], [], [], []
for method in methods:
for experiment in glob(f'{resultdir}/*-{method}-m{error_name}.pkl'):
true_prevalences, estim_prevalences, tr_prev, te_prev, te_prev_estim, best_params = pickle.load(open(experiment, 'rb'))
method_names.append(nicename(method))
true_prevs.append(true_prevalences)
estim_prevs.append(estim_prevalences)
tr_prevs.append(tr_prev)
return method_names, true_prevs, estim_prevs, tr_prevs
def plot_error_by_drift(methods, error_name, logscale=False, path=None):
print('plotting error by drift')
if path is not None:
path = join(path, f'error_by_drift_{error_name}.{plotext}')
method_names, true_prevs, estim_prevs, tr_prevs = gather_results(methods, error_name)
qp.plot.error_by_drift(
method_names,
true_prevs,
estim_prevs,
tr_prevs,
n_bins=20,
error_name=error_name,
show_std=False,
logscale=logscale,
title=f'Quantification error as a function of distribution shift',
savepath=path
)
def diagonal_plot(methods, error_name, path=None):
print('plotting diagonal plots')
if path is not None:
path = join(path, f'diag_{error_name}')
method_names, true_prevs, estim_prevs, tr_prevs = gather_results(methods, error_name)
qp.plot.binary_diagonal(method_names, true_prevs, estim_prevs, pos_class=0, title='Negative', legend=False, show_std=False, savepath=f'{path}_neg.{plotext}')
qp.plot.binary_diagonal(method_names, true_prevs, estim_prevs, pos_class=1, title='Neutral', legend=False, show_std=False, savepath=f'{path}_neu.{plotext}')
qp.plot.binary_diagonal(method_names, true_prevs, estim_prevs, pos_class=2, title='Positive', legend=True, show_std=False, savepath=f'{path}_pos.{plotext}')
def binary_bias_global(methods, error_name, path=None):
print('plotting bias global')
if path is not None:
path = join(path, f'globalbias_{error_name}')
method_names, true_prevs, estim_prevs, tr_prevs = gather_results(methods, error_name)
qp.plot.binary_bias_global(method_names, true_prevs, estim_prevs, pos_class=0, title='Negative', savepath=f'{path}_neg.{plotext}')
qp.plot.binary_bias_global(method_names, true_prevs, estim_prevs, pos_class=1, title='Neutral', savepath=f'{path}_neu.{plotext}')
qp.plot.binary_bias_global(method_names, true_prevs, estim_prevs, pos_class=2, title='Positive', savepath=f'{path}_pos.{plotext}')
def binary_bias_bins(methods, error_name, path=None):
print('plotting bias local')
if path is not None:
path = join(path, f'localbias_{error_name}')
method_names, true_prevs, estim_prevs, tr_prevs = gather_results(methods, error_name)
qp.plot.binary_bias_bins(method_names, true_prevs, estim_prevs, pos_class=0, title='Negative', legend=False, savepath=f'{path}_neg.{plotext}')
qp.plot.binary_bias_bins(method_names, true_prevs, estim_prevs, pos_class=1, title='Neutral', legend=False, savepath=f'{path}_neu.{plotext}')
qp.plot.binary_bias_bins(method_names, true_prevs, estim_prevs, pos_class=2, title='Positive', legend=True, savepath=f'{path}_pos.{plotext}')
gao_seb_methods = ['cc', 'acc', 'pcc', 'pacc', 'sld', 'svmq', 'svmkld', 'svmnkld']
new_methods_ae = ['svmmae' , 'epaccmaeptr', 'epaccmaemae', 'hdy', 'quanet']
new_methods_rae = ['svmmrae' , 'epaccmraeptr', 'epaccmraemrae', 'hdy', 'quanet']
plot_error_by_drift(gao_seb_methods+new_methods_ae, error_name='ae', path=plotdir)
plot_error_by_drift(gao_seb_methods+new_methods_rae, error_name='rae', logscale=True, path=plotdir)
diagonal_plot(gao_seb_methods+new_methods_ae, error_name='ae', path=plotdir)
diagonal_plot(gao_seb_methods+new_methods_rae, error_name='rae', path=plotdir)
binary_bias_global(gao_seb_methods+new_methods_ae, error_name='ae', path=plotdir)
binary_bias_global(gao_seb_methods+new_methods_rae, error_name='rae', path=plotdir)
#binary_bias_bins(gao_seb_methods+new_methods_ae, error_name='ae', path=plotdir)
#binary_bias_bins(gao_seb_methods+new_methods_rae, error_name='rae', path=plotdir)

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import quapy as qp
import numpy as np
from os import makedirs
import sys, os
import pickle
from experiments import result_path
from tabular import Table
import argparse
tables_path = './tables'
MAXTONE = 50 # sets the intensity of the maximum color reached by the worst (red) and best (green) results
makedirs(tables_path, exist_ok=True)
sample_size = 100
qp.environ['SAMPLE_SIZE'] = sample_size
nice = {
'mae':'AE',
'mrae':'RAE',
'ae':'AE',
'rae':'RAE',
'svmkld': 'SVM(KLD)',
'svmnkld': 'SVM(NKLD)',
'svmq': 'SVM(Q)',
'svmae': 'SVM(AE)',
'svmnae': 'SVM(NAE)',
'svmmae': 'SVM(AE)',
'svmmrae': 'SVM(RAE)',
'quanet': 'QuaNet',
'hdy': 'HDy',
'hdysld': 'HDy-SLD',
'dys': 'DyS',
'svmperf':'',
'sanders': 'Sanders',
'semeval13': 'SemEval13',
'semeval14': 'SemEval14',
'semeval15': 'SemEval15',
'semeval16': 'SemEval16',
'Average': 'Average'
}
def save_table(path, table):
print(f'saving results in {path}')
with open(path, 'wt') as foo:
foo.write(table)
def experiment_errors(path, dataset, method, loss):
path = result_path(path, dataset, method, 'm'+loss if not loss.startswith('m') else loss)
if os.path.exists(path):
true_prevs, estim_prevs, _, _, _, _ = pickle.load(open(path, 'rb'))
err_fn = getattr(qp.error, loss)
errors = err_fn(true_prevs, estim_prevs)
return errors
return None
def nicerm(key):
return '\mathrm{'+nice[key]+'}'
if __name__ == '__main__':
parser = argparse.ArgumentParser(description='Generate tables for Tweeter Sentiment Quantification')
parser.add_argument('results', metavar='RESULT_PATH', type=str,
help='path to the directory containing the results of the methods tested in Gao & Sebastiani')
parser.add_argument('newresults', metavar='RESULT_PATH', type=str,
help='path to the directory containing the results for the experimental methods')
args = parser.parse_args()
datasets = qp.datasets.TWITTER_SENTIMENT_DATASETS_TEST
evaluation_measures = [qp.error.ae, qp.error.rae]
gao_seb_methods = ['cc', 'acc', 'pcc', 'pacc', 'sld', 'svmq', 'svmkld', 'svmnkld']
new_methods = ['hdy'] # methods added to the Gao & Sebastiani methods
experimental_methods = ['hdysld'] # experimental
for i, eval_func in enumerate(evaluation_measures):
# Tables evaluation scores for AE and RAE (two tables)
# ----------------------------------------------------
eval_name = eval_func.__name__
added_methods = ['svmm' + eval_name] + new_methods
methods = gao_seb_methods + added_methods + experimental_methods
nold_methods = len(gao_seb_methods)
nnew_methods = len(added_methods)
nexp_methods = len(experimental_methods)
# fill data table
table = Table(benchmarks=datasets, methods=methods)
for dataset in datasets:
for method in methods:
if method in experimental_methods:
path = args.newresults
else:
path = args.results
table.add(dataset, method, experiment_errors(path, dataset, method, eval_name))
# write the latex table
tabular = """
\\begin{tabularx}{\\textwidth}{|c||""" + ('Y|'*nold_methods) + '|' + ('Y|'*nnew_methods) + '|' + ('Y|'*nexp_methods) + """} \hline
& \multicolumn{"""+str(nold_methods)+"""}{c||}{Methods tested in~\cite{Gao:2016uq}} &
\multicolumn{"""+str(nnew_methods)+"""}{c|}{} &
\multicolumn{"""+str(nexp_methods)+"""}{c|}{}\\\\ \hline
"""
rowreplace={dataset: nice.get(dataset, dataset.upper()) for dataset in datasets}
colreplace={method:'\side{' + nice.get(method, method.upper()) +'$^{' + nicerm(eval_name) + '}$} ' for method in methods}
tabular += table.latexTabular(benchmark_replace=rowreplace, method_replace=colreplace)
tabular += "\n\end{tabularx}"
save_table(f'./tables/tab_results_{eval_name}.new.tex', tabular)
# Tables ranks for AE and RAE (two tables)
# ----------------------------------------------------
# fill the data table
ranktable = Table(benchmarks=datasets, methods=methods, missing='--')
for dataset in datasets:
for method in methods:
ranktable.add(dataset, method, values=table.get(dataset, method, 'rank'))
# write the latex table
tabular = """
\\begin{tabularx}{\\textwidth}{|c||""" + ('Y|'*nold_methods) + '|' + ('Y|'*nnew_methods) + '|' + ('Y|'*nexp_methods) + """} \hline
& \multicolumn{"""+str(nold_methods)+"""}{c||}{Methods tested in~\cite{Gao:2016uq}} &
\multicolumn{"""+str(nnew_methods)+"""}{c|}{} &
\multicolumn{"""+str(nexp_methods)+"""}{c|}{}\\\\ \hline
"""
for method in methods:
tabular += ' & \side{' + nice.get(method, method.upper()) +'$^{' + nicerm(eval_name) + '}$} '
tabular += '\\\\\hline\n'
for dataset in datasets:
tabular += nice.get(dataset, dataset.upper()) + ' '
for method in methods:
newrank = ranktable.get(dataset, method)
if newrank != '--':
newrank = f'{int(newrank)}'
color = ranktable.get_color(dataset, method)
if color == '--':
color = ''
tabular += ' & ' + f'{newrank}' + color
tabular += '\\\\\hline\n'
tabular += '\hline\n'
tabular += 'Average '
for method in methods:
newrank = ranktable.get_average(method)
if newrank != '--':
newrank = f'{newrank:.1f}'
color = ranktable.get_average(method, 'color')
if color == '--':
color = ''
tabular += ' & ' + f'{newrank}' + color
tabular += '\\\\\hline\n'
tabular += "\end{tabularx}"
save_table(f'./tables/tab_rank_{eval_name}.new.tex', tabular)
print("[Done]")

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import numpy as np
from sklearn.base import BaseEstimator
from sklearn.decomposition import PCA
from sklearn.preprocessing import StandardScaler
import quapy as qp
from typing import Union
from quapy.data import LabelledCollection
from quapy.method.base import BaseQuantifier, BinaryQuantifier
from quapy.method.aggregative import PACC, EMQ, HDy
import quapy.functional as F
from tqdm import tqdm
from scipy.sparse import issparse, csr_matrix
import scipy
class PACCSLD(PACC):
"""
This method combines the EMQ improved posterior probabilities with PACC.
Note: the posterior probabilities are re-calibrated with EMQ only during prediction, and not also during fit since,
for PACC, the validation split is known to have the same prevalence as the training set (this is because the split
is stratified) and thus the posterior probabilities should not be re-calibrated for a different prior (it actually
happens to degrades performance).
"""
def fit(self, data: qp.data.LabelledCollection, fit_learner=True, val_split:Union[float, int, qp.data.LabelledCollection]=0.4):
self.train_prevalence = F.prevalence_from_labels(data.labels, data.n_classes)
return super(PACCSLD, self).fit(data, fit_learner, val_split)
def aggregate(self, classif_posteriors):
priors, posteriors = EMQ.EM(self.train_prevalence, classif_posteriors, epsilon=1e-4)
return super(PACCSLD, self).aggregate(posteriors)
class HDySLD(HDy):
"""
This method combines the EMQ improved posterior probabilities with HDy.
Note: [same as PACCSLD]
"""
def fit(self, data: qp.data.LabelledCollection, fit_learner=True,
val_split: Union[float, int, qp.data.LabelledCollection] = 0.4):
self.train_prevalence = F.prevalence_from_labels(data.labels, data.n_classes)
return super(HDySLD, self).fit(data, fit_learner, val_split)
def aggregate(self, classif_posteriors):
priors, posteriors = EMQ.EM(self.train_prevalence, classif_posteriors, epsilon=1e-4)
return super(HDySLD, self).aggregate(posteriors)
class AveragePoolQuantification(BinaryQuantifier):
def __init__(self, learner, sample_size, trials, n_components=-1, zscore=False):
self.learner = learner
self.sample_size = sample_size
self.trials = trials
self.do_zscore = zscore
self.zscore = StandardScaler() if self.do_zscore else None
self.do_pca = n_components>0
self.pca = PCA(n_components) if self.do_pca else None
def fit(self, data: LabelledCollection):
training, validation = data.split_stratified(train_prop=0.7)
X, y = [], []
nprevpoints = F.get_nprevpoints_approximation(self.trials, data.n_classes)
for sample in tqdm(
training.artificial_sampling_generator(self.sample_size, n_prevalences=nprevpoints, repeats=1),
desc='generating averages'
):
X.append(sample.instances.mean(axis=0))
y.append(sample.prevalence()[1])
while len(X) < self.trials:
sample = training.sampling(self.sample_size, F.uniform_simplex_sampling(data.n_classes))
X.append(sample.instances.mean(axis=0))
y.append(sample.prevalence())
X = np.asarray(np.vstack(X))
y = np.asarray(y)
if self.do_pca:
X = self.pca.fit_transform(X)
print(X.shape)
if self.do_zscore:
X = self.zscore.fit_transform(X)
print('training regressor...')
self.regressor = self.learner.fit(X, y)
# correction at 0:
print('getting corrections...')
X0 = np.asarray(np.vstack([validation.sampling(self.sample_size, 0., shuffle=False).instances.mean(axis=0) for _ in range(100)]))
X1 = np.asarray(np.vstack([validation.sampling(self.sample_size, 1., shuffle=False).instances.mean(axis=0) for _ in range(100)]))
if self.do_pca:
X0 = self.pca.transform(X0)
X1 = self.pca.transform(X1)
if self.do_zscore:
X0 = self.zscore.transform(X0)
X1 = self.zscore.transform(X1)
self.correction_0 = self.regressor.predict(X0).mean()
self.correction_1 = self.regressor.predict(X1).mean()
print('correction-0', self.correction_0)
print('correction-1', self.correction_1)
print('done')
def quantify(self, instances):
ave = np.asarray(instances.mean(axis=0))
if self.do_pca:
ave = self.pca.transform(ave)
if self.do_zscore:
ave = self.zscore.transform(ave)
phat = self.regressor.predict(ave).item()
phat = np.clip((phat-self.correction_0)/(self.correction_1-self.correction_0), 0, 1)
return np.asarray([1-phat, phat])
def set_params(self, **parameters):
self.learner.set_params(**parameters)
def get_params(self, deep=True):
return self.learner.get_params(deep=deep)
class WinnowOrthogonal(BaseEstimator):
def __init__(self):
pass
def fit(self, X, y):
self.classes_ = np.asarray(sorted(np.unique(y)))
w1 = np.asarray(X[y == 0].mean(axis=0)).flatten()
w2 = np.asarray(X[y == 1].mean(axis=0)).flatten()
diff = w2 - w1
orth = np.ones_like(diff)
orth[0] = -diff[1:].sum() / diff[0]
orth /= np.linalg.norm(orth)
self.w = orth
self.b = w1.dot(orth)
return self
def decision_function(self, X):
if issparse(X):
Z = X.dot(csr_matrix(self.w).T).toarray().flatten()
return Z - self.b
else:
return np.matmul(X, self.w) - self.b
def predict(self, X):
return 1 * (self.decision_function(X) > 0)
def split(self, X, y):
s = self.predict(X)
X0a = X[np.logical_and(y == 0, s == 0)]
X0b = X[np.logical_and(y == 0, s == 1)]
X1a = X[np.logical_and(y == 1, s == 0)]
X1b = X[np.logical_and(y == 1, s == 1)]
y0a = np.zeros(X0a.shape[0], dtype=np.int)
y0b = np.zeros(X0b.shape[0], dtype=np.int)
y1a = np.ones(X1a.shape[0], dtype=np.int)
y1b = np.ones(X1b.shape[0], dtype=np.int)
return X0a, X0b, X1a, X1b, y0a, y0b, y1a, y1b
def get_params(self):
return {}
def set_params(self, **params):
pass

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import multiprocessing
N_JOBS = -2 #multiprocessing.cpu_count()
ENSEMBLE_N_JOBS=1
SAMPLE_SIZE = 100

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from glob import glob
import pickle
import numpy as np
results = './results'
method_choices = {}
for file in glob(f'{results}/*'):
hyper = pickle.load(open(file, 'rb'))[-1]
if hyper:
dataset,method,optim = file.split('/')[-1].split('-')
key = str(hyper)
if method not in method_choices:
method_choices[method] = {}
if key not in method_choices[method]:
method_choices[method][key] = 0
method_choices[method][key] = method_choices[method][key]+1
for method, hyper_count_dict in method_choices.items():
hyper, counts = zip(*list(hyper_count_dict.items()))
order = np.argsort(counts)
counts = np.asarray(counts)[order][::-1]
hyper = np.asarray(hyper)[order][::-1]
print(method)
for hyper_i, count_i in zip(hyper, counts):
print('\t', hyper_i, count_i)

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import numpy as np
import itertools
from scipy.stats import ttest_ind_from_stats, wilcoxon
class Table:
VALID_TESTS = [None, "wilcoxon", "ttest"]
def __init__(self, benchmarks, methods, lower_is_better=True, ttest='ttest', prec_mean=3,
clean_zero=False, show_std=False, prec_std=3, average=True, missing=None, missing_str='--', color=True):
assert ttest in self.VALID_TESTS, f'unknown test, valid are {self.VALID_TESTS}'
self.benchmarks = np.asarray(benchmarks)
self.benchmark_index = {row:i for i, row in enumerate(benchmarks)}
self.methods = np.asarray(methods)
self.method_index = {col:j for j, col in enumerate(methods)}
self.map = {}
# keyed (#rows,#cols)-ndarrays holding computations from self.map['values']
self._addmap('values', dtype=object)
self.lower_is_better = lower_is_better
self.ttest = ttest
self.prec_mean = prec_mean
self.clean_zero = clean_zero
self.show_std = show_std
self.prec_std = prec_std
self.add_average = average
self.missing = missing
self.missing_str = missing_str
self.color = color
self.touch()
@property
def nbenchmarks(self):
return len(self.benchmarks)
@property
def nmethods(self):
return len(self.methods)
def touch(self):
self._modif = True
def update(self):
if self._modif:
self.compute()
def _getfilled(self):
return np.argwhere(self.map['fill'])
@property
def values(self):
return self.map['values']
def _indexes(self):
return itertools.product(range(self.nbenchmarks), range(self.nmethods))
def _addmap(self, map, dtype, func=None):
self.map[map] = np.empty((self.nbenchmarks, self.nmethods), dtype=dtype)
if func is None:
return
m = self.map[map]
f = func
indexes = self._indexes() if map == 'fill' else self._getfilled()
for i, j in indexes:
m[i, j] = f(self.values[i, j])
def _addrank(self):
for i in range(self.nbenchmarks):
filled_cols_idx = np.argwhere(self.map['fill'][i]).flatten()
col_means = [self.map['mean'][i,j] for j in filled_cols_idx]
ranked_cols_idx = filled_cols_idx[np.argsort(col_means)]
if not self.lower_is_better:
ranked_cols_idx = ranked_cols_idx[::-1]
self.map['rank'][i, ranked_cols_idx] = np.arange(1, len(filled_cols_idx)+1)
def _addcolor(self):
for i in range(self.nbenchmarks):
filled_cols_idx = np.argwhere(self.map['fill'][i]).flatten()
if filled_cols_idx.size==0:
continue
col_means = [self.map['mean'][i,j] for j in filled_cols_idx]
minval = min(col_means)
maxval = max(col_means)
for col_idx in filled_cols_idx:
val = self.map['mean'][i,col_idx]
norm = (maxval - minval)
if norm > 0:
normval = (val - minval) / norm
else:
normval = 0.5
if self.lower_is_better:
normval = 1 - normval
self.map['color'][i, col_idx] = color_red2green_01(normval)
def _run_ttest(self, row, col1, col2):
mean1 = self.map['mean'][row, col1]
std1 = self.map['std'][row, col1]
nobs1 = self.map['nobs'][row, col1]
mean2 = self.map['mean'][row, col2]
std2 = self.map['std'][row, col2]
nobs2 = self.map['nobs'][row, col2]
_, p_val = ttest_ind_from_stats(mean1, std1, nobs1, mean2, std2, nobs2)
return p_val
def _run_wilcoxon(self, row, col1, col2):
values1 = self.map['values'][row, col1]
values2 = self.map['values'][row, col2]
_, p_val = wilcoxon(values1, values2)
return p_val
def _add_statistical_test(self):
if self.ttest is None:
return
self.some_similar = [False]*self.nmethods
for i in range(self.nbenchmarks):
filled_cols_idx = np.argwhere(self.map['fill'][i]).flatten()
if len(filled_cols_idx) <= 1:
continue
col_means = [self.map['mean'][i,j] for j in filled_cols_idx]
best_pos = filled_cols_idx[np.argmin(col_means)]
for j in filled_cols_idx:
if j==best_pos:
continue
if self.ttest == 'ttest':
p_val = self._run_ttest(i, best_pos, j)
else:
p_val = self._run_wilcoxon(i, best_pos, j)
pval_outcome = pval_interpretation(p_val)
self.map['ttest'][i, j] = pval_outcome
if pval_outcome != 'Diff':
self.some_similar[j] = True
def compute(self):
self._addmap('fill', dtype=bool, func=lambda x: x is not None)
self._addmap('mean', dtype=float, func=np.mean)
self._addmap('std', dtype=float, func=np.std)
self._addmap('nobs', dtype=float, func=len)
self._addmap('rank', dtype=int, func=None)
self._addmap('color', dtype=object, func=None)
self._addmap('ttest', dtype=object, func=None)
self._addmap('latex', dtype=object, func=None)
self._addrank()
self._addcolor()
self._add_statistical_test()
if self.add_average:
self._addave()
self._modif = False
def _is_column_full(self, col):
return all(self.map['fill'][:, self.method_index[col]])
def _addave(self):
ave = Table(['ave'], self.methods, lower_is_better=self.lower_is_better, ttest=self.ttest, average=False,
missing=self.missing, missing_str=self.missing_str)
for col in self.methods:
values = None
if self._is_column_full(col):
if self.ttest == 'ttest':
values = np.asarray(self.map['mean'][:, self.method_index[col]])
else: # wilcoxon
values = np.concatenate(self.values[:, self.method_index[col]])
ave.add('ave', col, values)
self.average = ave
def add(self, benchmark, method, values):
if values is not None:
values = np.asarray(values)
if values.ndim==0:
values = values.flatten()
rid, cid = self._coordinates(benchmark, method)
self.map['values'][rid, cid] = values
self.touch()
def get(self, benchmark, method, attr='mean'):
self.update()
assert attr in self.map, f'unknwon attribute {attr}'
rid, cid = self._coordinates(benchmark, method)
if self.map['fill'][rid, cid]:
v = self.map[attr][rid, cid]
if v is None or (isinstance(v,float) and np.isnan(v)):
return self.missing
return v
else:
return self.missing
def _coordinates(self, benchmark, method):
assert benchmark in self.benchmark_index, f'benchmark {benchmark} out of range'
assert method in self.method_index, f'method {method} out of range'
rid = self.benchmark_index[benchmark]
cid = self.method_index[method]
return rid, cid
def get_average(self, method, attr='mean'):
self.update()
if self.add_average:
return self.average.get('ave', method, attr=attr)
return None
def get_color(self, benchmark, method):
color = self.get(benchmark, method, attr='color')
if color is None:
return ''
return color
def latex(self, benchmark, method):
self.update()
i,j = self._coordinates(benchmark, method)
if self.map['fill'][i,j] == False:
return self.missing_str
mean = self.map['mean'][i,j]
l = f" {mean:.{self.prec_mean}f}"
if self.clean_zero:
l = l.replace(' 0.', '.')
isbest = self.map['rank'][i,j] == 1
if isbest:
l = "\\textbf{"+l.strip()+"}"
stat = ''
if self.ttest is not None and self.some_similar[j]:
test_label = self.map['ttest'][i,j]
if test_label == 'Sim':
stat = '^{\dag\phantom{\dag}}'
elif test_label == 'Same':
stat = '^{\ddag}'
elif isbest or test_label == 'Diff':
stat = '^{\phantom{\ddag}}'
std = ''
if self.show_std:
std = self.map['std'][i,j]
std = f" {std:.{self.prec_std}f}"
if self.clean_zero:
std = std.replace(' 0.', '.')
std = f" \pm {std:{self.prec_std}}"
if stat!='' or std!='':
l = f'{l}${stat}{std}$'
if self.color:
l += ' ' + self.map['color'][i,j]
return l
def latexTabular(self, benchmark_replace={}, method_replace={}, average=True):
tab = ' & '
tab += ' & '.join([method_replace.get(col, col) for col in self.methods])
tab += ' \\\\\hline\n'
for row in self.benchmarks:
rowname = benchmark_replace.get(row, row)
tab += rowname + ' & '
tab += self.latexRow(row)
if average:
tab += '\hline\n'
tab += 'Average & '
tab += self.latexAverage()
return tab
def latexRow(self, benchmark, endl='\\\\\hline\n'):
s = [self.latex(benchmark, col) for col in self.methods]
s = ' & '.join(s)
s += ' ' + endl
return s
def latexAverage(self, endl='\\\\\hline\n'):
if self.add_average:
return self.average.latexRow('ave', endl=endl)
def getRankTable(self):
t = Table(benchmarks=self.benchmarks, methods=self.methods, prec_mean=0, average=True)
for rid, cid in self._getfilled():
row = self.benchmarks[rid]
col = self.methods[cid]
t.add(row, col, self.get(row, col, 'rank'))
t.compute()
return t
def dropMethods(self, methods):
drop_index = [self.method_index[m] for m in methods]
new_methods = np.delete(self.methods, drop_index)
new_index = {col:j for j, col in enumerate(new_methods)}
self.map['values'] = self.values[:,np.asarray([self.method_index[m] for m in new_methods], dtype=int)]
self.methods = new_methods
self.method_index = new_index
self.touch()
def pval_interpretation(p_val):
if 0.005 >= p_val:
return 'Diff'
elif 0.05 >= p_val > 0.005:
return 'Sim'
elif p_val > 0.05:
return 'Same'
def color_red2green_01(val, maxtone=50):
if np.isnan(val): return None
assert 0 <= val <= 1, f'val {val} out of range [0,1]'
# rescale to [-1,1]
val = val * 2 - 1
if val < 0:
color = 'red'
tone = maxtone * (-val)
else:
color = 'green'
tone = maxtone * val
return '\cellcolor{' + color + f'!{int(tone)}' + '}'

89
NewMethods/util.py Normal file
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@ -0,0 +1,89 @@
import numpy as np
nice = {
'mae':'AE',
'mrae':'RAE',
'ae':'AE',
'rae':'RAE',
'svmkld': 'SVM(KLD)',
'svmnkld': 'SVM(NKLD)',
'svmq': 'SVM(Q)',
'svmae': 'SVM(AE)',
'svmnae': 'SVM(NAE)',
'svmmae': 'SVM(AE)',
'svmmrae': 'SVM(RAE)',
'quanet': 'QuaNet',
'hdy': 'HDy',
'dys': 'DyS',
'epaccmaeptr': 'E(PACC)$_\mathrm{Ptr}$',
'epaccmaemae': 'E(PACC)$_\mathrm{AE}$',
'epaccmraeptr': 'E(PACC)$_\mathrm{Ptr}$',
'epaccmraemrae': 'E(PACC)$_\mathrm{RAE}$',
'svmperf':'',
'sanders': 'Sanders',
'semeval13': 'SemEval13',
'semeval14': 'SemEval14',
'semeval15': 'SemEval15',
'semeval16': 'SemEval16',
'Average': 'Average'
}
def nicerm(key):
return '\mathrm{'+nice[key]+'}'
def nicename(method, eval_name=None, side=False):
m = nice.get(method, method.upper())
if eval_name is not None:
o = '$^{' + nicerm(eval_name) + '}$'
m = (m+o).replace('$$','')
if side:
m = '\side{'+m+'}'
return m
def load_Gao_Sebastiani_previous_results():
def rename(method):
old2new = {
'kld': 'svmkld',
'nkld': 'svmnkld',
'qbeta2': 'svmq',
'em': 'sld'
}
return old2new.get(method, method)
gao_seb_results = {}
with open('./Gao_Sebastiani_results.txt', 'rt') as fin:
lines = fin.readlines()
for line in lines[1:]:
line = line.strip()
parts = line.lower().split()
if len(parts) == 4:
dataset, method, ae, rae = parts
else:
method, ae, rae = parts
learner, method = method.split('-')
method = rename(method)
gao_seb_results[f'{dataset}-{method}-ae'] = float(ae)
gao_seb_results[f'{dataset}-{method}-rae'] = float(rae)
return gao_seb_results
def get_ranks_from_Gao_Sebastiani():
gao_seb_results = load_Gao_Sebastiani_previous_results()
datasets = set([key.split('-')[0] for key in gao_seb_results.keys()])
methods = np.sort(np.unique([key.split('-')[1] for key in gao_seb_results.keys()]))
ranks = {}
for metric in ['ae', 'rae']:
for dataset in datasets:
scores = [gao_seb_results[f'{dataset}-{method}-{metric}'] for method in methods]
order = np.argsort(scores)
sorted_methods = methods[order]
for i, method in enumerate(sorted_methods):
ranks[f'{dataset}-{method}-{metric}'] = i+1
for method in methods:
rankave = np.mean([ranks[f'{dataset}-{method}-{metric}'] for dataset in datasets])
ranks[f'Average-{method}-{metric}'] = rankave
return ranks, gao_seb_results

149
README.md
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@ -1,92 +1,62 @@
# QuaPy
## version 0.2.1
QuaPy is an open source framework for quantification (a.k.a. supervised prevalence estimation, or learning to quantify)
QuaPy is an open source framework for Quantification (a.k.a. Supervised Prevalence Estimation)
written in Python.
QuaPy is based on the concept of "data sample", and provides implementations of the
most important aspects of the quantification workflow, such as (baseline and advanced)
quantification methods,
quantification-oriented model selection mechanisms, evaluation measures, and evaluations protocols
QuaPy roots on the concept of data sample, and provides implementations of
most important concepts in quantification literature, such as the most important
quantification baselines, many advanced quantification methods,
quantification-oriented model selection, many evaluation measures and protocols
used for evaluating quantification methods.
QuaPy also makes available commonly used datasets, and offers visualization tools
for facilitating the analysis and interpretation of the experimental results.
### Last updates:
* Version 0.2.1 is released! major changes can be consulted [here](CHANGE_LOG.txt).
* The developer API documentation is available [here](https://hlt-isti.github.io/QuaPy/index.html)
### Installation
```commandline
pip install quapy
```
### Cite QuaPy
If you find QuaPy useful (and we hope you will), please consider citing the original paper in your research:
```
@inproceedings{moreo2021quapy,
title={QuaPy: a python-based framework for quantification},
author={Moreo, Alejandro and Esuli, Andrea and Sebastiani, Fabrizio},
booktitle={Proceedings of the 30th ACM International Conference on Information \& Knowledge Management},
pages={4534--4543},
year={2021}
}
```
QuaPy also integrates commonly used datasets and offers visualization tools
for facilitating the analysis and interpretation of results.
## A quick example:
The following script fetches a dataset of tweets, trains, applies, and evaluates a quantifier based on the
_Adjusted Classify & Count_ quantification method, using, as the evaluation measure, the _Mean Absolute Error_ (MAE)
between the predicted and the true class prevalence values
The following script fetchs a Twitter dataset, trains and evaluates an
_Adjusted Classify & Count_ model in terms of the _Mean Absolute Error_ (MAE)
between the class prevalences estimated for the test set and the true prevalences
of the test set.
```python
import quapy as qp
from sklearn.linear_model import LogisticRegression
training, test = qp.datasets.fetch_UCIBinaryDataset("yeast").train_test
dataset = qp.datasets.fetch_twitter('semeval16')
# create an "Adjusted Classify & Count" quantifier
model = qp.method.aggregative.ACC()
Xtr, ytr = training.Xy
model.fit(Xtr, ytr)
model = qp.method.aggregative.ACC(LogisticRegression())
model.fit(dataset.training)
estim_prevalence = model.predict(test.X)
true_prevalence = test.prevalence()
estim_prevalences = model.quantify(dataset.test.instances)
true_prevalences = dataset.test.prevalence()
error = qp.error.mae(true_prevalences, estim_prevalences)
error = qp.error.mae(true_prevalence, estim_prevalence)
print(f'Mean Absolute Error (MAE)={error:.3f}')
```
Quantification is useful in scenarios characterized by prior probability shift. In other
words, we would be little interested in estimating the class prevalence values of the test set if
we could assume the IID assumption to hold, as this prevalence would be roughly equivalent to the
class prevalence of the training set. For this reason, any quantification model
should be tested across many samples, even ones characterized by class prevalence
values different or very different from those found in the training set.
QuaPy implements sampling procedures and evaluation protocols that automate this workflow.
See the [documentation](https://hlt-isti.github.io/QuaPy/manuals.html) for detailed examples.
Quantification is useful in scenarios of prior probability shift. In other
words, we would not be interested in estimating the class prevalences of the test set if
we could assume the IID assumption to hold, as this prevalence would simply coincide with the
class prevalence of the training set. For this reason, any Quantification model
should be tested across samples characterized by different class prevalences.
QuaPy implements sampling procedures and evaluation protocols that automates this endeavour.
See the [Wiki](https://github.com/HLT-ISTI/QuaPy/wiki) for detailed examples.
## Features
* Implementation of many popular quantification methods (Classify-&-Count and its variants, Expectation Maximization,
quantification methods based on structured output learning, HDy, QuaNet, quantification ensembles, among others).
* Support for uncertainty quantification via bootstrap-based and Bayesian methods, including confidence intervals and simplex-aware confidence regions.
* Versatile functionality for performing evaluation based on sampling generation protocols (e.g., APP, NPP, etc.).
* Implementation of most commonly used evaluation metrics (e.g., AE, RAE, NAE, NRAE, SE, KLD, NKLD, etc.).
* Datasets frequently used in quantification (textual and numeric), including:
* Implementation of most popular quantification methods (Classify-&-Count variants, Expectation-Maximization,
SVM-based variants for quantification, HDy, QuaNet, and Ensembles).
* Versatile functionality for performing evaluation based on artificial sampling protocols.
* Implementation of most commonly used evaluation metrics (e.g., MAE, MRAE, MSE, NKLD, etc.).
* Popular datasets for Quantification (textual and numeric) available, including:
* 32 UCI Machine Learning datasets.
* 11 Twitter quantification-by-sentiment datasets.
* 3 product reviews quantification-by-sentiment datasets.
* 4 tasks from LeQua 2022 competition and 4 tasks from LeQua 2024 competition
* IFCB for Plancton quantification
* Native support for binary and single-label multiclass quantification scenarios.
* Model selection functionality that minimizes quantification-oriented loss functions.
* Visualization tools for analysing the experimental results.
* 11 Twitter Sentiment datasets.
* 3 Reviews Sentiment datasets.
* Native supports for binary and single-label scenarios of quantification.
* Model selection functionality targeting quantification-oriented losses.
* Visualization tools for analysing results.
## Requirements
@ -98,29 +68,38 @@ quantification methods based on structured output learning, HDy, QuaNet, quantif
* pandas, xlrd
* matplotlib
## Contributing
## SVM-perf with quantification-oriented losses
In order to run experiments involving SVM(Q), SVM(KLD), SVM(NKLD),
SVM(AE), or SVM(RAE), you have to first download the
[svmperf](http://www.cs.cornell.edu/people/tj/svm_light/svm_perf.html)
package, apply the patch
[svm-perf-quantification-ext.patch](./svm-perf-quantification-ext.patch), and compile the sources.
The script [prepare_svmperf.sh](prepare_svmperf.sh) does all the job. Simply run:
In case you want to contribute improvements to quapy, please generate pull request to the "devel" branch.
```
./prepare_svmperf.sh
```
## Documentation
The resulting directory [svm_perf_quantification](./svm_perf_quantification) contains the
patched version of _svmperf_ with quantification-oriented losses.
Check out the [developer API documentation here](https://hlt-isti.github.io/QuaPy/index.html).
The [svm-perf-quantification-ext.patch](./svm-perf-quantification-ext.patch) is an extension of the patch made available by
[Esuli et al. 2015](https://dl.acm.org/doi/abs/10.1145/2700406?casa_token=8D2fHsGCVn0AAAAA:ZfThYOvrzWxMGfZYlQW_y8Cagg-o_l6X_PcF09mdETQ4Tu7jK98mxFbGSXp9ZSO14JkUIYuDGFG0)
that allows SVMperf to optimize for
the _Q_ measure as proposed by [Barranquero et al. 2015](https://www.sciencedirect.com/science/article/abs/pii/S003132031400291X)
and for the _KLD_ and _NKLD_ as proposed by [Esuli et al. 2015](https://dl.acm.org/doi/abs/10.1145/2700406?casa_token=8D2fHsGCVn0AAAAA:ZfThYOvrzWxMGfZYlQW_y8Cagg-o_l6X_PcF09mdETQ4Tu7jK98mxFbGSXp9ZSO14JkUIYuDGFG0)
for quantification.
This patch extends the former by also allowing SVMperf to optimize for
_AE_ and _RAE_.
Check out the [Manuals](https://hlt-isti.github.io/QuaPy/manuals.html), in which many code examples
## Wiki
Check out our [Wiki](https://github.com/HLT-ISTI/QuaPy/wiki) in which many examples
are provided:
* [Datasets](https://hlt-isti.github.io/QuaPy/manuals/datasets.html)
* [Evaluation](https://hlt-isti.github.io/QuaPy/manuals/evaluation.html)
* [Protocols](https://hlt-isti.github.io/QuaPy/manuals/protocols.html)
* [Methods](https://hlt-isti.github.io/QuaPy/manuals/methods.html)
* [SVMperf](https://hlt-isti.github.io/QuaPy/manuals/explicit-loss-minimization.html)
* [Model Selection](https://hlt-isti.github.io/QuaPy/manuals/model-selection.html)
* [Plotting](https://hlt-isti.github.io/QuaPy/manuals/plotting.html)
## Acknowledgments:
<img src="docs/source/SoBigData.png" alt="SoBigData++" width="250"/>
This work has been supported by the QuaDaSh project
_"Finanziato dall’Unione europea---Next Generation EU,
Missione 4 Componente 2 CUP B53D23026250001"_.
* [Datasets](https://github.com/HLT-ISTI/QuaPy/wiki/Datasets)
* [Evaluation](https://github.com/HLT-ISTI/QuaPy/wiki/Evaluation)
* [Methods](https://github.com/HLT-ISTI/QuaPy/wiki/Methods)
* [Model Selection](https://github.com/HLT-ISTI/QuaPy/wiki/Model-Selection)
* [Plotting](https://github.com/HLT-ISTI/QuaPy/wiki/Plotting)

40
TODO.txt
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@ -1,24 +1,16 @@
Solve the warnings issue; right now there is a warning ignore in method/__init__.py:
Add 'platt' to calib options in EMQ?
Allow n_prevpoints in APP to be specified by a user-defined grid?
Add the fix suggested by Alexander?
"For a more general application, I would maybe first establish a per-class threshold value of plausible prevalence
based on the number of actual positives and the required sample size; e.g., for sample_size=100 and actual
positives [10, 100, 500] -> [0.1, 1.0, 1.0], meaning that class 0 can be sampled at most at 0.1 prevalence, while
the others can be sampled up to 1. prevalence. Then, when a prevalence value is requested, e.g., [0.33, 0.33, 0.33],
we may either clip each value and normalize (as you suggest for the extreme case, e.g., [0.1, 0.33, 0.33]/sum) or
scale each value by per-class thresholds, i.e., [0.33*0.1, 0.33*1, 0.33*1]/sum."
- This affects LabelledCollection
- This functionality should be accessible via sampling protocols and evaluation functions
- [TODO] document confidence in manuals
- [TODO] add ensemble methods SC-MQ, MC-SQ, MC-MQ
- [TODO] add HistNetQ
- [TODO] add CDE-iteration and Bayes-CDE methods
- [TODO] add Friedman's method and DeBias
- [TODO] check ignore warning stuff
check https://docs.python.org/3/library/warnings.html#temporarily-suppressing-warnings
- [TODO] nmd and md are not selectable from qp.evaluation.evaluate as a string
Documentation with sphinx
Add NAE, NRAE
Add "measures for evaluating ordinal"?
Document methods with paper references
In binary quantification (hp, kindle, imdb) we used F1 in the minority class (which in kindle and hp happens to be the
negative class). This is not covered in this new implementation, in which the binary case is not treated as such, but as
an instance of single-label with 2 labels. Check
Add classnames to LabelledCollection ?
Add automatic reindex of class labels in LabelledCollection (currently, class indexes should be ordered and with no gaps)
Add datasets for topic.
Clarify whether QuaNet is an aggregative method or not.
Explore the hyperparameter "number of bins" in HDy
Rename EMQ to SLD ?
How many times is the system of equations for ACC and PACC not solved? How many times is it clipped? Do they sum up
to one always?
Parallelize the kFCV in ACC and PACC

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@ -1 +0,0 @@
build/

1
docs/.nojekyll
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@ -1 +0,0 @@

20
docs/Makefile
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@ -1,20 +0,0 @@
# Minimal makefile for Sphinx documentation
#
# You can set these variables from the command line, and also
# from the environment for the first two.
SPHINXOPTS ?=
SPHINXBUILD ?= sphinx-build
SOURCEDIR = source
BUILDDIR = build
# Put it first so that "make" without argument is like "make help".
help:
@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
.PHONY: help Makefile
# Catch-all target: route all unknown targets to Sphinx using the new
# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
%: Makefile
@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

464
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@ -1,464 +0,0 @@
<!DOCTYPE html>
<html lang="en" data-content_root="../" >
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Overview: module code &#8212; QuaPy: A Python-based open-source framework for quantification 0.2.1 documentation</title>
<script data-cfasync="false">
document.documentElement.dataset.mode = localStorage.getItem("mode") || "";
document.documentElement.dataset.theme = localStorage.getItem("theme") || "";
</script>
<!--
this give us a css class that will be invisible only if js is disabled
-->
<noscript>
<style>
.pst-js-only { display: none !important; }
</style>
</noscript>
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<link href="../_static/styles/theme.css?digest=90905a2f556bf617f1a9" rel="stylesheet" />
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<h1>Source code for quapy.classification.calibration</h1><div class="highlight"><pre>
<span></span><span class="kn">from</span><span class="w"> </span><span class="nn">copy</span><span class="w"> </span><span class="kn">import</span> <span class="n">deepcopy</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">sklearn.base</span><span class="w"> </span><span class="kn">import</span> <span class="n">BaseEstimator</span><span class="p">,</span> <span class="n">clone</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">sklearn.model_selection</span><span class="w"> </span><span class="kn">import</span> <span class="n">cross_val_predict</span><span class="p">,</span> <span class="n">train_test_split</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">sklearn.preprocessing</span><span class="w"> </span><span class="kn">import</span> <span class="n">LabelEncoder</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">sklearn.utils.validation</span><span class="w"> </span><span class="kn">import</span> <span class="n">check_X_y</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
<span class="c1"># Wrappers of calibration defined by Alexandari et al. in paper &lt;http://proceedings.mlr.press/v119/alexandari20a.html&gt;</span>
<span class="c1"># requires &quot;pip install abstension&quot;</span>
<span class="c1"># see https://github.com/kundajelab/abstention</span>
<span class="k">def</span><span class="w"> </span><span class="nf">_require_abstention_calibration</span><span class="p">():</span>
<span class="k">try</span><span class="p">:</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">abstention.calibration</span><span class="w"> </span><span class="kn">import</span> <span class="n">NoBiasVectorScaling</span><span class="p">,</span> <span class="n">TempScaling</span><span class="p">,</span> <span class="n">VectorScaling</span>
<span class="k">except</span> <span class="ne">ImportError</span> <span class="k">as</span> <span class="n">exc</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ImportError</span><span class="p">(</span>
<span class="s2">&quot;Calibration methods in quapy.classification.calibration require the optional &quot;</span>
<span class="s2">&quot;&#39;abstention&#39; package.&quot;</span>
<span class="p">)</span> <span class="kn">from</span><span class="w"> </span><span class="nn">exc</span>
<span class="k">return</span> <span class="n">NoBiasVectorScaling</span><span class="p">,</span> <span class="n">TempScaling</span><span class="p">,</span> <span class="n">VectorScaling</span>
<div class="viewcode-block" id="RecalibratedProbabilisticClassifier">
<a class="viewcode-back" href="../../../quapy.classification.html#quapy.classification.calibration.RecalibratedProbabilisticClassifier">[docs]</a>
<span class="k">class</span><span class="w"> </span><span class="nc">RecalibratedProbabilisticClassifier</span><span class="p">:</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Abstract class for (re)calibration method from `abstention.calibration`, as defined in</span>
<span class="sd"> `Alexandari, A., Kundaje, A., &amp; Shrikumar, A. (2020, November). Maximum likelihood with bias-corrected calibration</span>
<span class="sd"> is hard-to-beat at label shift adaptation. In International Conference on Machine Learning (pp. 222-232). PMLR.</span>
<span class="sd"> &lt;http://proceedings.mlr.press/v119/alexandari20a.html&gt;`_:</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">pass</span></div>
<div class="viewcode-block" id="RecalibratedProbabilisticClassifierBase">
<a class="viewcode-back" href="../../../quapy.classification.html#quapy.classification.calibration.RecalibratedProbabilisticClassifierBase">[docs]</a>
<span class="k">class</span><span class="w"> </span><span class="nc">RecalibratedProbabilisticClassifierBase</span><span class="p">(</span><span class="n">BaseEstimator</span><span class="p">,</span> <span class="n">RecalibratedProbabilisticClassifier</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Applies a (re)calibration method from `abstention.calibration`, as defined in</span>
<span class="sd"> `Alexandari et al. paper &lt;http://proceedings.mlr.press/v119/alexandari20a.html&gt;`_.</span>
<span class="sd"> :param classifier: a scikit-learn probabilistic classifier</span>
<span class="sd"> :param calibrator: the calibration object (an instance of abstention.calibration.CalibratorFactory)</span>
<span class="sd"> :param val_split: indicate an integer k for performing kFCV to obtain the posterior probabilities, or a float p</span>
<span class="sd"> in (0,1) to indicate that the posteriors are obtained in a stratified validation split containing p% of the</span>
<span class="sd"> training instances (the rest is used for training). In any case, the classifier is retrained in the whole</span>
<span class="sd"> training set afterwards. Default value is 5.</span>
<span class="sd"> :param n_jobs: indicate the number of parallel workers (only when val_split is an integer); default=None</span>
<span class="sd"> :param verbose: whether or not to display information in the standard output</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">classifier</span><span class="p">,</span> <span class="n">calibrator</span><span class="p">,</span> <span class="n">val_split</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">n_jobs</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">verbose</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">classifier</span> <span class="o">=</span> <span class="n">classifier</span>
<span class="bp">self</span><span class="o">.</span><span class="n">calibrator</span> <span class="o">=</span> <span class="n">calibrator</span>
<span class="bp">self</span><span class="o">.</span><span class="n">val_split</span> <span class="o">=</span> <span class="n">val_split</span>
<span class="bp">self</span><span class="o">.</span><span class="n">n_jobs</span> <span class="o">=</span> <span class="n">n_jobs</span>
<span class="bp">self</span><span class="o">.</span><span class="n">verbose</span> <span class="o">=</span> <span class="n">verbose</span>
<div class="viewcode-block" id="RecalibratedProbabilisticClassifierBase.fit">
<a class="viewcode-back" href="../../../quapy.classification.html#quapy.classification.calibration.RecalibratedProbabilisticClassifierBase.fit">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">fit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">,</span> <span class="n">y</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Fits the calibration for the probabilistic classifier.</span>
<span class="sd"> :param X: array-like of shape `(n_samples, n_features)` with the data instances</span>
<span class="sd"> :param y: array-like of shape `(n_samples,)` with the class labels</span>
<span class="sd"> :return: self</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">k</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">val_split</span>
<span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">k</span><span class="p">,</span> <span class="nb">int</span><span class="p">):</span>
<span class="k">if</span> <span class="n">k</span> <span class="o">&lt;</span> <span class="mi">2</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s1">&#39;wrong value for val_split: the number of folds must be &gt; 2&#39;</span><span class="p">)</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">fit_cv</span><span class="p">(</span><span class="n">X</span><span class="p">,</span> <span class="n">y</span><span class="p">)</span>
<span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">k</span><span class="p">,</span> <span class="nb">float</span><span class="p">):</span>
<span class="k">if</span> <span class="ow">not</span> <span class="p">(</span><span class="mi">0</span> <span class="o">&lt;</span> <span class="n">k</span> <span class="o">&lt;</span> <span class="mi">1</span><span class="p">):</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s1">&#39;wrong value for val_split: the proportion of validation documents must be in (0,1)&#39;</span><span class="p">)</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">fit_tr_val</span><span class="p">(</span><span class="n">X</span><span class="p">,</span> <span class="n">y</span><span class="p">)</span></div>
<div class="viewcode-block" id="RecalibratedProbabilisticClassifierBase.fit_cv">
<a class="viewcode-back" href="../../../quapy.classification.html#quapy.classification.calibration.RecalibratedProbabilisticClassifierBase.fit_cv">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">fit_cv</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">,</span> <span class="n">y</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Fits the calibration in a cross-validation manner, i.e., it generates posterior probabilities for all</span>
<span class="sd"> training instances via cross-validation, and then retrains the classifier on all training instances.</span>
<span class="sd"> The posterior probabilities thus generated are used for calibrating the outputs of the classifier.</span>
<span class="sd"> :param X: array-like of shape `(n_samples, n_features)` with the data instances</span>
<span class="sd"> :param y: array-like of shape `(n_samples,)` with the class labels</span>
<span class="sd"> :return: self</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">posteriors</span> <span class="o">=</span> <span class="n">cross_val_predict</span><span class="p">(</span>
<span class="bp">self</span><span class="o">.</span><span class="n">classifier</span><span class="p">,</span> <span class="n">X</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">cv</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">val_split</span><span class="p">,</span> <span class="n">n_jobs</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">n_jobs</span><span class="p">,</span> <span class="n">verbose</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">verbose</span><span class="p">,</span> <span class="n">method</span><span class="o">=</span><span class="s1">&#39;predict_proba&#39;</span>
<span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">classifier</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="n">X</span><span class="p">,</span> <span class="n">y</span><span class="p">)</span>
<span class="n">nclasses</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">unique</span><span class="p">(</span><span class="n">y</span><span class="p">))</span>
<span class="bp">self</span><span class="o">.</span><span class="n">calibration_function</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">calibrator</span><span class="p">(</span><span class="n">posteriors</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">eye</span><span class="p">(</span><span class="n">nclasses</span><span class="p">)[</span><span class="n">y</span><span class="p">],</span> <span class="n">posterior_supplied</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="k">return</span> <span class="bp">self</span></div>
<div class="viewcode-block" id="RecalibratedProbabilisticClassifierBase.fit_tr_val">
<a class="viewcode-back" href="../../../quapy.classification.html#quapy.classification.calibration.RecalibratedProbabilisticClassifierBase.fit_tr_val">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">fit_tr_val</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">,</span> <span class="n">y</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Fits the calibration in a train/val-split manner, i.e.t, it partitions the training instances into a</span>
<span class="sd"> training and a validation set, and then uses the training samples to learn classifier which is then used</span>
<span class="sd"> to generate posterior probabilities for the held-out validation data. These posteriors are used to calibrate</span>
<span class="sd"> the classifier. The classifier is not retrained on the whole dataset.</span>
<span class="sd"> :param X: array-like of shape `(n_samples, n_features)` with the data instances</span>
<span class="sd"> :param y: array-like of shape `(n_samples,)` with the class labels</span>
<span class="sd"> :return: self</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">Xtr</span><span class="p">,</span> <span class="n">Xva</span><span class="p">,</span> <span class="n">ytr</span><span class="p">,</span> <span class="n">yva</span> <span class="o">=</span> <span class="n">train_test_split</span><span class="p">(</span><span class="n">X</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">test_size</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">val_split</span><span class="p">,</span> <span class="n">stratify</span><span class="o">=</span><span class="n">y</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">classifier</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="n">Xtr</span><span class="p">,</span> <span class="n">ytr</span><span class="p">)</span>
<span class="n">posteriors</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">classifier</span><span class="o">.</span><span class="n">predict_proba</span><span class="p">(</span><span class="n">Xva</span><span class="p">)</span>
<span class="n">nclasses</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">unique</span><span class="p">(</span><span class="n">yva</span><span class="p">))</span>
<span class="bp">self</span><span class="o">.</span><span class="n">calibration_function</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">calibrator</span><span class="p">(</span><span class="n">posteriors</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">eye</span><span class="p">(</span><span class="n">nclasses</span><span class="p">)[</span><span class="n">yva</span><span class="p">],</span> <span class="n">posterior_supplied</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="k">return</span> <span class="bp">self</span></div>
<div class="viewcode-block" id="RecalibratedProbabilisticClassifierBase.predict">
<a class="viewcode-back" href="../../../quapy.classification.html#quapy.classification.calibration.RecalibratedProbabilisticClassifierBase.predict">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">predict</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Predicts class labels for the data instances in `X`</span>
<span class="sd"> :param X: array-like of shape `(n_samples, n_features)` with the data instances</span>
<span class="sd"> :return: array-like of shape `(n_samples,)` with the class label predictions</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">classifier</span><span class="o">.</span><span class="n">predict</span><span class="p">(</span><span class="n">X</span><span class="p">)</span></div>
<div class="viewcode-block" id="RecalibratedProbabilisticClassifierBase.predict_proba">
<a class="viewcode-back" href="../../../quapy.classification.html#quapy.classification.calibration.RecalibratedProbabilisticClassifierBase.predict_proba">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">predict_proba</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Generates posterior probabilities for the data instances in `X`</span>
<span class="sd"> :param X: array-like of shape `(n_samples, n_features)` with the data instances</span>
<span class="sd"> :return: array-like of shape `(n_samples, n_classes)` with posterior probabilities</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">posteriors</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">classifier</span><span class="o">.</span><span class="n">predict_proba</span><span class="p">(</span><span class="n">X</span><span class="p">)</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">calibration_function</span><span class="p">(</span><span class="n">posteriors</span><span class="p">)</span></div>
<span class="nd">@property</span>
<span class="k">def</span><span class="w"> </span><span class="nf">classes_</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Returns the classes on which the classifier has been trained on</span>
<span class="sd"> :return: array-like of shape `(n_classes)`</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">classifier</span><span class="o">.</span><span class="n">classes_</span></div>
<div class="viewcode-block" id="NBVSCalibration">
<a class="viewcode-back" href="../../../quapy.classification.html#quapy.classification.calibration.NBVSCalibration">[docs]</a>
<span class="k">class</span><span class="w"> </span><span class="nc">NBVSCalibration</span><span class="p">(</span><span class="n">RecalibratedProbabilisticClassifierBase</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Applies the No-Bias Vector Scaling (NBVS) calibration method from `abstention.calibration`, as defined in</span>
<span class="sd"> `Alexandari et al. paper &lt;http://proceedings.mlr.press/v119/alexandari20a.html&gt;`_:</span>
<span class="sd"> :param classifier: a scikit-learn probabilistic classifier</span>
<span class="sd"> :param val_split: indicate an integer k for performing kFCV to obtain the posterior prevalences, or a float p</span>
<span class="sd"> in (0,1) to indicate that the posteriors are obtained in a stratified validation split containing p% of the</span>
<span class="sd"> training instances (the rest is used for training). In any case, the classifier is retrained in the whole</span>
<span class="sd"> training set afterwards. Default value is 5.</span>
<span class="sd"> :param n_jobs: indicate the number of parallel workers (only when val_split is an integer)</span>
<span class="sd"> :param verbose: whether or not to display information in the standard output</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">classifier</span><span class="p">,</span> <span class="n">val_split</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">n_jobs</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">verbose</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
<span class="n">NoBiasVectorScaling</span><span class="p">,</span> <span class="n">_</span><span class="p">,</span> <span class="n">_</span> <span class="o">=</span> <span class="n">_require_abstention_calibration</span><span class="p">()</span>
<span class="bp">self</span><span class="o">.</span><span class="n">classifier</span> <span class="o">=</span> <span class="n">classifier</span>
<span class="bp">self</span><span class="o">.</span><span class="n">calibrator</span> <span class="o">=</span> <span class="n">NoBiasVectorScaling</span><span class="p">(</span><span class="n">verbose</span><span class="o">=</span><span class="n">verbose</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">val_split</span> <span class="o">=</span> <span class="n">val_split</span>
<span class="bp">self</span><span class="o">.</span><span class="n">n_jobs</span> <span class="o">=</span> <span class="n">n_jobs</span>
<span class="bp">self</span><span class="o">.</span><span class="n">verbose</span> <span class="o">=</span> <span class="n">verbose</span></div>
<div class="viewcode-block" id="BCTSCalibration">
<a class="viewcode-back" href="../../../quapy.classification.html#quapy.classification.calibration.BCTSCalibration">[docs]</a>
<span class="k">class</span><span class="w"> </span><span class="nc">BCTSCalibration</span><span class="p">(</span><span class="n">RecalibratedProbabilisticClassifierBase</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Applies the Bias-Corrected Temperature Scaling (BCTS) calibration method from `abstention.calibration`, as defined in</span>
<span class="sd"> `Alexandari et al. paper &lt;http://proceedings.mlr.press/v119/alexandari20a.html&gt;`_:</span>
<span class="sd"> :param classifier: a scikit-learn probabilistic classifier</span>
<span class="sd"> :param val_split: indicate an integer k for performing kFCV to obtain the posterior prevalences, or a float p</span>
<span class="sd"> in (0,1) to indicate that the posteriors are obtained in a stratified validation split containing p% of the</span>
<span class="sd"> training instances (the rest is used for training). In any case, the classifier is retrained in the whole</span>
<span class="sd"> training set afterwards. Default value is 5.</span>
<span class="sd"> :param n_jobs: indicate the number of parallel workers (only when val_split is an integer)</span>
<span class="sd"> :param verbose: whether or not to display information in the standard output</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">classifier</span><span class="p">,</span> <span class="n">val_split</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">n_jobs</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">verbose</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
<span class="n">_</span><span class="p">,</span> <span class="n">TempScaling</span><span class="p">,</span> <span class="n">_</span> <span class="o">=</span> <span class="n">_require_abstention_calibration</span><span class="p">()</span>
<span class="bp">self</span><span class="o">.</span><span class="n">classifier</span> <span class="o">=</span> <span class="n">classifier</span>
<span class="bp">self</span><span class="o">.</span><span class="n">calibrator</span> <span class="o">=</span> <span class="n">TempScaling</span><span class="p">(</span><span class="n">verbose</span><span class="o">=</span><span class="n">verbose</span><span class="p">,</span> <span class="n">bias_positions</span><span class="o">=</span><span class="s1">&#39;all&#39;</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">val_split</span> <span class="o">=</span> <span class="n">val_split</span>
<span class="bp">self</span><span class="o">.</span><span class="n">n_jobs</span> <span class="o">=</span> <span class="n">n_jobs</span>
<span class="bp">self</span><span class="o">.</span><span class="n">verbose</span> <span class="o">=</span> <span class="n">verbose</span></div>
<div class="viewcode-block" id="TSCalibration">
<a class="viewcode-back" href="../../../quapy.classification.html#quapy.classification.calibration.TSCalibration">[docs]</a>
<span class="k">class</span><span class="w"> </span><span class="nc">TSCalibration</span><span class="p">(</span><span class="n">RecalibratedProbabilisticClassifierBase</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Applies the Temperature Scaling (TS) calibration method from `abstention.calibration`, as defined in</span>
<span class="sd"> `Alexandari et al. paper &lt;http://proceedings.mlr.press/v119/alexandari20a.html&gt;`_:</span>
<span class="sd"> :param classifier: a scikit-learn probabilistic classifier</span>
<span class="sd"> :param val_split: indicate an integer k for performing kFCV to obtain the posterior prevalences, or a float p</span>
<span class="sd"> in (0,1) to indicate that the posteriors are obtained in a stratified validation split containing p% of the</span>
<span class="sd"> training instances (the rest is used for training). In any case, the classifier is retrained in the whole</span>
<span class="sd"> training set afterwards. Default value is 5.</span>
<span class="sd"> :param n_jobs: indicate the number of parallel workers (only when val_split is an integer)</span>
<span class="sd"> :param verbose: whether or not to display information in the standard output</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">classifier</span><span class="p">,</span> <span class="n">val_split</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">n_jobs</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">verbose</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
<span class="n">_</span><span class="p">,</span> <span class="n">TempScaling</span><span class="p">,</span> <span class="n">_</span> <span class="o">=</span> <span class="n">_require_abstention_calibration</span><span class="p">()</span>
<span class="bp">self</span><span class="o">.</span><span class="n">classifier</span> <span class="o">=</span> <span class="n">classifier</span>
<span class="bp">self</span><span class="o">.</span><span class="n">calibrator</span> <span class="o">=</span> <span class="n">TempScaling</span><span class="p">(</span><span class="n">verbose</span><span class="o">=</span><span class="n">verbose</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">val_split</span> <span class="o">=</span> <span class="n">val_split</span>
<span class="bp">self</span><span class="o">.</span><span class="n">n_jobs</span> <span class="o">=</span> <span class="n">n_jobs</span>
<span class="bp">self</span><span class="o">.</span><span class="n">verbose</span> <span class="o">=</span> <span class="n">verbose</span></div>
<div class="viewcode-block" id="VSCalibration">
<a class="viewcode-back" href="../../../quapy.classification.html#quapy.classification.calibration.VSCalibration">[docs]</a>
<span class="k">class</span><span class="w"> </span><span class="nc">VSCalibration</span><span class="p">(</span><span class="n">RecalibratedProbabilisticClassifierBase</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Applies the Vector Scaling (VS) calibration method from `abstention.calibration`, as defined in</span>
<span class="sd"> `Alexandari et al. paper &lt;http://proceedings.mlr.press/v119/alexandari20a.html&gt;`_:</span>
<span class="sd"> :param classifier: a scikit-learn probabilistic classifier</span>
<span class="sd"> :param val_split: indicate an integer k for performing kFCV to obtain the posterior prevalences, or a float p</span>
<span class="sd"> in (0,1) to indicate that the posteriors are obtained in a stratified validation split containing p% of the</span>
<span class="sd"> training instances (the rest is used for training). In any case, the classifier is retrained in the whole</span>
<span class="sd"> training set afterwards. Default value is 5.</span>
<span class="sd"> :param n_jobs: indicate the number of parallel workers (only when val_split is an integer)</span>
<span class="sd"> :param verbose: whether or not to display information in the standard output</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">classifier</span><span class="p">,</span> <span class="n">val_split</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">n_jobs</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">verbose</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
<span class="n">_</span><span class="p">,</span> <span class="n">_</span><span class="p">,</span> <span class="n">VectorScaling</span> <span class="o">=</span> <span class="n">_require_abstention_calibration</span><span class="p">()</span>
<span class="bp">self</span><span class="o">.</span><span class="n">classifier</span> <span class="o">=</span> <span class="n">classifier</span>
<span class="bp">self</span><span class="o">.</span><span class="n">calibrator</span> <span class="o">=</span> <span class="n">VectorScaling</span><span class="p">(</span><span class="n">verbose</span><span class="o">=</span><span class="n">verbose</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">val_split</span> <span class="o">=</span> <span class="n">val_split</span>
<span class="bp">self</span><span class="o">.</span><span class="n">n_jobs</span> <span class="o">=</span> <span class="n">n_jobs</span>
<span class="bp">self</span><span class="o">.</span><span class="n">verbose</span> <span class="o">=</span> <span class="n">verbose</span></div>
<div class="viewcode-block" id="TemperatureScalingFromLogits">
<a class="viewcode-back" href="../../../quapy.classification.html#quapy.classification.calibration.TemperatureScalingFromLogits">[docs]</a>
<span class="k">class</span><span class="w"> </span><span class="nc">TemperatureScalingFromLogits</span><span class="p">(</span><span class="n">BaseEstimator</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Calibrates a matrix of logits by learning a temperature-scaling mapping</span>
<span class="sd"> with the calibration methods from `abstention.calibration`.</span>
<span class="sd"> This estimator is useful when the inputs are already logits produced by a</span>
<span class="sd"> pretrained classifier, and the goal is to transform them directly into</span>
<span class="sd"> calibrated posterior probabilities without retraining the underlying model.</span>
<span class="sd"> :param bias_corrected: if True, uses Bias-Corrected Temperature Scaling</span>
<span class="sd"> (BCTS); otherwise, uses standard Temperature Scaling (TS)</span>
<span class="sd"> :param verbose: whether the underlying calibrator should display progress</span>
<span class="sd"> information</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">bias_corrected</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">verbose</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">bias_corrected</span> <span class="o">=</span> <span class="n">bias_corrected</span>
<span class="bp">self</span><span class="o">.</span><span class="n">verbose</span> <span class="o">=</span> <span class="n">verbose</span>
<div class="viewcode-block" id="TemperatureScalingFromLogits.fit">
<a class="viewcode-back" href="../../../quapy.classification.html#quapy.classification.calibration.TemperatureScalingFromLogits.fit">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">fit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">,</span> <span class="n">y</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Fits the logits calibrator.</span>
<span class="sd"> :param X: array-like of shape `(n_samples, n_classes)` containing</span>
<span class="sd"> logits</span>
<span class="sd"> :param y: array-like of shape `(n_samples,)` containing class labels</span>
<span class="sd"> :return: self</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">X</span><span class="p">,</span> <span class="n">y</span> <span class="o">=</span> <span class="n">check_X_y</span><span class="p">(</span><span class="n">X</span><span class="p">,</span> <span class="n">y</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">label_encoder_</span> <span class="o">=</span> <span class="n">LabelEncoder</span><span class="p">()</span>
<span class="n">y_enc</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">label_encoder_</span><span class="o">.</span><span class="n">fit_transform</span><span class="p">(</span><span class="n">y</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">classes_</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">label_encoder_</span><span class="o">.</span><span class="n">classes_</span>
<span class="n">n_classes</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">classes_</span><span class="p">)</span>
<span class="n">logits_dim</span> <span class="o">=</span> <span class="n">X</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
<span class="k">if</span> <span class="n">n_classes</span> <span class="o">!=</span> <span class="n">logits_dim</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
<span class="sa">f</span><span class="s1">&#39;mismatch between the number of classes (</span><span class="si">{</span><span class="n">n_classes</span><span class="si">}</span><span class="s1">) and the &#39;</span>
<span class="sa">f</span><span class="s1">&#39;dimensionality of the logits (</span><span class="si">{</span><span class="n">logits_dim</span><span class="si">}</span><span class="s1">)&#39;</span>
<span class="p">)</span>
<span class="n">_</span><span class="p">,</span> <span class="n">TempScaling</span><span class="p">,</span> <span class="n">_</span> <span class="o">=</span> <span class="n">_require_abstention_calibration</span><span class="p">()</span>
<span class="n">calibrator</span> <span class="o">=</span> <span class="n">TempScaling</span><span class="p">(</span>
<span class="n">verbose</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">verbose</span><span class="p">,</span>
<span class="n">bias_positions</span><span class="o">=</span><span class="s1">&#39;all&#39;</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">bias_corrected</span> <span class="k">else</span> <span class="p">[],</span>
<span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">calibrator_</span> <span class="o">=</span> <span class="n">calibrator</span>
<span class="bp">self</span><span class="o">.</span><span class="n">calibration_function_</span> <span class="o">=</span> <span class="n">calibrator</span><span class="p">(</span><span class="n">X</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">eye</span><span class="p">(</span><span class="n">n_classes</span><span class="p">)[</span><span class="n">y_enc</span><span class="p">])</span>
<span class="k">return</span> <span class="bp">self</span></div>
<div class="viewcode-block" id="TemperatureScalingFromLogits.predict_proba">
<a class="viewcode-back" href="../../../quapy.classification.html#quapy.classification.calibration.TemperatureScalingFromLogits.predict_proba">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">predict_proba</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Converts logits into calibrated posterior probabilities.</span>
<span class="sd"> :param X: array-like of shape `(n_samples, n_classes)` containing</span>
<span class="sd"> logits</span>
<span class="sd"> :return: array-like of shape `(n_samples, n_classes)` with calibrated</span>
<span class="sd"> posterior probabilities</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">calibration_function_</span><span class="p">(</span><span class="n">X</span><span class="p">)</span></div>
<div class="viewcode-block" id="TemperatureScalingFromLogits.predict">
<a class="viewcode-back" href="../../../quapy.classification.html#quapy.classification.calibration.TemperatureScalingFromLogits.predict">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">predict</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Predicts class labels after calibration.</span>
<span class="sd"> :param X: array-like of shape `(n_samples, n_classes)` containing</span>
<span class="sd"> logits</span>
<span class="sd"> :return: array-like of shape `(n_samples,)` with class label</span>
<span class="sd"> predictions</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">posteriors</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">predict_proba</span><span class="p">(</span><span class="n">X</span><span class="p">)</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">label_encoder_</span><span class="o">.</span><span class="n">inverse_transform</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">argmax</span><span class="p">(</span><span class="n">posteriors</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">))</span></div>
</div>
</pre></div>
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<h1>Source code for quapy.classification.methods</h1><div class="highlight"><pre>
<span></span><span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">sklearn.base</span><span class="w"> </span><span class="kn">import</span> <span class="n">BaseEstimator</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">sklearn.decomposition</span><span class="w"> </span><span class="kn">import</span> <span class="n">TruncatedSVD</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">sklearn.linear_model</span><span class="w"> </span><span class="kn">import</span> <span class="n">LogisticRegression</span>
<div class="viewcode-block" id="LowRankLogisticRegression">
<a class="viewcode-back" href="../../../quapy.classification.html#quapy.classification.methods.LowRankLogisticRegression">[docs]</a>
<span class="k">class</span><span class="w"> </span><span class="nc">LowRankLogisticRegression</span><span class="p">(</span><span class="n">BaseEstimator</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> An example of a classification method (i.e., an object that implements `fit`, `predict`, and `predict_proba`)</span>
<span class="sd"> that also generates embedded inputs (i.e., that implements `transform`), as those required for</span>
<span class="sd"> :class:`quapy.method.neural.QuaNet`. This is a mock method to allow for easily instantiating</span>
<span class="sd"> :class:`quapy.method.neural.QuaNet` on array-like real-valued instances.</span>
<span class="sd"> The transformation consists of applying :class:`sklearn.decomposition.TruncatedSVD`</span>
<span class="sd"> while classification is performed using :class:`sklearn.linear_model.LogisticRegression` on the low-rank space.</span>
<span class="sd"> :param n_components: the number of principal components to retain</span>
<span class="sd"> :param kwargs: parameters for the</span>
<span class="sd"> `Logistic Regression &lt;https://scikit-learn.org/stable/modules/generated/sklearn.linear_model.LogisticRegression.html&gt;`__ classifier</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">n_components</span><span class="o">=</span><span class="mi">100</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">n_components</span> <span class="o">=</span> <span class="n">n_components</span>
<span class="bp">self</span><span class="o">.</span><span class="n">classifier</span> <span class="o">=</span> <span class="n">LogisticRegression</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
<div class="viewcode-block" id="LowRankLogisticRegression.get_params">
<a class="viewcode-back" href="../../../quapy.classification.html#quapy.classification.methods.LowRankLogisticRegression.get_params">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">get_params</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Get hyper-parameters for this estimator.</span>
<span class="sd"> :return: a dictionary with parameter names mapped to their values</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">params</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;n_components&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">n_components</span><span class="p">}</span>
<span class="n">params</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">classifier</span><span class="o">.</span><span class="n">get_params</span><span class="p">())</span>
<span class="k">return</span> <span class="n">params</span></div>
<div class="viewcode-block" id="LowRankLogisticRegression.set_params">
<a class="viewcode-back" href="../../../quapy.classification.html#quapy.classification.methods.LowRankLogisticRegression.set_params">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">set_params</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">params</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Set the parameters of this estimator.</span>
<span class="sd"> :param parameters: a `**kwargs` dictionary with the estimator parameters for</span>
<span class="sd"> `Logistic Regression &lt;https://scikit-learn.org/stable/modules/generated/sklearn.linear_model.LogisticRegression.html&gt;`__</span>
<span class="sd"> and eventually also `n_components` for `TruncatedSVD`</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">params_</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="n">params</span><span class="p">)</span>
<span class="k">if</span> <span class="s1">&#39;n_components&#39;</span> <span class="ow">in</span> <span class="n">params_</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">n_components</span> <span class="o">=</span> <span class="n">params_</span><span class="p">[</span><span class="s1">&#39;n_components&#39;</span><span class="p">]</span>
<span class="k">del</span> <span class="n">params_</span><span class="p">[</span><span class="s1">&#39;n_components&#39;</span><span class="p">]</span>
<span class="bp">self</span><span class="o">.</span><span class="n">classifier</span><span class="o">.</span><span class="n">set_params</span><span class="p">(</span><span class="o">**</span><span class="n">params_</span><span class="p">)</span></div>
<div class="viewcode-block" id="LowRankLogisticRegression.fit">
<a class="viewcode-back" href="../../../quapy.classification.html#quapy.classification.methods.LowRankLogisticRegression.fit">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">fit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">,</span> <span class="n">y</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Fit the model according to the given training data. The fit consists of</span>
<span class="sd"> fitting `TruncatedSVD` and then `LogisticRegression` on the low-rank representation.</span>
<span class="sd"> :param X: array-like of shape `(n_samples, n_features)` with the instances</span>
<span class="sd"> :param y: array-like of shape `(n_samples, n_classes)` with the class labels</span>
<span class="sd"> :return: `self`</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">nF</span> <span class="o">=</span> <span class="n">X</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
<span class="bp">self</span><span class="o">.</span><span class="n">pca</span> <span class="o">=</span> <span class="kc">None</span>
<span class="k">if</span> <span class="n">nF</span> <span class="o">&gt;</span> <span class="bp">self</span><span class="o">.</span><span class="n">n_components</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">pca</span> <span class="o">=</span> <span class="n">TruncatedSVD</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">n_components</span><span class="p">)</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="n">X</span><span class="p">)</span>
<span class="n">X</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">transform</span><span class="p">(</span><span class="n">X</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">classifier</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="n">X</span><span class="p">,</span> <span class="n">y</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">classes_</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">classifier</span><span class="o">.</span><span class="n">classes_</span>
<span class="k">return</span> <span class="bp">self</span></div>
<div class="viewcode-block" id="LowRankLogisticRegression.predict">
<a class="viewcode-back" href="../../../quapy.classification.html#quapy.classification.methods.LowRankLogisticRegression.predict">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">predict</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Predicts labels for the instances `X` embedded into the low-rank space.</span>
<span class="sd"> :param X: array-like of shape `(n_samples, n_features)` instances to classify</span>
<span class="sd"> :return: a `numpy` array of length `n` containing the label predictions, where `n` is the number of</span>
<span class="sd"> instances in `X`</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">X</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">transform</span><span class="p">(</span><span class="n">X</span><span class="p">)</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">classifier</span><span class="o">.</span><span class="n">predict</span><span class="p">(</span><span class="n">X</span><span class="p">)</span></div>
<div class="viewcode-block" id="LowRankLogisticRegression.predict_proba">
<a class="viewcode-back" href="../../../quapy.classification.html#quapy.classification.methods.LowRankLogisticRegression.predict_proba">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">predict_proba</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Predicts posterior probabilities for the instances `X` embedded into the low-rank space.</span>
<span class="sd"> :param X: array-like of shape `(n_samples, n_features)` instances to classify</span>
<span class="sd"> :return: array-like of shape `(n_samples, n_classes)` with the posterior probabilities</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">X</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">transform</span><span class="p">(</span><span class="n">X</span><span class="p">)</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">classifier</span><span class="o">.</span><span class="n">predict_proba</span><span class="p">(</span><span class="n">X</span><span class="p">)</span></div>
<div class="viewcode-block" id="LowRankLogisticRegression.transform">
<a class="viewcode-back" href="../../../quapy.classification.html#quapy.classification.methods.LowRankLogisticRegression.transform">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">transform</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Returns the low-rank approximation of `X` with `n_components` dimensions, or `X` unaltered if</span>
<span class="sd"> `n_components` &gt;= `X.shape[1]`.</span>
<span class="sd"> </span>
<span class="sd"> :param X: array-like of shape `(n_samples, n_features)` instances to embed</span>
<span class="sd"> :return: array-like of shape `(n_samples, n_components)` with the embedded instances</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">pca</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="k">return</span> <span class="n">X</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">pca</span><span class="o">.</span><span class="n">transform</span><span class="p">(</span><span class="n">X</span><span class="p">)</span></div>
</div>
<div class="viewcode-block" id="MockClassifierFromPosteriors">
<a class="viewcode-back" href="../../../quapy.classification.html#quapy.classification.methods.MockClassifierFromPosteriors">[docs]</a>
<span class="k">class</span><span class="w"> </span><span class="nc">MockClassifierFromPosteriors</span><span class="p">(</span><span class="n">BaseEstimator</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Mock classifier that bypasses classifier training when the input instances</span>
<span class="sd"> are already posterior probabilities produced by a pretrained probabilistic</span>
<span class="sd"> classifier.</span>
<span class="sd"> :param X: arrays of shape `(n_samples, n_classes)` are interpreted as posterior probabilities</span>
<span class="sd"> &quot;&quot;&quot;</span>
<div class="viewcode-block" id="MockClassifierFromPosteriors.fit">
<a class="viewcode-back" href="../../../quapy.classification.html#quapy.classification.methods.MockClassifierFromPosteriors.fit">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">fit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">,</span> <span class="n">y</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">classes_</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sort</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">unique</span><span class="p">(</span><span class="n">y</span><span class="p">))</span>
<span class="k">return</span> <span class="bp">self</span></div>
<div class="viewcode-block" id="MockClassifierFromPosteriors.predict">
<a class="viewcode-back" href="../../../quapy.classification.html#quapy.classification.methods.MockClassifierFromPosteriors.predict">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">predict</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">):</span>
<span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">argmax</span><span class="p">(</span><span class="n">X</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span></div>
<div class="viewcode-block" id="MockClassifierFromPosteriors.predict_proba">
<a class="viewcode-back" href="../../../quapy.classification.html#quapy.classification.methods.MockClassifierFromPosteriors.predict_proba">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">predict_proba</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">):</span>
<span class="k">return</span> <span class="n">X</span></div>
</div>
</pre></div>
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<h1>Source code for quapy.classification.svmperf</h1><div class="highlight"><pre>
<span></span><span class="kn">import</span><span class="w"> </span><span class="nn">logging</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">random</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">shutil</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">subprocess</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">tempfile</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">os</span><span class="w"> </span><span class="kn">import</span> <span class="n">remove</span><span class="p">,</span> <span class="n">makedirs</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">os.path</span><span class="w"> </span><span class="kn">import</span> <span class="n">join</span><span class="p">,</span> <span class="n">exists</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">subprocess</span><span class="w"> </span><span class="kn">import</span> <span class="n">PIPE</span><span class="p">,</span> <span class="n">STDOUT</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">sklearn.base</span><span class="w"> </span><span class="kn">import</span> <span class="n">BaseEstimator</span><span class="p">,</span> <span class="n">ClassifierMixin</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">sklearn.datasets</span><span class="w"> </span><span class="kn">import</span> <span class="n">dump_svmlight_file</span>
<div class="viewcode-block" id="SVMperf">
<a class="viewcode-back" href="../../../quapy.classification.html#quapy.classification.svmperf.SVMperf">[docs]</a>
<span class="k">class</span><span class="w"> </span><span class="nc">SVMperf</span><span class="p">(</span><span class="n">BaseEstimator</span><span class="p">,</span> <span class="n">ClassifierMixin</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;A wrapper for the `SVM-perf package &lt;https://www.cs.cornell.edu/people/tj/svm_light/svm_perf.html&gt;`__ by Thorsten Joachims.</span>
<span class="sd"> When using losses for quantification, the source code has to be patched. See</span>
<span class="sd"> the `installation documentation &lt;https://hlt-isti.github.io/QuaPy/build/html/Installation.html#svm-perf-with-quantification-oriented-losses&gt;`__</span>
<span class="sd"> for further details.</span>
<span class="sd"> References:</span>
<span class="sd"> * `Esuli et al.2015 &lt;https://dl.acm.org/doi/abs/10.1145/2700406?casa_token=8D2fHsGCVn0AAAAA:ZfThYOvrzWxMGfZYlQW_y8Cagg-o_l6X_PcF09mdETQ4Tu7jK98mxFbGSXp9ZSO14JkUIYuDGFG0&gt;`__</span>
<span class="sd"> * `Barranquero et al.2015 &lt;https://www.sciencedirect.com/science/article/abs/pii/S003132031400291X&gt;`__</span>
<span class="sd"> :param svmperf_base: path to directory containing the binary files `svm_perf_learn` and `svm_perf_classify`</span>
<span class="sd"> :param C: trade-off between training error and margin (default 0.01)</span>
<span class="sd"> :param verbose: set to True to print svm-perf std outputs</span>
<span class="sd"> :param loss: the loss to optimize for. Available losses are &quot;01&quot;, &quot;f1&quot;, &quot;kld&quot;, &quot;nkld&quot;, &quot;q&quot;, &quot;qacc&quot;, &quot;qf1&quot;, &quot;qgm&quot;, &quot;mae&quot;, &quot;mrae&quot;.</span>
<span class="sd"> :param host_folder: directory where to store the trained model; set to None (default) for using a tmp directory</span>
<span class="sd"> (temporal directories are automatically deleted)</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="c1"># losses with their respective codes in svm_perf implementation</span>
<span class="n">valid_losses</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;01&#39;</span><span class="p">:</span><span class="mi">0</span><span class="p">,</span> <span class="s1">&#39;f1&#39;</span><span class="p">:</span><span class="mi">1</span><span class="p">,</span> <span class="s1">&#39;kld&#39;</span><span class="p">:</span><span class="mi">12</span><span class="p">,</span> <span class="s1">&#39;nkld&#39;</span><span class="p">:</span><span class="mi">13</span><span class="p">,</span> <span class="s1">&#39;q&#39;</span><span class="p">:</span><span class="mi">22</span><span class="p">,</span> <span class="s1">&#39;qacc&#39;</span><span class="p">:</span><span class="mi">23</span><span class="p">,</span> <span class="s1">&#39;qf1&#39;</span><span class="p">:</span><span class="mi">24</span><span class="p">,</span> <span class="s1">&#39;qgm&#39;</span><span class="p">:</span><span class="mi">25</span><span class="p">,</span> <span class="s1">&#39;mae&#39;</span><span class="p">:</span><span class="mi">26</span><span class="p">,</span> <span class="s1">&#39;mrae&#39;</span><span class="p">:</span><span class="mi">27</span><span class="p">}</span>
<span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">svmperf_base</span><span class="p">,</span> <span class="n">C</span><span class="o">=</span><span class="mf">0.01</span><span class="p">,</span> <span class="n">verbose</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">loss</span><span class="o">=</span><span class="s1">&#39;01&#39;</span><span class="p">,</span> <span class="n">host_folder</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<span class="k">assert</span> <span class="n">exists</span><span class="p">(</span><span class="n">svmperf_base</span><span class="p">),</span> \
<span class="p">(</span><span class="sa">f</span><span class="s1">&#39;path </span><span class="si">{</span><span class="n">svmperf_base</span><span class="si">}</span><span class="s1"> does not seem to point to a valid path;&#39;</span>
<span class="sa">f</span><span class="s1">&#39;did you install svm-perf? &#39;</span>
<span class="sa">f</span><span class="s1">&#39;see instructions in https://hlt-isti.github.io/QuaPy/manuals/explicit-loss-minimization.html&#39;</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">svmperf_base</span> <span class="o">=</span> <span class="n">svmperf_base</span>
<span class="bp">self</span><span class="o">.</span><span class="n">C</span> <span class="o">=</span> <span class="n">C</span>
<span class="bp">self</span><span class="o">.</span><span class="n">verbose</span> <span class="o">=</span> <span class="n">verbose</span>
<span class="bp">self</span><span class="o">.</span><span class="n">loss</span> <span class="o">=</span> <span class="n">loss</span>
<span class="bp">self</span><span class="o">.</span><span class="n">host_folder</span> <span class="o">=</span> <span class="n">host_folder</span>
<div class="viewcode-block" id="SVMperf.fit">
<a class="viewcode-back" href="../../../quapy.classification.html#quapy.classification.svmperf.SVMperf.fit">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">fit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">,</span> <span class="n">y</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Trains the SVM for the multivariate performance loss</span>
<span class="sd"> :param X: training instances</span>
<span class="sd"> :param y: a binary vector of labels</span>
<span class="sd"> :return: `self`</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">assert</span> <span class="bp">self</span><span class="o">.</span><span class="n">loss</span> <span class="ow">in</span> <span class="n">SVMperf</span><span class="o">.</span><span class="n">valid_losses</span><span class="p">,</span> \
<span class="sa">f</span><span class="s1">&#39;unsupported loss </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">loss</span><span class="si">}</span><span class="s1">, valid ones are </span><span class="si">{</span><span class="nb">list</span><span class="p">(</span><span class="n">SVMperf</span><span class="o">.</span><span class="n">valid_losses</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span><span class="si">}</span><span class="s1">&#39;</span>
<span class="bp">self</span><span class="o">.</span><span class="n">svmperf_learn</span> <span class="o">=</span> <span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">svmperf_base</span><span class="p">,</span> <span class="s1">&#39;svm_perf_learn&#39;</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">svmperf_classify</span> <span class="o">=</span> <span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">svmperf_base</span><span class="p">,</span> <span class="s1">&#39;svm_perf_classify&#39;</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">loss_cmd</span> <span class="o">=</span> <span class="s1">&#39;-w 3 -l &#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">valid_losses</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">loss</span><span class="p">])</span>
<span class="bp">self</span><span class="o">.</span><span class="n">c_cmd</span> <span class="o">=</span> <span class="s1">&#39;-c &#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">C</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">classes_</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">unique</span><span class="p">(</span><span class="n">y</span><span class="p">))</span>
<span class="bp">self</span><span class="o">.</span><span class="n">n_classes_</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">classes_</span><span class="p">)</span>
<span class="n">local_random</span> <span class="o">=</span> <span class="n">random</span><span class="o">.</span><span class="n">Random</span><span class="p">()</span>
<span class="c1"># this would allow to run parallel instances of predict</span>
<span class="n">random_code</span> <span class="o">=</span> <span class="s1">&#39;svmperfprocess&#39;</span><span class="o">+</span><span class="s1">&#39;-&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">local_random</span><span class="o">.</span><span class="n">randint</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1000000</span><span class="p">))</span> <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">5</span><span class="p">))</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">host_folder</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">tmpdir</span> <span class="o">=</span> <span class="n">join</span><span class="p">(</span><span class="n">tempfile</span><span class="o">.</span><span class="n">gettempdir</span><span class="p">(),</span> <span class="n">random_code</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">tmpdir</span> <span class="o">=</span> <span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">host_folder</span><span class="p">,</span> <span class="s1">&#39;.&#39;</span> <span class="o">+</span> <span class="n">random_code</span><span class="p">)</span>
<span class="n">makedirs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">tmpdir</span><span class="p">,</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">model</span> <span class="o">=</span> <span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">tmpdir</span><span class="p">,</span> <span class="s1">&#39;model-&#39;</span><span class="o">+</span><span class="n">random_code</span><span class="p">)</span>
<span class="n">traindat</span> <span class="o">=</span> <span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">tmpdir</span><span class="p">,</span> <span class="sa">f</span><span class="s1">&#39;train-</span><span class="si">{</span><span class="n">random_code</span><span class="si">}</span><span class="s1">.dat&#39;</span><span class="p">)</span>
<span class="n">dump_svmlight_file</span><span class="p">(</span><span class="n">X</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">traindat</span><span class="p">,</span> <span class="n">zero_based</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
<span class="n">cmd</span> <span class="o">=</span> <span class="s1">&#39; &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="bp">self</span><span class="o">.</span><span class="n">svmperf_learn</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">c_cmd</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">loss_cmd</span><span class="p">,</span> <span class="n">traindat</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="p">])</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">verbose</span><span class="p">:</span>
<span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="vm">__name__</span><span class="p">)</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;[Running] </span><span class="si">{</span><span class="n">cmd</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="n">p</span> <span class="o">=</span> <span class="n">subprocess</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="n">cmd</span><span class="o">.</span><span class="n">split</span><span class="p">(),</span> <span class="n">stdout</span><span class="o">=</span><span class="n">PIPE</span><span class="p">,</span> <span class="n">stderr</span><span class="o">=</span><span class="n">PIPE</span><span class="p">)</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">exists</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="p">):</span>
<span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="vm">__name__</span><span class="p">)</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="n">p</span><span class="o">.</span><span class="n">stderr</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">))</span>
<span class="n">remove</span><span class="p">(</span><span class="n">traindat</span><span class="p">)</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">verbose</span><span class="p">:</span>
<span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="vm">__name__</span><span class="p">)</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="n">p</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">))</span>
<span class="k">return</span> <span class="bp">self</span></div>
<div class="viewcode-block" id="SVMperf.predict">
<a class="viewcode-back" href="../../../quapy.classification.html#quapy.classification.svmperf.SVMperf.predict">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">predict</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Predicts labels for the instances `X`</span>
<span class="sd"> :param X: array-like of shape `(n_samples, n_features)` instances to classify</span>
<span class="sd"> :return: a `numpy` array of length `n` containing the label predictions, where `n` is the number of</span>
<span class="sd"> instances in `X`</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">confidence_scores</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">decision_function</span><span class="p">(</span><span class="n">X</span><span class="p">)</span>
<span class="n">predictions</span> <span class="o">=</span> <span class="p">(</span><span class="n">confidence_scores</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">)</span> <span class="o">*</span> <span class="mi">1</span>
<span class="k">return</span> <span class="n">predictions</span></div>
<div class="viewcode-block" id="SVMperf.decision_function">
<a class="viewcode-back" href="../../../quapy.classification.html#quapy.classification.svmperf.SVMperf.decision_function">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">decision_function</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">,</span> <span class="n">y</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Evaluate the decision function for the samples in `X`.</span>
<span class="sd"> :param X: array-like of shape `(n_samples, n_features)` containing the instances to classify</span>
<span class="sd"> :param y: unused</span>
<span class="sd"> :return: array-like of shape `(n_samples,)` containing the decision scores of the instances</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">assert</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;tmpdir&#39;</span><span class="p">),</span> <span class="s1">&#39;predict called before fit&#39;</span>
<span class="k">assert</span> <span class="bp">self</span><span class="o">.</span><span class="n">tmpdir</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">,</span> <span class="s1">&#39;model directory corrupted&#39;</span>
<span class="k">assert</span> <span class="n">exists</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="p">),</span> <span class="s1">&#39;model not found&#39;</span>
<span class="k">if</span> <span class="n">y</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="n">y</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="n">X</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
<span class="c1"># in order to allow for parallel runs of predict, a random code is assigned</span>
<span class="n">local_random</span> <span class="o">=</span> <span class="n">random</span><span class="o">.</span><span class="n">Random</span><span class="p">()</span>
<span class="n">random_code</span> <span class="o">=</span> <span class="s1">&#39;-&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">local_random</span><span class="o">.</span><span class="n">randint</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1000000</span><span class="p">))</span> <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">5</span><span class="p">))</span>
<span class="n">predictions_path</span> <span class="o">=</span> <span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">tmpdir</span><span class="p">,</span> <span class="s1">&#39;predictions&#39;</span> <span class="o">+</span> <span class="n">random_code</span> <span class="o">+</span> <span class="s1">&#39;.dat&#39;</span><span class="p">)</span>
<span class="n">testdat</span> <span class="o">=</span> <span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">tmpdir</span><span class="p">,</span> <span class="s1">&#39;test&#39;</span> <span class="o">+</span> <span class="n">random_code</span> <span class="o">+</span> <span class="s1">&#39;.dat&#39;</span><span class="p">)</span>
<span class="n">dump_svmlight_file</span><span class="p">(</span><span class="n">X</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">testdat</span><span class="p">,</span> <span class="n">zero_based</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
<span class="n">cmd</span> <span class="o">=</span> <span class="s1">&#39; &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="bp">self</span><span class="o">.</span><span class="n">svmperf_classify</span><span class="p">,</span> <span class="n">testdat</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="p">,</span> <span class="n">predictions_path</span><span class="p">])</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">verbose</span><span class="p">:</span>
<span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="vm">__name__</span><span class="p">)</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;[Running] </span><span class="si">{</span><span class="n">cmd</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="n">p</span> <span class="o">=</span> <span class="n">subprocess</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="n">cmd</span><span class="o">.</span><span class="n">split</span><span class="p">(),</span> <span class="n">stdout</span><span class="o">=</span><span class="n">PIPE</span><span class="p">,</span> <span class="n">stderr</span><span class="o">=</span><span class="n">STDOUT</span><span class="p">)</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">verbose</span><span class="p">:</span>
<span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="vm">__name__</span><span class="p">)</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="n">p</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">))</span>
<span class="n">scores</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">loadtxt</span><span class="p">(</span><span class="n">predictions_path</span><span class="p">)</span>
<span class="n">remove</span><span class="p">(</span><span class="n">testdat</span><span class="p">)</span>
<span class="n">remove</span><span class="p">(</span><span class="n">predictions_path</span><span class="p">)</span>
<span class="k">return</span> <span class="n">scores</span></div>
<span class="k">def</span><span class="w"> </span><span class="fm">__del__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;tmpdir&#39;</span><span class="p">):</span>
<span class="n">shutil</span><span class="o">.</span><span class="n">rmtree</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">tmpdir</span><span class="p">,</span> <span class="n">ignore_errors</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span></div>
</pre></div>
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<h1>Source code for quapy.data._ifcb</h1><div class="highlight"><pre>
<span></span><span class="kn">import</span> <span class="nn">os</span>
<span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
<span class="kn">from</span> <span class="nn">quapy.protocol</span> <span class="kn">import</span> <span class="n">AbstractProtocol</span>
<div class="viewcode-block" id="IFCBTrainSamplesFromDir">
<a class="viewcode-back" href="../../../quapy.data.html#quapy.data._ifcb.IFCBTrainSamplesFromDir">[docs]</a>
<span class="k">class</span> <span class="nc">IFCBTrainSamplesFromDir</span><span class="p">(</span><span class="n">AbstractProtocol</span><span class="p">):</span>
<span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">path_dir</span><span class="p">:</span><span class="nb">str</span><span class="p">,</span> <span class="n">classes</span><span class="p">:</span> <span class="nb">list</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">path_dir</span> <span class="o">=</span> <span class="n">path_dir</span>
<span class="bp">self</span><span class="o">.</span><span class="n">classes</span> <span class="o">=</span> <span class="n">classes</span>
<span class="bp">self</span><span class="o">.</span><span class="n">samples</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">filename</span> <span class="ow">in</span> <span class="n">os</span><span class="o">.</span><span class="n">listdir</span><span class="p">(</span><span class="n">path_dir</span><span class="p">):</span>
<span class="k">if</span> <span class="n">filename</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s1">&#39;.csv&#39;</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">samples</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
<span class="k">def</span> <span class="fm">__call__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">for</span> <span class="n">sample</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">samples</span><span class="p">:</span>
<span class="n">s</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">path_dir</span><span class="p">,</span><span class="n">sample</span><span class="p">))</span>
<span class="c1"># all columns but the first where we get the class</span>
<span class="n">X</span> <span class="o">=</span> <span class="n">s</span><span class="o">.</span><span class="n">iloc</span><span class="p">[:,</span> <span class="mi">1</span><span class="p">:]</span><span class="o">.</span><span class="n">to_numpy</span><span class="p">()</span>
<span class="n">y</span> <span class="o">=</span> <span class="n">s</span><span class="o">.</span><span class="n">iloc</span><span class="p">[:,</span> <span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">to_numpy</span><span class="p">()</span>
<span class="k">yield</span> <span class="n">X</span><span class="p">,</span> <span class="n">y</span>
<div class="viewcode-block" id="IFCBTrainSamplesFromDir.total">
<a class="viewcode-back" href="../../../quapy.data.html#quapy.data._ifcb.IFCBTrainSamplesFromDir.total">[docs]</a>
<span class="k">def</span> <span class="nf">total</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Returns the total number of samples that the protocol generates.</span>
<span class="sd"> :return: The number of training samples to generate.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">samples</span><span class="p">)</span></div>
</div>
<div class="viewcode-block" id="IFCBTestSamples">
<a class="viewcode-back" href="../../../quapy.data.html#quapy.data._ifcb.IFCBTestSamples">[docs]</a>
<span class="k">class</span> <span class="nc">IFCBTestSamples</span><span class="p">(</span><span class="n">AbstractProtocol</span><span class="p">):</span>
<span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">path_dir</span><span class="p">:</span><span class="nb">str</span><span class="p">,</span> <span class="n">test_prevalences_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">path_dir</span> <span class="o">=</span> <span class="n">path_dir</span>
<span class="bp">self</span><span class="o">.</span><span class="n">test_prevalences</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">path_dir</span><span class="p">,</span> <span class="n">test_prevalences_path</span><span class="p">))</span>
<span class="k">def</span> <span class="fm">__call__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">for</span> <span class="n">_</span><span class="p">,</span> <span class="n">test_sample</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">test_prevalences</span><span class="o">.</span><span class="n">iterrows</span><span class="p">():</span>
<span class="c1">#Load the sample from disk</span>
<span class="n">X</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">path_dir</span><span class="p">,</span><span class="n">test_sample</span><span class="p">[</span><span class="s1">&#39;sample&#39;</span><span class="p">]</span><span class="o">+</span><span class="s1">&#39;.csv&#39;</span><span class="p">))</span><span class="o">.</span><span class="n">to_numpy</span><span class="p">()</span>
<span class="n">prevalences</span> <span class="o">=</span> <span class="n">test_sample</span><span class="o">.</span><span class="n">iloc</span><span class="p">[</span><span class="mi">1</span><span class="p">:]</span><span class="o">.</span><span class="n">to_numpy</span><span class="p">()</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="nb">float</span><span class="p">)</span>
<span class="k">yield</span> <span class="n">X</span><span class="p">,</span> <span class="n">prevalences</span>
<div class="viewcode-block" id="IFCBTestSamples.total">
<a class="viewcode-back" href="../../../quapy.data.html#quapy.data._ifcb.IFCBTestSamples.total">[docs]</a>
<span class="k">def</span> <span class="nf">total</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Returns the total number of samples that the protocol generates.</span>
<span class="sd"> :return: The number of test samples to generate.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">test_prevalences</span><span class="o">.</span><span class="n">index</span><span class="p">)</span></div>
</div>
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<h1>Source code for quapy.data._lequa2022</h1><div class="highlight"><pre>
<span></span><span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Tuple</span><span class="p">,</span> <span class="n">Union</span>
<span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
<span class="kn">import</span> <span class="nn">os</span>
<span class="kn">from</span> <span class="nn">quapy.protocol</span> <span class="kn">import</span> <span class="n">AbstractProtocol</span>
<span class="n">DEV_SAMPLES</span> <span class="o">=</span> <span class="mi">1000</span>
<span class="n">TEST_SAMPLES</span> <span class="o">=</span> <span class="mi">5000</span>
<span class="n">ERROR_TOL</span> <span class="o">=</span> <span class="mf">1E-3</span>
<div class="viewcode-block" id="load_category_map">
<a class="viewcode-back" href="../../../quapy.data.html#quapy.data._lequa2022.load_category_map">[docs]</a>
<span class="k">def</span> <span class="nf">load_category_map</span><span class="p">(</span><span class="n">path</span><span class="p">):</span>
<span class="n">cat2code</span> <span class="o">=</span> <span class="p">{}</span>
<span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="s1">&#39;rt&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fin</span><span class="p">:</span>
<span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">fin</span><span class="p">:</span>
<span class="n">category</span><span class="p">,</span> <span class="n">code</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">()</span>
<span class="n">cat2code</span><span class="p">[</span><span class="n">category</span><span class="p">]</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">code</span><span class="p">)</span>
<span class="n">code2cat</span> <span class="o">=</span> <span class="p">[</span><span class="n">cat</span> <span class="k">for</span> <span class="n">cat</span><span class="p">,</span> <span class="n">code</span> <span class="ow">in</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">cat2code</span><span class="o">.</span><span class="n">items</span><span class="p">(),</span> <span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">])]</span>
<span class="k">return</span> <span class="n">cat2code</span><span class="p">,</span> <span class="n">code2cat</span></div>
<div class="viewcode-block" id="load_raw_documents">
<a class="viewcode-back" href="../../../quapy.data.html#quapy.data._lequa2022.load_raw_documents">[docs]</a>
<span class="k">def</span> <span class="nf">load_raw_documents</span><span class="p">(</span><span class="n">path</span><span class="p">):</span>
<span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">path</span><span class="p">)</span>
<span class="n">documents</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">df</span><span class="p">[</span><span class="s2">&quot;text&quot;</span><span class="p">]</span><span class="o">.</span><span class="n">values</span><span class="p">)</span>
<span class="n">labels</span> <span class="o">=</span> <span class="kc">None</span>
<span class="k">if</span> <span class="s2">&quot;label&quot;</span> <span class="ow">in</span> <span class="n">df</span><span class="o">.</span><span class="n">columns</span><span class="p">:</span>
<span class="n">labels</span> <span class="o">=</span> <span class="n">df</span><span class="p">[</span><span class="s2">&quot;label&quot;</span><span class="p">]</span><span class="o">.</span><span class="n">values</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="nb">int</span><span class="p">)</span>
<span class="k">return</span> <span class="n">documents</span><span class="p">,</span> <span class="n">labels</span></div>
<div class="viewcode-block" id="load_vector_documents">
<a class="viewcode-back" href="../../../quapy.data.html#quapy.data._lequa2022.load_vector_documents">[docs]</a>
<span class="k">def</span> <span class="nf">load_vector_documents</span><span class="p">(</span><span class="n">path</span><span class="p">):</span>
<span class="n">D</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">path</span><span class="p">)</span><span class="o">.</span><span class="n">to_numpy</span><span class="p">(</span><span class="n">dtype</span><span class="o">=</span><span class="nb">float</span><span class="p">)</span>
<span class="n">labelled</span> <span class="o">=</span> <span class="n">D</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">==</span> <span class="mi">301</span>
<span class="k">if</span> <span class="n">labelled</span><span class="p">:</span>
<span class="n">X</span><span class="p">,</span> <span class="n">y</span> <span class="o">=</span> <span class="n">D</span><span class="p">[:,</span> <span class="mi">1</span><span class="p">:],</span> <span class="n">D</span><span class="p">[:,</span> <span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="nb">int</span><span class="p">)</span><span class="o">.</span><span class="n">flatten</span><span class="p">()</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">X</span><span class="p">,</span> <span class="n">y</span> <span class="o">=</span> <span class="n">D</span><span class="p">,</span> <span class="kc">None</span>
<span class="k">return</span> <span class="n">X</span><span class="p">,</span> <span class="n">y</span></div>
<div class="viewcode-block" id="SamplesFromDir">
<a class="viewcode-back" href="../../../quapy.data.html#quapy.data._lequa2022.SamplesFromDir">[docs]</a>
<span class="k">class</span> <span class="nc">SamplesFromDir</span><span class="p">(</span><span class="n">AbstractProtocol</span><span class="p">):</span>
<span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">path_dir</span><span class="p">:</span><span class="nb">str</span><span class="p">,</span> <span class="n">ground_truth_path</span><span class="p">:</span><span class="nb">str</span><span class="p">,</span> <span class="n">load_fn</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">path_dir</span> <span class="o">=</span> <span class="n">path_dir</span>
<span class="bp">self</span><span class="o">.</span><span class="n">load_fn</span> <span class="o">=</span> <span class="n">load_fn</span>
<span class="bp">self</span><span class="o">.</span><span class="n">true_prevs</span> <span class="o">=</span> <span class="n">ResultSubmission</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">ground_truth_path</span><span class="p">)</span>
<span class="k">def</span> <span class="fm">__call__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">for</span> <span class="nb">id</span><span class="p">,</span> <span class="n">prevalence</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">true_prevs</span><span class="o">.</span><span class="n">iterrows</span><span class="p">():</span>
<span class="n">sample</span><span class="p">,</span> <span class="n">_</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">load_fn</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">path_dir</span><span class="p">,</span> <span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="nb">id</span><span class="si">}</span><span class="s1">.txt&#39;</span><span class="p">))</span>
<span class="k">yield</span> <span class="n">sample</span><span class="p">,</span> <span class="n">prevalence</span></div>
<div class="viewcode-block" id="ResultSubmission">
<a class="viewcode-back" href="../../../quapy.data.html#quapy.data._lequa2022.ResultSubmission">[docs]</a>
<span class="k">class</span> <span class="nc">ResultSubmission</span><span class="p">:</span>
<span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">df</span> <span class="o">=</span> <span class="kc">None</span>
<span class="k">def</span> <span class="nf">__init_df</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">categories</span><span class="p">:</span> <span class="nb">int</span><span class="p">):</span>
<span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">categories</span><span class="p">,</span> <span class="nb">int</span><span class="p">)</span> <span class="ow">or</span> <span class="n">categories</span> <span class="o">&lt;</span> <span class="mi">2</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">TypeError</span><span class="p">(</span><span class="s1">&#39;wrong format for categories: an int (&gt;=2) was expected&#39;</span><span class="p">)</span>
<span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">columns</span><span class="o">=</span><span class="nb">list</span><span class="p">(</span><span class="nb">range</span><span class="p">(</span><span class="n">categories</span><span class="p">)))</span>
<span class="n">df</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">set_names</span><span class="p">(</span><span class="s1">&#39;id&#39;</span><span class="p">,</span> <span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">df</span> <span class="o">=</span> <span class="n">df</span>
<span class="nd">@property</span>
<span class="k">def</span> <span class="nf">n_categories</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">columns</span><span class="o">.</span><span class="n">values</span><span class="p">)</span>
<div class="viewcode-block" id="ResultSubmission.add">
<a class="viewcode-back" href="../../../quapy.data.html#quapy.data._lequa2022.ResultSubmission.add">[docs]</a>
<span class="k">def</span> <span class="nf">add</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">sample_id</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span> <span class="n">prevalence_values</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">):</span>
<span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">sample_id</span><span class="p">,</span> <span class="nb">int</span><span class="p">):</span>
<span class="k">raise</span> <span class="ne">TypeError</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;error: expected int for sample_sample, found </span><span class="si">{</span><span class="nb">type</span><span class="p">(</span><span class="n">sample_id</span><span class="p">)</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">prevalence_values</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">):</span>
<span class="k">raise</span> <span class="ne">TypeError</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;error: expected np.ndarray for prevalence_values, found </span><span class="si">{</span><span class="nb">type</span><span class="p">(</span><span class="n">prevalence_values</span><span class="p">)</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">df</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">__init_df</span><span class="p">(</span><span class="n">categories</span><span class="o">=</span><span class="nb">len</span><span class="p">(</span><span class="n">prevalence_values</span><span class="p">))</span>
<span class="k">if</span> <span class="n">sample_id</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">values</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;error: prevalence values for &quot;</span><span class="si">{</span><span class="n">sample_id</span><span class="si">}</span><span class="s1">&quot; already added&#39;</span><span class="p">)</span>
<span class="k">if</span> <span class="n">prevalence_values</span><span class="o">.</span><span class="n">ndim</span> <span class="o">!=</span> <span class="mi">1</span> <span class="ow">and</span> <span class="n">prevalence_values</span><span class="o">.</span><span class="n">size</span> <span class="o">!=</span> <span class="bp">self</span><span class="o">.</span><span class="n">n_categories</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;error: wrong shape found for prevalence vector </span><span class="si">{</span><span class="n">prevalence_values</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="k">if</span> <span class="p">(</span><span class="n">prevalence_values</span> <span class="o">&lt;</span> <span class="mi">0</span><span class="p">)</span><span class="o">.</span><span class="n">any</span><span class="p">()</span> <span class="ow">or</span> <span class="p">(</span><span class="n">prevalence_values</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">)</span><span class="o">.</span><span class="n">any</span><span class="p">():</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;error: prevalence values out of range [0,1] for &quot;</span><span class="si">{</span><span class="n">sample_id</span><span class="si">}</span><span class="s1">&quot;&#39;</span><span class="p">)</span>
<span class="k">if</span> <span class="n">np</span><span class="o">.</span><span class="n">abs</span><span class="p">(</span><span class="n">prevalence_values</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span> <span class="o">-</span> <span class="mi">1</span><span class="p">)</span> <span class="o">&gt;</span> <span class="n">ERROR_TOL</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;error: prevalence values do not sum up to one for &quot;</span><span class="si">{</span><span class="n">sample_id</span><span class="si">}</span><span class="s1">&quot;&#39;</span>
<span class="sa">f</span><span class="s1">&#39;(error tolerance </span><span class="si">{</span><span class="n">ERROR_TOL</span><span class="si">}</span><span class="s1">)&#39;</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">sample_id</span><span class="p">]</span> <span class="o">=</span> <span class="n">prevalence_values</span></div>
<span class="k">def</span> <span class="fm">__len__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="p">)</span>
<div class="viewcode-block" id="ResultSubmission.load">
<a class="viewcode-back" href="../../../quapy.data.html#quapy.data._lequa2022.ResultSubmission.load">[docs]</a>
<span class="nd">@classmethod</span>
<span class="k">def</span> <span class="nf">load</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">path</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="s1">&#39;ResultSubmission&#39;</span><span class="p">:</span>
<span class="n">df</span> <span class="o">=</span> <span class="n">ResultSubmission</span><span class="o">.</span><span class="n">check_file_format</span><span class="p">(</span><span class="n">path</span><span class="p">)</span>
<span class="n">r</span> <span class="o">=</span> <span class="n">ResultSubmission</span><span class="p">()</span>
<span class="n">r</span><span class="o">.</span><span class="n">df</span> <span class="o">=</span> <span class="n">df</span>
<span class="k">return</span> <span class="n">r</span></div>
<div class="viewcode-block" id="ResultSubmission.dump">
<a class="viewcode-back" href="../../../quapy.data.html#quapy.data._lequa2022.ResultSubmission.dump">[docs]</a>
<span class="k">def</span> <span class="nf">dump</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">path</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
<span class="n">ResultSubmission</span><span class="o">.</span><span class="n">check_dataframe_format</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="n">path</span><span class="p">)</span></div>
<div class="viewcode-block" id="ResultSubmission.prevalence">
<a class="viewcode-back" href="../../../quapy.data.html#quapy.data._lequa2022.ResultSubmission.prevalence">[docs]</a>
<span class="k">def</span> <span class="nf">prevalence</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">sample_id</span><span class="p">:</span> <span class="nb">int</span><span class="p">):</span>
<span class="n">sel</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">sample_id</span><span class="p">]</span>
<span class="k">if</span> <span class="n">sel</span><span class="o">.</span><span class="n">empty</span><span class="p">:</span>
<span class="k">return</span> <span class="kc">None</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="n">sel</span><span class="o">.</span><span class="n">values</span><span class="o">.</span><span class="n">flatten</span><span class="p">()</span></div>
<div class="viewcode-block" id="ResultSubmission.iterrows">
<a class="viewcode-back" href="../../../quapy.data.html#quapy.data._lequa2022.ResultSubmission.iterrows">[docs]</a>
<span class="k">def</span> <span class="nf">iterrows</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">for</span> <span class="n">index</span><span class="p">,</span> <span class="n">row</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">iterrows</span><span class="p">():</span>
<span class="n">prevalence</span> <span class="o">=</span> <span class="n">row</span><span class="o">.</span><span class="n">values</span><span class="o">.</span><span class="n">flatten</span><span class="p">()</span>
<span class="k">yield</span> <span class="n">index</span><span class="p">,</span> <span class="n">prevalence</span></div>
<div class="viewcode-block" id="ResultSubmission.check_file_format">
<a class="viewcode-back" href="../../../quapy.data.html#quapy.data._lequa2022.ResultSubmission.check_file_format">[docs]</a>
<span class="nd">@classmethod</span>
<span class="k">def</span> <span class="nf">check_file_format</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">path</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Union</span><span class="p">[</span><span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="n">Tuple</span><span class="p">[</span><span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="nb">str</span><span class="p">]]:</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">index_col</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
<span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;the file </span><span class="si">{</span><span class="n">path</span><span class="si">}</span><span class="s1"> does not seem to be a valid csv file. &#39;</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">e</span><span class="p">)</span>
<span class="k">return</span> <span class="n">ResultSubmission</span><span class="o">.</span><span class="n">check_dataframe_format</span><span class="p">(</span><span class="n">df</span><span class="p">,</span> <span class="n">path</span><span class="o">=</span><span class="n">path</span><span class="p">)</span></div>
<div class="viewcode-block" id="ResultSubmission.check_dataframe_format">
<a class="viewcode-back" href="../../../quapy.data.html#quapy.data._lequa2022.ResultSubmission.check_dataframe_format">[docs]</a>
<span class="nd">@classmethod</span>
<span class="k">def</span> <span class="nf">check_dataframe_format</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">df</span><span class="p">,</span> <span class="n">path</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Union</span><span class="p">[</span><span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="n">Tuple</span><span class="p">[</span><span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="nb">str</span><span class="p">]]:</span>
<span class="n">hint_path</span> <span class="o">=</span> <span class="s1">&#39;&#39;</span> <span class="c1"># if given, show the data path in the error message</span>
<span class="k">if</span> <span class="n">path</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
<span class="n">hint_path</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">&#39; in </span><span class="si">{</span><span class="n">path</span><span class="si">}</span><span class="s1">&#39;</span>
<span class="k">if</span> <span class="n">df</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">name</span> <span class="o">!=</span> <span class="s1">&#39;id&#39;</span> <span class="ow">or</span> <span class="nb">len</span><span class="p">(</span><span class="n">df</span><span class="o">.</span><span class="n">columns</span><span class="p">)</span> <span class="o">&lt;</span> <span class="mi">2</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;wrong header</span><span class="si">{</span><span class="n">hint_path</span><span class="si">}</span><span class="s1">, &#39;</span>
<span class="sa">f</span><span class="s1">&#39;the format of the header should be &quot;id,0,...,n-1&quot;, &#39;</span>
<span class="sa">f</span><span class="s1">&#39;where n is the number of categories&#39;</span><span class="p">)</span>
<span class="k">if</span> <span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">ci</span><span class="p">)</span> <span class="k">for</span> <span class="n">ci</span> <span class="ow">in</span> <span class="n">df</span><span class="o">.</span><span class="n">columns</span><span class="o">.</span><span class="n">values</span><span class="p">]</span> <span class="o">!=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">df</span><span class="o">.</span><span class="n">columns</span><span class="p">))):</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;wrong header</span><span class="si">{</span><span class="n">hint_path</span><span class="si">}</span><span class="s1">, category ids should be 0,1,2,...,n-1, &#39;</span>
<span class="sa">f</span><span class="s1">&#39;where n is the number of categories&#39;</span><span class="p">)</span>
<span class="k">if</span> <span class="n">df</span><span class="o">.</span><span class="n">empty</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;error</span><span class="si">{</span><span class="n">hint_path</span><span class="si">}</span><span class="s1">: results file is empty&#39;</span><span class="p">)</span>
<span class="k">elif</span> <span class="nb">len</span><span class="p">(</span><span class="n">df</span><span class="p">)</span> <span class="o">!=</span> <span class="n">DEV_SAMPLES</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">df</span><span class="p">)</span> <span class="o">!=</span> <span class="n">TEST_SAMPLES</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;wrong number of prevalence values found</span><span class="si">{</span><span class="n">hint_path</span><span class="si">}</span><span class="s1">; &#39;</span>
<span class="sa">f</span><span class="s1">&#39;expected </span><span class="si">{</span><span class="n">DEV_SAMPLES</span><span class="si">}</span><span class="s1"> for development sets and &#39;</span>
<span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">TEST_SAMPLES</span><span class="si">}</span><span class="s1"> for test sets; found </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="n">df</span><span class="p">)</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="n">ids</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">df</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">values</span><span class="p">)</span>
<span class="n">expected_ids</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">df</span><span class="p">)))</span>
<span class="k">if</span> <span class="n">ids</span> <span class="o">!=</span> <span class="n">expected_ids</span><span class="p">:</span>
<span class="n">missing</span> <span class="o">=</span> <span class="n">expected_ids</span> <span class="o">-</span> <span class="n">ids</span>
<span class="k">if</span> <span class="n">missing</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;there are </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="n">missing</span><span class="p">)</span><span class="si">}</span><span class="s1"> missing ids</span><span class="si">{</span><span class="n">hint_path</span><span class="si">}</span><span class="s1">: </span><span class="si">{</span><span class="nb">sorted</span><span class="p">(</span><span class="n">missing</span><span class="p">)</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="n">unexpected</span> <span class="o">=</span> <span class="n">ids</span> <span class="o">-</span> <span class="n">expected_ids</span>
<span class="k">if</span> <span class="n">unexpected</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;there are </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="n">missing</span><span class="p">)</span><span class="si">}</span><span class="s1"> unexpected ids</span><span class="si">{</span><span class="n">hint_path</span><span class="si">}</span><span class="s1">: </span><span class="si">{</span><span class="nb">sorted</span><span class="p">(</span><span class="n">unexpected</span><span class="p">)</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="k">for</span> <span class="n">category_id</span> <span class="ow">in</span> <span class="n">df</span><span class="o">.</span><span class="n">columns</span><span class="p">:</span>
<span class="k">if</span> <span class="p">(</span><span class="n">df</span><span class="p">[</span><span class="n">category_id</span><span class="p">]</span> <span class="o">&lt;</span> <span class="mi">0</span><span class="p">)</span><span class="o">.</span><span class="n">any</span><span class="p">()</span> <span class="ow">or</span> <span class="p">(</span><span class="n">df</span><span class="p">[</span><span class="n">category_id</span><span class="p">]</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">)</span><span class="o">.</span><span class="n">any</span><span class="p">():</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;error</span><span class="si">{</span><span class="n">hint_path</span><span class="si">}</span><span class="s1"> column &quot;</span><span class="si">{</span><span class="n">category_id</span><span class="si">}</span><span class="s1">&quot; contains values out of range [0,1]&#39;</span><span class="p">)</span>
<span class="n">prevs</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">values</span>
<span class="n">round_errors</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">abs</span><span class="p">(</span><span class="n">prevs</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">axis</span><span class="o">=-</span><span class="mi">1</span><span class="p">)</span> <span class="o">-</span> <span class="mf">1.</span><span class="p">)</span> <span class="o">&gt;</span> <span class="n">ERROR_TOL</span>
<span class="k">if</span> <span class="n">round_errors</span><span class="o">.</span><span class="n">any</span><span class="p">():</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;warning: prevalence values in rows with id </span><span class="si">{</span><span class="n">np</span><span class="o">.</span><span class="n">where</span><span class="p">(</span><span class="n">round_errors</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">tolist</span><span class="p">()</span><span class="si">}</span><span class="s1"> &#39;</span>
<span class="sa">f</span><span class="s1">&#39;do not sum up to 1 (error tolerance </span><span class="si">{</span><span class="n">ERROR_TOL</span><span class="si">}</span><span class="s1">), &#39;</span>
<span class="sa">f</span><span class="s1">&#39;probably due to some rounding errors.&#39;</span><span class="p">)</span>
<span class="k">return</span> <span class="n">df</span></div>
</div>
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<h1>Source code for quapy.data.preprocessing</h1><div class="highlight"><pre>
<span></span><span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">scipy.sparse</span><span class="w"> </span><span class="kn">import</span> <span class="n">spmatrix</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">sklearn.feature_extraction.text</span><span class="w"> </span><span class="kn">import</span> <span class="n">TfidfVectorizer</span><span class="p">,</span> <span class="n">CountVectorizer</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">sklearn.preprocessing</span><span class="w"> </span><span class="kn">import</span> <span class="n">StandardScaler</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">tqdm</span><span class="w"> </span><span class="kn">import</span> <span class="n">tqdm</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">quapy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">qp</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">quapy.data.base</span><span class="w"> </span><span class="kn">import</span> <span class="n">Dataset</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">quapy.util</span><span class="w"> </span><span class="kn">import</span> <span class="n">map_parallel</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">.base</span><span class="w"> </span><span class="kn">import</span> <span class="n">LabelledCollection</span>
<div class="viewcode-block" id="instance_transformation">
<a class="viewcode-back" href="../../../quapy.data.html#quapy.data.preprocessing.instance_transformation">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">instance_transformation</span><span class="p">(</span><span class="n">dataset</span><span class="p">:</span><span class="n">Dataset</span><span class="p">,</span> <span class="n">transformer</span><span class="p">,</span> <span class="n">inplace</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Transforms a :class:`quapy.data.base.Dataset` applying the `fit_transform` and `transform` functions</span>
<span class="sd"> of a (sklearn&#39;s) transformer.</span>
<span class="sd"> :param dataset: a :class:`quapy.data.base.Dataset` where the instances of training and test collections are</span>
<span class="sd"> lists of str</span>
<span class="sd"> :param transformer: TransformerMixin implementing `fit_transform` and `transform` functions</span>
<span class="sd"> :param inplace: whether or not to apply the transformation inplace (True), or to a new copy (False, default)</span>
<span class="sd"> :return: a new :class:`quapy.data.base.Dataset` with transformed instances (if inplace=False) or a reference to the</span>
<span class="sd"> current Dataset (if inplace=True) where the instances have been transformed</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">training_transformed</span> <span class="o">=</span> <span class="n">transformer</span><span class="o">.</span><span class="n">fit_transform</span><span class="p">(</span><span class="o">*</span><span class="n">dataset</span><span class="o">.</span><span class="n">training</span><span class="o">.</span><span class="n">Xy</span><span class="p">)</span>
<span class="n">test_transformed</span> <span class="o">=</span> <span class="n">transformer</span><span class="o">.</span><span class="n">transform</span><span class="p">(</span><span class="n">dataset</span><span class="o">.</span><span class="n">test</span><span class="o">.</span><span class="n">X</span><span class="p">)</span>
<span class="n">orig_name</span> <span class="o">=</span> <span class="n">dataset</span><span class="o">.</span><span class="n">name</span>
<span class="k">if</span> <span class="n">inplace</span><span class="p">:</span>
<span class="n">dataset</span><span class="o">.</span><span class="n">training</span> <span class="o">=</span> <span class="n">LabelledCollection</span><span class="p">(</span><span class="n">training_transformed</span><span class="p">,</span> <span class="n">dataset</span><span class="o">.</span><span class="n">training</span><span class="o">.</span><span class="n">labels</span><span class="p">,</span> <span class="n">dataset</span><span class="o">.</span><span class="n">classes_</span><span class="p">)</span>
<span class="n">dataset</span><span class="o">.</span><span class="n">test</span> <span class="o">=</span> <span class="n">LabelledCollection</span><span class="p">(</span><span class="n">test_transformed</span><span class="p">,</span> <span class="n">dataset</span><span class="o">.</span><span class="n">test</span><span class="o">.</span><span class="n">labels</span><span class="p">,</span> <span class="n">dataset</span><span class="o">.</span><span class="n">classes_</span><span class="p">)</span>
<span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">transformer</span><span class="p">,</span> <span class="s1">&#39;vocabulary_&#39;</span><span class="p">):</span>
<span class="n">dataset</span><span class="o">.</span><span class="n">vocabulary</span> <span class="o">=</span> <span class="n">transformer</span><span class="o">.</span><span class="n">vocabulary_</span>
<span class="k">return</span> <span class="n">dataset</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">training</span> <span class="o">=</span> <span class="n">LabelledCollection</span><span class="p">(</span><span class="n">training_transformed</span><span class="p">,</span> <span class="n">dataset</span><span class="o">.</span><span class="n">training</span><span class="o">.</span><span class="n">labels</span><span class="o">.</span><span class="n">copy</span><span class="p">(),</span> <span class="n">dataset</span><span class="o">.</span><span class="n">classes_</span><span class="p">)</span>
<span class="n">test</span> <span class="o">=</span> <span class="n">LabelledCollection</span><span class="p">(</span><span class="n">test_transformed</span><span class="p">,</span> <span class="n">dataset</span><span class="o">.</span><span class="n">test</span><span class="o">.</span><span class="n">labels</span><span class="o">.</span><span class="n">copy</span><span class="p">(),</span> <span class="n">dataset</span><span class="o">.</span><span class="n">classes_</span><span class="p">)</span>
<span class="n">vocab</span> <span class="o">=</span> <span class="kc">None</span>
<span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">transformer</span><span class="p">,</span> <span class="s1">&#39;vocabulary_&#39;</span><span class="p">):</span>
<span class="n">vocab</span> <span class="o">=</span> <span class="n">transformer</span><span class="o">.</span><span class="n">vocabulary_</span>
<span class="k">return</span> <span class="n">Dataset</span><span class="p">(</span><span class="n">training</span><span class="p">,</span> <span class="n">test</span><span class="p">,</span> <span class="n">vocabulary</span><span class="o">=</span><span class="n">vocab</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="n">orig_name</span><span class="p">)</span></div>
<div class="viewcode-block" id="text2tfidf">
<a class="viewcode-back" href="../../../quapy.data.html#quapy.data.preprocessing.text2tfidf">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">text2tfidf</span><span class="p">(</span><span class="n">dataset</span><span class="p">:</span><span class="n">Dataset</span><span class="p">,</span> <span class="n">min_df</span><span class="o">=</span><span class="mi">3</span><span class="p">,</span> <span class="n">sublinear_tf</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">inplace</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Transforms a :class:`quapy.data.base.Dataset` of textual instances into a :class:`quapy.data.base.Dataset` of</span>
<span class="sd"> tfidf weighted sparse vectors</span>
<span class="sd"> :param dataset: a :class:`quapy.data.base.Dataset` where the instances of training and test collections are</span>
<span class="sd"> lists of str</span>
<span class="sd"> :param min_df: minimum number of occurrences for a word to be considered as part of the vocabulary (default 3)</span>
<span class="sd"> :param sublinear_tf: whether or not to apply the log scalling to the tf counters (default True)</span>
<span class="sd"> :param inplace: whether or not to apply the transformation inplace (True), or to a new copy (False, default)</span>
<span class="sd"> :param kwargs: the rest of parameters of the transformation (as for sklearn&#39;s</span>
<span class="sd"> `TfidfVectorizer &lt;https://scikit-learn.org/stable/modules/generated/sklearn.feature_extraction.text.TfidfVectorizer.html&gt;`_)</span>
<span class="sd"> :return: a new :class:`quapy.data.base.Dataset` in `csr_matrix` format (if inplace=False) or a reference to the</span>
<span class="sd"> current Dataset (if inplace=True) where the instances are stored in a `csr_matrix` of real-valued tfidf scores</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">__check_type</span><span class="p">(</span><span class="n">dataset</span><span class="o">.</span><span class="n">training</span><span class="o">.</span><span class="n">instances</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span> <span class="nb">str</span><span class="p">)</span>
<span class="n">__check_type</span><span class="p">(</span><span class="n">dataset</span><span class="o">.</span><span class="n">test</span><span class="o">.</span><span class="n">instances</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span> <span class="nb">str</span><span class="p">)</span>
<span class="n">vectorizer</span> <span class="o">=</span> <span class="n">TfidfVectorizer</span><span class="p">(</span><span class="n">min_df</span><span class="o">=</span><span class="n">min_df</span><span class="p">,</span> <span class="n">sublinear_tf</span><span class="o">=</span><span class="n">sublinear_tf</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
<span class="k">return</span> <span class="n">instance_transformation</span><span class="p">(</span><span class="n">dataset</span><span class="p">,</span> <span class="n">vectorizer</span><span class="p">,</span> <span class="n">inplace</span><span class="p">)</span></div>
<div class="viewcode-block" id="reduce_columns">
<a class="viewcode-back" href="../../../quapy.data.html#quapy.data.preprocessing.reduce_columns">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">reduce_columns</span><span class="p">(</span><span class="n">dataset</span><span class="p">:</span> <span class="n">Dataset</span><span class="p">,</span> <span class="n">min_df</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">inplace</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Reduces the dimensionality of the instances, represented as a `csr_matrix` (or any subtype of</span>
<span class="sd"> `scipy.sparse.spmatrix`), of training and test documents by removing the columns of words which are not present</span>
<span class="sd"> in at least `min_df` instances in the training set</span>
<span class="sd"> :param dataset: a :class:`quapy.data.base.Dataset` in which instances are represented in sparse format (any</span>
<span class="sd"> subtype of scipy.sparse.spmatrix)</span>
<span class="sd"> :param min_df: integer, minimum number of instances below which the columns are removed</span>
<span class="sd"> :param inplace: whether or not to apply the transformation inplace (True), or to a new copy (False, default)</span>
<span class="sd"> :return: a new :class:`quapy.data.base.Dataset` (if inplace=False) or a reference to the current</span>
<span class="sd"> :class:`quapy.data.base.Dataset` (inplace=True) where the dimensions corresponding to infrequent terms</span>
<span class="sd"> in the training set have been removed</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">__check_type</span><span class="p">(</span><span class="n">dataset</span><span class="o">.</span><span class="n">training</span><span class="o">.</span><span class="n">instances</span><span class="p">,</span> <span class="n">spmatrix</span><span class="p">)</span>
<span class="n">__check_type</span><span class="p">(</span><span class="n">dataset</span><span class="o">.</span><span class="n">test</span><span class="o">.</span><span class="n">instances</span><span class="p">,</span> <span class="n">spmatrix</span><span class="p">)</span>
<span class="k">assert</span> <span class="n">dataset</span><span class="o">.</span><span class="n">training</span><span class="o">.</span><span class="n">instances</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">==</span> <span class="n">dataset</span><span class="o">.</span><span class="n">test</span><span class="o">.</span><span class="n">instances</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="s1">&#39;unaligned vector spaces&#39;</span>
<span class="k">def</span><span class="w"> </span><span class="nf">filter_by_occurrences</span><span class="p">(</span><span class="n">X</span><span class="p">,</span> <span class="n">W</span><span class="p">):</span>
<span class="n">column_prevalence</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">((</span><span class="n">X</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">)</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">))</span><span class="o">.</span><span class="n">flatten</span><span class="p">()</span>
<span class="n">take_columns</span> <span class="o">=</span> <span class="n">column_prevalence</span> <span class="o">&gt;=</span> <span class="n">min_df</span>
<span class="n">X</span> <span class="o">=</span> <span class="n">X</span><span class="p">[:,</span> <span class="n">take_columns</span><span class="p">]</span>
<span class="n">W</span> <span class="o">=</span> <span class="n">W</span><span class="p">[:,</span> <span class="n">take_columns</span><span class="p">]</span>
<span class="k">return</span> <span class="n">X</span><span class="p">,</span> <span class="n">W</span>
<span class="n">Xtr</span><span class="p">,</span> <span class="n">Xte</span> <span class="o">=</span> <span class="n">filter_by_occurrences</span><span class="p">(</span><span class="n">dataset</span><span class="o">.</span><span class="n">training</span><span class="o">.</span><span class="n">instances</span><span class="p">,</span> <span class="n">dataset</span><span class="o">.</span><span class="n">test</span><span class="o">.</span><span class="n">instances</span><span class="p">)</span>
<span class="k">if</span> <span class="n">inplace</span><span class="p">:</span>
<span class="n">dataset</span><span class="o">.</span><span class="n">training</span><span class="o">.</span><span class="n">instances</span> <span class="o">=</span> <span class="n">Xtr</span>
<span class="n">dataset</span><span class="o">.</span><span class="n">test</span><span class="o">.</span><span class="n">instances</span> <span class="o">=</span> <span class="n">Xte</span>
<span class="k">return</span> <span class="n">dataset</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">training</span> <span class="o">=</span> <span class="n">LabelledCollection</span><span class="p">(</span><span class="n">Xtr</span><span class="p">,</span> <span class="n">dataset</span><span class="o">.</span><span class="n">training</span><span class="o">.</span><span class="n">labels</span><span class="o">.</span><span class="n">copy</span><span class="p">(),</span> <span class="n">dataset</span><span class="o">.</span><span class="n">classes_</span><span class="p">)</span>
<span class="n">test</span> <span class="o">=</span> <span class="n">LabelledCollection</span><span class="p">(</span><span class="n">Xte</span><span class="p">,</span> <span class="n">dataset</span><span class="o">.</span><span class="n">test</span><span class="o">.</span><span class="n">labels</span><span class="o">.</span><span class="n">copy</span><span class="p">(),</span> <span class="n">dataset</span><span class="o">.</span><span class="n">classes_</span><span class="p">)</span>
<span class="k">return</span> <span class="n">Dataset</span><span class="p">(</span><span class="n">training</span><span class="p">,</span> <span class="n">test</span><span class="p">)</span></div>
<div class="viewcode-block" id="standardize">
<a class="viewcode-back" href="../../../quapy.data.html#quapy.data.preprocessing.standardize">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">standardize</span><span class="p">(</span><span class="n">dataset</span><span class="p">:</span> <span class="n">Dataset</span><span class="p">,</span> <span class="n">inplace</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Standardizes the real-valued columns of a :class:`quapy.data.base.Dataset`.</span>
<span class="sd"> Standardization, aka z-scoring, of a variable `X` comes down to subtracting the average and normalizing by the</span>
<span class="sd"> standard deviation.</span>
<span class="sd"> :param dataset: a :class:`quapy.data.base.Dataset` object</span>
<span class="sd"> :param inplace: set to True if the transformation is to be applied inplace, or to False (default) if a new</span>
<span class="sd"> :class:`quapy.data.base.Dataset` is to be returned</span>
<span class="sd"> :return: an instance of :class:`quapy.data.base.Dataset`</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">s</span> <span class="o">=</span> <span class="n">StandardScaler</span><span class="p">()</span>
<span class="n">train</span><span class="p">,</span> <span class="n">test</span> <span class="o">=</span> <span class="n">dataset</span><span class="o">.</span><span class="n">train_test</span>
<span class="n">std_train_X</span> <span class="o">=</span> <span class="n">s</span><span class="o">.</span><span class="n">fit_transform</span><span class="p">(</span><span class="n">train</span><span class="o">.</span><span class="n">X</span><span class="p">)</span>
<span class="n">std_test_X</span> <span class="o">=</span> <span class="n">s</span><span class="o">.</span><span class="n">transform</span><span class="p">(</span><span class="n">test</span><span class="o">.</span><span class="n">X</span><span class="p">)</span>
<span class="k">if</span> <span class="n">inplace</span><span class="p">:</span>
<span class="n">dataset</span><span class="o">.</span><span class="n">training</span><span class="o">.</span><span class="n">instances</span> <span class="o">=</span> <span class="n">std_train_X</span>
<span class="n">dataset</span><span class="o">.</span><span class="n">test</span><span class="o">.</span><span class="n">instances</span> <span class="o">=</span> <span class="n">std_test_X</span>
<span class="k">return</span> <span class="n">dataset</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">training</span> <span class="o">=</span> <span class="n">LabelledCollection</span><span class="p">(</span><span class="n">std_train_X</span><span class="p">,</span> <span class="n">train</span><span class="o">.</span><span class="n">labels</span><span class="p">,</span> <span class="n">classes</span><span class="o">=</span><span class="n">train</span><span class="o">.</span><span class="n">classes_</span><span class="p">)</span>
<span class="n">test</span> <span class="o">=</span> <span class="n">LabelledCollection</span><span class="p">(</span><span class="n">std_test_X</span><span class="p">,</span> <span class="n">test</span><span class="o">.</span><span class="n">labels</span><span class="p">,</span> <span class="n">classes</span><span class="o">=</span><span class="n">test</span><span class="o">.</span><span class="n">classes_</span><span class="p">)</span>
<span class="k">return</span> <span class="n">Dataset</span><span class="p">(</span><span class="n">training</span><span class="p">,</span> <span class="n">test</span><span class="p">,</span> <span class="n">dataset</span><span class="o">.</span><span class="n">vocabulary</span><span class="p">,</span> <span class="n">dataset</span><span class="o">.</span><span class="n">name</span><span class="p">)</span></div>
<div class="viewcode-block" id="index">
<a class="viewcode-back" href="../../../quapy.data.html#quapy.data.preprocessing.index">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">index</span><span class="p">(</span><span class="n">dataset</span><span class="p">:</span> <span class="n">Dataset</span><span class="p">,</span> <span class="n">min_df</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">inplace</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Indexes the tokens of a textual :class:`quapy.data.base.Dataset` of string documents.</span>
<span class="sd"> To index a document means to replace each different token by a unique numerical index.</span>
<span class="sd"> Rare words (i.e., words occurring less than `min_df` times) are replaced by a special token `UNK`</span>
<span class="sd"> :param dataset: a :class:`quapy.data.base.Dataset` object where the instances of training and test documents</span>
<span class="sd"> are lists of str</span>
<span class="sd"> :param min_df: minimum number of occurrences below which the term is replaced by a `UNK` index</span>
<span class="sd"> :param inplace: whether or not to apply the transformation inplace (True), or to a new copy (False, default)</span>
<span class="sd"> :param kwargs: the rest of parameters of the transformation (as for sklearn&#39;s</span>
<span class="sd"> `CountVectorizer &lt;https://scikit-learn.org/stable/modules/generated/sklearn.feature_extraction.text.CountVectorizer.html&gt;_`)</span>
<span class="sd"> :return: a new :class:`quapy.data.base.Dataset` (if inplace=False) or a reference to the current</span>
<span class="sd"> :class:`quapy.data.base.Dataset` (inplace=True) consisting of lists of integer values representing indices.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">__check_type</span><span class="p">(</span><span class="n">dataset</span><span class="o">.</span><span class="n">training</span><span class="o">.</span><span class="n">instances</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span> <span class="nb">str</span><span class="p">)</span>
<span class="n">__check_type</span><span class="p">(</span><span class="n">dataset</span><span class="o">.</span><span class="n">test</span><span class="o">.</span><span class="n">instances</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span> <span class="nb">str</span><span class="p">)</span>
<span class="n">indexer</span> <span class="o">=</span> <span class="n">IndexTransformer</span><span class="p">(</span><span class="n">min_df</span><span class="o">=</span><span class="n">min_df</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
<span class="n">training_index</span> <span class="o">=</span> <span class="n">indexer</span><span class="o">.</span><span class="n">fit_transform</span><span class="p">(</span><span class="n">dataset</span><span class="o">.</span><span class="n">training</span><span class="o">.</span><span class="n">instances</span><span class="p">)</span>
<span class="n">test_index</span> <span class="o">=</span> <span class="n">indexer</span><span class="o">.</span><span class="n">transform</span><span class="p">(</span><span class="n">dataset</span><span class="o">.</span><span class="n">test</span><span class="o">.</span><span class="n">instances</span><span class="p">)</span>
<span class="n">training_index</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">training_index</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="nb">object</span><span class="p">)</span>
<span class="n">test_index</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">test_index</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="nb">object</span><span class="p">)</span>
<span class="k">if</span> <span class="n">inplace</span><span class="p">:</span>
<span class="n">dataset</span><span class="o">.</span><span class="n">training</span> <span class="o">=</span> <span class="n">LabelledCollection</span><span class="p">(</span><span class="n">training_index</span><span class="p">,</span> <span class="n">dataset</span><span class="o">.</span><span class="n">training</span><span class="o">.</span><span class="n">labels</span><span class="p">,</span> <span class="n">dataset</span><span class="o">.</span><span class="n">classes_</span><span class="p">)</span>
<span class="n">dataset</span><span class="o">.</span><span class="n">test</span> <span class="o">=</span> <span class="n">LabelledCollection</span><span class="p">(</span><span class="n">test_index</span><span class="p">,</span> <span class="n">dataset</span><span class="o">.</span><span class="n">test</span><span class="o">.</span><span class="n">labels</span><span class="p">,</span> <span class="n">dataset</span><span class="o">.</span><span class="n">classes_</span><span class="p">)</span>
<span class="n">dataset</span><span class="o">.</span><span class="n">vocabulary</span> <span class="o">=</span> <span class="n">indexer</span><span class="o">.</span><span class="n">vocabulary_</span>
<span class="k">return</span> <span class="n">dataset</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">training</span> <span class="o">=</span> <span class="n">LabelledCollection</span><span class="p">(</span><span class="n">training_index</span><span class="p">,</span> <span class="n">dataset</span><span class="o">.</span><span class="n">training</span><span class="o">.</span><span class="n">labels</span><span class="o">.</span><span class="n">copy</span><span class="p">(),</span> <span class="n">dataset</span><span class="o">.</span><span class="n">classes_</span><span class="p">)</span>
<span class="n">test</span> <span class="o">=</span> <span class="n">LabelledCollection</span><span class="p">(</span><span class="n">test_index</span><span class="p">,</span> <span class="n">dataset</span><span class="o">.</span><span class="n">test</span><span class="o">.</span><span class="n">labels</span><span class="o">.</span><span class="n">copy</span><span class="p">(),</span> <span class="n">dataset</span><span class="o">.</span><span class="n">classes_</span><span class="p">)</span>
<span class="k">return</span> <span class="n">Dataset</span><span class="p">(</span><span class="n">training</span><span class="p">,</span> <span class="n">test</span><span class="p">,</span> <span class="n">indexer</span><span class="o">.</span><span class="n">vocabulary_</span><span class="p">)</span></div>
<span class="k">def</span><span class="w"> </span><span class="nf">__check_type</span><span class="p">(</span><span class="n">container</span><span class="p">,</span> <span class="n">container_type</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">element_type</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<span class="k">if</span> <span class="n">container_type</span><span class="p">:</span>
<span class="k">assert</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">container</span><span class="p">,</span> <span class="n">container_type</span><span class="p">),</span> \
<span class="sa">f</span><span class="s1">&#39;unexpected type of container (expected </span><span class="si">{</span><span class="n">container_type</span><span class="si">}</span><span class="s1">, found </span><span class="si">{</span><span class="nb">type</span><span class="p">(</span><span class="n">container</span><span class="p">)</span><span class="si">}</span><span class="s1">)&#39;</span>
<span class="k">if</span> <span class="n">element_type</span><span class="p">:</span>
<span class="k">assert</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">container</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">element_type</span><span class="p">),</span> \
<span class="sa">f</span><span class="s1">&#39;unexpected type of element (expected </span><span class="si">{</span><span class="n">container_type</span><span class="si">}</span><span class="s1">, found </span><span class="si">{</span><span class="nb">type</span><span class="p">(</span><span class="n">container</span><span class="p">)</span><span class="si">}</span><span class="s1">)&#39;</span>
<div class="viewcode-block" id="IndexTransformer">
<a class="viewcode-back" href="../../../quapy.data.html#quapy.data.preprocessing.IndexTransformer">[docs]</a>
<span class="k">class</span><span class="w"> </span><span class="nc">IndexTransformer</span><span class="p">:</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> This class implements a sklearn&#39;s-style transformer that indexes text as numerical ids for the tokens it</span>
<span class="sd"> contains, and that would be generated by sklearn&#39;s</span>
<span class="sd"> `CountVectorizer &lt;https://scikit-learn.org/stable/modules/generated/sklearn.feature_extraction.text.CountVectorizer.html&gt;`_</span>
<span class="sd"> :param kwargs: keyworded arguments from</span>
<span class="sd"> `CountVectorizer &lt;https://scikit-learn.org/stable/modules/generated/sklearn.feature_extraction.text.CountVectorizer.html&gt;`_</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">vect</span> <span class="o">=</span> <span class="n">CountVectorizer</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">unk</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span> <span class="c1"># a valid index is assigned after fit</span>
<span class="bp">self</span><span class="o">.</span><span class="n">pad</span> <span class="o">=</span> <span class="o">-</span><span class="mi">2</span> <span class="c1"># a valid index is assigned after fit</span>
<div class="viewcode-block" id="IndexTransformer.fit">
<a class="viewcode-back" href="../../../quapy.data.html#quapy.data.preprocessing.IndexTransformer.fit">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">fit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Fits the transformer, i.e., decides on the vocabulary, given a list of strings.</span>
<span class="sd"> :param X: a list of strings</span>
<span class="sd"> :return: self</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="bp">self</span><span class="o">.</span><span class="n">vect</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="n">X</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">analyzer</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">vect</span><span class="o">.</span><span class="n">build_analyzer</span><span class="p">()</span>
<span class="bp">self</span><span class="o">.</span><span class="n">vocabulary_</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">vect</span><span class="o">.</span><span class="n">vocabulary_</span>
<span class="bp">self</span><span class="o">.</span><span class="n">unk</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">add_word</span><span class="p">(</span><span class="n">qp</span><span class="o">.</span><span class="n">environ</span><span class="p">[</span><span class="s1">&#39;UNK_TOKEN&#39;</span><span class="p">],</span> <span class="n">qp</span><span class="o">.</span><span class="n">environ</span><span class="p">[</span><span class="s1">&#39;UNK_INDEX&#39;</span><span class="p">])</span>
<span class="bp">self</span><span class="o">.</span><span class="n">pad</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">add_word</span><span class="p">(</span><span class="n">qp</span><span class="o">.</span><span class="n">environ</span><span class="p">[</span><span class="s1">&#39;PAD_TOKEN&#39;</span><span class="p">],</span> <span class="n">qp</span><span class="o">.</span><span class="n">environ</span><span class="p">[</span><span class="s1">&#39;PAD_INDEX&#39;</span><span class="p">])</span>
<span class="k">return</span> <span class="bp">self</span></div>
<div class="viewcode-block" id="IndexTransformer.transform">
<a class="viewcode-back" href="../../../quapy.data.html#quapy.data.preprocessing.IndexTransformer.transform">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">transform</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">,</span> <span class="n">n_jobs</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Transforms the strings in `X` as lists of numerical ids</span>
<span class="sd"> :param X: a list of strings</span>
<span class="sd"> :param n_jobs: the number of parallel workers to carry out this task</span>
<span class="sd"> :return: a `np.ndarray` of numerical ids</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="c1"># given the number of tasks and the number of jobs, generates the slices for the parallel processes</span>
<span class="k">assert</span> <span class="bp">self</span><span class="o">.</span><span class="n">unk</span> <span class="o">!=</span> <span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="s1">&#39;transform called before fit&#39;</span>
<span class="n">n_jobs</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">_get_njobs</span><span class="p">(</span><span class="n">n_jobs</span><span class="p">)</span>
<span class="k">return</span> <span class="n">map_parallel</span><span class="p">(</span><span class="n">func</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">_index</span><span class="p">,</span> <span class="n">args</span><span class="o">=</span><span class="n">X</span><span class="p">,</span> <span class="n">n_jobs</span><span class="o">=</span><span class="n">n_jobs</span><span class="p">)</span></div>
<span class="k">def</span><span class="w"> </span><span class="nf">_index</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">documents</span><span class="p">):</span>
<span class="n">vocab</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">vocabulary_</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
<span class="k">return</span> <span class="p">[[</span><span class="n">vocab</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">word</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">unk</span><span class="p">)</span> <span class="k">for</span> <span class="n">word</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">analyzer</span><span class="p">(</span><span class="n">doc</span><span class="p">)]</span> <span class="k">for</span> <span class="n">doc</span> <span class="ow">in</span> <span class="n">tqdm</span><span class="p">(</span><span class="n">documents</span><span class="p">,</span> <span class="s1">&#39;indexing&#39;</span><span class="p">)]</span>
<div class="viewcode-block" id="IndexTransformer.fit_transform">
<a class="viewcode-back" href="../../../quapy.data.html#quapy.data.preprocessing.IndexTransformer.fit_transform">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">fit_transform</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">,</span> <span class="n">n_jobs</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Fits the transform on `X` and transforms it.</span>
<span class="sd"> :param X: a list of strings</span>
<span class="sd"> :param n_jobs: the number of parallel workers to carry out this task</span>
<span class="sd"> :return: a `np.ndarray` of numerical ids</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="n">X</span><span class="p">)</span><span class="o">.</span><span class="n">transform</span><span class="p">(</span><span class="n">X</span><span class="p">,</span> <span class="n">n_jobs</span><span class="o">=</span><span class="n">n_jobs</span><span class="p">)</span></div>
<div class="viewcode-block" id="IndexTransformer.vocabulary_size">
<a class="viewcode-back" href="../../../quapy.data.html#quapy.data.preprocessing.IndexTransformer.vocabulary_size">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">vocabulary_size</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Gets the length of the vocabulary according to which the document tokens have been indexed</span>
<span class="sd"> :return: integer</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">vocabulary_</span><span class="p">)</span></div>
<div class="viewcode-block" id="IndexTransformer.add_word">
<a class="viewcode-back" href="../../../quapy.data.html#quapy.data.preprocessing.IndexTransformer.add_word">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">add_word</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">word</span><span class="p">,</span> <span class="nb">id</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">nogaps</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Adds a new token (regardless of whether it has been found in the text or not), with dedicated id.</span>
<span class="sd"> Useful to define special tokens for codifying unknown words, or padding tokens.</span>
<span class="sd"> :param word: string, surface form of the token</span>
<span class="sd"> :param id: integer, numerical value to assign to the token (leave as None for indicating the next valid id,</span>
<span class="sd"> default)</span>
<span class="sd"> :param nogaps: if set to True (default) asserts that the id indicated leads to no numerical gaps with</span>
<span class="sd"> precedent ids stored so far</span>
<span class="sd"> :return: integer, the numerical id for the new token</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">if</span> <span class="n">word</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">vocabulary_</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;word </span><span class="si">{</span><span class="n">word</span><span class="si">}</span><span class="s1"> already in dictionary&#39;</span><span class="p">)</span>
<span class="k">if</span> <span class="nb">id</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="c1"># add the word with the next id</span>
<span class="bp">self</span><span class="o">.</span><span class="n">vocabulary_</span><span class="p">[</span><span class="n">word</span><span class="p">]</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">vocabulary_</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">id2word</span> <span class="o">=</span> <span class="p">{</span><span class="n">id_</span><span class="p">:</span><span class="n">word_</span> <span class="k">for</span> <span class="n">word_</span><span class="p">,</span> <span class="n">id_</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">vocabulary_</span><span class="o">.</span><span class="n">items</span><span class="p">()}</span>
<span class="k">if</span> <span class="nb">id</span> <span class="ow">in</span> <span class="n">id2word</span><span class="p">:</span>
<span class="n">old_word</span> <span class="o">=</span> <span class="n">id2word</span><span class="p">[</span><span class="nb">id</span><span class="p">]</span>
<span class="bp">self</span><span class="o">.</span><span class="n">vocabulary_</span><span class="p">[</span><span class="n">word</span><span class="p">]</span> <span class="o">=</span> <span class="nb">id</span>
<span class="k">del</span> <span class="bp">self</span><span class="o">.</span><span class="n">vocabulary_</span><span class="p">[</span><span class="n">old_word</span><span class="p">]</span>
<span class="bp">self</span><span class="o">.</span><span class="n">add_word</span><span class="p">(</span><span class="n">old_word</span><span class="p">)</span>
<span class="k">elif</span> <span class="n">nogaps</span><span class="p">:</span>
<span class="k">if</span> <span class="nb">id</span> <span class="o">&gt;</span> <span class="bp">self</span><span class="o">.</span><span class="n">vocabulary_size</span><span class="p">()</span><span class="o">+</span><span class="mi">1</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;word </span><span class="si">{</span><span class="n">word</span><span class="si">}</span><span class="s1"> added with id </span><span class="si">{</span><span class="nb">id</span><span class="si">}</span><span class="s1">, while the current vocabulary size &#39;</span>
<span class="sa">f</span><span class="s1">&#39;is of </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">vocabulary_size</span><span class="p">()</span><span class="si">}</span><span class="s1">, and id gaps are not allowed&#39;</span><span class="p">)</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">vocabulary_</span><span class="p">[</span><span class="n">word</span><span class="p">]</span></div>
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<h1>Source code for quapy.data.reader</h1><div class="highlight"><pre>
<span></span><span class="kn">import</span><span class="w"> </span><span class="nn">logging</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">scipy.sparse</span><span class="w"> </span><span class="kn">import</span> <span class="n">dok_matrix</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">tqdm</span><span class="w"> </span><span class="kn">import</span> <span class="n">tqdm</span>
<div class="viewcode-block" id="from_text">
<a class="viewcode-back" href="../../../quapy.data.html#quapy.data.reader.from_text">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">from_text</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">encoding</span><span class="o">=</span><span class="s1">&#39;utf-8&#39;</span><span class="p">,</span> <span class="n">verbose</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">class2int</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Reads a labelled colletion of documents.</span>
<span class="sd"> File fomart &lt;0 or 1&gt;\t&lt;document&gt;\n</span>
<span class="sd"> :param path: path to the labelled collection</span>
<span class="sd"> :param encoding: the text encoding used to open the file</span>
<span class="sd"> :param verbose: if &gt;0 (default) shows some progress information in standard output</span>
<span class="sd"> :return: a list of sentences, and a list of labels</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">all_sentences</span><span class="p">,</span> <span class="n">all_labels</span> <span class="o">=</span> <span class="p">[],</span> <span class="p">[]</span>
<span class="k">if</span> <span class="n">verbose</span><span class="o">&gt;</span><span class="mi">0</span><span class="p">:</span>
<span class="n">file</span> <span class="o">=</span> <span class="n">tqdm</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="s1">&#39;rt&#39;</span><span class="p">,</span> <span class="n">encoding</span><span class="o">=</span><span class="n">encoding</span><span class="p">)</span><span class="o">.</span><span class="n">readlines</span><span class="p">(),</span> <span class="sa">f</span><span class="s1">&#39;loading </span><span class="si">{</span><span class="n">path</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">file</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="s1">&#39;rt&#39;</span><span class="p">,</span> <span class="n">encoding</span><span class="o">=</span><span class="n">encoding</span><span class="p">)</span><span class="o">.</span><span class="n">readlines</span><span class="p">()</span>
<span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">file</span><span class="p">:</span>
<span class="n">line</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
<span class="k">if</span> <span class="n">line</span><span class="p">:</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">label</span><span class="p">,</span> <span class="n">sentence</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="n">sentence</span> <span class="o">=</span> <span class="n">sentence</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
<span class="k">if</span> <span class="n">class2int</span><span class="p">:</span>
<span class="n">label</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">label</span><span class="p">)</span>
<span class="k">if</span> <span class="n">sentence</span><span class="p">:</span>
<span class="n">all_sentences</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">sentence</span><span class="p">)</span>
<span class="n">all_labels</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">label</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">ValueError</span><span class="p">:</span>
<span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="vm">__name__</span><span class="p">)</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;format error in </span><span class="si">{</span><span class="n">line</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="k">return</span> <span class="n">all_sentences</span><span class="p">,</span> <span class="n">all_labels</span></div>
<div class="viewcode-block" id="from_sparse">
<a class="viewcode-back" href="../../../quapy.data.html#quapy.data.reader.from_sparse">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">from_sparse</span><span class="p">(</span><span class="n">path</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Reads a labelled collection of real-valued instances expressed in sparse format</span>
<span class="sd"> File format &lt;-1 or 0 or 1&gt;[\s col(int):val(float)]\n</span>
<span class="sd"> :param path: path to the labelled collection</span>
<span class="sd"> :return: a `csr_matrix` containing the instances (rows), and a ndarray containing the labels</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">def</span><span class="w"> </span><span class="nf">split_col_val</span><span class="p">(</span><span class="n">col_val</span><span class="p">):</span>
<span class="n">col</span><span class="p">,</span> <span class="n">val</span> <span class="o">=</span> <span class="n">col_val</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;:&#39;</span><span class="p">)</span>
<span class="n">col</span><span class="p">,</span> <span class="n">val</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">col</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span><span class="p">,</span> <span class="nb">float</span><span class="p">(</span><span class="n">val</span><span class="p">)</span>
<span class="k">return</span> <span class="n">col</span><span class="p">,</span> <span class="n">val</span>
<span class="n">all_documents</span><span class="p">,</span> <span class="n">all_labels</span> <span class="o">=</span> <span class="p">[],</span> <span class="p">[]</span>
<span class="n">max_col</span> <span class="o">=</span> <span class="mi">0</span>
<span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">tqdm</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="s1">&#39;rt&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">readlines</span><span class="p">(),</span> <span class="sa">f</span><span class="s1">&#39;loading </span><span class="si">{</span><span class="n">path</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">):</span>
<span class="n">parts</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">()</span>
<span class="k">if</span> <span class="n">parts</span><span class="p">:</span>
<span class="n">all_labels</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">parts</span><span class="p">[</span><span class="mi">0</span><span class="p">]))</span>
<span class="n">cols</span><span class="p">,</span> <span class="n">vals</span> <span class="o">=</span> <span class="nb">zip</span><span class="p">(</span><span class="o">*</span><span class="p">[</span><span class="n">split_col_val</span><span class="p">(</span><span class="n">col_val</span><span class="p">)</span> <span class="k">for</span> <span class="n">col_val</span> <span class="ow">in</span> <span class="n">parts</span><span class="p">[</span><span class="mi">1</span><span class="p">:]])</span>
<span class="n">cols</span><span class="p">,</span> <span class="n">vals</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">cols</span><span class="p">),</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">vals</span><span class="p">)</span>
<span class="n">max_col</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="n">max_col</span><span class="p">,</span> <span class="n">cols</span><span class="o">.</span><span class="n">max</span><span class="p">())</span>
<span class="n">all_documents</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">cols</span><span class="p">,</span> <span class="n">vals</span><span class="p">))</span>
<span class="n">n_docs</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">all_labels</span><span class="p">)</span>
<span class="n">X</span> <span class="o">=</span> <span class="n">dok_matrix</span><span class="p">((</span><span class="n">n_docs</span><span class="p">,</span> <span class="n">max_col</span> <span class="o">+</span> <span class="mi">1</span><span class="p">),</span> <span class="n">dtype</span><span class="o">=</span><span class="nb">float</span><span class="p">)</span>
<span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="p">(</span><span class="n">cols</span><span class="p">,</span> <span class="n">vals</span><span class="p">)</span> <span class="ow">in</span> <span class="n">tqdm</span><span class="p">(</span><span class="nb">enumerate</span><span class="p">(</span><span class="n">all_documents</span><span class="p">),</span> <span class="n">total</span><span class="o">=</span><span class="nb">len</span><span class="p">(</span><span class="n">all_documents</span><span class="p">),</span>
<span class="n">desc</span><span class="o">=</span><span class="sa">f</span><span class="s1">&#39;\-- filling matrix of shape </span><span class="si">{</span><span class="n">X</span><span class="o">.</span><span class="n">shape</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">):</span>
<span class="n">X</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="n">cols</span><span class="p">]</span> <span class="o">=</span> <span class="n">vals</span>
<span class="n">X</span> <span class="o">=</span> <span class="n">X</span><span class="o">.</span><span class="n">tocsr</span><span class="p">()</span>
<span class="n">y</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">all_labels</span><span class="p">)</span> <span class="o">+</span> <span class="mi">1</span>
<span class="k">return</span> <span class="n">X</span><span class="p">,</span> <span class="n">y</span></div>
<div class="viewcode-block" id="from_csv">
<a class="viewcode-back" href="../../../quapy.data.html#quapy.data.reader.from_csv">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">from_csv</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">encoding</span><span class="o">=</span><span class="s1">&#39;utf-8&#39;</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Reads a csv file in which columns are separated by &#39;,&#39;.</span>
<span class="sd"> File format &lt;label&gt;,&lt;feat1&gt;,&lt;feat2&gt;,...,&lt;featn&gt;\n</span>
<span class="sd"> :param path: path to the csv file</span>
<span class="sd"> :param encoding: the text encoding used to open the file</span>
<span class="sd"> :return: a np.ndarray for the labels and a ndarray (float) for the covariates</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">X</span><span class="p">,</span> <span class="n">y</span> <span class="o">=</span> <span class="p">[],</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">instance</span> <span class="ow">in</span> <span class="n">tqdm</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="s1">&#39;rt&#39;</span><span class="p">,</span> <span class="n">encoding</span><span class="o">=</span><span class="n">encoding</span><span class="p">)</span><span class="o">.</span><span class="n">readlines</span><span class="p">(),</span> <span class="n">desc</span><span class="o">=</span><span class="sa">f</span><span class="s1">&#39;reading </span><span class="si">{</span><span class="n">path</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">):</span>
<span class="n">yi</span><span class="p">,</span> <span class="o">*</span><span class="n">xi</span> <span class="o">=</span> <span class="n">instance</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)</span>
<span class="n">X</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="nb">float</span><span class="p">,</span><span class="n">xi</span><span class="p">)))</span>
<span class="n">y</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">yi</span><span class="p">)</span>
<span class="n">X</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">X</span><span class="p">)</span>
<span class="n">y</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">y</span><span class="p">)</span>
<span class="k">return</span> <span class="n">X</span><span class="p">,</span> <span class="n">y</span></div>
<div class="viewcode-block" id="reindex_labels">
<a class="viewcode-back" href="../../../quapy.data.html#quapy.data.reader.reindex_labels">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">reindex_labels</span><span class="p">(</span><span class="n">y</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Re-indexes a list of labels as a list of indexes, and returns the classnames corresponding to the indexes.</span>
<span class="sd"> E.g.:</span>
<span class="sd"> &gt;&gt;&gt; reindex_labels([&#39;B&#39;, &#39;B&#39;, &#39;A&#39;, &#39;C&#39;])</span>
<span class="sd"> &gt;&gt;&gt; (array([1, 1, 0, 2]), array([&#39;A&#39;, &#39;B&#39;, &#39;C&#39;], dtype=&#39;&lt;U1&#39;))</span>
<span class="sd"> :param y: the list or array of original labels</span>
<span class="sd"> :return: a ndarray (int) of class indexes, and a ndarray of classnames corresponding to the indexes.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">y</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">y</span><span class="p">)</span>
<span class="n">classnames</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="nb">sorted</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">unique</span><span class="p">(</span><span class="n">y</span><span class="p">)))</span>
<span class="n">label2index</span> <span class="o">=</span> <span class="p">{</span><span class="n">label</span><span class="p">:</span> <span class="n">index</span> <span class="k">for</span> <span class="n">index</span><span class="p">,</span> <span class="n">label</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">classnames</span><span class="p">)}</span>
<span class="n">indexed</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">empty</span><span class="p">(</span><span class="n">y</span><span class="o">.</span><span class="n">shape</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="nb">int</span><span class="p">)</span>
<span class="k">for</span> <span class="n">label</span> <span class="ow">in</span> <span class="n">classnames</span><span class="p">:</span>
<span class="n">indexed</span><span class="p">[</span><span class="n">y</span><span class="o">==</span><span class="n">label</span><span class="p">]</span> <span class="o">=</span> <span class="n">label2index</span><span class="p">[</span><span class="n">label</span><span class="p">]</span>
<span class="k">return</span> <span class="n">indexed</span><span class="p">,</span> <span class="n">classnames</span></div>
<div class="viewcode-block" id="binarize">
<a class="viewcode-back" href="../../../quapy.data.html#quapy.data.reader.binarize">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">binarize</span><span class="p">(</span><span class="n">y</span><span class="p">,</span> <span class="n">pos_class</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Binarizes a categorical array-like collection of labels towards the positive class `pos_class`. E.g.,:</span>
<span class="sd"> &gt;&gt;&gt; binarize([1, 2, 3, 1, 1, 0], pos_class=2)</span>
<span class="sd"> &gt;&gt;&gt; array([0, 1, 0, 0, 0, 0])</span>
<span class="sd"> :param y: array-like of labels</span>
<span class="sd"> :param pos_class: integer, the positive class</span>
<span class="sd"> :return: a binary np.ndarray, in which values 1 corresponds to positions in whcih `y` had `pos_class` labels, and</span>
<span class="sd"> 0 otherwise</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">y</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">y</span><span class="p">)</span>
<span class="n">ybin</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="n">y</span><span class="o">.</span><span class="n">shape</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="nb">int</span><span class="p">)</span>
<span class="n">ybin</span><span class="p">[</span><span class="n">y</span> <span class="o">==</span> <span class="n">pos_class</span><span class="p">]</span> <span class="o">=</span> <span class="mi">1</span>
<span class="k">return</span> <span class="n">ybin</span></div>
</pre></div>
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<h1>Source code for quapy.evaluation</h1><div class="highlight"><pre>
<span></span><span class="kn">from</span><span class="w"> </span><span class="nn">typing</span><span class="w"> </span><span class="kn">import</span> <span class="n">Union</span><span class="p">,</span> <span class="n">Callable</span><span class="p">,</span> <span class="n">Iterable</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">tqdm</span><span class="w"> </span><span class="kn">import</span> <span class="n">tqdm</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">quapy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">qp</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">quapy.protocol</span><span class="w"> </span><span class="kn">import</span> <span class="n">AbstractProtocol</span><span class="p">,</span> <span class="n">OnLabelledCollectionProtocol</span><span class="p">,</span> <span class="n">IterateProtocol</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">quapy.method.base</span><span class="w"> </span><span class="kn">import</span> <span class="n">BaseQuantifier</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">pandas</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">pd</span>
<div class="viewcode-block" id="prediction">
<a class="viewcode-back" href="../../quapy.html#quapy.evaluation.prediction">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">prediction</span><span class="p">(</span>
<span class="n">model</span><span class="p">:</span> <span class="n">BaseQuantifier</span><span class="p">,</span>
<span class="n">protocol</span><span class="p">:</span> <span class="n">AbstractProtocol</span><span class="p">,</span>
<span class="n">aggr_speedup</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">bool</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;auto&#39;</span><span class="p">,</span>
<span class="n">verbose</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Uses a quantification model to generate predictions for the samples generated via a specific protocol.</span>
<span class="sd"> This function is central to all evaluation processes, and is endowed with an optimization to speed-up the</span>
<span class="sd"> prediction of protocols that generate samples from a large collection. The optimization applies to aggregative</span>
<span class="sd"> quantifiers only, and to OnLabelledCollectionProtocol protocols, and comes down to generating the classification</span>
<span class="sd"> predictions once and for all, and then generating samples over the classification predictions (instead of over</span>
<span class="sd"> the raw instances), so that the classifier prediction is never called again. This behaviour is obtained by</span>
<span class="sd"> setting `aggr_speedup` to &#39;auto&#39; or True, and is only carried out if the overall process is convenient in terms</span>
<span class="sd"> of computations (e.g., if the number of classification predictions needed for the original collection exceed the</span>
<span class="sd"> number of classification predictions needed for all samples, then the optimization is not undertaken).</span>
<span class="sd"> :param model: a quantifier, instance of :class:`quapy.method.base.BaseQuantifier`</span>
<span class="sd"> :param protocol: :class:`quapy.protocol.AbstractProtocol`; if this object is also instance of</span>
<span class="sd"> :class:`quapy.protocol.OnLabelledCollectionProtocol`, then the aggregation speed-up can be run. This is the protocol</span>
<span class="sd"> in charge of generating the samples for which the model has to issue class prevalence predictions.</span>
<span class="sd"> :param aggr_speedup: whether or not to apply the speed-up. Set to &quot;force&quot; for applying it even if the number of</span>
<span class="sd"> instances in the original collection on which the protocol acts is larger than the number of instances</span>
<span class="sd"> in the samples to be generated. Set to True or &quot;auto&quot; (default) for letting QuaPy decide whether it is</span>
<span class="sd"> convenient or not. Set to False to deactivate.</span>
<span class="sd"> :param verbose: boolean, show or not information in stdout</span>
<span class="sd"> :return: a tuple `(true_prevs, estim_prevs)` in which each element in the tuple is an array of shape</span>
<span class="sd"> `(n_samples, n_classes)` containing the true, or predicted, prevalence values for each sample</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">assert</span> <span class="n">aggr_speedup</span> <span class="ow">in</span> <span class="p">[</span><span class="kc">False</span><span class="p">,</span> <span class="kc">True</span><span class="p">,</span> <span class="s1">&#39;auto&#39;</span><span class="p">,</span> <span class="s1">&#39;force&#39;</span><span class="p">],</span> <span class="s1">&#39;invalid value for aggr_speedup&#39;</span>
<span class="n">sout</span> <span class="o">=</span> <span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="nb">print</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">if</span> <span class="n">verbose</span> <span class="k">else</span> <span class="kc">None</span>
<span class="n">apply_optimization</span> <span class="o">=</span> <span class="kc">False</span>
<span class="k">if</span> <span class="n">aggr_speedup</span> <span class="ow">in</span> <span class="p">[</span><span class="kc">True</span><span class="p">,</span> <span class="s1">&#39;auto&#39;</span><span class="p">,</span> <span class="s1">&#39;force&#39;</span><span class="p">]:</span>
<span class="c1"># checks whether the prediction can be made more efficiently; this check consists in verifying if the model is</span>
<span class="c1"># of type aggregative, if the protocol is based on LabelledCollection, and if the total number of documents to</span>
<span class="c1"># classify using the protocol would exceed the number of test documents in the original collection</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">quapy.method.aggregative</span><span class="w"> </span><span class="kn">import</span> <span class="n">AggregativeQuantifier</span>
<span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="n">AggregativeQuantifier</span><span class="p">)</span> <span class="ow">and</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">protocol</span><span class="p">,</span> <span class="n">OnLabelledCollectionProtocol</span><span class="p">):</span>
<span class="k">if</span> <span class="n">aggr_speedup</span> <span class="o">==</span> <span class="s1">&#39;force&#39;</span><span class="p">:</span>
<span class="n">apply_optimization</span> <span class="o">=</span> <span class="kc">True</span>
<span class="n">sout</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;forcing aggregative speedup&#39;</span><span class="p">)</span>
<span class="k">elif</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">protocol</span><span class="p">,</span> <span class="s1">&#39;sample_size&#39;</span><span class="p">):</span>
<span class="n">nD</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">protocol</span><span class="o">.</span><span class="n">get_labelled_collection</span><span class="p">())</span>
<span class="n">samplesD</span> <span class="o">=</span> <span class="n">protocol</span><span class="o">.</span><span class="n">total</span><span class="p">()</span> <span class="o">*</span> <span class="n">protocol</span><span class="o">.</span><span class="n">sample_size</span>
<span class="k">if</span> <span class="n">nD</span> <span class="o">&lt;</span> <span class="n">samplesD</span><span class="p">:</span>
<span class="n">apply_optimization</span> <span class="o">=</span> <span class="kc">True</span>
<span class="n">sout</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;speeding up the prediction for the aggregative quantifier, &#39;</span>
<span class="sa">f</span><span class="s1">&#39;total classifications </span><span class="si">{</span><span class="n">nD</span><span class="si">}</span><span class="s1"> instead of </span><span class="si">{</span><span class="n">samplesD</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="k">if</span> <span class="n">apply_optimization</span><span class="p">:</span>
<span class="n">pre_classified</span> <span class="o">=</span> <span class="n">model</span><span class="o">.</span><span class="n">classify</span><span class="p">(</span><span class="n">protocol</span><span class="o">.</span><span class="n">get_labelled_collection</span><span class="p">()</span><span class="o">.</span><span class="n">instances</span><span class="p">)</span>
<span class="n">protocol_with_predictions</span> <span class="o">=</span> <span class="n">protocol</span><span class="o">.</span><span class="n">on_preclassified_instances</span><span class="p">(</span><span class="n">pre_classified</span><span class="p">)</span>
<span class="k">return</span> <span class="n">__prediction_helper</span><span class="p">(</span><span class="n">model</span><span class="o">.</span><span class="n">aggregate</span><span class="p">,</span> <span class="n">protocol_with_predictions</span><span class="p">,</span> <span class="n">verbose</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="n">__prediction_helper</span><span class="p">(</span><span class="n">model</span><span class="o">.</span><span class="n">predict</span><span class="p">,</span> <span class="n">protocol</span><span class="p">,</span> <span class="n">verbose</span><span class="p">)</span></div>
<span class="k">def</span><span class="w"> </span><span class="nf">__prediction_helper</span><span class="p">(</span><span class="n">quantification_fn</span><span class="p">,</span> <span class="n">protocol</span><span class="p">:</span> <span class="n">AbstractProtocol</span><span class="p">,</span> <span class="n">verbose</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
<span class="n">true_prevs</span><span class="p">,</span> <span class="n">estim_prevs</span> <span class="o">=</span> <span class="p">[],</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">sample_instances</span><span class="p">,</span> <span class="n">sample_prev</span> <span class="ow">in</span> <span class="n">tqdm</span><span class="p">(</span><span class="n">protocol</span><span class="p">(),</span> <span class="n">total</span><span class="o">=</span><span class="n">protocol</span><span class="o">.</span><span class="n">total</span><span class="p">(),</span> <span class="n">desc</span><span class="o">=</span><span class="s1">&#39;predicting&#39;</span><span class="p">)</span> <span class="k">if</span> <span class="n">verbose</span> <span class="k">else</span> <span class="n">protocol</span><span class="p">():</span>
<span class="n">estim_prevs</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">quantification_fn</span><span class="p">(</span><span class="n">sample_instances</span><span class="p">))</span>
<span class="n">true_prevs</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">sample_prev</span><span class="p">)</span>
<span class="n">true_prevs</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">true_prevs</span><span class="p">)</span>
<span class="n">estim_prevs</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">estim_prevs</span><span class="p">)</span>
<span class="k">return</span> <span class="n">true_prevs</span><span class="p">,</span> <span class="n">estim_prevs</span>
<div class="viewcode-block" id="evaluation_report">
<a class="viewcode-back" href="../../quapy.html#quapy.evaluation.evaluation_report">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">evaluation_report</span><span class="p">(</span><span class="n">model</span><span class="p">:</span> <span class="n">BaseQuantifier</span><span class="p">,</span>
<span class="n">protocol</span><span class="p">:</span> <span class="n">AbstractProtocol</span><span class="p">,</span>
<span class="n">error_metrics</span><span class="p">:</span> <span class="n">Iterable</span><span class="p">[</span><span class="n">Union</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span><span class="n">Callable</span><span class="p">]]</span> <span class="o">=</span> <span class="s1">&#39;mae&#39;</span><span class="p">,</span>
<span class="n">aggr_speedup</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">bool</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;auto&#39;</span><span class="p">,</span>
<span class="n">verbose</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Generates a report (a pandas&#39; DataFrame) containing information of the evaluation of the model as according</span>
<span class="sd"> to a specific protocol and in terms of one or more evaluation metrics (errors).</span>
<span class="sd"> :param model: a quantifier, instance of :class:`quapy.method.base.BaseQuantifier`</span>
<span class="sd"> :param protocol: :class:`quapy.protocol.AbstractProtocol`; if this object is also instance of</span>
<span class="sd"> :class:`quapy.protocol.OnLabelledCollectionProtocol`, then the aggregation speed-up can be run. This is the protocol</span>
<span class="sd"> in charge of generating the samples in which the model is evaluated.</span>
<span class="sd"> :param error_metrics: a string, or list of strings, representing the name(s) of an error function in `qp.error`</span>
<span class="sd"> (e.g., &#39;mae&#39;, the default value), or a callable function, or a list of callable functions, implementing</span>
<span class="sd"> the error function itself.</span>
<span class="sd"> :param aggr_speedup: whether or not to apply the speed-up. Set to &quot;force&quot; for applying it even if the number of</span>
<span class="sd"> instances in the original collection on which the protocol acts is larger than the number of instances</span>
<span class="sd"> in the samples to be generated. Set to True or &quot;auto&quot; (default) for letting QuaPy decide whether it is</span>
<span class="sd"> convenient or not. Set to False to deactivate.</span>
<span class="sd"> :param verbose: boolean, show or not information in stdout</span>
<span class="sd"> :return: a pandas&#39; DataFrame containing the columns &#39;true-prev&#39; (the true prevalence of each sample),</span>
<span class="sd"> &#39;estim-prev&#39; (the prevalence estimated by the model for each sample), and as many columns as error metrics</span>
<span class="sd"> have been indicated, each displaying the score in terms of that metric for every sample.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">true_prevs</span><span class="p">,</span> <span class="n">estim_prevs</span> <span class="o">=</span> <span class="n">prediction</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="n">protocol</span><span class="p">,</span> <span class="n">aggr_speedup</span><span class="o">=</span><span class="n">aggr_speedup</span><span class="p">,</span> <span class="n">verbose</span><span class="o">=</span><span class="n">verbose</span><span class="p">)</span>
<span class="k">return</span> <span class="n">_prevalence_report</span><span class="p">(</span><span class="n">true_prevs</span><span class="p">,</span> <span class="n">estim_prevs</span><span class="p">,</span> <span class="n">error_metrics</span><span class="p">)</span></div>
<span class="k">def</span><span class="w"> </span><span class="nf">_prevalence_report</span><span class="p">(</span><span class="n">true_prevs</span><span class="p">,</span> <span class="n">estim_prevs</span><span class="p">,</span> <span class="n">error_metrics</span><span class="p">:</span> <span class="n">Iterable</span><span class="p">[</span><span class="n">Union</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Callable</span><span class="p">]]</span> <span class="o">=</span> <span class="s1">&#39;mae&#39;</span><span class="p">):</span>
<span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">error_metrics</span><span class="p">,</span> <span class="nb">str</span><span class="p">):</span>
<span class="n">error_metrics</span> <span class="o">=</span> <span class="p">[</span><span class="n">error_metrics</span><span class="p">]</span>
<span class="n">error_funcs</span> <span class="o">=</span> <span class="p">[</span><span class="n">qp</span><span class="o">.</span><span class="n">error</span><span class="o">.</span><span class="n">from_name</span><span class="p">(</span><span class="n">e</span><span class="p">)</span> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">e</span><span class="p">,</span> <span class="nb">str</span><span class="p">)</span> <span class="k">else</span> <span class="n">e</span> <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="n">error_metrics</span><span class="p">]</span>
<span class="k">assert</span> <span class="nb">all</span><span class="p">(</span><span class="nb">hasattr</span><span class="p">(</span><span class="n">e</span><span class="p">,</span> <span class="s1">&#39;__call__&#39;</span><span class="p">)</span> <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="n">error_funcs</span><span class="p">),</span> <span class="s1">&#39;invalid error functions&#39;</span>
<span class="n">error_names</span> <span class="o">=</span> <span class="p">[</span><span class="n">e</span><span class="o">.</span><span class="vm">__name__</span> <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="n">error_funcs</span><span class="p">]</span>
<span class="n">row_entries</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">true_prev</span><span class="p">,</span> <span class="n">estim_prev</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">true_prevs</span><span class="p">,</span> <span class="n">estim_prevs</span><span class="p">):</span>
<span class="n">series</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;true-prev&#39;</span><span class="p">:</span> <span class="n">true_prev</span><span class="p">,</span> <span class="s1">&#39;estim-prev&#39;</span><span class="p">:</span> <span class="n">estim_prev</span><span class="p">}</span>
<span class="k">for</span> <span class="n">error_name</span><span class="p">,</span> <span class="n">error_metric</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">error_names</span><span class="p">,</span> <span class="n">error_funcs</span><span class="p">):</span>
<span class="n">score</span> <span class="o">=</span> <span class="n">error_metric</span><span class="p">(</span><span class="n">true_prev</span><span class="p">,</span> <span class="n">estim_prev</span><span class="p">)</span>
<span class="n">series</span><span class="p">[</span><span class="n">error_name</span><span class="p">]</span> <span class="o">=</span> <span class="n">score</span>
<span class="n">row_entries</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">series</span><span class="p">)</span>
<span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="o">.</span><span class="n">from_records</span><span class="p">(</span><span class="n">row_entries</span><span class="p">)</span>
<span class="k">return</span> <span class="n">df</span>
<div class="viewcode-block" id="evaluate">
<a class="viewcode-back" href="../../quapy.html#quapy.evaluation.evaluate">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">evaluate</span><span class="p">(</span>
<span class="n">model</span><span class="p">:</span> <span class="n">BaseQuantifier</span><span class="p">,</span>
<span class="n">protocol</span><span class="p">:</span> <span class="n">AbstractProtocol</span><span class="p">,</span>
<span class="n">error_metric</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Callable</span><span class="p">],</span>
<span class="n">aggr_speedup</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">bool</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;auto&#39;</span><span class="p">,</span>
<span class="n">verbose</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Evaluates a quantification model according to a specific sample generation protocol and in terms of one</span>
<span class="sd"> evaluation metric (error).</span>
<span class="sd"> :param model: a quantifier, instance of :class:`quapy.method.base.BaseQuantifier`</span>
<span class="sd"> :param protocol: :class:`quapy.protocol.AbstractProtocol`; if this object is also instance of</span>
<span class="sd"> :class:`quapy.protocol.OnLabelledCollectionProtocol`, then the aggregation speed-up can be run. This is the</span>
<span class="sd"> protocol in charge of generating the samples in which the model is evaluated.</span>
<span class="sd"> :param error_metric: a string representing the name(s) of an error function in `qp.error`</span>
<span class="sd"> (e.g., &#39;mae&#39;), or a callable function implementing the error function itself.</span>
<span class="sd"> :param aggr_speedup: whether or not to apply the speed-up. Set to &quot;force&quot; for applying it even if the number of</span>
<span class="sd"> instances in the original collection on which the protocol acts is larger than the number of instances</span>
<span class="sd"> in the samples to be generated. Set to True or &quot;auto&quot; (default) for letting QuaPy decide whether it is</span>
<span class="sd"> convenient or not. Set to False to deactivate.</span>
<span class="sd"> :param verbose: boolean, show or not information in stdout</span>
<span class="sd"> :return: if the error metric is not averaged (e.g., &#39;ae&#39;, &#39;rae&#39;), returns an array of shape `(n_samples,)` with</span>
<span class="sd"> the error scores for each sample; if the error metric is averaged (e.g., &#39;mae&#39;, &#39;mrae&#39;) then returns</span>
<span class="sd"> a single float</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">error_metric</span><span class="p">,</span> <span class="nb">str</span><span class="p">):</span>
<span class="n">error_metric</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">error</span><span class="o">.</span><span class="n">from_name</span><span class="p">(</span><span class="n">error_metric</span><span class="p">)</span>
<span class="n">true_prevs</span><span class="p">,</span> <span class="n">estim_prevs</span> <span class="o">=</span> <span class="n">prediction</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="n">protocol</span><span class="p">,</span> <span class="n">aggr_speedup</span><span class="o">=</span><span class="n">aggr_speedup</span><span class="p">,</span> <span class="n">verbose</span><span class="o">=</span><span class="n">verbose</span><span class="p">)</span>
<span class="k">return</span> <span class="n">error_metric</span><span class="p">(</span><span class="n">true_prevs</span><span class="p">,</span> <span class="n">estim_prevs</span><span class="p">)</span></div>
<div class="viewcode-block" id="evaluate_on_samples">
<a class="viewcode-back" href="../../quapy.html#quapy.evaluation.evaluate_on_samples">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">evaluate_on_samples</span><span class="p">(</span>
<span class="n">model</span><span class="p">:</span> <span class="n">BaseQuantifier</span><span class="p">,</span>
<span class="n">samples</span><span class="p">:</span> <span class="n">Iterable</span><span class="p">[</span><span class="n">qp</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">LabelledCollection</span><span class="p">],</span>
<span class="n">error_metric</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Callable</span><span class="p">],</span>
<span class="n">verbose</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Evaluates a quantification model on a given set of samples and in terms of one evaluation metric (error).</span>
<span class="sd"> :param model: a quantifier, instance of :class:`quapy.method.base.BaseQuantifier`</span>
<span class="sd"> :param samples: a list of samples on which the quantifier is to be evaluated</span>
<span class="sd"> :param error_metric: a string representing the name(s) of an error function in `qp.error`</span>
<span class="sd"> (e.g., &#39;mae&#39;), or a callable function implementing the error function itself.</span>
<span class="sd"> :param verbose: boolean, show or not information in stdout</span>
<span class="sd"> :return: if the error metric is not averaged (e.g., &#39;ae&#39;, &#39;rae&#39;), returns an array of shape `(n_samples,)` with</span>
<span class="sd"> the error scores for each sample; if the error metric is averaged (e.g., &#39;mae&#39;, &#39;mrae&#39;) then returns</span>
<span class="sd"> a single float</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">return</span> <span class="n">evaluate</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="n">IterateProtocol</span><span class="p">(</span><span class="n">samples</span><span class="p">),</span> <span class="n">error_metric</span><span class="p">,</span> <span class="n">aggr_speedup</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">verbose</span><span class="o">=</span><span class="n">verbose</span><span class="p">)</span></div>
</pre></div>
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<h1>Source code for quapy.method._kdey</h1><div class="highlight"><pre>
<span></span><span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">numbers</span><span class="w"> </span><span class="kn">import</span> <span class="n">Real</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">sklearn.base</span><span class="w"> </span><span class="kn">import</span> <span class="n">BaseEstimator</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">sklearn.neighbors</span><span class="w"> </span><span class="kn">import</span> <span class="n">KernelDensity</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">quapy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">qp</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">quapy.method._helper</span><span class="w"> </span><span class="kn">import</span> <span class="n">_labels_to_indices</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">quapy.method.aggregative</span><span class="w"> </span><span class="kn">import</span> <span class="n">AggregativeSoftQuantifier</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">quapy.functional</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">F</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">scipy.special</span><span class="w"> </span><span class="kn">import</span> <span class="n">logsumexp</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">sklearn.metrics.pairwise</span><span class="w"> </span><span class="kn">import</span> <span class="n">rbf_kernel</span>
<div class="viewcode-block" id="KDEBase">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._kdey.KDEBase">[docs]</a>
<span class="k">class</span><span class="w"> </span><span class="nc">KDEBase</span><span class="p">:</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Common ancestor for KDE-based methods. Implements some common routines.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">BANDWIDTH_METHOD</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;scott&#39;</span><span class="p">,</span> <span class="s1">&#39;silverman&#39;</span><span class="p">]</span>
<span class="n">KERNELS</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;gaussian&#39;</span><span class="p">,</span> <span class="s1">&#39;aitchison&#39;</span><span class="p">,</span> <span class="s1">&#39;ilr&#39;</span><span class="p">]</span>
<span class="nd">@classmethod</span>
<span class="k">def</span><span class="w"> </span><span class="nf">_check_bandwidth</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">bandwidth</span><span class="p">,</span> <span class="n">kernel</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Checks that the bandwidth parameter is correct</span>
<span class="sd"> :param bandwidth: either a string (see BANDWIDTH_METHOD) or a float</span>
<span class="sd"> :return: the bandwidth if the check is passed, or raises an exception for invalid values</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">assert</span> <span class="n">bandwidth</span> <span class="ow">in</span> <span class="n">KDEBase</span><span class="o">.</span><span class="n">BANDWIDTH_METHOD</span> <span class="ow">or</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">bandwidth</span><span class="p">,</span> <span class="n">Real</span><span class="p">),</span> \
<span class="sa">f</span><span class="s1">&#39;invalid bandwidth, valid ones are </span><span class="si">{</span><span class="n">KDEBase</span><span class="o">.</span><span class="n">BANDWIDTH_METHOD</span><span class="si">}</span><span class="s1"> or float values&#39;</span>
<span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">bandwidth</span><span class="p">,</span> <span class="n">Real</span><span class="p">):</span>
<span class="n">bandwidth</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">bandwidth</span><span class="p">)</span>
<span class="k">return</span> <span class="n">bandwidth</span>
<span class="nd">@classmethod</span>
<span class="k">def</span><span class="w"> </span><span class="nf">_check_kernel</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">kernel</span><span class="p">):</span>
<span class="k">assert</span> <span class="n">kernel</span> <span class="ow">in</span> <span class="n">KDEBase</span><span class="o">.</span><span class="n">KERNELS</span><span class="p">,</span> <span class="sa">f</span><span class="s1">&#39;unknown </span><span class="si">{</span><span class="n">kernel</span><span class="si">=}</span><span class="s1">&#39;</span>
<span class="k">return</span> <span class="n">kernel</span>
<div class="viewcode-block" id="KDEBase.get_kde_function">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._kdey.KDEBase.get_kde_function">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">get_kde_function</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">,</span> <span class="n">bandwidth</span><span class="p">,</span> <span class="n">kernel</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Wraps the KDE function from scikit-learn.</span>
<span class="sd"> :param X: data for which the density function is to be estimated</span>
<span class="sd"> :param bandwidth: the bandwidth of the kernel</span>
<span class="sd"> :param kernel: the kernel family</span>
<span class="sd"> :return: a scikit-learn&#39;s KernelDensity object</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">X</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">transform_posteriors</span><span class="p">(</span><span class="n">X</span><span class="p">,</span> <span class="n">kernel</span><span class="p">)</span>
<span class="n">bandwidth</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">effective_bandwidth</span><span class="p">(</span><span class="n">bandwidth</span><span class="p">,</span> <span class="n">kernel</span><span class="p">)</span>
<span class="k">return</span> <span class="n">KernelDensity</span><span class="p">(</span><span class="n">bandwidth</span><span class="o">=</span><span class="n">bandwidth</span><span class="p">)</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="n">X</span><span class="p">)</span></div>
<div class="viewcode-block" id="KDEBase.pdf">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._kdey.KDEBase.pdf">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">pdf</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">kde</span><span class="p">,</span> <span class="n">X</span><span class="p">,</span> <span class="n">kernel</span><span class="p">,</span> <span class="n">log_densities</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Wraps the density evalution of scikit-learn&#39;s KDE. Scikit-learn returns log-scores (s), so this</span>
<span class="sd"> function returns :math:`e^{s}`</span>
<span class="sd"> :param kde: a previously fit KDE function</span>
<span class="sd"> :param X: the data for which the density is to be estimated</span>
<span class="sd"> :param kernel: the kernel family</span>
<span class="sd"> :return: np.ndarray with the densities</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">X</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">transform_posteriors</span><span class="p">(</span><span class="n">X</span><span class="p">,</span> <span class="n">kernel</span><span class="p">)</span>
<span class="n">log_density</span> <span class="o">=</span> <span class="n">kde</span><span class="o">.</span><span class="n">score_samples</span><span class="p">(</span><span class="n">X</span><span class="p">)</span>
<span class="k">if</span> <span class="n">log_densities</span><span class="p">:</span>
<span class="k">return</span> <span class="n">log_density</span>
<span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">exp</span><span class="p">(</span><span class="n">log_density</span><span class="p">)</span></div>
<div class="viewcode-block" id="KDEBase.get_mixture_components">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._kdey.KDEBase.get_mixture_components">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">get_mixture_components</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">classes</span><span class="p">,</span> <span class="n">bandwidth</span><span class="p">,</span> <span class="n">kernel</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Returns an array containing the mixture components, i.e., the KDE functions for each class.</span>
<span class="sd"> :param X: the data containing the covariates</span>
<span class="sd"> :param y: the class labels</span>
<span class="sd"> :param n_classes: integer, the number of classes</span>
<span class="sd"> :param bandwidth: float, the bandwidth of the kernel</span>
<span class="sd"> :param kernel: the kernel family</span>
<span class="sd"> :return: a list of KernelDensity objects, each fitted with the corresponding class-specific covariates</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">class_cond_X</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">cat</span> <span class="ow">in</span> <span class="n">classes</span><span class="p">:</span>
<span class="n">selX</span> <span class="o">=</span> <span class="n">X</span><span class="p">[</span><span class="n">y</span><span class="o">==</span><span class="n">cat</span><span class="p">]</span>
<span class="k">if</span> <span class="n">selX</span><span class="o">.</span><span class="n">size</span><span class="o">==</span><span class="mi">0</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;empty class </span><span class="si">{</span><span class="n">cat</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="n">class_cond_X</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">selX</span><span class="p">)</span>
<span class="k">return</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">get_kde_function</span><span class="p">(</span><span class="n">X_cond_yi</span><span class="p">,</span> <span class="n">bandwidth</span><span class="p">,</span> <span class="n">kernel</span><span class="p">)</span> <span class="k">for</span> <span class="n">X_cond_yi</span> <span class="ow">in</span> <span class="n">class_cond_X</span><span class="p">]</span></div>
<div class="viewcode-block" id="KDEBase.transform_posteriors">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._kdey.KDEBase.transform_posteriors">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">transform_posteriors</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">,</span> <span class="n">kernel</span><span class="p">):</span>
<span class="k">if</span> <span class="n">kernel</span> <span class="ow">in</span> <span class="p">{</span><span class="s1">&#39;aitchison&#39;</span><span class="p">,</span> <span class="s1">&#39;ilr&#39;</span><span class="p">}:</span>
<span class="n">X</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">shrink_posteriors</span><span class="p">(</span><span class="n">X</span><span class="p">)</span>
<span class="k">if</span> <span class="n">kernel</span> <span class="o">==</span> <span class="s1">&#39;aitchison&#39;</span><span class="p">:</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">clr_transform</span><span class="p">(</span><span class="n">X</span><span class="p">)</span>
<span class="k">if</span> <span class="n">kernel</span> <span class="o">==</span> <span class="s1">&#39;ilr&#39;</span><span class="p">:</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">ilr_transform</span><span class="p">(</span><span class="n">X</span><span class="p">)</span>
<span class="k">return</span> <span class="n">X</span></div>
<div class="viewcode-block" id="KDEBase.shrink_posteriors">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._kdey.KDEBase.shrink_posteriors">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">shrink_posteriors</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">):</span>
<span class="n">shrinkage</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;shrinkage&#39;</span><span class="p">,</span> <span class="mf">0.0</span><span class="p">)</span>
<span class="k">if</span> <span class="n">shrinkage</span> <span class="o">&lt;=</span> <span class="mi">0</span><span class="p">:</span>
<span class="k">return</span> <span class="n">X</span>
<span class="n">X</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">X</span><span class="p">)</span>
<span class="n">n_classes</span> <span class="o">=</span> <span class="n">X</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
<span class="n">uniform</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">full</span><span class="p">(</span><span class="n">n_classes</span><span class="p">,</span> <span class="mf">1.0</span> <span class="o">/</span> <span class="n">n_classes</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="n">X</span><span class="o">.</span><span class="n">dtype</span><span class="p">)</span>
<span class="k">return</span> <span class="p">(</span><span class="mf">1.0</span> <span class="o">-</span> <span class="n">shrinkage</span><span class="p">)</span> <span class="o">*</span> <span class="n">X</span> <span class="o">+</span> <span class="n">shrinkage</span> <span class="o">*</span> <span class="n">uniform</span></div>
<div class="viewcode-block" id="KDEBase.effective_bandwidth">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._kdey.KDEBase.effective_bandwidth">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">effective_bandwidth</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">bandwidth</span><span class="p">,</span> <span class="n">kernel</span><span class="p">):</span>
<span class="n">shrinkage</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;shrinkage&#39;</span><span class="p">,</span> <span class="mf">0.0</span><span class="p">)</span>
<span class="k">if</span> <span class="n">shrinkage</span> <span class="o">&gt;</span> <span class="mi">0</span> <span class="ow">and</span> <span class="n">kernel</span> <span class="ow">in</span> <span class="p">{</span><span class="s1">&#39;aitchison&#39;</span><span class="p">,</span> <span class="s1">&#39;ilr&#39;</span><span class="p">}</span> <span class="ow">and</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">bandwidth</span><span class="p">,</span> <span class="n">Real</span><span class="p">):</span>
<span class="k">return</span> <span class="p">(</span><span class="mf">1.0</span> <span class="o">-</span> <span class="n">shrinkage</span><span class="p">)</span> <span class="o">*</span> <span class="nb">float</span><span class="p">(</span><span class="n">bandwidth</span><span class="p">)</span>
<span class="k">return</span> <span class="n">bandwidth</span></div>
<div class="viewcode-block" id="KDEBase.clr_transform">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._kdey.KDEBase.clr_transform">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">clr_transform</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">):</span>
<span class="k">if</span> <span class="ow">not</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;clr&#39;</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">clr</span> <span class="o">=</span> <span class="n">F</span><span class="o">.</span><span class="n">CLRtransformation</span><span class="p">()</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">clr</span><span class="p">(</span><span class="n">X</span><span class="p">)</span></div>
<div class="viewcode-block" id="KDEBase.ilr_transform">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._kdey.KDEBase.ilr_transform">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">ilr_transform</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">):</span>
<span class="k">if</span> <span class="ow">not</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;ilr&#39;</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">ilr</span> <span class="o">=</span> <span class="n">F</span><span class="o">.</span><span class="n">ILRtransformation</span><span class="p">()</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">ilr</span><span class="p">(</span><span class="n">X</span><span class="p">)</span></div>
</div>
<div class="viewcode-block" id="KDEyML">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._kdey.KDEyML">[docs]</a>
<span class="k">class</span><span class="w"> </span><span class="nc">KDEyML</span><span class="p">(</span><span class="n">AggregativeSoftQuantifier</span><span class="p">,</span> <span class="n">KDEBase</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Kernel Density Estimation model for quantification (KDEy) relying on the Kullback-Leibler divergence (KLD) as</span>
<span class="sd"> the divergence measure to be minimized. This method was first proposed in the paper</span>
<span class="sd"> `Kernel Density Estimation for Multiclass Quantification &lt;https://link.springer.com/article/10.1007/s10994-024-06726-5&gt;`_ (`arXiv &lt;https://arxiv.org/abs/2401.00490&gt;`_), in which</span>
<span class="sd"> the authors show that minimizing the distribution mathing criterion for KLD is akin to performing</span>
<span class="sd"> maximum likelihood (ML).</span>
<span class="sd"> The distribution matching optimization problem comes down to solving:</span>
<span class="sd"> :math:`\\hat{\\alpha} = \\arg\\min_{\\alpha\\in\\Delta^{n-1}} \\mathcal{D}(\\boldsymbol{p}_{\\alpha}||q_{\\widetilde{U}})`</span>
<span class="sd"> where :math:`p_{\\alpha}` is the mixture of class-specific KDEs with mixture parameter (hence class prevalence)</span>
<span class="sd"> :math:`\\alpha` defined by</span>
<span class="sd"> :math:`\\boldsymbol{p}_{\\alpha}(\\widetilde{x}) = \\sum_{i=1}^n \\alpha_i p_{\\widetilde{L}_i}(\\widetilde{x})`</span>
<span class="sd"> where :math:`p_X(\\boldsymbol{x}) = \\frac{1}{|X|} \\sum_{x_i\\in X} K\\left(\\frac{x-x_i}{h}\\right)` is the</span>
<span class="sd"> KDE function that uses the datapoints in X as the kernel centers.</span>
<span class="sd"> In KDEy-ML, the divergence is taken to be the Kullback-Leibler Divergence. This is equivalent to solving:</span>
<span class="sd"> :math:`\\hat{\\alpha} = \\arg\\min_{\\alpha\\in\\Delta^{n-1}} -</span>
<span class="sd"> \\mathbb{E}_{q_{\\widetilde{U}}} \\left[ \\log \\boldsymbol{p}_{\\alpha}(\\widetilde{x}) \\right]`</span>
<span class="sd"> which corresponds to the maximum likelihood estimate.</span>
<span class="sd"> :param classifier: a scikit-learn&#39;s BaseEstimator, or None, in which case the classifier is taken to be</span>
<span class="sd"> the one indicated in `qp.environ[&#39;DEFAULT_CLS&#39;]`</span>
<span class="sd"> :param fit_classifier: whether to train the learner (default is True). Set to False if the</span>
<span class="sd"> learner has been trained outside the quantifier.</span>
<span class="sd"> :param val_split: specifies the data used for generating classifier predictions. This specification</span>
<span class="sd"> can be made as float in (0, 1) indicating the proportion of stratified held-out validation set to</span>
<span class="sd"> be extracted from the training set; or as an integer (default 5), indicating that the predictions</span>
<span class="sd"> are to be generated in a `k`-fold cross-validation manner (with this integer indicating the value</span>
<span class="sd"> for `k`); or as a tuple (X,y) defining the specific set of data to use for validation.</span>
<span class="sd"> :param bandwidth: float, the bandwidth of the Kernel</span>
<span class="sd"> :param kernel: kernel of KDE, valid ones are in KDEBase.KERNELS</span>
<span class="sd"> :param shrinkage: amount of shrinkage towards the uniform distribution to apply before</span>
<span class="sd"> Aitchison/ILR transformations. Must be in ``[0,1)``.</span>
<span class="sd"> :param random_state: a seed to be set before fitting any base quantifier (default None)</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">classifier</span><span class="p">:</span> <span class="n">BaseEstimator</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">fit_classifier</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">val_split</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">bandwidth</span><span class="o">=</span><span class="mf">0.1</span><span class="p">,</span>
<span class="n">kernel</span><span class="o">=</span><span class="s1">&#39;gaussian&#39;</span><span class="p">,</span> <span class="n">shrinkage</span><span class="o">=</span><span class="mf">0.0</span><span class="p">,</span> <span class="n">random_state</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">classifier</span><span class="p">,</span> <span class="n">fit_classifier</span><span class="p">,</span> <span class="n">val_split</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">bandwidth</span> <span class="o">=</span> <span class="n">KDEBase</span><span class="o">.</span><span class="n">_check_bandwidth</span><span class="p">(</span><span class="n">bandwidth</span><span class="p">,</span> <span class="n">kernel</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">kernel</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_check_kernel</span><span class="p">(</span><span class="n">kernel</span><span class="p">)</span>
<span class="k">assert</span> <span class="mi">0</span> <span class="o">&lt;=</span> <span class="n">shrinkage</span> <span class="o">&lt;</span> <span class="mi">1</span><span class="p">,</span> <span class="s1">&#39;shrinkage must be in [0,1)&#39;</span>
<span class="k">assert</span> <span class="bp">self</span><span class="o">.</span><span class="n">kernel</span> <span class="o">!=</span> <span class="s1">&#39;gaussian&#39;</span> <span class="ow">or</span> <span class="n">shrinkage</span> <span class="o">==</span> <span class="mi">0</span><span class="p">,</span> \
<span class="s1">&#39;shrinkage is only supported for Aitchison/ILR kernels&#39;</span>
<span class="bp">self</span><span class="o">.</span><span class="n">shrinkage</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">shrinkage</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">random_state</span><span class="o">=</span><span class="n">random_state</span>
<div class="viewcode-block" id="KDEyML.aggregation_fit">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._kdey.KDEyML.aggregation_fit">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">aggregation_fit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">classif_predictions</span><span class="p">,</span> <span class="n">labels</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">mix_densities</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_mixture_components</span><span class="p">(</span>
<span class="n">classif_predictions</span><span class="p">,</span>
<span class="n">labels</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">classes_</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">bandwidth</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">kernel</span><span class="p">,</span>
<span class="p">)</span>
<span class="k">return</span> <span class="bp">self</span></div>
<div class="viewcode-block" id="KDEyML.aggregate">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._kdey.KDEyML.aggregate">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">aggregate</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">posteriors</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Searches for the mixture model parameter (the sought prevalence values) that maximizes the likelihood</span>
<span class="sd"> of the data (i.e., that minimizes the negative log-likelihood)</span>
<span class="sd"> :param posteriors: instances in the sample converted into posterior probabilities</span>
<span class="sd"> :return: a vector of class prevalence estimates</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">with</span> <span class="n">qp</span><span class="o">.</span><span class="n">util</span><span class="o">.</span><span class="n">temp_seed</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">random_state</span><span class="p">):</span>
<span class="n">epsilon</span> <span class="o">=</span> <span class="mf">1e-12</span>
<span class="n">n_classes</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">mix_densities</span><span class="p">)</span>
<span class="k">if</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">kernel</span> <span class="o">!=</span> <span class="s1">&#39;gaussian&#39;</span> <span class="ow">and</span> <span class="n">n_classes</span> <span class="o">&gt;=</span> <span class="mi">20</span><span class="p">)</span> <span class="ow">or</span> <span class="n">n_classes</span> <span class="o">&gt;=</span> <span class="mi">30</span><span class="p">:</span>
<span class="n">test_log_densities</span> <span class="o">=</span> <span class="p">[</span>
<span class="bp">self</span><span class="o">.</span><span class="n">pdf</span><span class="p">(</span><span class="n">kde_i</span><span class="p">,</span> <span class="n">posteriors</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">kernel</span><span class="p">,</span> <span class="n">log_densities</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="k">for</span> <span class="n">kde_i</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">mix_densities</span>
<span class="p">]</span>
<span class="k">def</span><span class="w"> </span><span class="nf">neg_loglikelihood</span><span class="p">(</span><span class="n">prev</span><span class="p">):</span>
<span class="n">prev</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">error</span><span class="o">.</span><span class="n">smooth</span><span class="p">(</span><span class="n">prev</span><span class="p">,</span> <span class="n">eps</span><span class="o">=</span><span class="n">epsilon</span><span class="p">)</span>
<span class="n">test_loglikelihood</span> <span class="o">=</span> <span class="n">logsumexp</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">prev</span><span class="p">)[:,</span> <span class="kc">None</span><span class="p">]</span> <span class="o">+</span> <span class="n">test_log_densities</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
<span class="k">return</span> <span class="o">-</span><span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">test_loglikelihood</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">test_densities</span> <span class="o">=</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">pdf</span><span class="p">(</span><span class="n">kde_i</span><span class="p">,</span> <span class="n">posteriors</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">kernel</span><span class="p">)</span> <span class="k">for</span> <span class="n">kde_i</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">mix_densities</span><span class="p">]</span>
<span class="k">def</span><span class="w"> </span><span class="nf">neg_loglikelihood</span><span class="p">(</span><span class="n">prev</span><span class="p">):</span>
<span class="n">test_mixture_likelihood</span> <span class="o">=</span> <span class="n">prev</span> <span class="o">@</span> <span class="n">test_densities</span>
<span class="n">test_loglikelihood</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">test_mixture_likelihood</span> <span class="o">+</span> <span class="n">epsilon</span><span class="p">)</span>
<span class="k">return</span> <span class="o">-</span><span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">test_loglikelihood</span><span class="p">)</span>
<span class="k">return</span> <span class="n">F</span><span class="o">.</span><span class="n">optim_minimize</span><span class="p">(</span><span class="n">neg_loglikelihood</span><span class="p">,</span> <span class="n">n_classes</span><span class="p">)</span></div>
</div>
<div class="viewcode-block" id="KDEyHD">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._kdey.KDEyHD">[docs]</a>
<span class="k">class</span><span class="w"> </span><span class="nc">KDEyHD</span><span class="p">(</span><span class="n">AggregativeSoftQuantifier</span><span class="p">,</span> <span class="n">KDEBase</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Kernel Density Estimation model for quantification (KDEy) relying on the squared Hellinger Disntace (HD) as</span>
<span class="sd"> the divergence measure to be minimized. This method was first proposed in the paper</span>
<span class="sd"> `Kernel Density Estimation for Multiclass Quantification &lt;https://link.springer.com/article/10.1007/s10994-024-06726-5&gt;`_ (`arXiv &lt;https://arxiv.org/abs/2401.00490&gt;`_), in which</span>
<span class="sd"> the authors proposed a Monte Carlo approach for minimizing the divergence.</span>
<span class="sd"> The distribution matching optimization problem comes down to solving:</span>
<span class="sd"> :math:`\\hat{\\alpha} = \\arg\\min_{\\alpha\\in\\Delta^{n-1}} \\mathcal{D}(\\boldsymbol{p}_{\\alpha}||q_{\\widetilde{U}})`</span>
<span class="sd"> where :math:`p_{\\alpha}` is the mixture of class-specific KDEs with mixture parameter (hence class prevalence)</span>
<span class="sd"> :math:`\\alpha` defined by</span>
<span class="sd"> :math:`\\boldsymbol{p}_{\\alpha}(\\widetilde{x}) = \\sum_{i=1}^n \\alpha_i p_{\\widetilde{L}_i}(\\widetilde{x})`</span>
<span class="sd"> where :math:`p_X(\\boldsymbol{x}) = \\frac{1}{|X|} \\sum_{x_i\\in X} K\\left(\\frac{x-x_i}{h}\\right)` is the</span>
<span class="sd"> KDE function that uses the datapoints in X as the kernel centers.</span>
<span class="sd"> In KDEy-HD, the divergence is taken to be the squared Hellinger Distance, an f-divergence with corresponding</span>
<span class="sd"> f-generator function given by:</span>
<span class="sd"> :math:`f(u)=(\\sqrt{u}-1)^2`</span>
<span class="sd"> The authors proposed a Monte Carlo solution that relies on importance sampling:</span>
<span class="sd"> :math:`\\hat{D}_f(p||q)= \\frac{1}{t} \\sum_{i=1}^t f\\left(\\frac{p(x_i)}{q(x_i)}\\right) \\frac{q(x_i)}{r(x_i)}`</span>
<span class="sd"> where the datapoints (trials) :math:`x_1,\\ldots,x_t\\sim_{\\mathrm{iid}} r` with :math:`r` the</span>
<span class="sd"> uniform distribution.</span>
<span class="sd"> :param classifier: a scikit-learn&#39;s BaseEstimator, or None, in which case the classifier is taken to be</span>
<span class="sd"> the one indicated in `qp.environ[&#39;DEFAULT_CLS&#39;]`</span>
<span class="sd"> :param fit_classifier: whether to train the learner (default is True). Set to False if the</span>
<span class="sd"> learner has been trained outside the quantifier.</span>
<span class="sd"> :param val_split: specifies the data used for generating classifier predictions. This specification</span>
<span class="sd"> can be made as float in (0, 1) indicating the proportion of stratified held-out validation set to</span>
<span class="sd"> be extracted from the training set; or as an integer (default 5), indicating that the predictions</span>
<span class="sd"> are to be generated in a `k`-fold cross-validation manner (with this integer indicating the value</span>
<span class="sd"> for `k`); or as a tuple (X,y) defining the specific set of data to use for validation.</span>
<span class="sd"> :param bandwidth: float, the bandwidth of the Kernel</span>
<span class="sd"> :param random_state: a seed to be set before fitting any base quantifier (default None)</span>
<span class="sd"> :param montecarlo_trials: number of Monte Carlo trials (default 10000)</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">classifier</span><span class="p">:</span> <span class="n">BaseEstimator</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">fit_classifier</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">val_split</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">divergence</span><span class="p">:</span> <span class="nb">str</span><span class="o">=</span><span class="s1">&#39;HD&#39;</span><span class="p">,</span>
<span class="n">bandwidth</span><span class="o">=</span><span class="mf">0.1</span><span class="p">,</span> <span class="n">random_state</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">montecarlo_trials</span><span class="o">=</span><span class="mi">10000</span><span class="p">):</span>
<span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">classifier</span><span class="p">,</span> <span class="n">fit_classifier</span><span class="p">,</span> <span class="n">val_split</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">divergence</span> <span class="o">=</span> <span class="n">divergence</span>
<span class="bp">self</span><span class="o">.</span><span class="n">bandwidth</span> <span class="o">=</span> <span class="n">KDEBase</span><span class="o">.</span><span class="n">_check_bandwidth</span><span class="p">(</span><span class="n">bandwidth</span><span class="p">,</span> <span class="n">kernel</span><span class="o">=</span><span class="s1">&#39;gaussian&#39;</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">random_state</span><span class="o">=</span><span class="n">random_state</span>
<span class="bp">self</span><span class="o">.</span><span class="n">montecarlo_trials</span> <span class="o">=</span> <span class="n">montecarlo_trials</span>
<div class="viewcode-block" id="KDEyHD.aggregation_fit">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._kdey.KDEyHD.aggregation_fit">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">aggregation_fit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">classif_predictions</span><span class="p">,</span> <span class="n">labels</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">mix_densities</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_mixture_components</span><span class="p">(</span>
<span class="n">classif_predictions</span><span class="p">,</span> <span class="n">labels</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">classes_</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">bandwidth</span><span class="p">,</span> <span class="s1">&#39;gaussian&#39;</span>
<span class="p">)</span>
<span class="n">N</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">montecarlo_trials</span>
<span class="n">rs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">random_state</span>
<span class="n">n</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">classes_</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">reference_samples</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">vstack</span><span class="p">([</span><span class="n">kde_i</span><span class="o">.</span><span class="n">sample</span><span class="p">(</span><span class="n">N</span><span class="o">//</span><span class="n">n</span><span class="p">,</span> <span class="n">random_state</span><span class="o">=</span><span class="n">rs</span><span class="p">)</span> <span class="k">for</span> <span class="n">kde_i</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">mix_densities</span><span class="p">])</span>
<span class="bp">self</span><span class="o">.</span><span class="n">reference_classwise_densities</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span>
<span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">pdf</span><span class="p">(</span><span class="n">kde_j</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">reference_samples</span><span class="p">,</span> <span class="s1">&#39;gaussian&#39;</span><span class="p">)</span> <span class="k">for</span> <span class="n">kde_j</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">mix_densities</span><span class="p">]</span>
<span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">reference_density</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">reference_classwise_densities</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span> <span class="c1"># equiv. to (uniform @ self.reference_classwise_densities)</span>
<span class="k">return</span> <span class="bp">self</span></div>
<div class="viewcode-block" id="KDEyHD.aggregate">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._kdey.KDEyHD.aggregate">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">aggregate</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">posteriors</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">):</span>
<span class="c1"># we retain all n*N examples (sampled from a mixture with uniform parameter), and then</span>
<span class="c1"># apply importance sampling (IS). In this version we compute D(p_alpha||q) with IS</span>
<span class="n">n_classes</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">mix_densities</span><span class="p">)</span>
<span class="n">test_kde</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_kde_function</span><span class="p">(</span><span class="n">posteriors</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">bandwidth</span><span class="p">,</span> <span class="s1">&#39;gaussian&#39;</span><span class="p">)</span>
<span class="n">test_densities</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">pdf</span><span class="p">(</span><span class="n">test_kde</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">reference_samples</span><span class="p">,</span> <span class="s1">&#39;gaussian&#39;</span><span class="p">)</span>
<span class="k">def</span><span class="w"> </span><span class="nf">f_squared_hellinger</span><span class="p">(</span><span class="n">u</span><span class="p">):</span>
<span class="k">return</span> <span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="n">u</span><span class="p">)</span><span class="o">-</span><span class="mi">1</span><span class="p">)</span><span class="o">**</span><span class="mi">2</span>
<span class="c1"># todo: this will fail when self.divergence is a callable, and is not the right place to do it anyway</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">divergence</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">==</span> <span class="s1">&#39;hd&#39;</span><span class="p">:</span>
<span class="n">f</span> <span class="o">=</span> <span class="n">f_squared_hellinger</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s1">&#39;only squared HD is currently implemented&#39;</span><span class="p">)</span>
<span class="n">epsilon</span> <span class="o">=</span> <span class="mf">1e-10</span>
<span class="n">qs</span> <span class="o">=</span> <span class="n">test_densities</span> <span class="o">+</span> <span class="n">epsilon</span>
<span class="n">rs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">reference_density</span> <span class="o">+</span> <span class="n">epsilon</span>
<span class="n">iw</span> <span class="o">=</span> <span class="n">qs</span><span class="o">/</span><span class="n">rs</span> <span class="c1">#importance weights</span>
<span class="n">p_class</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">reference_classwise_densities</span> <span class="o">+</span> <span class="n">epsilon</span>
<span class="n">fracs</span> <span class="o">=</span> <span class="n">p_class</span><span class="o">/</span><span class="n">qs</span>
<span class="k">def</span><span class="w"> </span><span class="nf">divergence</span><span class="p">(</span><span class="n">prev</span><span class="p">):</span>
<span class="c1"># ps / qs = (prev @ p_class) / qs = prev @ (p_class / qs) = prev @ fracs</span>
<span class="n">ps_div_qs</span> <span class="o">=</span> <span class="n">prev</span> <span class="o">@</span> <span class="n">fracs</span>
<span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span> <span class="n">f</span><span class="p">(</span><span class="n">ps_div_qs</span><span class="p">)</span> <span class="o">*</span> <span class="n">iw</span> <span class="p">)</span>
<span class="k">return</span> <span class="n">F</span><span class="o">.</span><span class="n">optim_minimize</span><span class="p">(</span><span class="n">divergence</span><span class="p">,</span> <span class="n">n_classes</span><span class="p">)</span></div>
</div>
<div class="viewcode-block" id="KDEyCS">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._kdey.KDEyCS">[docs]</a>
<span class="k">class</span><span class="w"> </span><span class="nc">KDEyCS</span><span class="p">(</span><span class="n">AggregativeSoftQuantifier</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Kernel Density Estimation model for quantification (KDEy) relying on the Cauchy-Schwarz divergence (CS) as</span>
<span class="sd"> the divergence measure to be minimized. This method was first proposed in the paper</span>
<span class="sd"> `Kernel Density Estimation for Multiclass Quantification &lt;https://link.springer.com/article/10.1007/s10994-024-06726-5&gt;`_ (`arXiv &lt;https://arxiv.org/abs/2401.00490&gt;`_), in which</span>
<span class="sd"> the authors proposed a Monte Carlo approach for minimizing the divergence.</span>
<span class="sd"> The distribution matching optimization problem comes down to solving:</span>
<span class="sd"> :math:`\\hat{\\alpha} = \\arg\\min_{\\alpha\\in\\Delta^{n-1}} \\mathcal{D}(\\boldsymbol{p}_{\\alpha}||q_{\\widetilde{U}})`</span>
<span class="sd"> where :math:`p_{\\alpha}` is the mixture of class-specific KDEs with mixture parameter (hence class prevalence)</span>
<span class="sd"> :math:`\\alpha` defined by</span>
<span class="sd"> :math:`\\boldsymbol{p}_{\\alpha}(\\widetilde{x}) = \\sum_{i=1}^n \\alpha_i p_{\\widetilde{L}_i}(\\widetilde{x})`</span>
<span class="sd"> where :math:`p_X(\\boldsymbol{x}) = \\frac{1}{|X|} \\sum_{x_i\\in X} K\\left(\\frac{x-x_i}{h}\\right)` is the</span>
<span class="sd"> KDE function that uses the datapoints in X as the kernel centers.</span>
<span class="sd"> In KDEy-CS, the divergence is taken to be the Cauchy-Schwarz divergence given by:</span>
<span class="sd"> :math:`\\mathcal{D}_{\\mathrm{CS}}(p||q)=-\\log\\left(\\frac{\\int p(x)q(x)dx}{\\sqrt{\\int p(x)^2dx \\int q(x)^2dx}}\\right)`</span>
<span class="sd"> The authors showed that this distribution matching admits a closed-form solution</span>
<span class="sd"> :param classifier: a scikit-learn&#39;s BaseEstimator, or None, in which case the classifier is taken to be</span>
<span class="sd"> the one indicated in `qp.environ[&#39;DEFAULT_CLS&#39;]`</span>
<span class="sd"> :param fit_classifier: whether to train the learner (default is True). Set to False if the</span>
<span class="sd"> learner has been trained outside the quantifier.</span>
<span class="sd"> :param val_split: specifies the data used for generating classifier predictions. This specification</span>
<span class="sd"> can be made as float in (0, 1) indicating the proportion of stratified held-out validation set to</span>
<span class="sd"> be extracted from the training set; or as an integer (default 5), indicating that the predictions</span>
<span class="sd"> are to be generated in a `k`-fold cross-validation manner (with this integer indicating the value</span>
<span class="sd"> for `k`); or as a tuple (X,y) defining the specific set of data to use for validation.</span>
<span class="sd"> :param bandwidth: float, the bandwidth of the Kernel</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">classifier</span><span class="p">:</span> <span class="n">BaseEstimator</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">fit_classifier</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">val_split</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">bandwidth</span><span class="o">=</span><span class="mf">0.1</span><span class="p">):</span>
<span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">classifier</span><span class="p">,</span> <span class="n">fit_classifier</span><span class="p">,</span> <span class="n">val_split</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">bandwidth</span> <span class="o">=</span> <span class="n">KDEBase</span><span class="o">.</span><span class="n">_check_bandwidth</span><span class="p">(</span><span class="n">bandwidth</span><span class="p">,</span> <span class="n">kernel</span><span class="o">=</span><span class="s1">&#39;gaussian&#39;</span><span class="p">)</span>
<div class="viewcode-block" id="KDEyCS.gram_matrix_mix_sum">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._kdey.KDEyCS.gram_matrix_mix_sum">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">gram_matrix_mix_sum</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">,</span> <span class="n">Y</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<span class="c1"># this adapts the output of the rbf_kernel function (pairwise evaluations of Gaussian kernels k(x,y))</span>
<span class="c1"># to contain pairwise evaluations of N(x|mu,Sigma1+Sigma2) with mu=y and Sigma1 and Sigma2 are </span>
<span class="c1"># two &quot;scalar matrices&quot; (h^2)*I each, so Sigma1+Sigma2 has scalar 2(h^2) (h is the bandwidth)</span>
<span class="n">h</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">bandwidth</span>
<span class="n">variance</span> <span class="o">=</span> <span class="mi">2</span> <span class="o">*</span> <span class="p">(</span><span class="n">h</span><span class="o">**</span><span class="mi">2</span><span class="p">)</span>
<span class="n">nD</span> <span class="o">=</span> <span class="n">X</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
<span class="n">gamma</span> <span class="o">=</span> <span class="mi">1</span><span class="o">/</span><span class="p">(</span><span class="mi">2</span><span class="o">*</span><span class="n">variance</span><span class="p">)</span>
<span class="n">norm_factor</span> <span class="o">=</span> <span class="mi">1</span><span class="o">/</span><span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(((</span><span class="mi">2</span><span class="o">*</span><span class="n">np</span><span class="o">.</span><span class="n">pi</span><span class="p">)</span><span class="o">**</span><span class="n">nD</span><span class="p">)</span> <span class="o">*</span> <span class="p">(</span><span class="n">variance</span><span class="o">**</span><span class="p">(</span><span class="n">nD</span><span class="p">)))</span>
<span class="n">gram</span> <span class="o">=</span> <span class="n">norm_factor</span> <span class="o">*</span> <span class="n">rbf_kernel</span><span class="p">(</span><span class="n">X</span><span class="p">,</span> <span class="n">Y</span><span class="p">,</span> <span class="n">gamma</span><span class="o">=</span><span class="n">gamma</span><span class="p">)</span>
<span class="k">return</span> <span class="n">gram</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span></div>
<div class="viewcode-block" id="KDEyCS.aggregation_fit">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._kdey.KDEyCS.aggregation_fit">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">aggregation_fit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">classif_predictions</span><span class="p">,</span> <span class="n">labels</span><span class="p">):</span>
<span class="n">P</span><span class="p">,</span> <span class="n">y</span> <span class="o">=</span> <span class="n">classif_predictions</span><span class="p">,</span> <span class="n">labels</span>
<span class="n">n</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">classes_</span><span class="p">)</span>
<span class="n">y</span> <span class="o">=</span> <span class="n">_labels_to_indices</span><span class="p">(</span><span class="n">y</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">classes_</span><span class="p">)</span>
<span class="c1"># counts_inv keeps track of the relative weight of each datapoint within its class</span>
<span class="c1"># (i.e., the weight in its KDE model)</span>
<span class="n">counts_inv</span> <span class="o">=</span> <span class="mi">1</span> <span class="o">/</span> <span class="p">(</span><span class="n">F</span><span class="o">.</span><span class="n">counts_from_labels</span><span class="p">(</span><span class="n">y</span><span class="p">,</span> <span class="n">classes</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="n">n</span><span class="p">)))</span>
<span class="c1"># tr_tr_sums corresponds to symbol \overline{B} in the paper</span>
<span class="n">tr_tr_sums</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="n">shape</span><span class="o">=</span><span class="p">(</span><span class="n">n</span><span class="p">,</span><span class="n">n</span><span class="p">),</span> <span class="n">dtype</span><span class="o">=</span><span class="nb">float</span><span class="p">)</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">n</span><span class="p">):</span>
<span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">n</span><span class="p">):</span>
<span class="k">if</span> <span class="n">i</span> <span class="o">&gt;</span> <span class="n">j</span><span class="p">:</span>
<span class="n">tr_tr_sums</span><span class="p">[</span><span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">]</span> <span class="o">=</span> <span class="n">tr_tr_sums</span><span class="p">[</span><span class="n">j</span><span class="p">,</span><span class="n">i</span><span class="p">]</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">block</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">gram_matrix_mix_sum</span><span class="p">(</span><span class="n">P</span><span class="p">[</span><span class="n">y</span> <span class="o">==</span> <span class="n">i</span><span class="p">],</span> <span class="n">P</span><span class="p">[</span><span class="n">y</span> <span class="o">==</span> <span class="n">j</span><span class="p">]</span> <span class="k">if</span> <span class="n">i</span><span class="o">!=</span><span class="n">j</span> <span class="k">else</span> <span class="kc">None</span><span class="p">)</span>
<span class="n">tr_tr_sums</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">]</span> <span class="o">=</span> <span class="n">block</span>
<span class="c1"># keep track of these data structures for the test phase</span>
<span class="bp">self</span><span class="o">.</span><span class="n">Ptr</span> <span class="o">=</span> <span class="n">P</span>
<span class="bp">self</span><span class="o">.</span><span class="n">ytr</span> <span class="o">=</span> <span class="n">y</span>
<span class="bp">self</span><span class="o">.</span><span class="n">tr_tr_sums</span> <span class="o">=</span> <span class="n">tr_tr_sums</span>
<span class="bp">self</span><span class="o">.</span><span class="n">counts_inv</span> <span class="o">=</span> <span class="n">counts_inv</span>
<span class="k">return</span> <span class="bp">self</span></div>
<div class="viewcode-block" id="KDEyCS.aggregate">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._kdey.KDEyCS.aggregate">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">aggregate</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">posteriors</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">):</span>
<span class="n">Ptr</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">Ptr</span>
<span class="n">Pte</span> <span class="o">=</span> <span class="n">posteriors</span>
<span class="n">y</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ytr</span>
<span class="n">tr_tr_sums</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">tr_tr_sums</span>
<span class="n">M</span><span class="p">,</span> <span class="n">nD</span> <span class="o">=</span> <span class="n">Pte</span><span class="o">.</span><span class="n">shape</span>
<span class="n">Minv</span> <span class="o">=</span> <span class="p">(</span><span class="mi">1</span><span class="o">/</span><span class="n">M</span><span class="p">)</span> <span class="c1"># t in the paper</span>
<span class="n">n</span> <span class="o">=</span> <span class="n">Ptr</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
<span class="c1"># becomes a constant that does not affect the optimization, no need to compute it</span>
<span class="c1"># partC = 0.5*np.log(self.gram_matrix_mix_sum(Pte) * Kinv * Kinv)</span>
<span class="c1"># tr_te_sums corresponds to \overline{a}*(1/Li)*(1/M) in the paper (note the constants</span>
<span class="c1"># are already aggregated to tr_te_sums, so these multiplications are not carried out</span>
<span class="c1"># at each iteration of the optimization phase)</span>
<span class="n">tr_te_sums</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="n">shape</span><span class="o">=</span><span class="n">n</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="nb">float</span><span class="p">)</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">n</span><span class="p">):</span>
<span class="n">tr_te_sums</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">gram_matrix_mix_sum</span><span class="p">(</span><span class="n">Ptr</span><span class="p">[</span><span class="n">y</span><span class="o">==</span><span class="n">i</span><span class="p">],</span> <span class="n">Pte</span><span class="p">)</span>
<span class="k">def</span><span class="w"> </span><span class="nf">divergence</span><span class="p">(</span><span class="n">alpha</span><span class="p">):</span>
<span class="c1"># called \overline{r} in the paper</span>
<span class="n">alpha_ratio</span> <span class="o">=</span> <span class="n">alpha</span> <span class="o">*</span> <span class="bp">self</span><span class="o">.</span><span class="n">counts_inv</span>
<span class="c1"># recall that tr_te_sums already accounts for the constant terms (1/Li)*(1/M)</span>
<span class="n">partA</span> <span class="o">=</span> <span class="o">-</span><span class="n">np</span><span class="o">.</span><span class="n">log</span><span class="p">((</span><span class="n">alpha_ratio</span> <span class="o">@</span> <span class="n">tr_te_sums</span><span class="p">)</span> <span class="o">*</span> <span class="n">Minv</span><span class="p">)</span>
<span class="n">partB</span> <span class="o">=</span> <span class="mf">0.5</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">alpha_ratio</span> <span class="o">@</span> <span class="n">tr_tr_sums</span> <span class="o">@</span> <span class="n">alpha_ratio</span><span class="p">)</span>
<span class="k">return</span> <span class="n">partA</span> <span class="o">+</span> <span class="n">partB</span> <span class="c1">#+ partC</span>
<span class="k">return</span> <span class="n">F</span><span class="o">.</span><span class="n">optim_minimize</span><span class="p">(</span><span class="n">divergence</span><span class="p">,</span> <span class="n">n</span><span class="p">)</span></div>
</div>
</pre></div>
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<h1>Source code for quapy.method._neural</h1><div class="highlight"><pre>
<span></span><span class="kn">import</span><span class="w"> </span><span class="nn">logging</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">os</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">pathlib</span><span class="w"> </span><span class="kn">import</span> <span class="n">Path</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">random</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">torch</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">torch.nn</span><span class="w"> </span><span class="kn">import</span> <span class="n">MSELoss</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">torch.nn.functional</span><span class="w"> </span><span class="kn">import</span> <span class="n">relu</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">quapy.protocol</span><span class="w"> </span><span class="kn">import</span> <span class="n">UPP</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">quapy.method.aggregative</span><span class="w"> </span><span class="kn">import</span> <span class="o">*</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">quapy.util</span><span class="w"> </span><span class="kn">import</span> <span class="n">EarlyStop</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">tqdm</span><span class="w"> </span><span class="kn">import</span> <span class="n">tqdm</span>
<div class="viewcode-block" id="QuaNetTrainer">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._neural.QuaNetTrainer">[docs]</a>
<span class="k">class</span><span class="w"> </span><span class="nc">QuaNetTrainer</span><span class="p">(</span><span class="n">BaseQuantifier</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Implementation of `QuaNet &lt;https://dl.acm.org/doi/abs/10.1145/3269206.3269287&gt;`_, a neural network for</span>
<span class="sd"> quantification. This implementation uses `PyTorch &lt;https://pytorch.org/&gt;`_ and can take advantage of GPU</span>
<span class="sd"> for speeding-up the training phase.</span>
<span class="sd"> Example:</span>
<span class="sd"> &gt;&gt;&gt; import quapy as qp</span>
<span class="sd"> &gt;&gt;&gt; from quapy.method.meta import QuaNet</span>
<span class="sd"> &gt;&gt;&gt; from quapy.classification.neural import NeuralClassifierTrainer, CNNnet</span>
<span class="sd"> &gt;&gt;&gt;</span>
<span class="sd"> &gt;&gt;&gt; # use samples of 100 elements</span>
<span class="sd"> &gt;&gt;&gt; qp.environ[&#39;SAMPLE_SIZE&#39;] = 100</span>
<span class="sd"> &gt;&gt;&gt;</span>
<span class="sd"> &gt;&gt;&gt; # load the Kindle dataset as text, and convert words to numerical indexes</span>
<span class="sd"> &gt;&gt;&gt; dataset = qp.datasets.fetch_reviews(&#39;kindle&#39;, pickle=True)</span>
<span class="sd"> &gt;&gt;&gt; qp.train.preprocessing.index(dataset, min_df=5, inplace=True)</span>
<span class="sd"> &gt;&gt;&gt;</span>
<span class="sd"> &gt;&gt;&gt; # the text classifier is a CNN trained by NeuralClassifierTrainer</span>
<span class="sd"> &gt;&gt;&gt; cnn = CNNnet(dataset.vocabulary_size, dataset.n_classes)</span>
<span class="sd"> &gt;&gt;&gt; classifier = NeuralClassifierTrainer(cnn, device=&#39;cuda&#39;)</span>
<span class="sd"> &gt;&gt;&gt;</span>
<span class="sd"> &gt;&gt;&gt; # train QuaNet (QuaNet is an alias to QuaNetTrainer)</span>
<span class="sd"> &gt;&gt;&gt; model = QuaNet(classifier, qp.environ[&#39;SAMPLE_SIZE&#39;], device=&#39;cuda&#39;)</span>
<span class="sd"> &gt;&gt;&gt; model.fit(*dataset.training.Xy)</span>
<span class="sd"> &gt;&gt;&gt; estim_prevalence = model.predict(dataset.test.instances)</span>
<span class="sd"> :param classifier: an object implementing `fit` (i.e., that can be trained on labelled data),</span>
<span class="sd"> `predict_proba` (i.e., that can generate posterior probabilities of unlabelled examples) and</span>
<span class="sd"> `transform` (i.e., that can generate embedded representations of the unlabelled instances).</span>
<span class="sd"> :param fit_classifier: whether to train the learner (default is True). Set to False if the</span>
<span class="sd"> learner has been trained outside the quantifier.</span>
<span class="sd"> :param sample_size: integer, the sample size; default is None, meaning that the sample size should be</span>
<span class="sd"> taken from qp.environ[&quot;SAMPLE_SIZE&quot;]</span>
<span class="sd"> :param n_epochs: integer, maximum number of training epochs</span>
<span class="sd"> :param tr_iter_per_poch: integer, number of training iterations before considering an epoch complete</span>
<span class="sd"> :param va_iter_per_poch: integer, number of validation iterations to perform after each epoch</span>
<span class="sd"> :param lr: float, the learning rate</span>
<span class="sd"> :param lstm_hidden_size: integer, hidden dimensionality of the LSTM cells</span>
<span class="sd"> :param lstm_nlayers: integer, number of LSTM layers</span>
<span class="sd"> :param ff_layers: list of integers, dimensions of the densely-connected FF layers on top of the</span>
<span class="sd"> quantification embedding</span>
<span class="sd"> :param bidirectional: boolean, indicates whether the LSTM is bidirectional or not</span>
<span class="sd"> :param qdrop_p: float, dropout probability</span>
<span class="sd"> :param patience: integer, number of epochs showing no improvement in the validation set before stopping the</span>
<span class="sd"> training phase (early stopping)</span>
<span class="sd"> :param checkpointdir: string, a path where to store models&#39; checkpoints</span>
<span class="sd"> :param checkpointname: string (optional), the name of the model&#39;s checkpoint</span>
<span class="sd"> :param device: string, indicate &quot;cpu&quot; or &quot;cuda&quot;</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span>
<span class="n">classifier</span><span class="p">,</span>
<span class="n">fit_classifier</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
<span class="n">sample_size</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
<span class="n">n_epochs</span><span class="o">=</span><span class="mi">100</span><span class="p">,</span>
<span class="n">tr_iter_per_poch</span><span class="o">=</span><span class="mi">500</span><span class="p">,</span>
<span class="n">va_iter_per_poch</span><span class="o">=</span><span class="mi">100</span><span class="p">,</span>
<span class="n">lr</span><span class="o">=</span><span class="mf">1e-3</span><span class="p">,</span>
<span class="n">lstm_hidden_size</span><span class="o">=</span><span class="mi">64</span><span class="p">,</span>
<span class="n">lstm_nlayers</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
<span class="n">ff_layers</span><span class="o">=</span><span class="p">[</span><span class="mi">1024</span><span class="p">,</span> <span class="mi">512</span><span class="p">],</span>
<span class="n">bidirectional</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
<span class="n">qdrop_p</span><span class="o">=</span><span class="mf">0.5</span><span class="p">,</span>
<span class="n">patience</span><span class="o">=</span><span class="mi">10</span><span class="p">,</span>
<span class="n">checkpointdir</span><span class="o">=</span><span class="s1">&#39;../checkpoint&#39;</span><span class="p">,</span>
<span class="n">checkpointname</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
<span class="n">device</span><span class="o">=</span><span class="s1">&#39;cuda&#39;</span><span class="p">):</span>
<span class="k">assert</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">classifier</span><span class="p">,</span> <span class="s1">&#39;transform&#39;</span><span class="p">),</span> \
<span class="sa">f</span><span class="s1">&#39;the classifier </span><span class="si">{</span><span class="n">classifier</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="si">}</span><span class="s1"> does not seem to be able to produce document embeddings &#39;</span> \
<span class="sa">f</span><span class="s1">&#39;since it does not implement the method &quot;transform&quot;&#39;</span>
<span class="k">assert</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">classifier</span><span class="p">,</span> <span class="s1">&#39;predict_proba&#39;</span><span class="p">),</span> \
<span class="sa">f</span><span class="s1">&#39;the classifier </span><span class="si">{</span><span class="n">classifier</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="si">}</span><span class="s1"> does not seem to be able to produce posterior probabilities &#39;</span> \
<span class="sa">f</span><span class="s1">&#39;since it does not implement the method &quot;predict_proba&quot;&#39;</span>
<span class="bp">self</span><span class="o">.</span><span class="n">classifier</span> <span class="o">=</span> <span class="n">classifier</span>
<span class="bp">self</span><span class="o">.</span><span class="n">fit_classifier</span> <span class="o">=</span> <span class="n">fit_classifier</span>
<span class="bp">self</span><span class="o">.</span><span class="n">sample_size</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">_get_sample_size</span><span class="p">(</span><span class="n">sample_size</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">n_epochs</span> <span class="o">=</span> <span class="n">n_epochs</span>
<span class="bp">self</span><span class="o">.</span><span class="n">tr_iter</span> <span class="o">=</span> <span class="n">tr_iter_per_poch</span>
<span class="bp">self</span><span class="o">.</span><span class="n">va_iter</span> <span class="o">=</span> <span class="n">va_iter_per_poch</span>
<span class="bp">self</span><span class="o">.</span><span class="n">lr</span> <span class="o">=</span> <span class="n">lr</span>
<span class="bp">self</span><span class="o">.</span><span class="n">quanet_params</span> <span class="o">=</span> <span class="p">{</span>
<span class="s1">&#39;lstm_hidden_size&#39;</span><span class="p">:</span> <span class="n">lstm_hidden_size</span><span class="p">,</span>
<span class="s1">&#39;lstm_nlayers&#39;</span><span class="p">:</span> <span class="n">lstm_nlayers</span><span class="p">,</span>
<span class="s1">&#39;ff_layers&#39;</span><span class="p">:</span> <span class="n">ff_layers</span><span class="p">,</span>
<span class="s1">&#39;bidirectional&#39;</span><span class="p">:</span> <span class="n">bidirectional</span><span class="p">,</span>
<span class="s1">&#39;qdrop_p&#39;</span><span class="p">:</span> <span class="n">qdrop_p</span>
<span class="p">}</span>
<span class="bp">self</span><span class="o">.</span><span class="n">patience</span> <span class="o">=</span> <span class="n">patience</span>
<span class="k">if</span> <span class="n">checkpointname</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="n">local_random</span> <span class="o">=</span> <span class="n">random</span><span class="o">.</span><span class="n">Random</span><span class="p">()</span>
<span class="n">random_code</span> <span class="o">=</span> <span class="s1">&#39;-&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">local_random</span><span class="o">.</span><span class="n">randint</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1000000</span><span class="p">))</span> <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">5</span><span class="p">))</span>
<span class="n">checkpointname</span> <span class="o">=</span> <span class="s1">&#39;QuaNet-&#39;</span><span class="o">+</span><span class="n">random_code</span>
<span class="bp">self</span><span class="o">.</span><span class="n">checkpointdir</span> <span class="o">=</span> <span class="n">checkpointdir</span>
<span class="bp">self</span><span class="o">.</span><span class="n">checkpoint</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">checkpointdir</span><span class="p">,</span> <span class="n">checkpointname</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">device</span> <span class="o">=</span> <span class="n">torch</span><span class="o">.</span><span class="n">device</span><span class="p">(</span><span class="n">device</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">__check_params_colision</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">quanet_params</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">classifier</span><span class="o">.</span><span class="n">get_params</span><span class="p">())</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_classes_</span> <span class="o">=</span> <span class="kc">None</span>
<div class="viewcode-block" id="QuaNetTrainer.fit">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._neural.QuaNetTrainer.fit">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">fit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">,</span> <span class="n">y</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Trains QuaNet.</span>
<span class="sd"> :param X: the training instances on which to train QuaNet. If `fit_classifier=True`, the data will be split in</span>
<span class="sd"> 40/40/20 for training the classifier, training QuaNet, and validating QuaNet, respectively. If</span>
<span class="sd"> `fit_classifier=False`, the data will be split in 66/34 for training QuaNet and validating it, respectively.</span>
<span class="sd"> :param y: the labels of X</span>
<span class="sd"> :return: self</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">data</span> <span class="o">=</span> <span class="n">LabelledCollection</span><span class="p">(</span><span class="n">X</span><span class="p">,</span> <span class="n">y</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_classes_</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">classes_</span>
<span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">checkpointdir</span><span class="p">,</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">fit_classifier</span><span class="p">:</span>
<span class="n">classifier_data</span><span class="p">,</span> <span class="n">unused_data</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">split_stratified</span><span class="p">(</span><span class="mf">0.4</span><span class="p">)</span>
<span class="n">train_data</span><span class="p">,</span> <span class="n">valid_data</span> <span class="o">=</span> <span class="n">unused_data</span><span class="o">.</span><span class="n">split_stratified</span><span class="p">(</span><span class="mf">0.66</span><span class="p">)</span> <span class="c1"># 0.66 split of 60% makes 40% and 20%</span>
<span class="bp">self</span><span class="o">.</span><span class="n">classifier</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="o">*</span><span class="n">classifier_data</span><span class="o">.</span><span class="n">Xy</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">classifier_data</span> <span class="o">=</span> <span class="kc">None</span>
<span class="n">train_data</span><span class="p">,</span> <span class="n">valid_data</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">split_stratified</span><span class="p">(</span><span class="mf">0.66</span><span class="p">)</span>
<span class="c1"># estimate the hard and soft stats tpr and fpr of the classifier</span>
<span class="bp">self</span><span class="o">.</span><span class="n">tr_prev</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">prevalence</span><span class="p">()</span>
<span class="c1"># compute the posterior probabilities of the instances</span>
<span class="n">valid_posteriors</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">classifier</span><span class="o">.</span><span class="n">predict_proba</span><span class="p">(</span><span class="n">valid_data</span><span class="o">.</span><span class="n">instances</span><span class="p">)</span>
<span class="n">train_posteriors</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">classifier</span><span class="o">.</span><span class="n">predict_proba</span><span class="p">(</span><span class="n">train_data</span><span class="o">.</span><span class="n">instances</span><span class="p">)</span>
<span class="c1"># turn instances&#39; original representations into embeddings</span>
<span class="n">valid_data_embed</span> <span class="o">=</span> <span class="n">LabelledCollection</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">classifier</span><span class="o">.</span><span class="n">transform</span><span class="p">(</span><span class="n">valid_data</span><span class="o">.</span><span class="n">instances</span><span class="p">),</span> <span class="n">valid_data</span><span class="o">.</span><span class="n">labels</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_classes_</span><span class="p">)</span>
<span class="n">train_data_embed</span> <span class="o">=</span> <span class="n">LabelledCollection</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">classifier</span><span class="o">.</span><span class="n">transform</span><span class="p">(</span><span class="n">train_data</span><span class="o">.</span><span class="n">instances</span><span class="p">),</span> <span class="n">train_data</span><span class="o">.</span><span class="n">labels</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_classes_</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">quantifiers</span> <span class="o">=</span> <span class="p">{</span>
<span class="s1">&#39;cc&#39;</span><span class="p">:</span> <span class="n">CC</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">classifier</span><span class="p">,</span> <span class="n">fit_classifier</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="o">*</span><span class="n">valid_data</span><span class="o">.</span><span class="n">Xy</span><span class="p">),</span>
<span class="s1">&#39;acc&#39;</span><span class="p">:</span> <span class="n">ACC</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">classifier</span><span class="p">,</span> <span class="n">fit_classifier</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="o">*</span><span class="n">valid_data</span><span class="o">.</span><span class="n">Xy</span><span class="p">),</span>
<span class="s1">&#39;pcc&#39;</span><span class="p">:</span> <span class="n">PCC</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">classifier</span><span class="p">,</span> <span class="n">fit_classifier</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="o">*</span><span class="n">valid_data</span><span class="o">.</span><span class="n">Xy</span><span class="p">),</span>
<span class="s1">&#39;pacc&#39;</span><span class="p">:</span> <span class="n">PACC</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">classifier</span><span class="p">,</span> <span class="n">fit_classifier</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="o">*</span><span class="n">valid_data</span><span class="o">.</span><span class="n">Xy</span><span class="p">),</span>
<span class="p">}</span>
<span class="k">if</span> <span class="n">classifier_data</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">quantifiers</span><span class="p">[</span><span class="s1">&#39;emq&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">EMQ</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">classifier</span><span class="p">,</span> <span class="n">fit_classifier</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="o">*</span><span class="n">valid_data</span><span class="o">.</span><span class="n">Xy</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">status</span> <span class="o">=</span> <span class="p">{</span>
<span class="s1">&#39;tr-loss&#39;</span><span class="p">:</span> <span class="o">-</span><span class="mi">1</span><span class="p">,</span>
<span class="s1">&#39;va-loss&#39;</span><span class="p">:</span> <span class="o">-</span><span class="mi">1</span><span class="p">,</span>
<span class="s1">&#39;tr-mae&#39;</span><span class="p">:</span> <span class="o">-</span><span class="mi">1</span><span class="p">,</span>
<span class="s1">&#39;va-mae&#39;</span><span class="p">:</span> <span class="o">-</span><span class="mi">1</span><span class="p">,</span>
<span class="p">}</span>
<span class="n">nQ</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">quantifiers</span><span class="p">)</span>
<span class="n">nC</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">n_classes</span>
<span class="bp">self</span><span class="o">.</span><span class="n">quanet</span> <span class="o">=</span> <span class="n">QuaNetModule</span><span class="p">(</span>
<span class="n">doc_embedding_size</span><span class="o">=</span><span class="n">train_data_embed</span><span class="o">.</span><span class="n">instances</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
<span class="n">n_classes</span><span class="o">=</span><span class="n">data</span><span class="o">.</span><span class="n">n_classes</span><span class="p">,</span>
<span class="n">stats_size</span><span class="o">=</span><span class="n">nQ</span><span class="o">*</span><span class="n">nC</span><span class="p">,</span>
<span class="n">order_by</span><span class="o">=</span><span class="mi">0</span> <span class="k">if</span> <span class="n">data</span><span class="o">.</span><span class="n">binary</span> <span class="k">else</span> <span class="kc">None</span><span class="p">,</span>
<span class="o">**</span><span class="bp">self</span><span class="o">.</span><span class="n">quanet_params</span>
<span class="p">)</span><span class="o">.</span><span class="n">to</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">device</span><span class="p">)</span>
<span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="vm">__name__</span><span class="p">)</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">quanet</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">optim</span> <span class="o">=</span> <span class="n">torch</span><span class="o">.</span><span class="n">optim</span><span class="o">.</span><span class="n">Adam</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">quanet</span><span class="o">.</span><span class="n">parameters</span><span class="p">(),</span> <span class="n">lr</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">lr</span><span class="p">)</span>
<span class="n">early_stop</span> <span class="o">=</span> <span class="n">EarlyStop</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">patience</span><span class="p">,</span> <span class="n">lower_is_better</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="n">checkpoint</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">checkpoint</span>
<span class="k">for</span> <span class="n">epoch_i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">n_epochs</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_epoch</span><span class="p">(</span><span class="n">train_data_embed</span><span class="p">,</span> <span class="n">train_posteriors</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">tr_iter</span><span class="p">,</span> <span class="n">epoch_i</span><span class="p">,</span> <span class="n">early_stop</span><span class="p">,</span> <span class="n">train</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_epoch</span><span class="p">(</span><span class="n">valid_data_embed</span><span class="p">,</span> <span class="n">valid_posteriors</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">va_iter</span><span class="p">,</span> <span class="n">epoch_i</span><span class="p">,</span> <span class="n">early_stop</span><span class="p">,</span> <span class="n">train</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
<span class="n">early_stop</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">status</span><span class="p">[</span><span class="s1">&#39;va-loss&#39;</span><span class="p">],</span> <span class="n">epoch_i</span><span class="p">)</span>
<span class="k">if</span> <span class="n">early_stop</span><span class="o">.</span><span class="n">IMPROVED</span><span class="p">:</span>
<span class="n">torch</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">quanet</span><span class="o">.</span><span class="n">state_dict</span><span class="p">(),</span> <span class="n">checkpoint</span><span class="p">)</span>
<span class="k">elif</span> <span class="n">early_stop</span><span class="o">.</span><span class="n">STOP</span><span class="p">:</span>
<span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="vm">__name__</span><span class="p">)</span><span class="o">.</span><span class="n">info</span><span class="p">(</span>
<span class="sa">f</span><span class="s1">&#39;training ended by patience exhausted; loading best model parameters in </span><span class="si">{</span><span class="n">checkpoint</span><span class="si">}</span><span class="s1"> &#39;</span>
<span class="sa">f</span><span class="s1">&#39;for epoch </span><span class="si">{</span><span class="n">early_stop</span><span class="o">.</span><span class="n">best_epoch</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">quanet</span><span class="o">.</span><span class="n">load_state_dict</span><span class="p">(</span><span class="n">torch</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">checkpoint</span><span class="p">))</span>
<span class="k">break</span>
<span class="k">return</span> <span class="bp">self</span></div>
<span class="k">def</span><span class="w"> </span><span class="nf">_get_aggregative_estims</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">posteriors</span><span class="p">):</span>
<span class="n">label_predictions</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">argmax</span><span class="p">(</span><span class="n">posteriors</span><span class="p">,</span> <span class="n">axis</span><span class="o">=-</span><span class="mi">1</span><span class="p">)</span>
<span class="n">prevs_estim</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">quantifier</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">quantifiers</span><span class="o">.</span><span class="n">values</span><span class="p">():</span>
<span class="n">predictions</span> <span class="o">=</span> <span class="n">posteriors</span> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">quantifier</span><span class="p">,</span> <span class="n">AggregativeSoftQuantifier</span><span class="p">)</span> <span class="k">else</span> <span class="n">label_predictions</span>
<span class="n">prevs_estim</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">quantifier</span><span class="o">.</span><span class="n">aggregate</span><span class="p">(</span><span class="n">predictions</span><span class="p">))</span>
<span class="c1"># there is no real need for adding static estims like the TPR or FPR from training since those are constant</span>
<span class="k">return</span> <span class="n">prevs_estim</span>
<div class="viewcode-block" id="QuaNetTrainer.predict">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._neural.QuaNetTrainer.predict">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">predict</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">):</span>
<span class="n">posteriors</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">classifier</span><span class="o">.</span><span class="n">predict_proba</span><span class="p">(</span><span class="n">X</span><span class="p">)</span>
<span class="n">embeddings</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">classifier</span><span class="o">.</span><span class="n">transform</span><span class="p">(</span><span class="n">X</span><span class="p">)</span>
<span class="n">quant_estims</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_aggregative_estims</span><span class="p">(</span><span class="n">posteriors</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">quanet</span><span class="o">.</span><span class="n">eval</span><span class="p">()</span>
<span class="k">with</span> <span class="n">torch</span><span class="o">.</span><span class="n">no_grad</span><span class="p">():</span>
<span class="n">prevalence</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">quanet</span><span class="o">.</span><span class="n">forward</span><span class="p">(</span><span class="n">embeddings</span><span class="p">,</span> <span class="n">posteriors</span><span class="p">,</span> <span class="n">quant_estims</span><span class="p">)</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">device</span> <span class="o">==</span> <span class="n">torch</span><span class="o">.</span><span class="n">device</span><span class="p">(</span><span class="s1">&#39;cuda&#39;</span><span class="p">):</span>
<span class="n">prevalence</span> <span class="o">=</span> <span class="n">prevalence</span><span class="o">.</span><span class="n">cpu</span><span class="p">()</span>
<span class="n">prevalence</span> <span class="o">=</span> <span class="n">prevalence</span><span class="o">.</span><span class="n">numpy</span><span class="p">()</span><span class="o">.</span><span class="n">flatten</span><span class="p">()</span>
<span class="k">return</span> <span class="n">prevalence</span></div>
<span class="k">def</span><span class="w"> </span><span class="nf">_epoch</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">data</span><span class="p">:</span> <span class="n">LabelledCollection</span><span class="p">,</span> <span class="n">posteriors</span><span class="p">,</span> <span class="n">iterations</span><span class="p">,</span> <span class="n">epoch</span><span class="p">,</span> <span class="n">early_stop</span><span class="p">,</span> <span class="n">train</span><span class="p">):</span>
<span class="n">mse_loss</span> <span class="o">=</span> <span class="n">MSELoss</span><span class="p">()</span>
<span class="bp">self</span><span class="o">.</span><span class="n">quanet</span><span class="o">.</span><span class="n">train</span><span class="p">(</span><span class="n">mode</span><span class="o">=</span><span class="n">train</span><span class="p">)</span>
<span class="n">losses</span> <span class="o">=</span> <span class="p">[]</span>
<span class="n">mae_errors</span> <span class="o">=</span> <span class="p">[]</span>
<span class="n">sampler</span> <span class="o">=</span> <span class="n">UPP</span><span class="p">(</span>
<span class="n">data</span><span class="p">,</span>
<span class="n">sample_size</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">sample_size</span><span class="p">,</span>
<span class="n">repeats</span><span class="o">=</span><span class="n">iterations</span><span class="p">,</span>
<span class="n">random_state</span><span class="o">=</span><span class="kc">None</span> <span class="k">if</span> <span class="n">train</span> <span class="k">else</span> <span class="mi">0</span> <span class="c1"># different samples during train, same samples during validation</span>
<span class="p">)</span>
<span class="n">pbar</span> <span class="o">=</span> <span class="n">tqdm</span><span class="p">(</span><span class="n">sampler</span><span class="o">.</span><span class="n">samples_parameters</span><span class="p">(),</span> <span class="n">total</span><span class="o">=</span><span class="n">sampler</span><span class="o">.</span><span class="n">total</span><span class="p">())</span>
<span class="k">for</span> <span class="n">it</span><span class="p">,</span> <span class="n">index</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">pbar</span><span class="p">):</span>
<span class="n">sample_data</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">sampling_from_index</span><span class="p">(</span><span class="n">index</span><span class="p">)</span>
<span class="n">sample_posteriors</span> <span class="o">=</span> <span class="n">posteriors</span><span class="p">[</span><span class="n">index</span><span class="p">]</span>
<span class="n">quant_estims</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_aggregative_estims</span><span class="p">(</span><span class="n">sample_posteriors</span><span class="p">)</span>
<span class="n">ptrue</span> <span class="o">=</span> <span class="n">torch</span><span class="o">.</span><span class="n">as_tensor</span><span class="p">([</span><span class="n">sample_data</span><span class="o">.</span><span class="n">prevalence</span><span class="p">()],</span> <span class="n">dtype</span><span class="o">=</span><span class="n">torch</span><span class="o">.</span><span class="n">float</span><span class="p">,</span> <span class="n">device</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">device</span><span class="p">)</span>
<span class="k">if</span> <span class="n">train</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">optim</span><span class="o">.</span><span class="n">zero_grad</span><span class="p">()</span>
<span class="n">phat</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">quanet</span><span class="o">.</span><span class="n">forward</span><span class="p">(</span><span class="n">sample_data</span><span class="o">.</span><span class="n">instances</span><span class="p">,</span> <span class="n">sample_posteriors</span><span class="p">,</span> <span class="n">quant_estims</span><span class="p">)</span>
<span class="n">loss</span> <span class="o">=</span> <span class="n">mse_loss</span><span class="p">(</span><span class="n">phat</span><span class="p">,</span> <span class="n">ptrue</span><span class="p">)</span>
<span class="n">mae</span> <span class="o">=</span> <span class="n">mae_loss</span><span class="p">(</span><span class="n">phat</span><span class="p">,</span> <span class="n">ptrue</span><span class="p">)</span>
<span class="n">loss</span><span class="o">.</span><span class="n">backward</span><span class="p">()</span>
<span class="bp">self</span><span class="o">.</span><span class="n">optim</span><span class="o">.</span><span class="n">step</span><span class="p">()</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">with</span> <span class="n">torch</span><span class="o">.</span><span class="n">no_grad</span><span class="p">():</span>
<span class="n">phat</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">quanet</span><span class="o">.</span><span class="n">forward</span><span class="p">(</span><span class="n">sample_data</span><span class="o">.</span><span class="n">instances</span><span class="p">,</span> <span class="n">sample_posteriors</span><span class="p">,</span> <span class="n">quant_estims</span><span class="p">)</span>
<span class="n">loss</span> <span class="o">=</span> <span class="n">mse_loss</span><span class="p">(</span><span class="n">phat</span><span class="p">,</span> <span class="n">ptrue</span><span class="p">)</span>
<span class="n">mae</span> <span class="o">=</span> <span class="n">mae_loss</span><span class="p">(</span><span class="n">phat</span><span class="p">,</span> <span class="n">ptrue</span><span class="p">)</span>
<span class="n">losses</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">loss</span><span class="o">.</span><span class="n">item</span><span class="p">())</span>
<span class="n">mae_errors</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">mae</span><span class="o">.</span><span class="n">item</span><span class="p">())</span>
<span class="n">mse</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">losses</span><span class="p">)</span>
<span class="n">mae</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">mae_errors</span><span class="p">)</span>
<span class="k">if</span> <span class="n">train</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">status</span><span class="p">[</span><span class="s1">&#39;tr-loss&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">mse</span>
<span class="bp">self</span><span class="o">.</span><span class="n">status</span><span class="p">[</span><span class="s1">&#39;tr-mae&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">mae</span>
<span class="k">else</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">status</span><span class="p">[</span><span class="s1">&#39;va-loss&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">mse</span>
<span class="bp">self</span><span class="o">.</span><span class="n">status</span><span class="p">[</span><span class="s1">&#39;va-mae&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">mae</span>
<span class="k">if</span> <span class="n">train</span><span class="p">:</span>
<span class="n">pbar</span><span class="o">.</span><span class="n">set_description</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;[QuaNet] &#39;</span>
<span class="sa">f</span><span class="s1">&#39;epoch=</span><span class="si">{</span><span class="n">epoch</span><span class="si">}</span><span class="s1"> [it=</span><span class="si">{</span><span class="n">it</span><span class="si">}</span><span class="s1">/</span><span class="si">{</span><span class="n">iterations</span><span class="si">}</span><span class="s1">]</span><span class="se">\t</span><span class="s1">&#39;</span>
<span class="sa">f</span><span class="s1">&#39;tr-mseloss=</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">status</span><span class="p">[</span><span class="s2">&quot;tr-loss&quot;</span><span class="p">]</span><span class="si">:</span><span class="s1">.5f</span><span class="si">}</span><span class="s1"> tr-maeloss=</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">status</span><span class="p">[</span><span class="s2">&quot;tr-mae&quot;</span><span class="p">]</span><span class="si">:</span><span class="s1">.5f</span><span class="si">}</span><span class="se">\t</span><span class="s1">&#39;</span>
<span class="sa">f</span><span class="s1">&#39;val-mseloss=</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">status</span><span class="p">[</span><span class="s2">&quot;va-loss&quot;</span><span class="p">]</span><span class="si">:</span><span class="s1">.5f</span><span class="si">}</span><span class="s1"> val-maeloss=</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">status</span><span class="p">[</span><span class="s2">&quot;va-mae&quot;</span><span class="p">]</span><span class="si">:</span><span class="s1">.5f</span><span class="si">}</span><span class="s1"> &#39;</span>
<span class="sa">f</span><span class="s1">&#39;patience=</span><span class="si">{</span><span class="n">early_stop</span><span class="o">.</span><span class="n">patience</span><span class="si">}</span><span class="s1">/</span><span class="si">{</span><span class="n">early_stop</span><span class="o">.</span><span class="n">PATIENCE_LIMIT</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
<div class="viewcode-block" id="QuaNetTrainer.get_params">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._neural.QuaNetTrainer.get_params">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">get_params</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">deep</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
<span class="n">classifier_params</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">classifier</span><span class="o">.</span><span class="n">get_params</span><span class="p">()</span>
<span class="n">classifier_params</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;classifier__&#39;</span><span class="o">+</span><span class="n">k</span><span class="p">:</span><span class="n">v</span> <span class="k">for</span> <span class="n">k</span><span class="p">,</span><span class="n">v</span> <span class="ow">in</span> <span class="n">classifier_params</span><span class="o">.</span><span class="n">items</span><span class="p">()}</span>
<span class="k">return</span> <span class="p">{</span><span class="o">**</span><span class="n">classifier_params</span><span class="p">,</span> <span class="o">**</span><span class="bp">self</span><span class="o">.</span><span class="n">quanet_params</span><span class="p">}</span></div>
<div class="viewcode-block" id="QuaNetTrainer.set_params">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._neural.QuaNetTrainer.set_params">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">set_params</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">parameters</span><span class="p">):</span>
<span class="n">learner_params</span> <span class="o">=</span> <span class="p">{}</span>
<span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">val</span> <span class="ow">in</span> <span class="n">parameters</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
<span class="k">if</span> <span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">quanet_params</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">quanet_params</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">val</span>
<span class="k">elif</span> <span class="n">key</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;classifier__&#39;</span><span class="p">):</span>
<span class="n">learner_params</span><span class="p">[</span><span class="n">key</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;classifier__&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)]</span> <span class="o">=</span> <span class="n">val</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s1">&#39;unknown parameter &#39;</span><span class="p">,</span> <span class="n">key</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">classifier</span><span class="o">.</span><span class="n">set_params</span><span class="p">(</span><span class="o">**</span><span class="n">learner_params</span><span class="p">)</span></div>
<span class="k">def</span><span class="w"> </span><span class="nf">__check_params_colision</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">quanet_params</span><span class="p">,</span> <span class="n">learner_params</span><span class="p">):</span>
<span class="n">quanet_keys</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">quanet_params</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
<span class="n">learner_keys</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">learner_params</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
<span class="n">intersection</span> <span class="o">=</span> <span class="n">quanet_keys</span><span class="o">.</span><span class="n">intersection</span><span class="p">(</span><span class="n">learner_keys</span><span class="p">)</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">intersection</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;the use of parameters </span><span class="si">{</span><span class="n">intersection</span><span class="si">}</span><span class="s1"> is ambiguous sine those can refer to &#39;</span>
<span class="sa">f</span><span class="s1">&#39;the parameters of QuaNet or the learner </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">classifier</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
<div class="viewcode-block" id="QuaNetTrainer.clean_checkpoint">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._neural.QuaNetTrainer.clean_checkpoint">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">clean_checkpoint</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Removes the checkpoint</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">os</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">checkpoint</span><span class="p">)</span></div>
<div class="viewcode-block" id="QuaNetTrainer.clean_checkpoint_dir">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._neural.QuaNetTrainer.clean_checkpoint_dir">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">clean_checkpoint_dir</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Removes anything contained in the checkpoint directory</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">shutil</span>
<span class="n">shutil</span><span class="o">.</span><span class="n">rmtree</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">checkpointdir</span><span class="p">,</span> <span class="n">ignore_errors</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span></div>
<span class="nd">@property</span>
<span class="k">def</span><span class="w"> </span><span class="nf">classes_</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_classes_</span></div>
<div class="viewcode-block" id="mae_loss">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._neural.mae_loss">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">mae_loss</span><span class="p">(</span><span class="n">output</span><span class="p">,</span> <span class="n">target</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Torch-like wrapper for the Mean Absolute Error</span>
<span class="sd"> :param output: predictions</span>
<span class="sd"> :param target: ground truth values</span>
<span class="sd"> :return: mean absolute error loss</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">return</span> <span class="n">torch</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">torch</span><span class="o">.</span><span class="n">abs</span><span class="p">(</span><span class="n">output</span> <span class="o">-</span> <span class="n">target</span><span class="p">))</span></div>
<div class="viewcode-block" id="QuaNetModule">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._neural.QuaNetModule">[docs]</a>
<span class="k">class</span><span class="w"> </span><span class="nc">QuaNetModule</span><span class="p">(</span><span class="n">torch</span><span class="o">.</span><span class="n">nn</span><span class="o">.</span><span class="n">Module</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Implements the `QuaNet &lt;https://dl.acm.org/doi/abs/10.1145/3269206.3269287&gt;`_ forward pass.</span>
<span class="sd"> See :class:`QuaNetTrainer` for training QuaNet.</span>
<span class="sd"> :param doc_embedding_size: integer, the dimensionality of the document embeddings</span>
<span class="sd"> :param n_classes: integer, number of classes</span>
<span class="sd"> :param stats_size: integer, number of statistics estimated by simple quantification methods</span>
<span class="sd"> :param lstm_hidden_size: integer, hidden dimensionality of the LSTM cell</span>
<span class="sd"> :param lstm_nlayers: integer, number of LSTM layers</span>
<span class="sd"> :param ff_layers: list of integers, dimensions of the densely-connected FF layers on top of the</span>
<span class="sd"> quantification embedding</span>
<span class="sd"> :param bidirectional: boolean, whether or not to use bidirectional LSTM</span>
<span class="sd"> :param qdrop_p: float, dropout probability</span>
<span class="sd"> :param order_by: integer, class for which the document embeddings are to be sorted</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span>
<span class="n">doc_embedding_size</span><span class="p">,</span>
<span class="n">n_classes</span><span class="p">,</span>
<span class="n">stats_size</span><span class="p">,</span>
<span class="n">lstm_hidden_size</span><span class="o">=</span><span class="mi">64</span><span class="p">,</span>
<span class="n">lstm_nlayers</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
<span class="n">ff_layers</span><span class="o">=</span><span class="p">[</span><span class="mi">1024</span><span class="p">,</span> <span class="mi">512</span><span class="p">],</span>
<span class="n">bidirectional</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
<span class="n">qdrop_p</span><span class="o">=</span><span class="mf">0.5</span><span class="p">,</span>
<span class="n">order_by</span><span class="o">=</span><span class="mi">0</span><span class="p">):</span>
<span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">()</span>
<span class="bp">self</span><span class="o">.</span><span class="n">n_classes</span> <span class="o">=</span> <span class="n">n_classes</span>
<span class="bp">self</span><span class="o">.</span><span class="n">order_by</span> <span class="o">=</span> <span class="n">order_by</span>
<span class="bp">self</span><span class="o">.</span><span class="n">hidden_size</span> <span class="o">=</span> <span class="n">lstm_hidden_size</span>
<span class="bp">self</span><span class="o">.</span><span class="n">nlayers</span> <span class="o">=</span> <span class="n">lstm_nlayers</span>
<span class="bp">self</span><span class="o">.</span><span class="n">bidirectional</span> <span class="o">=</span> <span class="n">bidirectional</span>
<span class="bp">self</span><span class="o">.</span><span class="n">ndirections</span> <span class="o">=</span> <span class="mi">2</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">bidirectional</span> <span class="k">else</span> <span class="mi">1</span>
<span class="bp">self</span><span class="o">.</span><span class="n">qdrop_p</span> <span class="o">=</span> <span class="n">qdrop_p</span>
<span class="bp">self</span><span class="o">.</span><span class="n">lstm</span> <span class="o">=</span> <span class="n">torch</span><span class="o">.</span><span class="n">nn</span><span class="o">.</span><span class="n">LSTM</span><span class="p">(</span><span class="n">doc_embedding_size</span> <span class="o">+</span> <span class="n">n_classes</span><span class="p">,</span> <span class="c1"># +n_classes stands for the posterior probs. (concatenated)</span>
<span class="n">lstm_hidden_size</span><span class="p">,</span> <span class="n">lstm_nlayers</span><span class="p">,</span> <span class="n">bidirectional</span><span class="o">=</span><span class="n">bidirectional</span><span class="p">,</span>
<span class="n">dropout</span><span class="o">=</span><span class="n">qdrop_p</span><span class="p">,</span> <span class="n">batch_first</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">dropout</span> <span class="o">=</span> <span class="n">torch</span><span class="o">.</span><span class="n">nn</span><span class="o">.</span><span class="n">Dropout</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">qdrop_p</span><span class="p">)</span>
<span class="n">lstm_output_size</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">hidden_size</span> <span class="o">*</span> <span class="bp">self</span><span class="o">.</span><span class="n">ndirections</span>
<span class="n">ff_input_size</span> <span class="o">=</span> <span class="n">lstm_output_size</span> <span class="o">+</span> <span class="n">stats_size</span>
<span class="n">prev_size</span> <span class="o">=</span> <span class="n">ff_input_size</span>
<span class="bp">self</span><span class="o">.</span><span class="n">ff_layers</span> <span class="o">=</span> <span class="n">torch</span><span class="o">.</span><span class="n">nn</span><span class="o">.</span><span class="n">ModuleList</span><span class="p">()</span>
<span class="k">for</span> <span class="n">lin_size</span> <span class="ow">in</span> <span class="n">ff_layers</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">ff_layers</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">torch</span><span class="o">.</span><span class="n">nn</span><span class="o">.</span><span class="n">Linear</span><span class="p">(</span><span class="n">prev_size</span><span class="p">,</span> <span class="n">lin_size</span><span class="p">))</span>
<span class="n">prev_size</span> <span class="o">=</span> <span class="n">lin_size</span>
<span class="bp">self</span><span class="o">.</span><span class="n">output</span> <span class="o">=</span> <span class="n">torch</span><span class="o">.</span><span class="n">nn</span><span class="o">.</span><span class="n">Linear</span><span class="p">(</span><span class="n">prev_size</span><span class="p">,</span> <span class="n">n_classes</span><span class="p">)</span>
<span class="nd">@property</span>
<span class="k">def</span><span class="w"> </span><span class="nf">device</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="n">torch</span><span class="o">.</span><span class="n">device</span><span class="p">(</span><span class="s1">&#39;cuda&#39;</span><span class="p">)</span> <span class="k">if</span> <span class="nb">next</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parameters</span><span class="p">())</span><span class="o">.</span><span class="n">is_cuda</span> <span class="k">else</span> <span class="n">torch</span><span class="o">.</span><span class="n">device</span><span class="p">(</span><span class="s1">&#39;cpu&#39;</span><span class="p">)</span>
<span class="k">def</span><span class="w"> </span><span class="nf">_init_hidden</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="n">directions</span> <span class="o">=</span> <span class="mi">2</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">bidirectional</span> <span class="k">else</span> <span class="mi">1</span>
<span class="n">var_hidden</span> <span class="o">=</span> <span class="n">torch</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">nlayers</span> <span class="o">*</span> <span class="n">directions</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">hidden_size</span><span class="p">)</span>
<span class="n">var_cell</span> <span class="o">=</span> <span class="n">torch</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">nlayers</span> <span class="o">*</span> <span class="n">directions</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">hidden_size</span><span class="p">)</span>
<span class="k">if</span> <span class="nb">next</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">lstm</span><span class="o">.</span><span class="n">parameters</span><span class="p">())</span><span class="o">.</span><span class="n">is_cuda</span><span class="p">:</span>
<span class="n">var_hidden</span><span class="p">,</span> <span class="n">var_cell</span> <span class="o">=</span> <span class="n">var_hidden</span><span class="o">.</span><span class="n">cuda</span><span class="p">(),</span> <span class="n">var_cell</span><span class="o">.</span><span class="n">cuda</span><span class="p">()</span>
<span class="k">return</span> <span class="n">var_hidden</span><span class="p">,</span> <span class="n">var_cell</span>
<div class="viewcode-block" id="QuaNetModule.forward">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._neural.QuaNetModule.forward">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">forward</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">doc_embeddings</span><span class="p">,</span> <span class="n">doc_posteriors</span><span class="p">,</span> <span class="n">statistics</span><span class="p">):</span>
<span class="n">device</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">device</span>
<span class="n">doc_embeddings</span> <span class="o">=</span> <span class="n">torch</span><span class="o">.</span><span class="n">as_tensor</span><span class="p">(</span><span class="n">doc_embeddings</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="n">torch</span><span class="o">.</span><span class="n">float</span><span class="p">,</span> <span class="n">device</span><span class="o">=</span><span class="n">device</span><span class="p">)</span>
<span class="n">doc_posteriors</span> <span class="o">=</span> <span class="n">torch</span><span class="o">.</span><span class="n">as_tensor</span><span class="p">(</span><span class="n">doc_posteriors</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="n">torch</span><span class="o">.</span><span class="n">float</span><span class="p">,</span> <span class="n">device</span><span class="o">=</span><span class="n">device</span><span class="p">)</span>
<span class="n">statistics</span> <span class="o">=</span> <span class="n">torch</span><span class="o">.</span><span class="n">as_tensor</span><span class="p">(</span><span class="n">statistics</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="n">torch</span><span class="o">.</span><span class="n">float</span><span class="p">,</span> <span class="n">device</span><span class="o">=</span><span class="n">device</span><span class="p">)</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">order_by</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
<span class="n">order</span> <span class="o">=</span> <span class="n">torch</span><span class="o">.</span><span class="n">argsort</span><span class="p">(</span><span class="n">doc_posteriors</span><span class="p">[:,</span> <span class="bp">self</span><span class="o">.</span><span class="n">order_by</span><span class="p">])</span>
<span class="n">doc_embeddings</span> <span class="o">=</span> <span class="n">doc_embeddings</span><span class="p">[</span><span class="n">order</span><span class="p">]</span>
<span class="n">doc_posteriors</span> <span class="o">=</span> <span class="n">doc_posteriors</span><span class="p">[</span><span class="n">order</span><span class="p">]</span>
<span class="n">embeded_posteriors</span> <span class="o">=</span> <span class="n">torch</span><span class="o">.</span><span class="n">cat</span><span class="p">((</span><span class="n">doc_embeddings</span><span class="p">,</span> <span class="n">doc_posteriors</span><span class="p">),</span> <span class="n">dim</span><span class="o">=-</span><span class="mi">1</span><span class="p">)</span>
<span class="c1"># the entire set represents only one instance in quapy contexts, and so the batch_size=1</span>
<span class="c1"># the shape should be (1, number-of-instances, embedding-size + n_classes)</span>
<span class="n">embeded_posteriors</span> <span class="o">=</span> <span class="n">embeded_posteriors</span><span class="o">.</span><span class="n">unsqueeze</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">lstm</span><span class="o">.</span><span class="n">flatten_parameters</span><span class="p">()</span>
<span class="n">_</span><span class="p">,</span> <span class="p">(</span><span class="n">rnn_hidden</span><span class="p">,</span><span class="n">_</span><span class="p">)</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">lstm</span><span class="p">(</span><span class="n">embeded_posteriors</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_init_hidden</span><span class="p">())</span>
<span class="n">rnn_hidden</span> <span class="o">=</span> <span class="n">rnn_hidden</span><span class="o">.</span><span class="n">view</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">nlayers</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">ndirections</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">hidden_size</span><span class="p">)</span>
<span class="n">quant_embedding</span> <span class="o">=</span> <span class="n">rnn_hidden</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">view</span><span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">)</span>
<span class="n">quant_embedding</span> <span class="o">=</span> <span class="n">torch</span><span class="o">.</span><span class="n">cat</span><span class="p">((</span><span class="n">quant_embedding</span><span class="p">,</span> <span class="n">statistics</span><span class="p">))</span>
<span class="n">abstracted</span> <span class="o">=</span> <span class="n">quant_embedding</span><span class="o">.</span><span class="n">unsqueeze</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
<span class="k">for</span> <span class="n">linear</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">ff_layers</span><span class="p">:</span>
<span class="n">abstracted</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">dropout</span><span class="p">(</span><span class="n">relu</span><span class="p">(</span><span class="n">linear</span><span class="p">(</span><span class="n">abstracted</span><span class="p">)))</span>
<span class="n">logits</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">output</span><span class="p">(</span><span class="n">abstracted</span><span class="p">)</span><span class="o">.</span><span class="n">view</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">)</span>
<span class="n">prevalence</span> <span class="o">=</span> <span class="n">torch</span><span class="o">.</span><span class="n">softmax</span><span class="p">(</span><span class="n">logits</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">)</span>
<span class="k">return</span> <span class="n">prevalence</span></div>
</div>
</pre></div>
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<h1>Source code for quapy.method._threshold_optim</h1><div class="highlight"><pre>
<span></span><span class="kn">from</span><span class="w"> </span><span class="nn">abc</span><span class="w"> </span><span class="kn">import</span> <span class="n">abstractmethod</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">sklearn.base</span><span class="w"> </span><span class="kn">import</span> <span class="n">BaseEstimator</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">quapy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">qp</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">quapy.functional</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">F</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">quapy.data</span><span class="w"> </span><span class="kn">import</span> <span class="n">LabelledCollection</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">quapy.method.aggregative</span><span class="w"> </span><span class="kn">import</span> <span class="n">BinaryAggregativeQuantifier</span>
<div class="viewcode-block" id="ThresholdOptimization">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._threshold_optim.ThresholdOptimization">[docs]</a>
<span class="k">class</span><span class="w"> </span><span class="nc">ThresholdOptimization</span><span class="p">(</span><span class="n">BinaryAggregativeQuantifier</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Abstract class of Threshold Optimization variants for :class:`ACC` as proposed by</span>
<span class="sd"> `Forman 2006 &lt;https://dl.acm.org/doi/abs/10.1145/1150402.1150423&gt;`_ and</span>
<span class="sd"> `Forman 2008 &lt;https://link.springer.com/article/10.1007/s10618-008-0097-y&gt;`_.</span>
<span class="sd"> The goal is to bring improved stability to the denominator of the adjustment.</span>
<span class="sd"> The different variants are based on different heuristics for choosing a decision threshold</span>
<span class="sd"> that would allow for more true positives and many more false positives, on the grounds this</span>
<span class="sd"> would deliver larger denominators.</span>
<span class="sd"> :param classifier: a scikit-learn&#39;s BaseEstimator, or None, in which case the classifier is taken to be</span>
<span class="sd"> the one indicated in `qp.environ[&#39;DEFAULT_CLS&#39;]`</span>
<span class="sd"> :param fit_classifier: whether to train the learner (default is True). Set to False if the</span>
<span class="sd"> learner has been trained outside the quantifier.</span>
<span class="sd"> :param val_split: specifies the data used for generating classifier predictions. This specification</span>
<span class="sd"> can be made as float in (0, 1) indicating the proportion of stratified held-out validation set to</span>
<span class="sd"> be extracted from the training set; or as an integer (default 5), indicating that the predictions</span>
<span class="sd"> are to be generated in a `k`-fold cross-validation manner (with this integer indicating the value</span>
<span class="sd"> for `k`); or as a tuple (X,y) defining the specific set of data to use for validation.</span>
<span class="sd"> :param n_jobs: number of parallel workers</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">classifier</span><span class="p">:</span> <span class="n">BaseEstimator</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">fit_classifier</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">val_split</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">n_jobs</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">classifier</span><span class="p">,</span> <span class="n">fit_classifier</span><span class="p">,</span> <span class="n">val_split</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">n_jobs</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">_get_njobs</span><span class="p">(</span><span class="n">n_jobs</span><span class="p">)</span>
<div class="viewcode-block" id="ThresholdOptimization.condition">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._threshold_optim.ThresholdOptimization.condition">[docs]</a>
<span class="nd">@abstractmethod</span>
<span class="k">def</span><span class="w"> </span><span class="nf">condition</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">tpr</span><span class="p">,</span> <span class="n">fpr</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">float</span><span class="p">:</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Implements the criterion according to which the threshold should be selected.</span>
<span class="sd"> This function should return the (float) score to be minimized.</span>
<span class="sd"> :param tpr: float, true positive rate</span>
<span class="sd"> :param fpr: float, false positive rate</span>
<span class="sd"> :return: float, a score for the given `tpr` and `fpr`</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="o">...</span></div>
<div class="viewcode-block" id="ThresholdOptimization.discard">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._threshold_optim.ThresholdOptimization.discard">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">discard</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">tpr</span><span class="p">,</span> <span class="n">fpr</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">bool</span><span class="p">:</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Indicates whether a combination of tpr and fpr should be discarded</span>
<span class="sd"> :param tpr: float, true positive rate</span>
<span class="sd"> :param fpr: float, false positive rate</span>
<span class="sd"> :return: true if the combination is to be discarded, false otherwise</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">return</span> <span class="p">(</span><span class="n">tpr</span> <span class="o">-</span> <span class="n">fpr</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span></div>
<span class="k">def</span><span class="w"> </span><span class="nf">_eval_candidate_thresholds</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">decision_scores</span><span class="p">,</span> <span class="n">y</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Seeks for the best `tpr` and `fpr` according to the score obtained at different</span>
<span class="sd"> decision thresholds. The scoring function is implemented in function `_condition`.</span>
<span class="sd"> :param decision_scores: array-like with the classification scores</span>
<span class="sd"> :param y: predicted labels for the validation set (or for the training set via `k`-fold cross validation)</span>
<span class="sd"> :return: best `tpr` and `fpr` and `threshold` according to `_condition`</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">candidate_thresholds</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">unique</span><span class="p">(</span><span class="n">decision_scores</span><span class="p">)</span>
<span class="n">candidates</span> <span class="o">=</span> <span class="p">[]</span>
<span class="n">scores</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">candidate_threshold</span> <span class="ow">in</span> <span class="n">candidate_thresholds</span><span class="p">:</span>
<span class="n">y_</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">classes_</span><span class="p">[</span><span class="mi">1</span> <span class="o">*</span> <span class="p">(</span><span class="n">decision_scores</span> <span class="o">&gt;=</span> <span class="n">candidate_threshold</span><span class="p">)]</span>
<span class="n">TP</span><span class="p">,</span> <span class="n">FP</span><span class="p">,</span> <span class="n">FN</span><span class="p">,</span> <span class="n">TN</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_compute_table</span><span class="p">(</span><span class="n">y</span><span class="p">,</span> <span class="n">y_</span><span class="p">)</span>
<span class="n">tpr</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_compute_tpr</span><span class="p">(</span><span class="n">TP</span><span class="p">,</span> <span class="n">FN</span><span class="p">)</span>
<span class="n">fpr</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_compute_fpr</span><span class="p">(</span><span class="n">FP</span><span class="p">,</span> <span class="n">TN</span><span class="p">)</span>
<span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">discard</span><span class="p">(</span><span class="n">tpr</span><span class="p">,</span> <span class="n">fpr</span><span class="p">):</span>
<span class="n">candidate_score</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">condition</span><span class="p">(</span><span class="n">tpr</span><span class="p">,</span> <span class="n">fpr</span><span class="p">)</span>
<span class="n">candidates</span><span class="o">.</span><span class="n">append</span><span class="p">([</span><span class="n">tpr</span><span class="p">,</span> <span class="n">fpr</span><span class="p">,</span> <span class="n">candidate_threshold</span><span class="p">])</span>
<span class="n">scores</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">candidate_score</span><span class="p">)</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">candidates</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="c1"># if no candidate gives rise to a valid combination of tpr and fpr, this method defaults to the standard</span>
<span class="c1"># classify &amp; count; this is akin to assign tpr=1, fpr=0, threshold=0</span>
<span class="n">tpr</span><span class="p">,</span> <span class="n">fpr</span><span class="p">,</span> <span class="n">threshold</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span>
<span class="n">candidates</span><span class="o">.</span><span class="n">append</span><span class="p">([</span><span class="n">tpr</span><span class="p">,</span> <span class="n">fpr</span><span class="p">,</span> <span class="n">threshold</span><span class="p">])</span>
<span class="n">scores</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
<span class="n">candidates</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">candidates</span><span class="p">)</span>
<span class="n">candidates</span> <span class="o">=</span> <span class="n">candidates</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">argsort</span><span class="p">(</span><span class="n">scores</span><span class="p">)]</span> <span class="c1"># sort candidates by candidate_score</span>
<span class="k">return</span> <span class="n">candidates</span>
<div class="viewcode-block" id="ThresholdOptimization.aggregate_with_threshold">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._threshold_optim.ThresholdOptimization.aggregate_with_threshold">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">aggregate_with_threshold</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">classif_predictions</span><span class="p">,</span> <span class="n">tprs</span><span class="p">,</span> <span class="n">fprs</span><span class="p">,</span> <span class="n">thresholds</span><span class="p">):</span>
<span class="c1"># This function performs the adjusted count for given tpr, fpr, and threshold.</span>
<span class="c1"># Note that, due to broadcasting, tprs, fprs, and thresholds could be arrays of length &gt; 1</span>
<span class="n">prevs_estims</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">classif_predictions</span><span class="p">[:,</span> <span class="kc">None</span><span class="p">]</span> <span class="o">&gt;=</span> <span class="n">thresholds</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
<span class="n">prevs_estims</span> <span class="o">=</span> <span class="p">(</span><span class="n">prevs_estims</span> <span class="o">-</span> <span class="n">fprs</span><span class="p">)</span> <span class="o">/</span> <span class="p">(</span><span class="n">tprs</span> <span class="o">-</span> <span class="n">fprs</span><span class="p">)</span>
<span class="n">prevs_estims</span> <span class="o">=</span> <span class="n">F</span><span class="o">.</span><span class="n">as_binary_prevalence</span><span class="p">(</span><span class="n">prevs_estims</span><span class="p">,</span> <span class="n">clip_if_necessary</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="k">return</span> <span class="n">prevs_estims</span><span class="o">.</span><span class="n">squeeze</span><span class="p">()</span></div>
<span class="k">def</span><span class="w"> </span><span class="nf">_compute_table</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">y_</span><span class="p">):</span>
<span class="n">TP</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">logical_and</span><span class="p">(</span><span class="n">y</span> <span class="o">==</span> <span class="n">y_</span><span class="p">,</span> <span class="n">y</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">pos_label</span><span class="p">)</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span>
<span class="n">FP</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">logical_and</span><span class="p">(</span><span class="n">y</span> <span class="o">!=</span> <span class="n">y_</span><span class="p">,</span> <span class="n">y</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">neg_label</span><span class="p">)</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span>
<span class="n">FN</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">logical_and</span><span class="p">(</span><span class="n">y</span> <span class="o">!=</span> <span class="n">y_</span><span class="p">,</span> <span class="n">y</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">pos_label</span><span class="p">)</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span>
<span class="n">TN</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">logical_and</span><span class="p">(</span><span class="n">y</span> <span class="o">==</span> <span class="n">y_</span><span class="p">,</span> <span class="n">y</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">neg_label</span><span class="p">)</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span>
<span class="k">return</span> <span class="n">TP</span><span class="p">,</span> <span class="n">FP</span><span class="p">,</span> <span class="n">FN</span><span class="p">,</span> <span class="n">TN</span>
<span class="k">def</span><span class="w"> </span><span class="nf">_compute_tpr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">TP</span><span class="p">,</span> <span class="n">FN</span><span class="p">):</span>
<span class="k">if</span> <span class="n">TP</span> <span class="o">+</span> <span class="n">FN</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="k">return</span> <span class="mi">1</span>
<span class="k">return</span> <span class="n">TP</span> <span class="o">/</span> <span class="p">(</span><span class="n">TP</span> <span class="o">+</span> <span class="n">FN</span><span class="p">)</span>
<span class="k">def</span><span class="w"> </span><span class="nf">_compute_fpr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">FP</span><span class="p">,</span> <span class="n">TN</span><span class="p">):</span>
<span class="k">if</span> <span class="n">FP</span> <span class="o">+</span> <span class="n">TN</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="k">return</span> <span class="mi">0</span>
<span class="k">return</span> <span class="n">FP</span> <span class="o">/</span> <span class="p">(</span><span class="n">FP</span> <span class="o">+</span> <span class="n">TN</span><span class="p">)</span>
<div class="viewcode-block" id="ThresholdOptimization.aggregation_fit">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._threshold_optim.ThresholdOptimization.aggregation_fit">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">aggregation_fit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">classif_predictions</span><span class="p">,</span> <span class="n">labels</span><span class="p">):</span>
<span class="n">decision_scores</span><span class="p">,</span> <span class="n">y</span> <span class="o">=</span> <span class="n">classif_predictions</span><span class="p">,</span> <span class="n">labels</span>
<span class="c1"># the standard behavior is to keep the best threshold only</span>
<span class="bp">self</span><span class="o">.</span><span class="n">tpr</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">fpr</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">threshold</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_eval_candidate_thresholds</span><span class="p">(</span><span class="n">decision_scores</span><span class="p">,</span> <span class="n">y</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
<span class="k">return</span> <span class="bp">self</span></div>
<div class="viewcode-block" id="ThresholdOptimization.aggregate">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._threshold_optim.ThresholdOptimization.aggregate">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">aggregate</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">classif_predictions</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">):</span>
<span class="c1"># the standard behavior is to compute the adjusted count using the best threshold found</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">aggregate_with_threshold</span><span class="p">(</span><span class="n">classif_predictions</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">tpr</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">fpr</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">threshold</span><span class="p">)</span></div>
</div>
<div class="viewcode-block" id="T50">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._threshold_optim.T50">[docs]</a>
<span class="k">class</span><span class="w"> </span><span class="nc">T50</span><span class="p">(</span><span class="n">ThresholdOptimization</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Threshold Optimization variant for :class:`ACC` as proposed by</span>
<span class="sd"> `Forman 2006 &lt;https://dl.acm.org/doi/abs/10.1145/1150402.1150423&gt;`_ and</span>
<span class="sd"> `Forman 2008 &lt;https://link.springer.com/article/10.1007/s10618-008-0097-y&gt;`_ that looks</span>
<span class="sd"> for the threshold that makes `tpr` closest to 0.5.</span>
<span class="sd"> The goal is to bring improved stability to the denominator of the adjustment.</span>
<span class="sd"> :param classifier: a scikit-learn&#39;s BaseEstimator, or None, in which case the classifier is taken to be</span>
<span class="sd"> the one indicated in `qp.environ[&#39;DEFAULT_CLS&#39;]`</span>
<span class="sd"> :param fit_classifier: whether to train the learner (default is True). Set to False if the</span>
<span class="sd"> learner has been trained outside the quantifier.</span>
<span class="sd"> :param val_split: specifies the data used for generating classifier predictions. This specification</span>
<span class="sd"> can be made as float in (0, 1) indicating the proportion of stratified held-out validation set to</span>
<span class="sd"> be extracted from the training set; or as an integer (default 5), indicating that the predictions</span>
<span class="sd"> are to be generated in a `k`-fold cross-validation manner (with this integer indicating the value</span>
<span class="sd"> for `k`); or as a tuple (X,y) defining the specific set of data to use for validation.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">classifier</span><span class="p">:</span> <span class="n">BaseEstimator</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">fit_classifier</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">val_split</span><span class="o">=</span><span class="mi">5</span><span class="p">):</span>
<span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">classifier</span><span class="p">,</span> <span class="n">fit_classifier</span><span class="p">,</span> <span class="n">val_split</span><span class="p">)</span>
<div class="viewcode-block" id="T50.condition">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._threshold_optim.T50.condition">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">condition</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">tpr</span><span class="p">,</span> <span class="n">fpr</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">float</span><span class="p">:</span>
<span class="k">return</span> <span class="nb">abs</span><span class="p">(</span><span class="n">tpr</span> <span class="o">-</span> <span class="mf">0.5</span><span class="p">)</span></div>
</div>
<div class="viewcode-block" id="MAX">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._threshold_optim.MAX">[docs]</a>
<span class="k">class</span><span class="w"> </span><span class="nc">MAX</span><span class="p">(</span><span class="n">ThresholdOptimization</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Threshold Optimization variant for :class:`ACC` as proposed by</span>
<span class="sd"> `Forman 2006 &lt;https://dl.acm.org/doi/abs/10.1145/1150402.1150423&gt;`_ and</span>
<span class="sd"> `Forman 2008 &lt;https://link.springer.com/article/10.1007/s10618-008-0097-y&gt;`_ that looks</span>
<span class="sd"> for the threshold that maximizes `tpr-fpr`.</span>
<span class="sd"> The goal is to bring improved stability to the denominator of the adjustment.</span>
<span class="sd"> :param classifier: a scikit-learn&#39;s BaseEstimator, or None, in which case the classifier is taken to be</span>
<span class="sd"> the one indicated in `qp.environ[&#39;DEFAULT_CLS&#39;]`</span>
<span class="sd"> :param fit_classifier: whether to train the learner (default is True). Set to False if the</span>
<span class="sd"> learner has been trained outside the quantifier.</span>
<span class="sd"> :param val_split: specifies the data used for generating classifier predictions. This specification</span>
<span class="sd"> can be made as float in (0, 1) indicating the proportion of stratified held-out validation set to</span>
<span class="sd"> be extracted from the training set; or as an integer (default 5), indicating that the predictions</span>
<span class="sd"> are to be generated in a `k`-fold cross-validation manner (with this integer indicating the value</span>
<span class="sd"> for `k`); or as a tuple (X,y) defining the specific set of data to use for validation.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">classifier</span><span class="p">:</span> <span class="n">BaseEstimator</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">fit_classifier</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">val_split</span><span class="o">=</span><span class="mi">5</span><span class="p">):</span>
<span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">classifier</span><span class="p">,</span> <span class="n">fit_classifier</span><span class="p">,</span> <span class="n">val_split</span><span class="p">)</span>
<div class="viewcode-block" id="MAX.condition">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._threshold_optim.MAX.condition">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">condition</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">tpr</span><span class="p">,</span> <span class="n">fpr</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">float</span><span class="p">:</span>
<span class="c1"># MAX strives to maximize (tpr - fpr), which is equivalent to minimize (fpr - tpr)</span>
<span class="k">return</span> <span class="p">(</span><span class="n">fpr</span> <span class="o">-</span> <span class="n">tpr</span><span class="p">)</span></div>
</div>
<div class="viewcode-block" id="X">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._threshold_optim.X">[docs]</a>
<span class="k">class</span><span class="w"> </span><span class="nc">X</span><span class="p">(</span><span class="n">ThresholdOptimization</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Threshold Optimization variant for :class:`ACC` as proposed by</span>
<span class="sd"> `Forman 2006 &lt;https://dl.acm.org/doi/abs/10.1145/1150402.1150423&gt;`_ and</span>
<span class="sd"> `Forman 2008 &lt;https://link.springer.com/article/10.1007/s10618-008-0097-y&gt;`_ that looks</span>
<span class="sd"> for the threshold that yields `tpr=1-fpr`.</span>
<span class="sd"> The goal is to bring improved stability to the denominator of the adjustment.</span>
<span class="sd"> :param classifier: a scikit-learn&#39;s BaseEstimator, or None, in which case the classifier is taken to be</span>
<span class="sd"> the one indicated in `qp.environ[&#39;DEFAULT_CLS&#39;]`</span>
<span class="sd"> :param fit_classifier: whether to train the learner (default is True). Set to False if the</span>
<span class="sd"> learner has been trained outside the quantifier.</span>
<span class="sd"> :param val_split: specifies the data used for generating classifier predictions. This specification</span>
<span class="sd"> can be made as float in (0, 1) indicating the proportion of stratified held-out validation set to</span>
<span class="sd"> be extracted from the training set; or as an integer (default 5), indicating that the predictions</span>
<span class="sd"> are to be generated in a `k`-fold cross-validation manner (with this integer indicating the value</span>
<span class="sd"> for `k`); or as a tuple (X,y) defining the specific set of data to use for validation.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">classifier</span><span class="p">:</span> <span class="n">BaseEstimator</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">fit_classifier</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">val_split</span><span class="o">=</span><span class="mi">5</span><span class="p">):</span>
<span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">classifier</span><span class="p">,</span> <span class="n">fit_classifier</span><span class="p">,</span> <span class="n">val_split</span><span class="p">)</span>
<div class="viewcode-block" id="X.condition">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._threshold_optim.X.condition">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">condition</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">tpr</span><span class="p">,</span> <span class="n">fpr</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">float</span><span class="p">:</span>
<span class="k">return</span> <span class="nb">abs</span><span class="p">(</span><span class="mi">1</span> <span class="o">-</span> <span class="p">(</span><span class="n">tpr</span> <span class="o">+</span> <span class="n">fpr</span><span class="p">))</span></div>
</div>
<div class="viewcode-block" id="MS">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._threshold_optim.MS">[docs]</a>
<span class="k">class</span><span class="w"> </span><span class="nc">MS</span><span class="p">(</span><span class="n">ThresholdOptimization</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Median Sweep. Threshold Optimization variant for :class:`ACC` as proposed by</span>
<span class="sd"> `Forman 2006 &lt;https://dl.acm.org/doi/abs/10.1145/1150402.1150423&gt;`_ and</span>
<span class="sd"> `Forman 2008 &lt;https://link.springer.com/article/10.1007/s10618-008-0097-y&gt;`_ that generates</span>
<span class="sd"> class prevalence estimates for all decision thresholds and returns the median of them all.</span>
<span class="sd"> The goal is to bring improved stability to the denominator of the adjustment.</span>
<span class="sd"> :param classifier: a scikit-learn&#39;s BaseEstimator, or None, in which case the classifier is taken to be</span>
<span class="sd"> the one indicated in `qp.environ[&#39;DEFAULT_CLS&#39;]`</span>
<span class="sd"> :param fit_classifier: whether to train the learner (default is True). Set to False if the</span>
<span class="sd"> learner has been trained outside the quantifier.</span>
<span class="sd"> :param val_split: specifies the data used for generating classifier predictions. This specification</span>
<span class="sd"> can be made as float in (0, 1) indicating the proportion of stratified held-out validation set to</span>
<span class="sd"> be extracted from the training set; or as an integer (default 5), indicating that the predictions</span>
<span class="sd"> are to be generated in a `k`-fold cross-validation manner (with this integer indicating the value</span>
<span class="sd"> for `k`); or as a tuple (X,y) defining the specific set of data to use for validation.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">classifier</span><span class="p">:</span> <span class="n">BaseEstimator</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">fit_classifier</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">val_split</span><span class="o">=</span><span class="mi">5</span><span class="p">):</span>
<span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">classifier</span><span class="p">,</span> <span class="n">fit_classifier</span><span class="p">,</span> <span class="n">val_split</span><span class="p">)</span>
<div class="viewcode-block" id="MS.condition">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._threshold_optim.MS.condition">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">condition</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">tpr</span><span class="p">,</span> <span class="n">fpr</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">float</span><span class="p">:</span>
<span class="k">return</span> <span class="mi">1</span></div>
<div class="viewcode-block" id="MS.aggregation_fit">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._threshold_optim.MS.aggregation_fit">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">aggregation_fit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">classif_predictions</span><span class="p">,</span> <span class="n">labels</span><span class="p">):</span>
<span class="n">decision_scores</span><span class="p">,</span> <span class="n">y</span> <span class="o">=</span> <span class="n">classif_predictions</span><span class="p">,</span> <span class="n">labels</span>
<span class="c1"># keeps all candidates</span>
<span class="n">tprs_fprs_thresholds</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_eval_candidate_thresholds</span><span class="p">(</span><span class="n">decision_scores</span><span class="p">,</span> <span class="n">y</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">tprs</span> <span class="o">=</span> <span class="n">tprs_fprs_thresholds</span><span class="p">[:,</span> <span class="mi">0</span><span class="p">]</span>
<span class="bp">self</span><span class="o">.</span><span class="n">fprs</span> <span class="o">=</span> <span class="n">tprs_fprs_thresholds</span><span class="p">[:,</span> <span class="mi">1</span><span class="p">]</span>
<span class="bp">self</span><span class="o">.</span><span class="n">thresholds</span> <span class="o">=</span> <span class="n">tprs_fprs_thresholds</span><span class="p">[:,</span> <span class="mi">2</span><span class="p">]</span>
<span class="k">return</span> <span class="bp">self</span></div>
<div class="viewcode-block" id="MS.aggregate">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._threshold_optim.MS.aggregate">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">aggregate</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">classif_predictions</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">):</span>
<span class="n">prevalences</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">aggregate_with_threshold</span><span class="p">(</span><span class="n">classif_predictions</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">tprs</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">fprs</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">thresholds</span><span class="p">)</span>
<span class="k">if</span> <span class="n">prevalences</span><span class="o">.</span><span class="n">ndim</span><span class="o">==</span><span class="mi">2</span><span class="p">:</span>
<span class="n">prevalences</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">median</span><span class="p">(</span><span class="n">prevalences</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
<span class="k">return</span> <span class="n">prevalences</span></div>
</div>
<div class="viewcode-block" id="MS2">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._threshold_optim.MS2">[docs]</a>
<span class="k">class</span><span class="w"> </span><span class="nc">MS2</span><span class="p">(</span><span class="n">MS</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Median Sweep 2. Threshold Optimization variant for :class:`ACC` as proposed by</span>
<span class="sd"> `Forman 2006 &lt;https://dl.acm.org/doi/abs/10.1145/1150402.1150423&gt;`_ and</span>
<span class="sd"> `Forman 2008 &lt;https://link.springer.com/article/10.1007/s10618-008-0097-y&gt;`_ that generates</span>
<span class="sd"> class prevalence estimates for all decision thresholds and returns the median of for cases in</span>
<span class="sd"> which `tpr-fpr&gt;0.25`</span>
<span class="sd"> The goal is to bring improved stability to the denominator of the adjustment.</span>
<span class="sd"> :param classifier: a scikit-learn&#39;s BaseEstimator, or None, in which case the classifier is taken to be</span>
<span class="sd"> the one indicated in `qp.environ[&#39;DEFAULT_CLS&#39;]`</span>
<span class="sd"> :param fit_classifier: whether to train the learner (default is True). Set to False if the</span>
<span class="sd"> learner has been trained outside the quantifier.</span>
<span class="sd"> :param val_split: specifies the data used for generating classifier predictions. This specification</span>
<span class="sd"> can be made as float in (0, 1) indicating the proportion of stratified held-out validation set to</span>
<span class="sd"> be extracted from the training set; or as an integer (default 5), indicating that the predictions</span>
<span class="sd"> are to be generated in a `k`-fold cross-validation manner (with this integer indicating the value</span>
<span class="sd"> for `k`); or as a tuple (X,y) defining the specific set of data to use for validation.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">classifier</span><span class="p">:</span> <span class="n">BaseEstimator</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">fit_classifier</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">val_split</span><span class="o">=</span><span class="mi">5</span><span class="p">):</span>
<span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">classifier</span><span class="p">,</span> <span class="n">fit_classifier</span><span class="p">,</span> <span class="n">val_split</span><span class="p">)</span>
<div class="viewcode-block" id="MS2.discard">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method._threshold_optim.MS2.discard">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">discard</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">tpr</span><span class="p">,</span> <span class="n">fpr</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">bool</span><span class="p">:</span>
<span class="k">return</span> <span class="p">(</span><span class="n">tpr</span><span class="o">-</span><span class="n">fpr</span><span class="p">)</span> <span class="o">&lt;=</span> <span class="mf">0.25</span></div>
</div>
</pre></div>
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<h1>Source code for quapy.method.base</h1><div class="highlight"><pre>
<span></span><span class="kn">import</span><span class="w"> </span><span class="nn">warnings</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">abc</span><span class="w"> </span><span class="kn">import</span> <span class="n">ABCMeta</span><span class="p">,</span> <span class="n">abstractmethod</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">copy</span><span class="w"> </span><span class="kn">import</span> <span class="n">deepcopy</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">joblib</span><span class="w"> </span><span class="kn">import</span> <span class="n">Parallel</span><span class="p">,</span> <span class="n">delayed</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">sklearn.base</span><span class="w"> </span><span class="kn">import</span> <span class="n">BaseEstimator</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">quapy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">qp</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">quapy.data</span><span class="w"> </span><span class="kn">import</span> <span class="n">LabelledCollection</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
<span class="c1"># Base Quantifier abstract class</span>
<span class="c1"># ------------------------------------</span>
<div class="viewcode-block" id="BaseQuantifier">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method.base.BaseQuantifier">[docs]</a>
<span class="k">class</span><span class="w"> </span><span class="nc">BaseQuantifier</span><span class="p">(</span><span class="n">BaseEstimator</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Abstract Quantifier. A quantifier is defined as an object of a class that implements the method :meth:`fit` on</span>
<span class="sd"> a pair X, y, the method :meth:`predict`, and the :meth:`set_params` and</span>
<span class="sd"> :meth:`get_params` for model selection (see :meth:`quapy.model_selection.GridSearchQ`)</span>
<span class="sd"> &quot;&quot;&quot;</span>
<div class="viewcode-block" id="BaseQuantifier.fit">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method.base.BaseQuantifier.fit">[docs]</a>
<span class="nd">@abstractmethod</span>
<span class="k">def</span><span class="w"> </span><span class="nf">fit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">,</span> <span class="n">y</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Generates a quantifier.</span>
<span class="sd"> :param X: array-like, the training instances</span>
<span class="sd"> :param y: array-like, the labels</span>
<span class="sd"> :return: self</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="o">...</span></div>
<div class="viewcode-block" id="BaseQuantifier.predict">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method.base.BaseQuantifier.predict">[docs]</a>
<span class="nd">@abstractmethod</span>
<span class="k">def</span><span class="w"> </span><span class="nf">predict</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Generate class prevalence estimates for the sample&#39;s instances</span>
<span class="sd"> :param X: array-like, the test instances</span>
<span class="sd"> :return: `np.ndarray` of shape `(n_classes,)` with class prevalence estimates.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="o">...</span></div>
<div class="viewcode-block" id="BaseQuantifier.quantify">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method.base.BaseQuantifier.quantify">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">quantify</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Alias to :meth:`predict`, for old compatibility</span>
<span class="sd"> :param X: array-like</span>
<span class="sd"> :return: `np.ndarray` of shape `(n_classes,)` with class prevalence estimates.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">predict</span><span class="p">(</span><span class="n">X</span><span class="p">)</span></div>
</div>
<div class="viewcode-block" id="BinaryQuantifier">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method.base.BinaryQuantifier">[docs]</a>
<span class="k">class</span><span class="w"> </span><span class="nc">BinaryQuantifier</span><span class="p">(</span><span class="n">BaseQuantifier</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Abstract class of binary quantifiers, i.e., quantifiers estimating class prevalence values for only two classes</span>
<span class="sd"> (typically, to be interpreted as one class and its complement).</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">def</span><span class="w"> </span><span class="nf">_check_binary</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">quantifier_name</span><span class="p">):</span>
<span class="n">n_classes</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">y</span><span class="p">))</span>
<span class="k">assert</span> <span class="n">n_classes</span><span class="o">==</span><span class="mi">2</span><span class="p">,</span> <span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">quantifier_name</span><span class="si">}</span><span class="s1"> works only on problems of binary classification. &#39;</span> \
<span class="sa">f</span><span class="s1">&#39;Use the class OneVsAll to enable </span><span class="si">{</span><span class="n">quantifier_name</span><span class="si">}</span><span class="s1"> work on single-label data.&#39;</span></div>
<div class="viewcode-block" id="OneVsAll">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method.base.OneVsAll">[docs]</a>
<span class="k">class</span><span class="w"> </span><span class="nc">OneVsAll</span><span class="p">:</span>
<span class="k">pass</span></div>
<div class="viewcode-block" id="newOneVsAll">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method.base.newOneVsAll">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">newOneVsAll</span><span class="p">(</span><span class="n">binary_quantifier</span><span class="p">:</span> <span class="n">BaseQuantifier</span><span class="p">,</span> <span class="n">n_jobs</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<span class="k">assert</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">binary_quantifier</span><span class="p">,</span> <span class="n">BaseQuantifier</span><span class="p">),</span> \
<span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">binary_quantifier</span><span class="si">}</span><span class="s1"> does not seem to be a Quantifier&#39;</span>
<span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">binary_quantifier</span><span class="p">,</span> <span class="n">qp</span><span class="o">.</span><span class="n">method</span><span class="o">.</span><span class="n">aggregative</span><span class="o">.</span><span class="n">AggregativeQuantifier</span><span class="p">):</span>
<span class="k">return</span> <span class="n">qp</span><span class="o">.</span><span class="n">method</span><span class="o">.</span><span class="n">aggregative</span><span class="o">.</span><span class="n">OneVsAllAggregative</span><span class="p">(</span><span class="n">binary_quantifier</span><span class="p">,</span> <span class="n">n_jobs</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="n">OneVsAllGeneric</span><span class="p">(</span><span class="n">binary_quantifier</span><span class="p">,</span> <span class="n">n_jobs</span><span class="p">)</span></div>
<div class="viewcode-block" id="OneVsAllGeneric">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method.base.OneVsAllGeneric">[docs]</a>
<span class="k">class</span><span class="w"> </span><span class="nc">OneVsAllGeneric</span><span class="p">(</span><span class="n">OneVsAll</span><span class="p">,</span> <span class="n">BaseQuantifier</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Allows any binary quantifier to perform quantification on single-label datasets. The method maintains one binary</span>
<span class="sd"> quantifier for each class, and then l1-normalizes the outputs so that the class prevalence values sum up to 1.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">binary_quantifier</span><span class="p">:</span> <span class="n">BaseQuantifier</span><span class="p">,</span> <span class="n">n_jobs</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<span class="k">assert</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">binary_quantifier</span><span class="p">,</span> <span class="n">BaseQuantifier</span><span class="p">),</span> \
<span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">binary_quantifier</span><span class="si">}</span><span class="s1"> does not seem to be a Quantifier&#39;</span>
<span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">binary_quantifier</span><span class="p">,</span> <span class="n">qp</span><span class="o">.</span><span class="n">method</span><span class="o">.</span><span class="n">aggregative</span><span class="o">.</span><span class="n">AggregativeQuantifier</span><span class="p">):</span>
<span class="n">warnings</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span><span class="s1">&#39;the quantifier seems to be an instance of qp.method.aggregative.AggregativeQuantifier; &#39;</span>
<span class="sa">f</span><span class="s1">&#39;you might prefer instantiating </span><span class="si">{</span><span class="n">qp</span><span class="o">.</span><span class="n">method</span><span class="o">.</span><span class="n">aggregative</span><span class="o">.</span><span class="n">OneVsAllAggregative</span><span class="o">.</span><span class="vm">__name__</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">binary_quantifier</span> <span class="o">=</span> <span class="n">binary_quantifier</span>
<span class="bp">self</span><span class="o">.</span><span class="n">n_jobs</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">_get_njobs</span><span class="p">(</span><span class="n">n_jobs</span><span class="p">)</span>
<div class="viewcode-block" id="OneVsAllGeneric.fit">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method.base.OneVsAllGeneric.fit">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">fit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">,</span> <span class="n">y</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">classes</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">unique</span><span class="p">(</span><span class="n">y</span><span class="p">))</span>
<span class="k">assert</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">classes</span><span class="p">)</span><span class="o">!=</span><span class="mi">2</span><span class="p">,</span> <span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="si">}</span><span class="s1"> expect non-binary data&#39;</span>
<span class="bp">self</span><span class="o">.</span><span class="n">dict_binary_quantifiers</span> <span class="o">=</span> <span class="p">{</span><span class="n">c</span><span class="p">:</span> <span class="n">deepcopy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">binary_quantifier</span><span class="p">)</span> <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">classes</span><span class="p">}</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_parallel</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_delayed_binary_fit</span><span class="p">,</span> <span class="n">X</span><span class="p">,</span> <span class="n">y</span><span class="p">)</span>
<span class="k">return</span> <span class="bp">self</span></div>
<span class="k">def</span><span class="w"> </span><span class="nf">_parallel</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">func</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
<span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span>
<span class="n">Parallel</span><span class="p">(</span><span class="n">n_jobs</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">n_jobs</span><span class="p">,</span> <span class="n">backend</span><span class="o">=</span><span class="s1">&#39;threading&#39;</span><span class="p">)(</span>
<span class="n">delayed</span><span class="p">(</span><span class="n">func</span><span class="p">)(</span><span class="n">c</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span> <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">classes</span>
<span class="p">)</span>
<span class="p">)</span>
<div class="viewcode-block" id="OneVsAllGeneric.predict">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method.base.OneVsAllGeneric.predict">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">predict</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">):</span>
<span class="n">prevalences</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_parallel</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_delayed_binary_predict</span><span class="p">,</span> <span class="n">X</span><span class="p">)</span>
<span class="k">return</span> <span class="n">qp</span><span class="o">.</span><span class="n">functional</span><span class="o">.</span><span class="n">normalize_prevalence</span><span class="p">(</span><span class="n">prevalences</span><span class="p">)</span></div>
<span class="c1"># @property</span>
<span class="c1"># def classes_(self):</span>
<span class="c1"># return sorted(self.dict_binary_quantifiers.keys())</span>
<span class="k">def</span><span class="w"> </span><span class="nf">_delayed_binary_predict</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">c</span><span class="p">,</span> <span class="n">X</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">dict_binary_quantifiers</span><span class="p">[</span><span class="n">c</span><span class="p">]</span><span class="o">.</span><span class="n">predict</span><span class="p">(</span><span class="n">X</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span>
<span class="k">def</span><span class="w"> </span><span class="nf">_delayed_binary_fit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">c</span><span class="p">,</span> <span class="n">X</span><span class="p">,</span> <span class="n">y</span><span class="p">):</span>
<span class="n">bindata</span> <span class="o">=</span> <span class="n">LabelledCollection</span><span class="p">(</span><span class="n">X</span><span class="p">,</span> <span class="n">y</span> <span class="o">==</span> <span class="n">c</span><span class="p">,</span> <span class="n">classes</span><span class="o">=</span><span class="p">[</span><span class="kc">False</span><span class="p">,</span> <span class="kc">True</span><span class="p">])</span>
<span class="bp">self</span><span class="o">.</span><span class="n">dict_binary_quantifiers</span><span class="p">[</span><span class="n">c</span><span class="p">]</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="o">*</span><span class="n">bindata</span><span class="o">.</span><span class="n">Xy</span><span class="p">)</span></div>
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<h1>Source code for quapy.method.non_aggregative</h1><div class="highlight"><pre>
<span></span><span class="kn">from</span><span class="w"> </span><span class="nn">itertools</span><span class="w"> </span><span class="kn">import</span> <span class="n">product</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">tqdm</span><span class="w"> </span><span class="kn">import</span> <span class="n">tqdm</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">typing</span><span class="w"> </span><span class="kn">import</span> <span class="n">Union</span><span class="p">,</span> <span class="n">Callable</span><span class="p">,</span> <span class="n">Counter</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">sklearn.feature_extraction.text</span><span class="w"> </span><span class="kn">import</span> <span class="n">CountVectorizer</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">sklearn.utils</span><span class="w"> </span><span class="kn">import</span> <span class="n">resample</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">sklearn.preprocessing</span><span class="w"> </span><span class="kn">import</span> <span class="n">normalize</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">quapy.method.confidence</span><span class="w"> </span><span class="kn">import</span> <span class="n">WithConfidenceABC</span><span class="p">,</span> <span class="n">ConfidenceRegionABC</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">quapy.functional</span><span class="w"> </span><span class="kn">import</span> <span class="n">get_divergence</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">quapy.method.base</span><span class="w"> </span><span class="kn">import</span> <span class="n">BaseQuantifier</span><span class="p">,</span> <span class="n">BinaryQuantifier</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">quapy.method._helper</span><span class="w"> </span><span class="kn">import</span> <span class="n">_labels_to_indices</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">quapy.method._energy</span><span class="w"> </span><span class="kn">import</span> <span class="n">_EnergyDistanceCore</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">quapy.functional</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">F</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">scipy.optimize</span><span class="w"> </span><span class="kn">import</span> <span class="n">lsq_linear</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">scipy</span><span class="w"> </span><span class="kn">import</span> <span class="n">sparse</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">quapy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">qp</span>
<div class="viewcode-block" id="MaximumLikelihoodPrevalenceEstimation">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method.non_aggregative.MaximumLikelihoodPrevalenceEstimation">[docs]</a>
<span class="k">class</span><span class="w"> </span><span class="nc">MaximumLikelihoodPrevalenceEstimation</span><span class="p">(</span><span class="n">BaseQuantifier</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> The `Maximum Likelihood Prevalence Estimation` (MLPE) method is a lazy method that assumes there is no prior</span>
<span class="sd"> probability shift between training and test instances (put it other way, that the i.i.d. assumpion holds).</span>
<span class="sd"> The estimation of class prevalence values for any test sample is always (i.e., irrespective of the test sample</span>
<span class="sd"> itself) the class prevalence seen during training. This method is considered to be a lower-bound quantifier that</span>
<span class="sd"> any quantification method should beat.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_classes_</span> <span class="o">=</span> <span class="kc">None</span>
<div class="viewcode-block" id="MaximumLikelihoodPrevalenceEstimation.fit">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method.non_aggregative.MaximumLikelihoodPrevalenceEstimation.fit">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">fit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">,</span> <span class="n">y</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Computes the training prevalence and stores it.</span>
<span class="sd"> :param X: array-like of shape `(n_samples, n_features)`, the training instances</span>
<span class="sd"> :param y: array-like of shape `(n_samples,)`, the labels</span>
<span class="sd"> :return: self</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_classes_</span> <span class="o">=</span> <span class="n">F</span><span class="o">.</span><span class="n">classes_from_labels</span><span class="p">(</span><span class="n">labels</span><span class="o">=</span><span class="n">y</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">estimated_prevalence</span> <span class="o">=</span> <span class="n">F</span><span class="o">.</span><span class="n">prevalence_from_labels</span><span class="p">(</span><span class="n">y</span><span class="p">,</span> <span class="n">classes</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">_classes_</span><span class="p">)</span>
<span class="k">return</span> <span class="bp">self</span></div>
<div class="viewcode-block" id="MaximumLikelihoodPrevalenceEstimation.predict">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method.non_aggregative.MaximumLikelihoodPrevalenceEstimation.predict">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">predict</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Ignores the input instances and returns, as the class prevalence estimantes, the training prevalence.</span>
<span class="sd"> :param X: array-like (ignored)</span>
<span class="sd"> :return: the class prevalence seen during training</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">estimated_prevalence</span></div>
</div>
<div class="viewcode-block" id="DMx">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method.non_aggregative.DMx">[docs]</a>
<span class="k">class</span><span class="w"> </span><span class="nc">DMx</span><span class="p">(</span><span class="n">BaseQuantifier</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Generic Distribution Matching quantifier for binary or multiclass quantification based on the space of covariates.</span>
<span class="sd"> This implementation takes the number of bins, the divergence, and the possibility to work on CDF as hyperparameters.</span>
<span class="sd"> :param nbins: number of bins used to discretize the distributions (default 8)</span>
<span class="sd"> :param divergence: a string representing a divergence measure (currently, &quot;HD&quot; and &quot;topsoe&quot; are implemented)</span>
<span class="sd"> or a callable function taking two ndarrays of the same dimension as input (default &quot;HD&quot;, meaning Hellinger</span>
<span class="sd"> Distance)</span>
<span class="sd"> :param cdf: whether to use CDF instead of PDF (default False)</span>
<span class="sd"> :param search: string indicating the search strategy used to estimate the prevalence values.</span>
<span class="sd"> Valid options are `optim_minimize` (default, works for binary and multiclass problems),</span>
<span class="sd"> `linear_search` (binary only), and `ternary_search` (binary only)</span>
<span class="sd"> :param n_jobs: number of parallel workers (default None)</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">nbins</span><span class="o">=</span><span class="mi">8</span><span class="p">,</span> <span class="n">divergence</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Callable</span><span class="p">]</span><span class="o">=</span><span class="s1">&#39;HD&#39;</span><span class="p">,</span> <span class="n">cdf</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">search</span><span class="o">=</span><span class="s1">&#39;optim_minimize&#39;</span><span class="p">,</span> <span class="n">n_jobs</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">nbins</span> <span class="o">=</span> <span class="n">nbins</span>
<span class="bp">self</span><span class="o">.</span><span class="n">divergence</span> <span class="o">=</span> <span class="n">divergence</span>
<span class="bp">self</span><span class="o">.</span><span class="n">cdf</span> <span class="o">=</span> <span class="n">cdf</span>
<span class="bp">self</span><span class="o">.</span><span class="n">search</span> <span class="o">=</span> <span class="n">search</span>
<span class="bp">self</span><span class="o">.</span><span class="n">n_jobs</span> <span class="o">=</span> <span class="n">n_jobs</span>
<div class="viewcode-block" id="DMx.HDx">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method.non_aggregative.DMx.HDx">[docs]</a>
<span class="nd">@classmethod</span>
<span class="k">def</span><span class="w"> </span><span class="nf">HDx</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">n_jobs</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> `Hellinger Distance x &lt;https://www.sciencedirect.com/science/article/pii/S0020025512004069&gt;`_ (HDx).</span>
<span class="sd"> HDx is a method for training binary quantifiers, that models quantification as the problem of</span>
<span class="sd"> minimizing the average divergence (in terms of the Hellinger Distance) across the feature-specific normalized</span>
<span class="sd"> histograms of two representations, one for the unlabelled examples, and another generated from the training</span>
<span class="sd"> examples as a mixture model of the class-specific representations. The parameters of the mixture thus represent</span>
<span class="sd"> the estimates of the class prevalence values.</span>
<span class="sd"> The method computes all matchings for nbins in [10, 20, ..., 110] and reports the mean of the median.</span>
<span class="sd"> The best prevalence is searched via linear search, from 0 to 1 stepping by 0.01.</span>
<span class="sd"> :param n_jobs: number of parallel workers</span>
<span class="sd"> :return: an instance of this class setup to mimick the performance of the HDx as originally proposed by</span>
<span class="sd"> González-Castro, Alaiz-Rodríguez, Alegre (2013)</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">quapy.method.meta</span><span class="w"> </span><span class="kn">import</span> <span class="n">MedianEstimator</span>
<span class="n">dmx</span> <span class="o">=</span> <span class="n">DMx</span><span class="p">(</span><span class="n">divergence</span><span class="o">=</span><span class="s1">&#39;HD&#39;</span><span class="p">,</span> <span class="n">cdf</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">search</span><span class="o">=</span><span class="s1">&#39;linear_search&#39;</span><span class="p">)</span>
<span class="n">nbins</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;nbins&#39;</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">linspace</span><span class="p">(</span><span class="mi">10</span><span class="p">,</span> <span class="mi">110</span><span class="p">,</span> <span class="mi">11</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="nb">int</span><span class="p">)}</span>
<span class="n">hdx</span> <span class="o">=</span> <span class="n">MedianEstimator</span><span class="p">(</span><span class="n">base_quantifier</span><span class="o">=</span><span class="n">dmx</span><span class="p">,</span> <span class="n">param_grid</span><span class="o">=</span><span class="n">nbins</span><span class="p">,</span> <span class="n">n_jobs</span><span class="o">=</span><span class="n">n_jobs</span><span class="p">)</span>
<span class="k">return</span> <span class="n">hdx</span></div>
<span class="k">def</span><span class="w"> </span><span class="nf">__get_distributions</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">):</span>
<span class="n">histograms</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">feat_idx</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">nfeats</span><span class="p">):</span>
<span class="n">feature</span> <span class="o">=</span> <span class="n">X</span><span class="p">[:,</span> <span class="n">feat_idx</span><span class="p">]</span>
<span class="n">feat_range</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">feat_ranges</span><span class="p">[</span><span class="n">feat_idx</span><span class="p">]</span>
<span class="n">hist</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">histogram</span><span class="p">(</span><span class="n">feature</span><span class="p">,</span> <span class="n">bins</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">nbins</span><span class="p">,</span> <span class="nb">range</span><span class="o">=</span><span class="n">feat_range</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
<span class="n">norm_hist</span> <span class="o">=</span> <span class="n">hist</span> <span class="o">/</span> <span class="n">hist</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span>
<span class="n">histograms</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">norm_hist</span><span class="p">)</span>
<span class="n">distributions</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">vstack</span><span class="p">(</span><span class="n">histograms</span><span class="p">)</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">cdf</span><span class="p">:</span>
<span class="n">distributions</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">cumsum</span><span class="p">(</span><span class="n">distributions</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="k">return</span> <span class="n">distributions</span>
<div class="viewcode-block" id="DMx.fit">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method.non_aggregative.DMx.fit">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">fit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">,</span> <span class="n">y</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Generates the validation distributions out of the training data (covariates).</span>
<span class="sd"> The validation distributions have shape `(n, nfeats, nbins)`, with `n` the number of classes, `nfeats`</span>
<span class="sd"> the number of features, and `nbins` the number of bins.</span>
<span class="sd"> In particular, let `V` be the validation distributions; then `di=V[i]` are the distributions obtained from</span>
<span class="sd"> training data labelled with class `i`; while `dij = di[j]` is the discrete distribution for feature j in</span>
<span class="sd"> training data labelled with class `i`, and `dij[k]` is the fraction of instances with a value in the `k`-th bin.</span>
<span class="sd"> :param X: array-like of shape `(n_samples, n_features)`, the training instances</span>
<span class="sd"> :param y: array-like of shape `(n_samples,)`, the labels</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="bp">self</span><span class="o">.</span><span class="n">nfeats</span> <span class="o">=</span> <span class="n">X</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
<span class="bp">self</span><span class="o">.</span><span class="n">feat_ranges</span> <span class="o">=</span> <span class="n">_get_features_range</span><span class="p">(</span><span class="n">X</span><span class="p">)</span>
<span class="n">classes</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">unique</span><span class="p">(</span><span class="n">y</span><span class="p">)</span>
<span class="n">y</span> <span class="o">=</span> <span class="n">_labels_to_indices</span><span class="p">(</span><span class="n">y</span><span class="p">,</span> <span class="n">classes</span><span class="p">)</span>
<span class="n">n_classes</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">classes</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">validation_distribution</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span>
<span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">__get_distributions</span><span class="p">(</span><span class="n">X</span><span class="p">[</span><span class="n">y</span><span class="o">==</span><span class="n">cat</span><span class="p">])</span> <span class="k">for</span> <span class="n">cat</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">n_classes</span><span class="p">)]</span>
<span class="p">)</span>
<span class="k">return</span> <span class="bp">self</span></div>
<div class="viewcode-block" id="DMx.predict">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method.non_aggregative.DMx.predict">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">predict</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Searches for the mixture model parameter (the sought prevalence values) that yields a validation distribution</span>
<span class="sd"> (the mixture) that best matches the test distribution, in terms of the divergence measure of choice.</span>
<span class="sd"> The matching is computed as the average dissimilarity (in terms of the dissimilarity measure of choice)</span>
<span class="sd"> between all feature-specific discrete distributions.</span>
<span class="sd"> :param X: instances in the sample</span>
<span class="sd"> :return: a vector of class prevalence estimates</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">assert</span> <span class="n">X</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">nfeats</span><span class="p">,</span> <span class="sa">f</span><span class="s1">&#39;wrong shape; expected </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">nfeats</span><span class="si">}</span><span class="s1">, found </span><span class="si">{</span><span class="n">X</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="si">}</span><span class="s1">&#39;</span>
<span class="n">test_distribution</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">__get_distributions</span><span class="p">(</span><span class="n">X</span><span class="p">)</span>
<span class="n">divergence</span> <span class="o">=</span> <span class="n">get_divergence</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">divergence</span><span class="p">)</span>
<span class="n">n_classes</span><span class="p">,</span> <span class="n">n_feats</span><span class="p">,</span> <span class="n">nbins</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">validation_distribution</span><span class="o">.</span><span class="n">shape</span>
<span class="k">def</span><span class="w"> </span><span class="nf">loss</span><span class="p">(</span><span class="n">prev</span><span class="p">):</span>
<span class="n">prev</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">expand_dims</span><span class="p">(</span><span class="n">prev</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
<span class="n">mixture_distribution</span> <span class="o">=</span> <span class="p">(</span><span class="n">prev</span> <span class="o">@</span> <span class="bp">self</span><span class="o">.</span><span class="n">validation_distribution</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="n">n_classes</span><span class="p">,</span><span class="o">-</span><span class="mi">1</span><span class="p">))</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="n">n_feats</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">)</span>
<span class="n">divs</span> <span class="o">=</span> <span class="p">[</span><span class="n">divergence</span><span class="p">(</span><span class="n">test_distribution</span><span class="p">[</span><span class="n">feat</span><span class="p">],</span> <span class="n">mixture_distribution</span><span class="p">[</span><span class="n">feat</span><span class="p">])</span> <span class="k">for</span> <span class="n">feat</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">n_feats</span><span class="p">)]</span>
<span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">divs</span><span class="p">)</span>
<span class="k">return</span> <span class="n">F</span><span class="o">.</span><span class="n">argmin_prevalence</span><span class="p">(</span><span class="n">loss</span><span class="p">,</span> <span class="n">n_classes</span><span class="p">,</span> <span class="n">method</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">search</span><span class="p">)</span></div>
</div>
<div class="viewcode-block" id="EDx">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method.non_aggregative.EDx">[docs]</a>
<span class="k">class</span><span class="w"> </span><span class="nc">EDx</span><span class="p">(</span><span class="n">_EnergyDistanceCore</span><span class="p">,</span> <span class="n">BaseQuantifier</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Energy Distance x (EDx), a covariate-space distribution-matching</span>
<span class="sd"> quantifier based on energy distance.</span>
<span class="sd"> EDx is the classifier-free counterpart of :class:`quapy.method.aggregative.EDy`.</span>
<span class="sd"> Instead of representing each class through posterior-probability vectors, it</span>
<span class="sd"> represents each class by the cloud of raw feature vectors observed in the</span>
<span class="sd"> training set and estimates the test prevalence vector by solving the same</span>
<span class="sd"> energy-distance quadratic program directly in feature space.</span>
<span class="sd"> This implementation works for binary and multiclass single-label</span>
<span class="sd"> quantification and relies on the optional ``quadprog`` dependency. The</span>
<span class="sd"> current QuaPy adaptation shares its numerical core with EDy and keeps</span>
<span class="sd"> credit to the original implementation available in</span>
<span class="sd"> `quantificationlib &lt;https://github.com/AICGijon/quantificationlib&gt;`_.</span>
<span class="sd"> The formulation follows the same references as EDy, namely:</span>
<span class="sd"> * Alberto Castaño, Laura Morán-Fernández, Jaime Alonso,</span>
<span class="sd"> Verónica Bolón-Canedo, Amparo Alonso-Betanzos, and Juan José del Coz.</span>
<span class="sd"> *An analysis of quantification methods based on matching distributions*.</span>
<span class="sd"> * Hideko Kawakubo, Marthinus Christoffel du Plessis, and Masashi Sugiyama</span>
<span class="sd"> (2016). *Computationally efficient class-prior estimation under class</span>
<span class="sd"> balance change using energy distance*. IEICE Transactions on Information</span>
<span class="sd"> and Systems, 99(1):176-186.</span>
<span class="sd"> :param distance: distance used to compare feature vectors. Valid string</span>
<span class="sd"> aliases are ``&#39;manhattan&#39;`` (default) and ``&#39;euclidean&#39;``; a custom</span>
<span class="sd"> callable compatible with pairwise-distance signatures can also be used</span>
<span class="sd"> :param n_jobs: number of parallel workers (default ``None``, meaning the</span>
<span class="sd"> value is taken from the environment)</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">distance</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Callable</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;manhattan&#39;</span><span class="p">,</span> <span class="n">n_jobs</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">distance</span> <span class="o">=</span> <span class="n">distance</span>
<span class="bp">self</span><span class="o">.</span><span class="n">n_jobs</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">_get_njobs</span><span class="p">(</span><span class="n">n_jobs</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">classes_</span> <span class="o">=</span> <span class="kc">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">n_features_in_</span> <span class="o">=</span> <span class="kc">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">train_distrib_</span> <span class="o">=</span> <span class="kc">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">train_n_cls_i_</span> <span class="o">=</span> <span class="kc">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">K_</span> <span class="o">=</span> <span class="kc">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">G_</span> <span class="o">=</span> <span class="kc">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">C_</span> <span class="o">=</span> <span class="kc">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">b_</span> <span class="o">=</span> <span class="kc">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">a_</span> <span class="o">=</span> <span class="kc">None</span>
<div class="viewcode-block" id="EDx.fit">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method.non_aggregative.EDx.fit">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">fit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">,</span> <span class="n">y</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Fit class-conditional feature-space distributions from training data.&quot;&quot;&quot;</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_check_ed_init_parameters</span><span class="p">()</span>
<span class="n">labels</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">y</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">classes_</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">unique</span><span class="p">(</span><span class="n">labels</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">n_features_in_</span> <span class="o">=</span> <span class="n">X</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
<span class="n">train_distrib</span> <span class="o">=</span> <span class="p">[</span><span class="n">X</span><span class="p">[</span><span class="n">labels</span> <span class="o">==</span> <span class="n">class_</span><span class="p">]</span> <span class="k">for</span> <span class="n">class_</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">classes_</span><span class="p">]</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_fit_energy_model</span><span class="p">(</span><span class="n">train_distrib</span><span class="p">)</span></div>
<div class="viewcode-block" id="EDx.predict">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method.non_aggregative.EDx.predict">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">predict</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Estimate class prevalences for a test sample of raw instances.&quot;&quot;&quot;</span>
<span class="k">assert</span> <span class="n">X</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">n_features_in_</span><span class="p">,</span> <span class="p">(</span>
<span class="sa">f</span><span class="s1">&#39;wrong shape; expected </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">n_features_in_</span><span class="si">}</span><span class="s1">, found </span><span class="si">{</span><span class="n">X</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="si">}</span><span class="s1">&#39;</span>
<span class="p">)</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_predict_energy</span><span class="p">(</span><span class="n">X</span><span class="p">)</span></div>
</div>
<div class="viewcode-block" id="ReadMe">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method.non_aggregative.ReadMe">[docs]</a>
<span class="k">class</span><span class="w"> </span><span class="nc">ReadMe</span><span class="p">(</span><span class="n">BaseQuantifier</span><span class="p">,</span> <span class="n">WithConfidenceABC</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> ReadMe is a non-aggregative quantification system proposed by</span>
<span class="sd"> `Daniel Hopkins and Gary King, 2007. A method of automated nonparametric content analysis for</span>
<span class="sd"> social science. American Journal of Political Science, 54(1):229–247.</span>
<span class="sd"> &lt;https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1540-5907.2009.00428.x&gt;`_.</span>
<span class="sd"> The idea is to estimate `Q(Y=i)` directly from:</span>
<span class="sd"> :math:`Q(X)=\\sum_{i=1} Q(X|Y=i) Q(Y=i)`</span>
<span class="sd"> via least-squares regression, i.e., without incurring the cost of computing posterior probabilities.</span>
<span class="sd"> However, this poses a very difficult representation in which the vector `Q(X)` and the matrix `Q(X|Y=i)`</span>
<span class="sd"> can be of very high dimensions. In order to render the problem tracktable, ReadMe performs bagging in</span>
<span class="sd"> the feature space. ReadMe also combines bagging with bootstrap in order to derive confidence intervals</span>
<span class="sd"> around point estimations.</span>
<span class="sd"> We use the same default parameters as in the official</span>
<span class="sd"> `R implementation &lt;https://github.com/iqss-research/ReadMeV1/blob/master/R/prototype.R&gt;`_.</span>
<span class="sd"> :param prob_model: str (&#39;naive&#39;, or &#39;full&#39;), selects the modality in which the probabilities `Q(X)` and</span>
<span class="sd"> `Q(X|Y)` are to be modelled. Options include &quot;full&quot;, which corresponds to the original formulation of</span>
<span class="sd"> ReadMe, in which X is constrained to be a binary matrix (e.g., of term presence/absence) and in which</span>
<span class="sd"> `Q(X)` and `Q(X|Y)` are modelled, respectively, as matrices of `(2^K, 1)` and `(2^K, n)` values, where</span>
<span class="sd"> `K` is the number of columns in the data matrix (i.e., `bagging_range`), and `n` is the number of classes.</span>
<span class="sd"> Of course, this approach is computationally prohibited for large `K`, so the authors advised against computing it</span>
<span class="sd"> for matrices with `K&gt;25` (although we recommend even smaller values of `K`). A much faster model is &quot;naive&quot;, which</span>
<span class="sd"> considers the `Q(X)` and `Q(X|Y)` be multinomial distributions under the `bag-of-words` perspective. In this</span>
<span class="sd"> case, `bagging_range` can be set to much larger values. Default is &quot;full&quot; (i.e., original ReadMe behavior).</span>
<span class="sd"> :param bootstrap_trials: int, number of bootstrap trials (default 300)</span>
<span class="sd"> :param bagging_trials: int, number of bagging trials (default 300)</span>
<span class="sd"> :param bagging_range: int, number of features to keep for each bagging trial (default 15)</span>
<span class="sd"> :param confidence_level: float, a value in (0,1) reflecting the desired confidence level (default 0.95)</span>
<span class="sd"> :param region: str in &#39;intervals&#39;, &#39;ellipse&#39;, &#39;ellipse-clr&#39;; indicates the preferred method for</span>
<span class="sd"> defining the confidence region (see :class:`WithConfidenceABC`)</span>
<span class="sd"> :param bonferroni: bool (default False), whether to apply Bonferroni correction when</span>
<span class="sd"> `region=&#39;intervals&#39;`. This parameter has no effect for ellipse-based regions.</span>
<span class="sd"> :param random_state: int or None, allows replicability (default None)</span>
<span class="sd"> :param verbose: bool, whether to display information during the process (default False)</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">MAX_FEATURES_FOR_EMPIRICAL_ESTIMATION</span> <span class="o">=</span> <span class="mi">25</span>
<span class="n">PROBABILISTIC_MODELS</span> <span class="o">=</span> <span class="p">[</span><span class="s2">&quot;naive&quot;</span><span class="p">,</span> <span class="s2">&quot;full&quot;</span><span class="p">]</span>
<span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span>
<span class="n">prob_model</span><span class="o">=</span><span class="s2">&quot;full&quot;</span><span class="p">,</span>
<span class="n">bootstrap_trials</span><span class="o">=</span><span class="mi">300</span><span class="p">,</span>
<span class="n">bagging_trials</span><span class="o">=</span><span class="mi">300</span><span class="p">,</span>
<span class="n">bagging_range</span><span class="o">=</span><span class="mi">15</span><span class="p">,</span>
<span class="n">confidence_level</span><span class="o">=</span><span class="mf">0.95</span><span class="p">,</span>
<span class="n">region</span><span class="o">=</span><span class="s1">&#39;intervals&#39;</span><span class="p">,</span>
<span class="n">bonferroni</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
<span class="n">random_state</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
<span class="n">verbose</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
<span class="k">assert</span> <span class="n">prob_model</span> <span class="ow">in</span> <span class="n">ReadMe</span><span class="o">.</span><span class="n">PROBABILISTIC_MODELS</span><span class="p">,</span> \
<span class="sa">f</span><span class="s1">&#39;unknown </span><span class="si">{</span><span class="n">prob_model</span><span class="si">=}</span><span class="s1">, valid ones are </span><span class="si">{</span><span class="n">ReadMe</span><span class="o">.</span><span class="n">PROBABILISTIC_MODELS</span><span class="si">=}</span><span class="s1">&#39;</span>
<span class="bp">self</span><span class="o">.</span><span class="n">prob_model</span> <span class="o">=</span> <span class="n">prob_model</span>
<span class="bp">self</span><span class="o">.</span><span class="n">bootstrap_trials</span> <span class="o">=</span> <span class="n">bootstrap_trials</span>
<span class="bp">self</span><span class="o">.</span><span class="n">bagging_trials</span> <span class="o">=</span> <span class="n">bagging_trials</span>
<span class="bp">self</span><span class="o">.</span><span class="n">bagging_range</span> <span class="o">=</span> <span class="n">bagging_range</span>
<span class="bp">self</span><span class="o">.</span><span class="n">confidence_level</span> <span class="o">=</span> <span class="n">confidence_level</span>
<span class="bp">self</span><span class="o">.</span><span class="n">region</span> <span class="o">=</span> <span class="n">region</span>
<span class="bp">self</span><span class="o">.</span><span class="n">bonferroni</span> <span class="o">=</span> <span class="n">bonferroni</span>
<span class="bp">self</span><span class="o">.</span><span class="n">random_state</span> <span class="o">=</span> <span class="n">random_state</span>
<span class="bp">self</span><span class="o">.</span><span class="n">verbose</span> <span class="o">=</span> <span class="n">verbose</span>
<div class="viewcode-block" id="ReadMe.fit">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method.non_aggregative.ReadMe.fit">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">fit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">,</span> <span class="n">y</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_check_matrix</span><span class="p">(</span><span class="n">X</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">rng</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">default_rng</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">random_state</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">classes_</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">unique</span><span class="p">(</span><span class="n">y</span><span class="p">)</span>
<span class="n">Xsize</span> <span class="o">=</span> <span class="n">X</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
<span class="c1"># Bootstrap loop</span>
<span class="bp">self</span><span class="o">.</span><span class="n">Xboots</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">yboots</span> <span class="o">=</span> <span class="p">[],</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bootstrap_trials</span><span class="p">):</span>
<span class="n">idx</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">rng</span><span class="o">.</span><span class="n">choice</span><span class="p">(</span><span class="n">Xsize</span><span class="p">,</span> <span class="n">size</span><span class="o">=</span><span class="n">Xsize</span><span class="p">,</span> <span class="n">replace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">Xboots</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">X</span><span class="p">[</span><span class="n">idx</span><span class="p">])</span>
<span class="bp">self</span><span class="o">.</span><span class="n">yboots</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">y</span><span class="p">[</span><span class="n">idx</span><span class="p">])</span>
<span class="k">return</span> <span class="bp">self</span></div>
<div class="viewcode-block" id="ReadMe.predict_conf">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method.non_aggregative.ReadMe.predict_conf">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">predict_conf</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">,</span> <span class="n">confidence_level</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span> <span class="n">ConfidenceRegionABC</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_check_matrix</span><span class="p">(</span><span class="n">X</span><span class="p">)</span>
<span class="k">if</span> <span class="n">confidence_level</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="n">confidence_level</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">confidence_level</span>
<span class="n">n_features</span> <span class="o">=</span> <span class="n">X</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
<span class="n">boots_prevalences</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">Xboots</span><span class="p">,</span> <span class="n">yboots</span> <span class="ow">in</span> <span class="n">tqdm</span><span class="p">(</span>
<span class="nb">zip</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">Xboots</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">yboots</span><span class="p">),</span>
<span class="n">desc</span><span class="o">=</span><span class="s1">&#39;bootstrap predictions&#39;</span><span class="p">,</span> <span class="n">total</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">bootstrap_trials</span><span class="p">,</span> <span class="n">disable</span><span class="o">=</span><span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">verbose</span>
<span class="p">):</span>
<span class="n">bagging_estimates</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bagging_trials</span><span class="p">):</span>
<span class="n">feat_idx</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">rng</span><span class="o">.</span><span class="n">choice</span><span class="p">(</span><span class="n">n_features</span><span class="p">,</span> <span class="n">size</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">bagging_range</span><span class="p">,</span> <span class="n">replace</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
<span class="n">Xboots_bagging</span> <span class="o">=</span> <span class="n">Xboots</span><span class="p">[:,</span> <span class="n">feat_idx</span><span class="p">]</span>
<span class="n">X_boots_bagging</span> <span class="o">=</span> <span class="n">X</span><span class="p">[:,</span> <span class="n">feat_idx</span><span class="p">]</span>
<span class="n">bagging_prev</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_quantify_iteration</span><span class="p">(</span><span class="n">Xboots_bagging</span><span class="p">,</span> <span class="n">yboots</span><span class="p">,</span> <span class="n">X_boots_bagging</span><span class="p">)</span>
<span class="n">bagging_estimates</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">bagging_prev</span><span class="p">)</span>
<span class="n">boots_prevalences</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">bagging_estimates</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">))</span>
<span class="n">conf</span> <span class="o">=</span> <span class="n">WithConfidenceABC</span><span class="o">.</span><span class="n">construct_region</span><span class="p">(</span><span class="n">boots_prevalences</span><span class="p">,</span> <span class="n">confidence_level</span><span class="p">,</span> <span class="n">method</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">region</span><span class="p">,</span> <span class="n">bonferroni</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">bonferroni</span><span class="p">)</span>
<span class="n">prev_estim</span> <span class="o">=</span> <span class="n">conf</span><span class="o">.</span><span class="n">point_estimate</span><span class="p">()</span>
<span class="k">return</span> <span class="n">prev_estim</span><span class="p">,</span> <span class="n">conf</span></div>
<div class="viewcode-block" id="ReadMe.predict">
<a class="viewcode-back" href="../../../quapy.method.html#quapy.method.non_aggregative.ReadMe.predict">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">predict</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">):</span>
<span class="n">prev_estim</span><span class="p">,</span> <span class="n">_</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">predict_conf</span><span class="p">(</span><span class="n">X</span><span class="p">)</span>
<span class="k">return</span> <span class="n">prev_estim</span></div>
<span class="k">def</span><span class="w"> </span><span class="nf">_quantify_iteration</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">Xtr</span><span class="p">,</span> <span class="n">ytr</span><span class="p">,</span> <span class="n">Xte</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Single ReadMe estimate.&quot;&quot;&quot;</span>
<span class="n">PX_given_Y</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">([</span><span class="bp">self</span><span class="o">.</span><span class="n">_compute_P</span><span class="p">(</span><span class="n">Xtr</span><span class="p">[</span><span class="n">ytr</span> <span class="o">==</span> <span class="n">c</span><span class="p">])</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">c</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">classes_</span><span class="p">)])</span>
<span class="n">PX</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_compute_P</span><span class="p">(</span><span class="n">Xte</span><span class="p">)</span>
<span class="n">res</span> <span class="o">=</span> <span class="n">lsq_linear</span><span class="p">(</span><span class="n">A</span><span class="o">=</span><span class="n">PX_given_Y</span><span class="o">.</span><span class="n">T</span><span class="p">,</span> <span class="n">b</span><span class="o">=</span><span class="n">PX</span><span class="p">,</span> <span class="n">bounds</span><span class="o">=</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">))</span>
<span class="n">pY</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">maximum</span><span class="p">(</span><span class="n">res</span><span class="o">.</span><span class="n">x</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span>
<span class="k">return</span> <span class="n">pY</span> <span class="o">/</span> <span class="n">pY</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span>
<span class="k">def</span><span class="w"> </span><span class="nf">_check_matrix</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;the &quot;full&quot; model requires estimating empirical distributions; due to the high computational cost,</span>
<span class="sd"> this function is only made available for binary matrices&quot;&quot;&quot;</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">prob_model</span> <span class="o">==</span> <span class="s1">&#39;full&#39;</span> <span class="ow">and</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">_is_binary_matrix</span><span class="p">(</span><span class="n">X</span><span class="p">):</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s1">&#39;the empirical distribution can only be computed efficiently on binary matrices&#39;</span><span class="p">)</span>
<span class="k">def</span><span class="w"> </span><span class="nf">_is_binary_matrix</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">):</span>
<span class="n">data</span> <span class="o">=</span> <span class="n">X</span><span class="o">.</span><span class="n">data</span> <span class="k">if</span> <span class="n">sparse</span><span class="o">.</span><span class="n">issparse</span><span class="p">(</span><span class="n">X</span><span class="p">)</span> <span class="k">else</span> <span class="n">X</span>
<span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">all</span><span class="p">((</span><span class="n">data</span> <span class="o">==</span> <span class="mi">0</span><span class="p">)</span> <span class="o">|</span> <span class="p">(</span><span class="n">data</span> <span class="o">==</span> <span class="mi">1</span><span class="p">))</span>
<span class="k">def</span><span class="w"> </span><span class="nf">_compute_P</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">):</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">prob_model</span> <span class="o">==</span> <span class="s1">&#39;naive&#39;</span><span class="p">:</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_multinomial_distribution</span><span class="p">(</span><span class="n">X</span><span class="p">)</span>
<span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">prob_model</span> <span class="o">==</span> <span class="s1">&#39;full&#39;</span><span class="p">:</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_empirical_distribution</span><span class="p">(</span><span class="n">X</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;unknown </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">prob_model</span><span class="si">}</span><span class="s1">; valid ones are </span><span class="si">{</span><span class="n">ReadMe</span><span class="o">.</span><span class="n">PROBABILISTIC_MODELS</span><span class="si">=}</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="k">def</span><span class="w"> </span><span class="nf">_empirical_distribution</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">):</span>
<span class="k">if</span> <span class="n">X</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">&gt;</span> <span class="bp">self</span><span class="o">.</span><span class="n">MAX_FEATURES_FOR_EMPIRICAL_ESTIMATION</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;the empirical distribution can only be computed efficiently for dimensions &#39;</span>
<span class="sa">f</span><span class="s1">&#39;less or equal than </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">MAX_FEATURES_FOR_EMPIRICAL_ESTIMATION</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="c1"># we first convert every binary row (e.g., 0 0 1 0 1) into the equivalent number (e.g., 5);</span>
<span class="c1"># this will speed up subsequent comparisons a lot</span>
<span class="n">K</span> <span class="o">=</span> <span class="n">X</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
<span class="n">binary_powers</span> <span class="o">=</span> <span class="mi">1</span> <span class="o">&lt;&lt;</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="n">K</span><span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">)</span> <span class="c1"># (2^K, ..., 32, 16, 8, 4, 2, 1)</span>
<span class="n">X_as_binary_numbers</span> <span class="o">=</span> <span class="n">X</span> <span class="o">@</span> <span class="n">binary_powers</span> <span class="c1"># e.g., [0 0 1 0 1] @ [16, 8, 4, 2, 1] = 5</span>
<span class="c1"># count occurrences and compute probs</span>
<span class="n">counts</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">bincount</span><span class="p">(</span><span class="n">X_as_binary_numbers</span><span class="p">,</span> <span class="n">minlength</span><span class="o">=</span><span class="mi">2</span> <span class="o">**</span> <span class="n">K</span><span class="p">)</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="nb">float</span><span class="p">)</span>
<span class="n">probs</span> <span class="o">=</span> <span class="n">counts</span> <span class="o">/</span> <span class="n">counts</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span>
<span class="k">return</span> <span class="n">probs</span>
<span class="k">def</span><span class="w"> </span><span class="nf">_multinomial_distribution</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">):</span>
<span class="n">PX</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">X</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">))</span>
<span class="n">PX</span> <span class="o">=</span> <span class="n">normalize</span><span class="p">(</span><span class="n">PX</span><span class="p">,</span> <span class="n">norm</span><span class="o">=</span><span class="s1">&#39;l1&#39;</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="k">return</span> <span class="n">PX</span><span class="o">.</span><span class="n">ravel</span><span class="p">()</span></div>
<span class="k">def</span><span class="w"> </span><span class="nf">_get_features_range</span><span class="p">(</span><span class="n">X</span><span class="p">):</span>
<span class="n">feat_ranges</span> <span class="o">=</span> <span class="p">[]</span>
<span class="n">ncols</span> <span class="o">=</span> <span class="n">X</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
<span class="k">for</span> <span class="n">col_idx</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">ncols</span><span class="p">):</span>
<span class="n">feature</span> <span class="o">=</span> <span class="n">X</span><span class="p">[:,</span><span class="n">col_idx</span><span class="p">]</span>
<span class="n">feat_ranges</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">np</span><span class="o">.</span><span class="n">min</span><span class="p">(</span><span class="n">feature</span><span class="p">),</span> <span class="n">np</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="n">feature</span><span class="p">)))</span>
<span class="k">return</span> <span class="n">feat_ranges</span>
<span class="c1">#---------------------------------------------------------------</span>
<span class="c1"># aliases</span>
<span class="c1">#---------------------------------------------------------------</span>
<span class="n">HDx</span> <span class="o">=</span> <span class="n">DMx</span><span class="o">.</span><span class="n">HDx</span>
<span class="n">DistributionMatchingX</span> <span class="o">=</span> <span class="n">DMx</span>
<span class="n">EnergyDistanceX</span> <span class="o">=</span> <span class="n">EDx</span>
<span class="n">HellingerDistanceX</span> <span class="o">=</span> <span class="n">HDx</span>
</pre></div>
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<h1>Source code for quapy.model_selection</h1><div class="highlight"><pre>
<span></span><span class="kn">import</span><span class="w"> </span><span class="nn">itertools</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">logging</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">signal</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">copy</span><span class="w"> </span><span class="kn">import</span> <span class="n">deepcopy</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">enum</span><span class="w"> </span><span class="kn">import</span> <span class="n">Enum</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">typing</span><span class="w"> </span><span class="kn">import</span> <span class="n">Union</span><span class="p">,</span> <span class="n">Callable</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">functools</span><span class="w"> </span><span class="kn">import</span> <span class="n">wraps</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">sklearn</span><span class="w"> </span><span class="kn">import</span> <span class="n">clone</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">quapy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">qp</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">quapy</span><span class="w"> </span><span class="kn">import</span> <span class="n">evaluation</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">quapy.protocol</span><span class="w"> </span><span class="kn">import</span> <span class="n">AbstractProtocol</span><span class="p">,</span> <span class="n">OnLabelledCollectionProtocol</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">quapy.data.base</span><span class="w"> </span><span class="kn">import</span> <span class="n">LabelledCollection</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">quapy.method.aggregative</span><span class="w"> </span><span class="kn">import</span> <span class="n">BaseQuantifier</span><span class="p">,</span> <span class="n">AggregativeQuantifier</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">quapy.util</span><span class="w"> </span><span class="kn">import</span> <span class="n">timeout</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">time</span><span class="w"> </span><span class="kn">import</span> <span class="n">time</span>
<div class="viewcode-block" id="Status">
<a class="viewcode-back" href="../../quapy.html#quapy.model_selection.Status">[docs]</a>
<span class="k">class</span><span class="w"> </span><span class="nc">Status</span><span class="p">(</span><span class="n">Enum</span><span class="p">):</span>
<span class="n">SUCCESS</span> <span class="o">=</span> <span class="mi">1</span>
<span class="n">TIMEOUT</span> <span class="o">=</span> <span class="mi">2</span>
<span class="n">INVALID</span> <span class="o">=</span> <span class="mi">3</span>
<span class="n">ERROR</span> <span class="o">=</span> <span class="mi">4</span></div>
<div class="viewcode-block" id="ConfigStatus">
<a class="viewcode-back" href="../../quapy.html#quapy.model_selection.ConfigStatus">[docs]</a>
<span class="k">class</span><span class="w"> </span><span class="nc">ConfigStatus</span><span class="p">:</span>
<span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">params</span><span class="p">,</span> <span class="n">status</span><span class="p">,</span> <span class="n">msg</span><span class="o">=</span><span class="s1">&#39;&#39;</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">params</span> <span class="o">=</span> <span class="n">params</span>
<span class="bp">self</span><span class="o">.</span><span class="n">status</span> <span class="o">=</span> <span class="n">status</span>
<span class="bp">self</span><span class="o">.</span><span class="n">msg</span> <span class="o">=</span> <span class="n">msg</span>
<span class="k">def</span><span class="w"> </span><span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="sa">f</span><span class="s1">&#39;:params:</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="si">}</span><span class="s1"> :status:</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">status</span><span class="si">}</span><span class="s1"> &#39;</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">msg</span>
<span class="k">def</span><span class="w"> </span><span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
<div class="viewcode-block" id="ConfigStatus.success">
<a class="viewcode-back" href="../../quapy.html#quapy.model_selection.ConfigStatus.success">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">success</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">status</span> <span class="o">==</span> <span class="n">Status</span><span class="o">.</span><span class="n">SUCCESS</span></div>
<div class="viewcode-block" id="ConfigStatus.failed">
<a class="viewcode-back" href="../../quapy.html#quapy.model_selection.ConfigStatus.failed">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">failed</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">status</span> <span class="o">!=</span> <span class="n">Status</span><span class="o">.</span><span class="n">SUCCESS</span></div>
</div>
<div class="viewcode-block" id="GridSearchQ">
<a class="viewcode-back" href="../../quapy.html#quapy.model_selection.GridSearchQ">[docs]</a>
<span class="k">class</span><span class="w"> </span><span class="nc">GridSearchQ</span><span class="p">(</span><span class="n">BaseQuantifier</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Grid Search optimization targeting a quantification-oriented metric.</span>
<span class="sd"> Optimizes the hyperparameters of a quantification method, based on an evaluation method and on an evaluation</span>
<span class="sd"> protocol for quantification.</span>
<span class="sd"> :param model: the quantifier to optimize</span>
<span class="sd"> :type model: BaseQuantifier</span>
<span class="sd"> :param param_grid: a dictionary with keys the parameter names and values the list of values to explore</span>
<span class="sd"> :param protocol: a sample generation protocol, an instance of :class:`quapy.protocol.AbstractProtocol`</span>
<span class="sd"> :param error: an error function (callable) or a string indicating the name of an error function (valid ones</span>
<span class="sd"> are those in :class:`quapy.error.QUANTIFICATION_ERROR`</span>
<span class="sd"> :param refit: whether to refit the model on the whole labelled collection (training+validation) with</span>
<span class="sd"> the best chosen hyperparameter combination. Ignored if protocol=&#39;gen&#39;</span>
<span class="sd"> :param timeout: establishes a timer (in seconds) for each of the hyperparameters configurations being tested.</span>
<span class="sd"> Whenever a run takes longer than this timer, that configuration will be ignored. If all configurations end up</span>
<span class="sd"> being ignored, a TimeoutError exception is raised. If -1 (default) then no time bound is set.</span>
<span class="sd"> :param raise_errors: boolean, if True then raises an exception when a param combination yields any error, if</span>
<span class="sd"> otherwise is False (default), then the combination is marked with an error status, but the process goes on.</span>
<span class="sd"> However, if no configuration yields a valid model, then a ValueError exception will be raised.</span>
<span class="sd"> :param verbose: set to True to get information through the stdout</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span>
<span class="n">model</span><span class="p">:</span> <span class="n">BaseQuantifier</span><span class="p">,</span>
<span class="n">param_grid</span><span class="p">:</span> <span class="nb">dict</span><span class="p">,</span>
<span class="n">protocol</span><span class="p">:</span> <span class="n">AbstractProtocol</span><span class="p">,</span>
<span class="n">error</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="n">Callable</span><span class="p">,</span> <span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">error</span><span class="o">.</span><span class="n">mae</span><span class="p">,</span>
<span class="n">refit</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
<span class="n">timeout</span><span class="o">=-</span><span class="mi">1</span><span class="p">,</span>
<span class="n">n_jobs</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
<span class="n">raise_errors</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
<span class="n">verbose</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">model</span> <span class="o">=</span> <span class="n">model</span>
<span class="bp">self</span><span class="o">.</span><span class="n">param_grid</span> <span class="o">=</span> <span class="n">param_grid</span>
<span class="bp">self</span><span class="o">.</span><span class="n">protocol</span> <span class="o">=</span> <span class="n">protocol</span>
<span class="bp">self</span><span class="o">.</span><span class="n">refit</span> <span class="o">=</span> <span class="n">refit</span>
<span class="bp">self</span><span class="o">.</span><span class="n">timeout</span> <span class="o">=</span> <span class="n">timeout</span>
<span class="bp">self</span><span class="o">.</span><span class="n">n_jobs</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">_get_njobs</span><span class="p">(</span><span class="n">n_jobs</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">raise_errors</span> <span class="o">=</span> <span class="n">raise_errors</span>
<span class="bp">self</span><span class="o">.</span><span class="n">verbose</span> <span class="o">=</span> <span class="n">verbose</span>
<span class="bp">self</span><span class="o">.</span><span class="n">__check_error_measure</span><span class="p">(</span><span class="n">error</span><span class="p">)</span>
<span class="k">assert</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">protocol</span><span class="p">,</span> <span class="n">AbstractProtocol</span><span class="p">),</span> <span class="s1">&#39;unknown protocol&#39;</span>
<span class="k">def</span><span class="w"> </span><span class="nf">_sout</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">msg</span><span class="p">):</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">verbose</span><span class="p">:</span>
<span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="vm">__name__</span><span class="p">)</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;[</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="si">}</span><span class="s1">:</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="si">}</span><span class="s1">]: </span><span class="si">{</span><span class="n">msg</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="k">def</span><span class="w"> </span><span class="nf">__check_error_measure</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">error</span><span class="p">):</span>
<span class="k">if</span> <span class="n">error</span> <span class="ow">in</span> <span class="n">qp</span><span class="o">.</span><span class="n">error</span><span class="o">.</span><span class="n">QUANTIFICATION_ERROR</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">error</span> <span class="o">=</span> <span class="n">error</span>
<span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">error</span><span class="p">,</span> <span class="nb">str</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">error</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">error</span><span class="o">.</span><span class="n">from_name</span><span class="p">(</span><span class="n">error</span><span class="p">)</span>
<span class="k">elif</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">error</span><span class="p">,</span> <span class="s1">&#39;__call__&#39;</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">error</span> <span class="o">=</span> <span class="n">error</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;unexpected error type; must either be a callable function or a str representing</span><span class="se">\n</span><span class="s1">&#39;</span>
<span class="sa">f</span><span class="s1">&#39;the name of an error function in </span><span class="si">{</span><span class="n">qp</span><span class="o">.</span><span class="n">error</span><span class="o">.</span><span class="n">QUANTIFICATION_ERROR_NAMES</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="k">def</span><span class="w"> </span><span class="nf">_prepare_classifier</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">cls_params</span><span class="p">):</span>
<span class="n">model</span> <span class="o">=</span> <span class="n">deepcopy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="p">)</span>
<span class="k">def</span><span class="w"> </span><span class="nf">job</span><span class="p">(</span><span class="n">cls_params</span><span class="p">):</span>
<span class="n">model</span><span class="o">.</span><span class="n">set_params</span><span class="p">(</span><span class="o">**</span><span class="n">cls_params</span><span class="p">)</span>
<span class="n">predictions</span> <span class="o">=</span> <span class="n">model</span><span class="o">.</span><span class="n">classifier_fit_predict</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_training_X</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_training_y</span><span class="p">)</span>
<span class="k">return</span> <span class="n">predictions</span>
<span class="n">predictions</span><span class="p">,</span> <span class="n">status</span><span class="p">,</span> <span class="n">took</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_error_handler</span><span class="p">(</span><span class="n">job</span><span class="p">,</span> <span class="n">cls_params</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_sout</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;[classifier fit] hyperparams=</span><span class="si">{</span><span class="n">cls_params</span><span class="si">}</span><span class="s1"> [took </span><span class="si">{</span><span class="n">took</span><span class="si">:</span><span class="s1">.3f</span><span class="si">}</span><span class="s1">s]&#39;</span><span class="p">)</span>
<span class="k">return</span> <span class="n">model</span><span class="p">,</span> <span class="n">predictions</span><span class="p">,</span> <span class="n">status</span><span class="p">,</span> <span class="n">took</span>
<span class="k">def</span><span class="w"> </span><span class="nf">_prepare_aggregation</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">args</span><span class="p">):</span>
<span class="n">model</span><span class="p">,</span> <span class="n">predictions</span><span class="p">,</span> <span class="n">cls_took</span><span class="p">,</span> <span class="n">cls_params</span><span class="p">,</span> <span class="n">q_params</span> <span class="o">=</span> <span class="n">args</span>
<span class="n">model</span> <span class="o">=</span> <span class="n">deepcopy</span><span class="p">(</span><span class="n">model</span><span class="p">)</span>
<span class="n">params</span> <span class="o">=</span> <span class="p">{</span><span class="o">**</span><span class="n">cls_params</span><span class="p">,</span> <span class="o">**</span><span class="n">q_params</span><span class="p">}</span>
<span class="k">def</span><span class="w"> </span><span class="nf">job</span><span class="p">(</span><span class="n">q_params</span><span class="p">):</span>
<span class="n">model</span><span class="o">.</span><span class="n">set_params</span><span class="p">(</span><span class="o">**</span><span class="n">q_params</span><span class="p">)</span>
<span class="n">P</span><span class="p">,</span> <span class="n">y</span> <span class="o">=</span> <span class="n">predictions</span>
<span class="n">model</span><span class="o">.</span><span class="n">aggregation_fit</span><span class="p">(</span><span class="n">P</span><span class="p">,</span> <span class="n">y</span><span class="p">)</span>
<span class="n">score</span> <span class="o">=</span> <span class="n">evaluation</span><span class="o">.</span><span class="n">evaluate</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="n">protocol</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">protocol</span><span class="p">,</span> <span class="n">error_metric</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">error</span><span class="p">)</span>
<span class="k">return</span> <span class="n">score</span>
<span class="n">score</span><span class="p">,</span> <span class="n">status</span><span class="p">,</span> <span class="n">aggr_took</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_error_handler</span><span class="p">(</span><span class="n">job</span><span class="p">,</span> <span class="n">q_params</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_print_status</span><span class="p">(</span><span class="n">params</span><span class="p">,</span> <span class="n">score</span><span class="p">,</span> <span class="n">status</span><span class="p">,</span> <span class="n">aggr_took</span><span class="p">)</span>
<span class="k">return</span> <span class="n">model</span><span class="p">,</span> <span class="n">params</span><span class="p">,</span> <span class="n">score</span><span class="p">,</span> <span class="n">status</span><span class="p">,</span> <span class="p">(</span><span class="n">cls_took</span><span class="o">+</span><span class="n">aggr_took</span><span class="p">)</span>
<span class="k">def</span><span class="w"> </span><span class="nf">_prepare_nonaggr_model</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">params</span><span class="p">):</span>
<span class="n">model</span> <span class="o">=</span> <span class="n">deepcopy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="p">)</span>
<span class="k">def</span><span class="w"> </span><span class="nf">job</span><span class="p">(</span><span class="n">params</span><span class="p">):</span>
<span class="n">model</span><span class="o">.</span><span class="n">set_params</span><span class="p">(</span><span class="o">**</span><span class="n">params</span><span class="p">)</span>
<span class="n">model</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_training_X</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_training_y</span><span class="p">)</span>
<span class="n">score</span> <span class="o">=</span> <span class="n">evaluation</span><span class="o">.</span><span class="n">evaluate</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="n">protocol</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">protocol</span><span class="p">,</span> <span class="n">error_metric</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">error</span><span class="p">)</span>
<span class="k">return</span> <span class="n">score</span>
<span class="n">score</span><span class="p">,</span> <span class="n">status</span><span class="p">,</span> <span class="n">took</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_error_handler</span><span class="p">(</span><span class="n">job</span><span class="p">,</span> <span class="n">params</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_print_status</span><span class="p">(</span><span class="n">params</span><span class="p">,</span> <span class="n">score</span><span class="p">,</span> <span class="n">status</span><span class="p">,</span> <span class="n">took</span><span class="p">)</span>
<span class="k">return</span> <span class="n">model</span><span class="p">,</span> <span class="n">params</span><span class="p">,</span> <span class="n">score</span><span class="p">,</span> <span class="n">status</span><span class="p">,</span> <span class="n">took</span>
<span class="k">def</span><span class="w"> </span><span class="nf">_break_down_fit</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Decides whether to break down the fit phase in two (classifier-fit followed by aggregation-fit).</span>
<span class="sd"> In order to do so, some conditions should be met: a) the quantifier is of type aggregative,</span>
<span class="sd"> b) the set of hyperparameters can be split into two disjoint non-empty groups.</span>
<span class="sd"> :return: True if the conditions are met, False otherwise</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="p">,</span> <span class="n">AggregativeQuantifier</span><span class="p">):</span>
<span class="k">return</span> <span class="kc">False</span>
<span class="n">cls_configs</span><span class="p">,</span> <span class="n">q_configs</span> <span class="o">=</span> <span class="n">group_params</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">param_grid</span><span class="p">)</span>
<span class="k">if</span> <span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">cls_configs</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">)</span> <span class="ow">or</span> <span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">q_configs</span><span class="p">)</span><span class="o">==</span><span class="mi">1</span><span class="p">):</span>
<span class="k">return</span> <span class="kc">False</span>
<span class="k">return</span> <span class="kc">True</span>
<span class="k">def</span><span class="w"> </span><span class="nf">_compute_scores_aggregative</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">,</span> <span class="n">y</span><span class="p">):</span>
<span class="c1"># break down the set of hyperparameters into two: classifier-specific, quantifier-specific</span>
<span class="n">cls_configs</span><span class="p">,</span> <span class="n">q_configs</span> <span class="o">=</span> <span class="n">group_params</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">param_grid</span><span class="p">)</span>
<span class="c1"># train all classifiers and get the predictions</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_training_X</span> <span class="o">=</span> <span class="n">X</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_training_y</span> <span class="o">=</span> <span class="n">y</span>
<span class="n">cls_outs</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">util</span><span class="o">.</span><span class="n">parallel</span><span class="p">(</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_prepare_classifier</span><span class="p">,</span>
<span class="n">cls_configs</span><span class="p">,</span>
<span class="n">seed</span><span class="o">=</span><span class="n">qp</span><span class="o">.</span><span class="n">environ</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;_R_SEED&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">),</span>
<span class="n">n_jobs</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">n_jobs</span><span class="p">,</span>
<span class="n">asarray</span><span class="o">=</span><span class="kc">False</span>
<span class="p">)</span>
<span class="c1"># filter out classifier configurations that yielded any error</span>
<span class="n">success_outs</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="n">predictions</span><span class="p">,</span> <span class="n">status</span><span class="p">,</span> <span class="n">took</span><span class="p">),</span> <span class="n">cls_config</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">cls_outs</span><span class="p">,</span> <span class="n">cls_configs</span><span class="p">):</span>
<span class="k">if</span> <span class="n">status</span><span class="o">.</span><span class="n">success</span><span class="p">():</span>
<span class="n">success_outs</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">model</span><span class="p">,</span> <span class="n">predictions</span><span class="p">,</span> <span class="n">took</span><span class="p">,</span> <span class="n">cls_config</span><span class="p">))</span>
<span class="k">else</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">error_collector</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">status</span><span class="p">)</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">success_outs</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s1">&#39;No valid configuration found for the classifier!&#39;</span><span class="p">)</span>
<span class="c1"># explore the quantifier-specific hyperparameters for each valid training configuration</span>
<span class="n">aggr_configs</span> <span class="o">=</span> <span class="p">[(</span><span class="o">*</span><span class="n">out</span><span class="p">,</span> <span class="n">q_config</span><span class="p">)</span> <span class="k">for</span> <span class="n">out</span><span class="p">,</span> <span class="n">q_config</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="n">success_outs</span><span class="p">,</span> <span class="n">q_configs</span><span class="p">)]</span>
<span class="n">aggr_outs</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">util</span><span class="o">.</span><span class="n">parallel</span><span class="p">(</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_prepare_aggregation</span><span class="p">,</span>
<span class="n">aggr_configs</span><span class="p">,</span>
<span class="n">seed</span><span class="o">=</span><span class="n">qp</span><span class="o">.</span><span class="n">environ</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;_R_SEED&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">),</span>
<span class="n">n_jobs</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">n_jobs</span>
<span class="p">)</span>
<span class="k">return</span> <span class="n">aggr_outs</span>
<span class="k">def</span><span class="w"> </span><span class="nf">_compute_scores_nonaggregative</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">,</span> <span class="n">y</span><span class="p">):</span>
<span class="n">configs</span> <span class="o">=</span> <span class="n">expand_grid</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">param_grid</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_training_X</span> <span class="o">=</span> <span class="n">X</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_training_y</span> <span class="o">=</span> <span class="n">y</span>
<span class="n">scores</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">util</span><span class="o">.</span><span class="n">parallel</span><span class="p">(</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_prepare_nonaggr_model</span><span class="p">,</span>
<span class="n">configs</span><span class="p">,</span>
<span class="n">seed</span><span class="o">=</span><span class="n">qp</span><span class="o">.</span><span class="n">environ</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;_R_SEED&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">),</span>
<span class="n">n_jobs</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">n_jobs</span>
<span class="p">)</span>
<span class="k">return</span> <span class="n">scores</span>
<span class="k">def</span><span class="w"> </span><span class="nf">_print_status</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">params</span><span class="p">,</span> <span class="n">score</span><span class="p">,</span> <span class="n">status</span><span class="p">,</span> <span class="n">took</span><span class="p">):</span>
<span class="k">if</span> <span class="n">status</span><span class="o">.</span><span class="n">success</span><span class="p">():</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_sout</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;hyperparams=[</span><span class="si">{</span><span class="n">params</span><span class="si">}</span><span class="s1">]</span><span class="se">\t</span><span class="s1"> got </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">error</span><span class="o">.</span><span class="vm">__name__</span><span class="si">}</span><span class="s1"> = </span><span class="si">{</span><span class="n">score</span><span class="si">:</span><span class="s1">.5f</span><span class="si">}</span><span class="s1"> [took </span><span class="si">{</span><span class="n">took</span><span class="si">:</span><span class="s1">.3f</span><span class="si">}</span><span class="s1">s]&#39;</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_sout</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;error=</span><span class="si">{</span><span class="n">status</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
<div class="viewcode-block" id="GridSearchQ.fit">
<a class="viewcode-back" href="../../quapy.html#quapy.model_selection.GridSearchQ.fit">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">fit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">,</span> <span class="n">y</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot; Learning routine. Fits methods with all combinations of hyperparameters and selects the one minimizing</span>
<span class="sd"> the error metric.</span>
<span class="sd"> :param X: array-like, training covariates</span>
<span class="sd"> :param y: array-like, labels of training data</span>
<span class="sd"> :return: self</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">refit</span> <span class="ow">and</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">protocol</span><span class="p">,</span> <span class="n">OnLabelledCollectionProtocol</span><span class="p">):</span>
<span class="k">raise</span> <span class="ne">RuntimeWarning</span><span class="p">(</span>
<span class="sa">f</span><span class="s1">&#39;&quot;refit&quot; was requested, but the protocol does not implement &#39;</span>
<span class="sa">f</span><span class="s1">&#39;the </span><span class="si">{</span><span class="n">OnLabelledCollectionProtocol</span><span class="o">.</span><span class="vm">__name__</span><span class="si">}</span><span class="s1"> interface&#39;</span>
<span class="p">)</span>
<span class="n">tinit</span> <span class="o">=</span> <span class="n">time</span><span class="p">()</span>
<span class="bp">self</span><span class="o">.</span><span class="n">error_collector</span> <span class="o">=</span> <span class="p">[]</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_sout</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;starting model selection with n_jobs=</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">n_jobs</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_break_down_fit</span><span class="p">():</span>
<span class="n">results</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_compute_scores_aggregative</span><span class="p">(</span><span class="n">X</span><span class="p">,</span> <span class="n">y</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">results</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_compute_scores_nonaggregative</span><span class="p">(</span><span class="n">X</span><span class="p">,</span> <span class="n">y</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">param_scores_</span> <span class="o">=</span> <span class="p">{}</span>
<span class="bp">self</span><span class="o">.</span><span class="n">best_score_</span> <span class="o">=</span> <span class="kc">None</span>
<span class="k">for</span> <span class="n">model</span><span class="p">,</span> <span class="n">params</span><span class="p">,</span> <span class="n">score</span><span class="p">,</span> <span class="n">status</span><span class="p">,</span> <span class="n">took</span> <span class="ow">in</span> <span class="n">results</span><span class="p">:</span>
<span class="k">if</span> <span class="n">status</span><span class="o">.</span><span class="n">success</span><span class="p">():</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">best_score_</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="n">score</span> <span class="o">&lt;</span> <span class="bp">self</span><span class="o">.</span><span class="n">best_score_</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">best_score_</span> <span class="o">=</span> <span class="n">score</span>
<span class="bp">self</span><span class="o">.</span><span class="n">best_params_</span> <span class="o">=</span> <span class="n">params</span>
<span class="bp">self</span><span class="o">.</span><span class="n">best_model_</span> <span class="o">=</span> <span class="n">model</span>
<span class="bp">self</span><span class="o">.</span><span class="n">param_scores_</span><span class="p">[</span><span class="nb">str</span><span class="p">(</span><span class="n">params</span><span class="p">)]</span> <span class="o">=</span> <span class="n">score</span>
<span class="k">else</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">param_scores_</span><span class="p">[</span><span class="nb">str</span><span class="p">(</span><span class="n">params</span><span class="p">)]</span> <span class="o">=</span> <span class="n">status</span><span class="o">.</span><span class="n">status</span>
<span class="bp">self</span><span class="o">.</span><span class="n">error_collector</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">status</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">fit_time_</span> <span class="o">=</span> <span class="n">time</span><span class="p">()</span><span class="o">-</span><span class="n">tinit</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">best_score_</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s1">&#39;no combination of hyperparameters seemed to work&#39;</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_sout</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;optimization finished: best params </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">best_params_</span><span class="si">}</span><span class="s1"> (score=</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">best_score_</span><span class="si">:</span><span class="s1">.5f</span><span class="si">}</span><span class="s1">) &#39;</span>
<span class="sa">f</span><span class="s1">&#39;[took </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">fit_time_</span><span class="si">:</span><span class="s1">.4f</span><span class="si">}</span><span class="s1">s]&#39;</span><span class="p">)</span>
<span class="n">no_errors</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">error_collector</span><span class="p">)</span>
<span class="k">if</span> <span class="n">no_errors</span><span class="o">&gt;</span><span class="mi">0</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_sout</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;warning: </span><span class="si">{</span><span class="n">no_errors</span><span class="si">}</span><span class="s1"> errors found&#39;</span><span class="p">)</span>
<span class="k">for</span> <span class="n">err</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">error_collector</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_sout</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;</span><span class="se">\t</span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">err</span><span class="p">)</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">refit</span><span class="p">:</span>
<span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">protocol</span><span class="p">,</span> <span class="n">OnLabelledCollectionProtocol</span><span class="p">):</span>
<span class="n">tinit</span> <span class="o">=</span> <span class="n">time</span><span class="p">()</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_sout</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;refitting on the whole development set&#39;</span><span class="p">)</span>
<span class="n">validation_collection</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">protocol</span><span class="o">.</span><span class="n">get_labelled_collection</span><span class="p">()</span>
<span class="n">training_collection</span> <span class="o">=</span> <span class="n">LabelledCollection</span><span class="p">(</span><span class="n">X</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">classes</span><span class="o">=</span><span class="n">validation_collection</span><span class="o">.</span><span class="n">classes</span><span class="p">)</span>
<span class="n">devel_collection</span> <span class="o">=</span> <span class="n">training_collection</span> <span class="o">+</span> <span class="n">validation_collection</span>
<span class="bp">self</span><span class="o">.</span><span class="n">best_model_</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="o">*</span><span class="n">devel_collection</span><span class="o">.</span><span class="n">Xy</span><span class="p">)</span>
<span class="n">tend</span> <span class="o">=</span> <span class="n">time</span><span class="p">()</span> <span class="o">-</span> <span class="n">tinit</span>
<span class="bp">self</span><span class="o">.</span><span class="n">refit_time_</span> <span class="o">=</span> <span class="n">tend</span>
<span class="k">else</span><span class="p">:</span>
<span class="c1"># already checked</span>
<span class="k">raise</span> <span class="ne">RuntimeWarning</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;the model cannot be refit on the whole dataset&#39;</span><span class="p">)</span>
<span class="k">return</span> <span class="bp">self</span></div>
<div class="viewcode-block" id="GridSearchQ.predict">
<a class="viewcode-back" href="../../quapy.html#quapy.model_selection.GridSearchQ.predict">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">predict</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Estimate class prevalence values using the best model found after calling the :meth:`fit` method.</span>
<span class="sd"> :param X: sample contanining the instances</span>
<span class="sd"> :return: a ndarray of shape `(n_classes)` with class prevalence estimates as according to the best model found</span>
<span class="sd"> by the model selection process.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">assert</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;best_model_&#39;</span><span class="p">),</span> <span class="s1">&#39;quantify called before fit&#39;</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">best_model</span><span class="p">()</span><span class="o">.</span><span class="n">predict</span><span class="p">(</span><span class="n">X</span><span class="p">)</span></div>
<div class="viewcode-block" id="GridSearchQ.set_params">
<a class="viewcode-back" href="../../quapy.html#quapy.model_selection.GridSearchQ.set_params">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">set_params</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">parameters</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Sets the hyper-parameters to explore.</span>
<span class="sd"> :param parameters: a dictionary with keys the parameter names and values the list of values to explore</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="bp">self</span><span class="o">.</span><span class="n">param_grid</span> <span class="o">=</span> <span class="n">parameters</span></div>
<div class="viewcode-block" id="GridSearchQ.get_params">
<a class="viewcode-back" href="../../quapy.html#quapy.model_selection.GridSearchQ.get_params">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">get_params</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">deep</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Returns the dictionary of hyper-parameters to explore (`param_grid`)</span>
<span class="sd"> :param deep: Unused</span>
<span class="sd"> :return: the dictionary `param_grid`</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">param_grid</span></div>
<div class="viewcode-block" id="GridSearchQ.best_model">
<a class="viewcode-back" href="../../quapy.html#quapy.model_selection.GridSearchQ.best_model">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">best_model</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Returns the best model found after calling the :meth:`fit` method, i.e., the one trained on the combination</span>
<span class="sd"> of hyper-parameters that minimized the error function.</span>
<span class="sd"> :return: a trained quantifier</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;best_model_&#39;</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">best_model_</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s1">&#39;best_model called before fit&#39;</span><span class="p">)</span></div>
<span class="k">def</span><span class="w"> </span><span class="nf">_error_handler</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">func</span><span class="p">,</span> <span class="n">params</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Endorses one job with two returned values: the status, and the time of execution</span>
<span class="sd"> :param func: the function to be called</span>
<span class="sd"> :param params: parameters of the function</span>
<span class="sd"> :return: `tuple(out, status, time)` where `out` is the function output,</span>
<span class="sd"> `status` is an enum value from `Status`, and `time` is the time it</span>
<span class="sd"> took to complete the call</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">output</span> <span class="o">=</span> <span class="kc">None</span>
<span class="k">def</span><span class="w"> </span><span class="nf">_handle</span><span class="p">(</span><span class="n">status</span><span class="p">,</span> <span class="n">exception</span><span class="p">):</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_errors</span><span class="p">:</span>
<span class="k">raise</span> <span class="n">exception</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="n">ConfigStatus</span><span class="p">(</span><span class="n">params</span><span class="p">,</span> <span class="n">status</span><span class="p">,</span> <span class="n">msg</span><span class="o">=</span><span class="nb">str</span><span class="p">(</span><span class="n">exception</span><span class="p">))</span>
<span class="k">try</span><span class="p">:</span>
<span class="k">with</span> <span class="n">timeout</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">timeout</span><span class="p">):</span>
<span class="n">tinit</span> <span class="o">=</span> <span class="n">time</span><span class="p">()</span>
<span class="n">output</span> <span class="o">=</span> <span class="n">func</span><span class="p">(</span><span class="n">params</span><span class="p">)</span>
<span class="n">status</span> <span class="o">=</span> <span class="n">ConfigStatus</span><span class="p">(</span><span class="n">params</span><span class="p">,</span> <span class="n">Status</span><span class="o">.</span><span class="n">SUCCESS</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">TimeoutError</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
<span class="n">status</span> <span class="o">=</span> <span class="n">_handle</span><span class="p">(</span><span class="n">Status</span><span class="o">.</span><span class="n">TIMEOUT</span><span class="p">,</span> <span class="n">e</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">ValueError</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
<span class="n">status</span> <span class="o">=</span> <span class="n">_handle</span><span class="p">(</span><span class="n">Status</span><span class="o">.</span><span class="n">INVALID</span><span class="p">,</span> <span class="n">e</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
<span class="n">status</span> <span class="o">=</span> <span class="n">_handle</span><span class="p">(</span><span class="n">Status</span><span class="o">.</span><span class="n">ERROR</span><span class="p">,</span> <span class="n">e</span><span class="p">)</span>
<span class="n">took</span> <span class="o">=</span> <span class="n">time</span><span class="p">()</span> <span class="o">-</span> <span class="n">tinit</span>
<span class="k">return</span> <span class="n">output</span><span class="p">,</span> <span class="n">status</span><span class="p">,</span> <span class="n">took</span></div>
<div class="viewcode-block" id="cross_val_predict">
<a class="viewcode-back" href="../../quapy.html#quapy.model_selection.cross_val_predict">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">cross_val_predict</span><span class="p">(</span><span class="n">quantifier</span><span class="p">:</span> <span class="n">BaseQuantifier</span><span class="p">,</span> <span class="n">data</span><span class="p">:</span> <span class="n">LabelledCollection</span><span class="p">,</span> <span class="n">nfolds</span><span class="o">=</span><span class="mi">3</span><span class="p">,</span> <span class="n">random_state</span><span class="o">=</span><span class="mi">0</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Akin to `scikit-learn&#39;s cross_val_predict &lt;https://scikit-learn.org/stable/modules/generated/sklearn.model_selection.cross_val_predict.html&gt;`_</span>
<span class="sd"> but for quantification.</span>
<span class="sd"> :param quantifier: a quantifier issuing class prevalence values</span>
<span class="sd"> :param data: a labelled collection</span>
<span class="sd"> :param nfolds: number of folds for k-fold cross validation generation</span>
<span class="sd"> :param random_state: random seed for reproducibility</span>
<span class="sd"> :return: a vector of class prevalence values</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">total_prev</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="n">shape</span><span class="o">=</span><span class="n">data</span><span class="o">.</span><span class="n">n_classes</span><span class="p">)</span>
<span class="k">for</span> <span class="n">train</span><span class="p">,</span> <span class="n">test</span> <span class="ow">in</span> <span class="n">data</span><span class="o">.</span><span class="n">kFCV</span><span class="p">(</span><span class="n">nfolds</span><span class="o">=</span><span class="n">nfolds</span><span class="p">,</span> <span class="n">random_state</span><span class="o">=</span><span class="n">random_state</span><span class="p">):</span>
<span class="n">quantifier</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="o">*</span><span class="n">train</span><span class="o">.</span><span class="n">Xy</span><span class="p">)</span>
<span class="n">fold_prev</span> <span class="o">=</span> <span class="n">quantifier</span><span class="o">.</span><span class="n">predict</span><span class="p">(</span><span class="n">test</span><span class="o">.</span><span class="n">X</span><span class="p">)</span>
<span class="n">rel_size</span> <span class="o">=</span> <span class="mf">1.</span> <span class="o">*</span> <span class="nb">len</span><span class="p">(</span><span class="n">test</span><span class="p">)</span> <span class="o">/</span> <span class="nb">len</span><span class="p">(</span><span class="n">data</span><span class="p">)</span>
<span class="n">total_prev</span> <span class="o">+=</span> <span class="n">fold_prev</span><span class="o">*</span><span class="n">rel_size</span>
<span class="k">return</span> <span class="n">total_prev</span></div>
<div class="viewcode-block" id="expand_grid">
<a class="viewcode-back" href="../../quapy.html#quapy.model_selection.expand_grid">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">expand_grid</span><span class="p">(</span><span class="n">param_grid</span><span class="p">:</span> <span class="nb">dict</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Expands a param_grid dictionary as a list of configurations.</span>
<span class="sd"> Example:</span>
<span class="sd"> &gt;&gt;&gt; combinations = expand_grid({&#39;A&#39;: [1, 10, 100], &#39;B&#39;: [True, False]})</span>
<span class="sd"> &gt;&gt;&gt; print(combinations)</span>
<span class="sd"> &gt;&gt;&gt; [{&#39;A&#39;: 1, &#39;B&#39;: True}, {&#39;A&#39;: 1, &#39;B&#39;: False}, {&#39;A&#39;: 10, &#39;B&#39;: True}, {&#39;A&#39;: 10, &#39;B&#39;: False}, {&#39;A&#39;: 100, &#39;B&#39;: True}, {&#39;A&#39;: 100, &#39;B&#39;: False}]</span>
<span class="sd"> :param param_grid: dictionary with keys representing hyper-parameter names, and values representing the range</span>
<span class="sd"> to explore for that hyper-parameter</span>
<span class="sd"> :return: a list of configurations, i.e., combinations of hyper-parameter assignments in the grid.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">params_keys</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">param_grid</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
<span class="n">params_values</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">param_grid</span><span class="o">.</span><span class="n">values</span><span class="p">())</span>
<span class="n">configs</span> <span class="o">=</span> <span class="p">[{</span><span class="n">k</span><span class="p">:</span> <span class="n">combs</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">k</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">params_keys</span><span class="p">)}</span> <span class="k">for</span> <span class="n">combs</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="o">*</span><span class="n">params_values</span><span class="p">)]</span>
<span class="k">return</span> <span class="n">configs</span></div>
<div class="viewcode-block" id="group_params">
<a class="viewcode-back" href="../../quapy.html#quapy.model_selection.group_params">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">group_params</span><span class="p">(</span><span class="n">param_grid</span><span class="p">:</span> <span class="nb">dict</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Partitions a param_grid dictionary as two lists of configurations, one for the classifier-specific</span>
<span class="sd"> hyper-parameters, and another for que quantifier-specific hyper-parameters</span>
<span class="sd"> :param param_grid: dictionary with keys representing hyper-parameter names, and values representing the range</span>
<span class="sd"> to explore for that hyper-parameter</span>
<span class="sd"> :return: two expanded grids of configurations, one for the classifier, another for the quantifier</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">classifier_params</span><span class="p">,</span> <span class="n">quantifier_params</span> <span class="o">=</span> <span class="p">{},</span> <span class="p">{}</span>
<span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">values</span> <span class="ow">in</span> <span class="n">param_grid</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
<span class="k">if</span> <span class="n">key</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;classifier__&#39;</span><span class="p">)</span> <span class="ow">or</span> <span class="n">key</span> <span class="o">==</span> <span class="s1">&#39;val_split&#39;</span><span class="p">:</span>
<span class="n">classifier_params</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">values</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">quantifier_params</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">values</span>
<span class="n">classifier_configs</span> <span class="o">=</span> <span class="n">expand_grid</span><span class="p">(</span><span class="n">classifier_params</span><span class="p">)</span>
<span class="n">quantifier_configs</span> <span class="o">=</span> <span class="n">expand_grid</span><span class="p">(</span><span class="n">quantifier_params</span><span class="p">)</span>
<span class="k">return</span> <span class="n">classifier_configs</span><span class="p">,</span> <span class="n">quantifier_configs</span></div>
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<h1>Source code for quapy.tests.test_base</h1><div class="highlight"><pre>
<span></span><span class="kn">import</span> <span class="nn">pytest</span>
<div class="viewcode-block" id="test_import">
<a class="viewcode-back" href="../../../quapy.tests.html#quapy.tests.test_base.test_import">[docs]</a>
<span class="k">def</span> <span class="nf">test_import</span><span class="p">():</span>
<span class="kn">import</span> <span class="nn">quapy</span> <span class="k">as</span> <span class="nn">qp</span>
<span class="k">assert</span> <span class="n">qp</span><span class="o">.</span><span class="n">__version__</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span></div>
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<h1>Source code for quapy.tests.test_datasets</h1><div class="highlight"><pre>
<span></span><span class="kn">import</span> <span class="nn">pytest</span>
<span class="kn">from</span> <span class="nn">quapy.data.datasets</span> <span class="kn">import</span> <span class="n">REVIEWS_SENTIMENT_DATASETS</span><span class="p">,</span> <span class="n">TWITTER_SENTIMENT_DATASETS_TEST</span><span class="p">,</span> \
<span class="n">TWITTER_SENTIMENT_DATASETS_TRAIN</span><span class="p">,</span> <span class="n">UCI_BINARY_DATASETS</span><span class="p">,</span> <span class="n">LEQUA2022_TASKS</span><span class="p">,</span> <span class="n">UCI_MULTICLASS_DATASETS</span><span class="p">,</span>\
<span class="n">fetch_reviews</span><span class="p">,</span> <span class="n">fetch_twitter</span><span class="p">,</span> <span class="n">fetch_UCIBinaryDataset</span><span class="p">,</span> <span class="n">fetch_lequa2022</span><span class="p">,</span> <span class="n">fetch_UCIMulticlassLabelledCollection</span>
<div class="viewcode-block" id="test_fetch_reviews">
<a class="viewcode-back" href="../../../quapy.tests.html#quapy.tests.test_datasets.test_fetch_reviews">[docs]</a>
<span class="nd">@pytest</span><span class="o">.</span><span class="n">mark</span><span class="o">.</span><span class="n">parametrize</span><span class="p">(</span><span class="s1">&#39;dataset_name&#39;</span><span class="p">,</span> <span class="n">REVIEWS_SENTIMENT_DATASETS</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">test_fetch_reviews</span><span class="p">(</span><span class="n">dataset_name</span><span class="p">):</span>
<span class="n">dataset</span> <span class="o">=</span> <span class="n">fetch_reviews</span><span class="p">(</span><span class="n">dataset_name</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;Dataset </span><span class="si">{</span><span class="n">dataset_name</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Training set stats&#39;</span><span class="p">)</span>
<span class="n">dataset</span><span class="o">.</span><span class="n">training</span><span class="o">.</span><span class="n">stats</span><span class="p">()</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Test set stats&#39;</span><span class="p">)</span>
<span class="n">dataset</span><span class="o">.</span><span class="n">test</span><span class="o">.</span><span class="n">stats</span><span class="p">()</span></div>
<div class="viewcode-block" id="test_fetch_twitter">
<a class="viewcode-back" href="../../../quapy.tests.html#quapy.tests.test_datasets.test_fetch_twitter">[docs]</a>
<span class="nd">@pytest</span><span class="o">.</span><span class="n">mark</span><span class="o">.</span><span class="n">parametrize</span><span class="p">(</span><span class="s1">&#39;dataset_name&#39;</span><span class="p">,</span> <span class="n">TWITTER_SENTIMENT_DATASETS_TEST</span> <span class="o">+</span> <span class="n">TWITTER_SENTIMENT_DATASETS_TRAIN</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">test_fetch_twitter</span><span class="p">(</span><span class="n">dataset_name</span><span class="p">):</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">dataset</span> <span class="o">=</span> <span class="n">fetch_twitter</span><span class="p">(</span><span class="n">dataset_name</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">ValueError</span> <span class="k">as</span> <span class="n">ve</span><span class="p">:</span>
<span class="k">if</span> <span class="n">dataset_name</span> <span class="o">==</span> <span class="s1">&#39;semeval&#39;</span> <span class="ow">and</span> <span class="n">ve</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span>
<span class="s1">&#39;dataset &quot;semeval&quot; can only be used for model selection.&#39;</span><span class="p">):</span>
<span class="n">dataset</span> <span class="o">=</span> <span class="n">fetch_twitter</span><span class="p">(</span><span class="n">dataset_name</span><span class="p">,</span> <span class="n">for_model_selection</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;Dataset </span><span class="si">{</span><span class="n">dataset_name</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Training set stats&#39;</span><span class="p">)</span>
<span class="n">dataset</span><span class="o">.</span><span class="n">training</span><span class="o">.</span><span class="n">stats</span><span class="p">()</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Test set stats&#39;</span><span class="p">)</span></div>
<div class="viewcode-block" id="test_fetch_UCIDataset">
<a class="viewcode-back" href="../../../quapy.tests.html#quapy.tests.test_datasets.test_fetch_UCIDataset">[docs]</a>
<span class="nd">@pytest</span><span class="o">.</span><span class="n">mark</span><span class="o">.</span><span class="n">parametrize</span><span class="p">(</span><span class="s1">&#39;dataset_name&#39;</span><span class="p">,</span> <span class="n">UCI_BINARY_DATASETS</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">test_fetch_UCIDataset</span><span class="p">(</span><span class="n">dataset_name</span><span class="p">):</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">dataset</span> <span class="o">=</span> <span class="n">fetch_UCIBinaryDataset</span><span class="p">(</span><span class="n">dataset_name</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">FileNotFoundError</span> <span class="k">as</span> <span class="n">fnfe</span><span class="p">:</span>
<span class="k">if</span> <span class="n">dataset_name</span> <span class="o">==</span> <span class="s1">&#39;pageblocks.5&#39;</span> <span class="ow">and</span> <span class="n">fnfe</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">find</span><span class="p">(</span>
<span class="s1">&#39;If this is the first time you attempt to load this dataset&#39;</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">:</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">&#39;The pageblocks.5 dataset requires some hand processing to be usable, skipping this test.&#39;</span><span class="p">)</span>
<span class="k">return</span>
<span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;Dataset </span><span class="si">{</span><span class="n">dataset_name</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Training set stats&#39;</span><span class="p">)</span>
<span class="n">dataset</span><span class="o">.</span><span class="n">training</span><span class="o">.</span><span class="n">stats</span><span class="p">()</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Test set stats&#39;</span><span class="p">)</span></div>
<div class="viewcode-block" id="test_fetch_UCIMultiDataset">
<a class="viewcode-back" href="../../../quapy.tests.html#quapy.tests.test_datasets.test_fetch_UCIMultiDataset">[docs]</a>
<span class="nd">@pytest</span><span class="o">.</span><span class="n">mark</span><span class="o">.</span><span class="n">parametrize</span><span class="p">(</span><span class="s1">&#39;dataset_name&#39;</span><span class="p">,</span> <span class="n">UCI_MULTICLASS_DATASETS</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">test_fetch_UCIMultiDataset</span><span class="p">(</span><span class="n">dataset_name</span><span class="p">):</span>
<span class="n">dataset</span> <span class="o">=</span> <span class="n">fetch_UCIMulticlassLabelledCollection</span><span class="p">(</span><span class="n">dataset_name</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;Dataset </span><span class="si">{</span><span class="n">dataset_name</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Training set stats&#39;</span><span class="p">)</span>
<span class="n">dataset</span><span class="o">.</span><span class="n">stats</span><span class="p">()</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Test set stats&#39;</span><span class="p">)</span></div>
<div class="viewcode-block" id="test_fetch_lequa2022">
<a class="viewcode-back" href="../../../quapy.tests.html#quapy.tests.test_datasets.test_fetch_lequa2022">[docs]</a>
<span class="nd">@pytest</span><span class="o">.</span><span class="n">mark</span><span class="o">.</span><span class="n">parametrize</span><span class="p">(</span><span class="s1">&#39;dataset_name&#39;</span><span class="p">,</span> <span class="n">LEQUA2022_TASKS</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">test_fetch_lequa2022</span><span class="p">(</span><span class="n">dataset_name</span><span class="p">):</span>
<span class="n">train</span><span class="p">,</span> <span class="n">gen_val</span><span class="p">,</span> <span class="n">gen_test</span> <span class="o">=</span> <span class="n">fetch_lequa2022</span><span class="p">(</span><span class="n">dataset_name</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">train</span><span class="o">.</span><span class="n">stats</span><span class="p">())</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Val:&#39;</span><span class="p">,</span> <span class="n">gen_val</span><span class="o">.</span><span class="n">total</span><span class="p">())</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Test:&#39;</span><span class="p">,</span> <span class="n">gen_test</span><span class="o">.</span><span class="n">total</span><span class="p">())</span></div>
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<h1>Source code for quapy.tests.test_evaluation</h1><div class="highlight"><pre>
<span></span><span class="kn">import</span> <span class="nn">unittest</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
<span class="kn">import</span> <span class="nn">quapy</span> <span class="k">as</span> <span class="nn">qp</span>
<span class="kn">from</span> <span class="nn">sklearn.linear_model</span> <span class="kn">import</span> <span class="n">LogisticRegression</span>
<span class="kn">from</span> <span class="nn">time</span> <span class="kn">import</span> <span class="n">time</span>
<span class="kn">from</span> <span class="nn">quapy.error</span> <span class="kn">import</span> <span class="n">QUANTIFICATION_ERROR_SINGLE</span><span class="p">,</span> <span class="n">QUANTIFICATION_ERROR</span><span class="p">,</span> <span class="n">QUANTIFICATION_ERROR_NAMES</span><span class="p">,</span> \
<span class="n">QUANTIFICATION_ERROR_SINGLE_NAMES</span>
<span class="kn">from</span> <span class="nn">quapy.method.aggregative</span> <span class="kn">import</span> <span class="n">EMQ</span><span class="p">,</span> <span class="n">PCC</span>
<span class="kn">from</span> <span class="nn">quapy.method.base</span> <span class="kn">import</span> <span class="n">BaseQuantifier</span>
<div class="viewcode-block" id="EvalTestCase">
<a class="viewcode-back" href="../../../quapy.tests.html#quapy.tests.test_evaluation.EvalTestCase">[docs]</a>
<span class="k">class</span> <span class="nc">EvalTestCase</span><span class="p">(</span><span class="n">unittest</span><span class="o">.</span><span class="n">TestCase</span><span class="p">):</span>
<div class="viewcode-block" id="EvalTestCase.test_eval_speedup">
<a class="viewcode-back" href="../../../quapy.tests.html#quapy.tests.test_evaluation.EvalTestCase.test_eval_speedup">[docs]</a>
<span class="k">def</span> <span class="nf">test_eval_speedup</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="n">data</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">datasets</span><span class="o">.</span><span class="n">fetch_reviews</span><span class="p">(</span><span class="s1">&#39;hp&#39;</span><span class="p">,</span> <span class="n">tfidf</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">min_df</span><span class="o">=</span><span class="mi">10</span><span class="p">,</span> <span class="n">pickle</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="n">train</span><span class="p">,</span> <span class="n">test</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">training</span><span class="p">,</span> <span class="n">data</span><span class="o">.</span><span class="n">test</span>
<span class="n">protocol</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">protocol</span><span class="o">.</span><span class="n">APP</span><span class="p">(</span><span class="n">test</span><span class="p">,</span> <span class="n">sample_size</span><span class="o">=</span><span class="mi">1000</span><span class="p">,</span> <span class="n">n_prevalences</span><span class="o">=</span><span class="mi">11</span><span class="p">,</span> <span class="n">repeats</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">random_state</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="k">class</span> <span class="nc">SlowLR</span><span class="p">(</span><span class="n">LogisticRegression</span><span class="p">):</span>
<span class="k">def</span> <span class="nf">predict_proba</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">):</span>
<span class="kn">import</span> <span class="nn">time</span>
<span class="n">time</span><span class="o">.</span><span class="n">sleep</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span>
<span class="k">return</span> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="n">predict_proba</span><span class="p">(</span><span class="n">X</span><span class="p">)</span>
<span class="n">emq</span> <span class="o">=</span> <span class="n">EMQ</span><span class="p">(</span><span class="n">SlowLR</span><span class="p">())</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="n">train</span><span class="p">)</span>
<span class="n">tinit</span> <span class="o">=</span> <span class="n">time</span><span class="p">()</span>
<span class="n">score</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">evaluation</span><span class="o">.</span><span class="n">evaluate</span><span class="p">(</span><span class="n">emq</span><span class="p">,</span> <span class="n">protocol</span><span class="p">,</span> <span class="n">error_metric</span><span class="o">=</span><span class="s1">&#39;mae&#39;</span><span class="p">,</span> <span class="n">verbose</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">aggr_speedup</span><span class="o">=</span><span class="s1">&#39;force&#39;</span><span class="p">)</span>
<span class="n">tend_optim</span> <span class="o">=</span> <span class="n">time</span><span class="p">()</span><span class="o">-</span><span class="n">tinit</span>
<span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;evaluation (with optimization) took </span><span class="si">{</span><span class="n">tend_optim</span><span class="si">}</span><span class="s1">s [MAE=</span><span class="si">{</span><span class="n">score</span><span class="si">:</span><span class="s1">.4f</span><span class="si">}</span><span class="s1">]&#39;</span><span class="p">)</span>
<span class="k">class</span> <span class="nc">NonAggregativeEMQ</span><span class="p">(</span><span class="n">BaseQuantifier</span><span class="p">):</span>
<span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="bp">cls</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">emq</span> <span class="o">=</span> <span class="n">EMQ</span><span class="p">(</span><span class="bp">cls</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">quantify</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">instances</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">emq</span><span class="o">.</span><span class="n">quantify</span><span class="p">(</span><span class="n">instances</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">fit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">data</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">emq</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="n">data</span><span class="p">)</span>
<span class="k">return</span> <span class="bp">self</span>
<span class="n">emq</span> <span class="o">=</span> <span class="n">NonAggregativeEMQ</span><span class="p">(</span><span class="n">SlowLR</span><span class="p">())</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="n">train</span><span class="p">)</span>
<span class="n">tinit</span> <span class="o">=</span> <span class="n">time</span><span class="p">()</span>
<span class="n">score</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">evaluation</span><span class="o">.</span><span class="n">evaluate</span><span class="p">(</span><span class="n">emq</span><span class="p">,</span> <span class="n">protocol</span><span class="p">,</span> <span class="n">error_metric</span><span class="o">=</span><span class="s1">&#39;mae&#39;</span><span class="p">,</span> <span class="n">verbose</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="n">tend_no_optim</span> <span class="o">=</span> <span class="n">time</span><span class="p">()</span> <span class="o">-</span> <span class="n">tinit</span>
<span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;evaluation (w/o optimization) took </span><span class="si">{</span><span class="n">tend_no_optim</span><span class="si">}</span><span class="s1">s [MAE=</span><span class="si">{</span><span class="n">score</span><span class="si">:</span><span class="s1">.4f</span><span class="si">}</span><span class="s1">]&#39;</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertEqual</span><span class="p">(</span><span class="n">tend_no_optim</span><span class="o">&gt;</span><span class="p">(</span><span class="n">tend_optim</span><span class="o">/</span><span class="mi">2</span><span class="p">),</span> <span class="kc">True</span><span class="p">)</span></div>
<div class="viewcode-block" id="EvalTestCase.test_evaluation_output">
<a class="viewcode-back" href="../../../quapy.tests.html#quapy.tests.test_evaluation.EvalTestCase.test_evaluation_output">[docs]</a>
<span class="k">def</span> <span class="nf">test_evaluation_output</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="n">data</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">datasets</span><span class="o">.</span><span class="n">fetch_reviews</span><span class="p">(</span><span class="s1">&#39;hp&#39;</span><span class="p">,</span> <span class="n">tfidf</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">min_df</span><span class="o">=</span><span class="mi">10</span><span class="p">,</span> <span class="n">pickle</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="n">train</span><span class="p">,</span> <span class="n">test</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">training</span><span class="p">,</span> <span class="n">data</span><span class="o">.</span><span class="n">test</span>
<span class="n">qp</span><span class="o">.</span><span class="n">environ</span><span class="p">[</span><span class="s1">&#39;SAMPLE_SIZE&#39;</span><span class="p">]</span><span class="o">=</span><span class="mi">100</span>
<span class="n">protocol</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">protocol</span><span class="o">.</span><span class="n">APP</span><span class="p">(</span><span class="n">test</span><span class="p">,</span> <span class="n">random_state</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
<span class="n">q</span> <span class="o">=</span> <span class="n">PCC</span><span class="p">(</span><span class="n">LogisticRegression</span><span class="p">())</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="n">train</span><span class="p">)</span>
<span class="n">single_errors</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">QUANTIFICATION_ERROR_SINGLE_NAMES</span><span class="p">)</span>
<span class="n">averaged_errors</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;m&#39;</span><span class="o">+</span><span class="n">e</span> <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="n">single_errors</span><span class="p">]</span>
<span class="n">single_errors</span> <span class="o">=</span> <span class="n">single_errors</span> <span class="o">+</span> <span class="p">[</span><span class="n">qp</span><span class="o">.</span><span class="n">error</span><span class="o">.</span><span class="n">from_name</span><span class="p">(</span><span class="n">e</span><span class="p">)</span> <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="n">single_errors</span><span class="p">]</span>
<span class="n">averaged_errors</span> <span class="o">=</span> <span class="n">averaged_errors</span> <span class="o">+</span> <span class="p">[</span><span class="n">qp</span><span class="o">.</span><span class="n">error</span><span class="o">.</span><span class="n">from_name</span><span class="p">(</span><span class="n">e</span><span class="p">)</span> <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="n">averaged_errors</span><span class="p">]</span>
<span class="k">for</span> <span class="n">error_metric</span><span class="p">,</span> <span class="n">averaged_error_metric</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">single_errors</span><span class="p">,</span> <span class="n">averaged_errors</span><span class="p">):</span>
<span class="n">score</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">evaluation</span><span class="o">.</span><span class="n">evaluate</span><span class="p">(</span><span class="n">q</span><span class="p">,</span> <span class="n">protocol</span><span class="p">,</span> <span class="n">error_metric</span><span class="o">=</span><span class="n">averaged_error_metric</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertTrue</span><span class="p">(</span><span class="nb">isinstance</span><span class="p">(</span><span class="n">score</span><span class="p">,</span> <span class="nb">float</span><span class="p">))</span>
<span class="n">scores</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">evaluation</span><span class="o">.</span><span class="n">evaluate</span><span class="p">(</span><span class="n">q</span><span class="p">,</span> <span class="n">protocol</span><span class="p">,</span> <span class="n">error_metric</span><span class="o">=</span><span class="n">error_metric</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertTrue</span><span class="p">(</span><span class="nb">isinstance</span><span class="p">(</span><span class="n">scores</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">))</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertEqual</span><span class="p">(</span><span class="n">scores</span><span class="o">.</span><span class="n">mean</span><span class="p">(),</span> <span class="n">score</span><span class="p">)</span></div>
</div>
<span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s1">&#39;__main__&#39;</span><span class="p">:</span>
<span class="n">unittest</span><span class="o">.</span><span class="n">main</span><span class="p">()</span>
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<h1>Source code for quapy.tests.test_hierarchy</h1><div class="highlight"><pre>
<span></span><span class="kn">import</span> <span class="nn">unittest</span>
<span class="kn">from</span> <span class="nn">sklearn.linear_model</span> <span class="kn">import</span> <span class="n">LogisticRegression</span>
<span class="kn">from</span> <span class="nn">quapy.method.aggregative</span> <span class="kn">import</span> <span class="o">*</span>
<div class="viewcode-block" id="HierarchyTestCase">
<a class="viewcode-back" href="../../../quapy.tests.html#quapy.tests.test_hierarchy.HierarchyTestCase">[docs]</a>
<span class="k">class</span> <span class="nc">HierarchyTestCase</span><span class="p">(</span><span class="n">unittest</span><span class="o">.</span><span class="n">TestCase</span><span class="p">):</span>
<div class="viewcode-block" id="HierarchyTestCase.test_aggregative">
<a class="viewcode-back" href="../../../quapy.tests.html#quapy.tests.test_hierarchy.HierarchyTestCase.test_aggregative">[docs]</a>
<span class="k">def</span> <span class="nf">test_aggregative</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="n">lr</span> <span class="o">=</span> <span class="n">LogisticRegression</span><span class="p">()</span>
<span class="k">for</span> <span class="n">m</span> <span class="ow">in</span> <span class="p">[</span><span class="n">CC</span><span class="p">(</span><span class="n">lr</span><span class="p">),</span> <span class="n">PCC</span><span class="p">(</span><span class="n">lr</span><span class="p">),</span> <span class="n">ACC</span><span class="p">(</span><span class="n">lr</span><span class="p">),</span> <span class="n">PACC</span><span class="p">(</span><span class="n">lr</span><span class="p">)]:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertEqual</span><span class="p">(</span><span class="nb">isinstance</span><span class="p">(</span><span class="n">m</span><span class="p">,</span> <span class="n">AggregativeQuantifier</span><span class="p">),</span> <span class="kc">True</span><span class="p">)</span></div>
<div class="viewcode-block" id="HierarchyTestCase.test_binary">
<a class="viewcode-back" href="../../../quapy.tests.html#quapy.tests.test_hierarchy.HierarchyTestCase.test_binary">[docs]</a>
<span class="k">def</span> <span class="nf">test_binary</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="n">lr</span> <span class="o">=</span> <span class="n">LogisticRegression</span><span class="p">()</span>
<span class="k">for</span> <span class="n">m</span> <span class="ow">in</span> <span class="p">[</span><span class="n">HDy</span><span class="p">(</span><span class="n">lr</span><span class="p">)]:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertEqual</span><span class="p">(</span><span class="nb">isinstance</span><span class="p">(</span><span class="n">m</span><span class="p">,</span> <span class="n">BinaryQuantifier</span><span class="p">),</span> <span class="kc">True</span><span class="p">)</span></div>
<div class="viewcode-block" id="HierarchyTestCase.test_probabilistic">
<a class="viewcode-back" href="../../../quapy.tests.html#quapy.tests.test_hierarchy.HierarchyTestCase.test_probabilistic">[docs]</a>
<span class="k">def</span> <span class="nf">test_probabilistic</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="n">lr</span> <span class="o">=</span> <span class="n">LogisticRegression</span><span class="p">()</span>
<span class="k">for</span> <span class="n">m</span> <span class="ow">in</span> <span class="p">[</span><span class="n">CC</span><span class="p">(</span><span class="n">lr</span><span class="p">),</span> <span class="n">ACC</span><span class="p">(</span><span class="n">lr</span><span class="p">)]:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertEqual</span><span class="p">(</span><span class="nb">isinstance</span><span class="p">(</span><span class="n">m</span><span class="p">,</span> <span class="n">AggregativeCrispQuantifier</span><span class="p">),</span> <span class="kc">True</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertEqual</span><span class="p">(</span><span class="nb">isinstance</span><span class="p">(</span><span class="n">m</span><span class="p">,</span> <span class="n">AggregativeSoftQuantifier</span><span class="p">),</span> <span class="kc">False</span><span class="p">)</span>
<span class="k">for</span> <span class="n">m</span> <span class="ow">in</span> <span class="p">[</span><span class="n">PCC</span><span class="p">(</span><span class="n">lr</span><span class="p">),</span> <span class="n">PACC</span><span class="p">(</span><span class="n">lr</span><span class="p">)]:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertEqual</span><span class="p">(</span><span class="nb">isinstance</span><span class="p">(</span><span class="n">m</span><span class="p">,</span> <span class="n">AggregativeCrispQuantifier</span><span class="p">),</span> <span class="kc">False</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertEqual</span><span class="p">(</span><span class="nb">isinstance</span><span class="p">(</span><span class="n">m</span><span class="p">,</span> <span class="n">AggregativeSoftQuantifier</span><span class="p">),</span> <span class="kc">True</span><span class="p">)</span></div>
</div>
<span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s1">&#39;__main__&#39;</span><span class="p">:</span>
<span class="n">unittest</span><span class="o">.</span><span class="n">main</span><span class="p">()</span>
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<h1>Source code for quapy.tests.test_labelcollection</h1><div class="highlight"><pre>
<span></span><span class="kn">import</span> <span class="nn">unittest</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
<span class="kn">from</span> <span class="nn">scipy.sparse</span> <span class="kn">import</span> <span class="n">csr_matrix</span>
<span class="kn">import</span> <span class="nn">quapy</span> <span class="k">as</span> <span class="nn">qp</span>
<div class="viewcode-block" id="LabelCollectionTestCase">
<a class="viewcode-back" href="../../../quapy.tests.html#quapy.tests.test_labelcollection.LabelCollectionTestCase">[docs]</a>
<span class="k">class</span> <span class="nc">LabelCollectionTestCase</span><span class="p">(</span><span class="n">unittest</span><span class="o">.</span><span class="n">TestCase</span><span class="p">):</span>
<div class="viewcode-block" id="LabelCollectionTestCase.test_split">
<a class="viewcode-back" href="../../../quapy.tests.html#quapy.tests.test_labelcollection.LabelCollectionTestCase.test_split">[docs]</a>
<span class="k">def</span> <span class="nf">test_split</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">100</span><span class="p">)</span>
<span class="n">y</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">randint</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="mi">5</span><span class="p">,</span><span class="mi">100</span><span class="p">)</span>
<span class="n">data</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">LabelledCollection</span><span class="p">(</span><span class="n">x</span><span class="p">,</span><span class="n">y</span><span class="p">)</span>
<span class="n">tr</span><span class="p">,</span> <span class="n">te</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">split_random</span><span class="p">(</span><span class="mf">0.7</span><span class="p">)</span>
<span class="n">check_prev</span> <span class="o">=</span> <span class="n">tr</span><span class="o">.</span><span class="n">prevalence</span><span class="p">()</span><span class="o">*</span><span class="mf">0.7</span> <span class="o">+</span> <span class="n">te</span><span class="o">.</span><span class="n">prevalence</span><span class="p">()</span><span class="o">*</span><span class="mf">0.3</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertEqual</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">tr</span><span class="p">),</span> <span class="mi">70</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertEqual</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">te</span><span class="p">),</span> <span class="mi">30</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertEqual</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">allclose</span><span class="p">(</span><span class="n">check_prev</span><span class="p">,</span> <span class="n">data</span><span class="o">.</span><span class="n">prevalence</span><span class="p">()),</span> <span class="kc">True</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertEqual</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">tr</span><span class="o">+</span><span class="n">te</span><span class="p">),</span> <span class="nb">len</span><span class="p">(</span><span class="n">data</span><span class="p">))</span></div>
<div class="viewcode-block" id="LabelCollectionTestCase.test_join">
<a class="viewcode-back" href="../../../quapy.tests.html#quapy.tests.test_labelcollection.LabelCollectionTestCase.test_join">[docs]</a>
<span class="k">def</span> <span class="nf">test_join</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">50</span><span class="p">)</span>
<span class="n">y</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">randint</span><span class="p">(</span><span class="mi">2</span><span class="p">,</span> <span class="mi">5</span><span class="p">,</span> <span class="mi">50</span><span class="p">)</span>
<span class="n">data1</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">LabelledCollection</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">)</span>
<span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">200</span><span class="p">)</span>
<span class="n">y</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">randint</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">200</span><span class="p">)</span>
<span class="n">data2</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">LabelledCollection</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">)</span>
<span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">100</span><span class="p">)</span>
<span class="n">y</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">randint</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">6</span><span class="p">,</span> <span class="mi">100</span><span class="p">)</span>
<span class="n">data3</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">LabelledCollection</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">)</span>
<span class="n">combined</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">LabelledCollection</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">data1</span><span class="p">,</span> <span class="n">data2</span><span class="p">,</span> <span class="n">data3</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertEqual</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">combined</span><span class="p">),</span> <span class="nb">len</span><span class="p">(</span><span class="n">data1</span><span class="p">)</span><span class="o">+</span><span class="nb">len</span><span class="p">(</span><span class="n">data2</span><span class="p">)</span><span class="o">+</span><span class="nb">len</span><span class="p">(</span><span class="n">data3</span><span class="p">))</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertEqual</span><span class="p">(</span><span class="nb">all</span><span class="p">(</span><span class="n">combined</span><span class="o">.</span><span class="n">classes_</span> <span class="o">==</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">6</span><span class="p">)),</span> <span class="kc">True</span><span class="p">)</span>
<span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">rand</span><span class="p">(</span><span class="mi">10</span><span class="p">,</span> <span class="mi">3</span><span class="p">)</span>
<span class="n">y</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">randint</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">10</span><span class="p">)</span>
<span class="n">data4</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">LabelledCollection</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">)</span>
<span class="k">with</span> <span class="bp">self</span><span class="o">.</span><span class="n">assertRaises</span><span class="p">(</span><span class="ne">Exception</span><span class="p">):</span>
<span class="n">combined</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">LabelledCollection</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">data1</span><span class="p">,</span> <span class="n">data2</span><span class="p">,</span> <span class="n">data3</span><span class="p">,</span> <span class="n">data4</span><span class="p">)</span>
<span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">rand</span><span class="p">(</span><span class="mi">20</span><span class="p">,</span> <span class="mi">3</span><span class="p">)</span>
<span class="n">y</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">randint</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">20</span><span class="p">)</span>
<span class="n">data5</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">LabelledCollection</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">)</span>
<span class="n">combined</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">LabelledCollection</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">data4</span><span class="p">,</span> <span class="n">data5</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertEqual</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">combined</span><span class="p">),</span> <span class="nb">len</span><span class="p">(</span><span class="n">data4</span><span class="p">)</span><span class="o">+</span><span class="nb">len</span><span class="p">(</span><span class="n">data5</span><span class="p">))</span>
<span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">rand</span><span class="p">(</span><span class="mi">10</span><span class="p">,</span> <span class="mi">4</span><span class="p">)</span>
<span class="n">y</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">randint</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">10</span><span class="p">)</span>
<span class="n">data6</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">LabelledCollection</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">)</span>
<span class="k">with</span> <span class="bp">self</span><span class="o">.</span><span class="n">assertRaises</span><span class="p">(</span><span class="ne">Exception</span><span class="p">):</span>
<span class="n">combined</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">LabelledCollection</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">data4</span><span class="p">,</span> <span class="n">data5</span><span class="p">,</span> <span class="n">data6</span><span class="p">)</span>
<span class="n">data4</span><span class="o">.</span><span class="n">instances</span> <span class="o">=</span> <span class="n">csr_matrix</span><span class="p">(</span><span class="n">data4</span><span class="o">.</span><span class="n">instances</span><span class="p">)</span>
<span class="k">with</span> <span class="bp">self</span><span class="o">.</span><span class="n">assertRaises</span><span class="p">(</span><span class="ne">Exception</span><span class="p">):</span>
<span class="n">combined</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">LabelledCollection</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">data4</span><span class="p">,</span> <span class="n">data5</span><span class="p">)</span>
<span class="n">data5</span><span class="o">.</span><span class="n">instances</span> <span class="o">=</span> <span class="n">csr_matrix</span><span class="p">(</span><span class="n">data5</span><span class="o">.</span><span class="n">instances</span><span class="p">)</span>
<span class="n">combined</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">LabelledCollection</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">data4</span><span class="p">,</span> <span class="n">data5</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertEqual</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">combined</span><span class="p">),</span> <span class="nb">len</span><span class="p">(</span><span class="n">data4</span><span class="p">)</span> <span class="o">+</span> <span class="nb">len</span><span class="p">(</span><span class="n">data5</span><span class="p">))</span></div>
</div>
<span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s1">&#39;__main__&#39;</span><span class="p">:</span>
<span class="n">unittest</span><span class="o">.</span><span class="n">main</span><span class="p">()</span>
</pre></div>
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<h1>Source code for quapy.tests.test_methods</h1><div class="highlight"><pre>
<span></span><span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
<span class="kn">import</span> <span class="nn">pytest</span>
<span class="kn">from</span> <span class="nn">sklearn.linear_model</span> <span class="kn">import</span> <span class="n">LogisticRegression</span>
<span class="kn">from</span> <span class="nn">sklearn.svm</span> <span class="kn">import</span> <span class="n">LinearSVC</span>
<span class="kn">import</span> <span class="nn">method.aggregative</span>
<span class="kn">import</span> <span class="nn">quapy</span> <span class="k">as</span> <span class="nn">qp</span>
<span class="kn">from</span> <span class="nn">quapy.model_selection</span> <span class="kn">import</span> <span class="n">GridSearchQ</span>
<span class="kn">from</span> <span class="nn">quapy.method.base</span> <span class="kn">import</span> <span class="n">BinaryQuantifier</span>
<span class="kn">from</span> <span class="nn">quapy.data</span> <span class="kn">import</span> <span class="n">Dataset</span><span class="p">,</span> <span class="n">LabelledCollection</span>
<span class="kn">from</span> <span class="nn">quapy.method</span> <span class="kn">import</span> <span class="n">AGGREGATIVE_METHODS</span><span class="p">,</span> <span class="n">NON_AGGREGATIVE_METHODS</span>
<span class="kn">from</span> <span class="nn">quapy.method.meta</span> <span class="kn">import</span> <span class="n">Ensemble</span>
<span class="kn">from</span> <span class="nn">quapy.protocol</span> <span class="kn">import</span> <span class="n">APP</span>
<span class="kn">from</span> <span class="nn">quapy.method.aggregative</span> <span class="kn">import</span> <span class="n">DMy</span>
<span class="kn">from</span> <span class="nn">quapy.method.meta</span> <span class="kn">import</span> <span class="n">MedianEstimator</span>
<span class="c1"># datasets = [pytest.param(qp.datasets.fetch_twitter(&#39;hcr&#39;, pickle=True), id=&#39;hcr&#39;),</span>
<span class="c1"># pytest.param(qp.datasets.fetch_UCIDataset(&#39;ionosphere&#39;), id=&#39;ionosphere&#39;)]</span>
<span class="n">tinydatasets</span> <span class="o">=</span> <span class="p">[</span><span class="n">pytest</span><span class="o">.</span><span class="n">param</span><span class="p">(</span><span class="n">qp</span><span class="o">.</span><span class="n">datasets</span><span class="o">.</span><span class="n">fetch_twitter</span><span class="p">(</span><span class="s1">&#39;hcr&#39;</span><span class="p">,</span> <span class="n">pickle</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span><span class="o">.</span><span class="n">reduce</span><span class="p">(),</span> <span class="nb">id</span><span class="o">=</span><span class="s1">&#39;tiny_hcr&#39;</span><span class="p">),</span>
<span class="n">pytest</span><span class="o">.</span><span class="n">param</span><span class="p">(</span><span class="n">qp</span><span class="o">.</span><span class="n">datasets</span><span class="o">.</span><span class="n">fetch_UCIBinaryDataset</span><span class="p">(</span><span class="s1">&#39;ionosphere&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">reduce</span><span class="p">(),</span> <span class="nb">id</span><span class="o">=</span><span class="s1">&#39;tiny_ionosphere&#39;</span><span class="p">)]</span>
<span class="n">learners</span> <span class="o">=</span> <span class="p">[</span><span class="n">LogisticRegression</span><span class="p">,</span> <span class="n">LinearSVC</span><span class="p">]</span>
<div class="viewcode-block" id="test_aggregative_methods">
<a class="viewcode-back" href="../../../quapy.tests.html#quapy.tests.test_methods.test_aggregative_methods">[docs]</a>
<span class="nd">@pytest</span><span class="o">.</span><span class="n">mark</span><span class="o">.</span><span class="n">parametrize</span><span class="p">(</span><span class="s1">&#39;dataset&#39;</span><span class="p">,</span> <span class="n">tinydatasets</span><span class="p">)</span>
<span class="nd">@pytest</span><span class="o">.</span><span class="n">mark</span><span class="o">.</span><span class="n">parametrize</span><span class="p">(</span><span class="s1">&#39;aggregative_method&#39;</span><span class="p">,</span> <span class="n">AGGREGATIVE_METHODS</span><span class="p">)</span>
<span class="nd">@pytest</span><span class="o">.</span><span class="n">mark</span><span class="o">.</span><span class="n">parametrize</span><span class="p">(</span><span class="s1">&#39;learner&#39;</span><span class="p">,</span> <span class="n">learners</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">test_aggregative_methods</span><span class="p">(</span><span class="n">dataset</span><span class="p">:</span> <span class="n">Dataset</span><span class="p">,</span> <span class="n">aggregative_method</span><span class="p">,</span> <span class="n">learner</span><span class="p">):</span>
<span class="n">model</span> <span class="o">=</span> <span class="n">aggregative_method</span><span class="p">(</span><span class="n">learner</span><span class="p">())</span>
<span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="n">BinaryQuantifier</span><span class="p">)</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">dataset</span><span class="o">.</span><span class="n">binary</span><span class="p">:</span>
<span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;skipping the test of binary model </span><span class="si">{</span><span class="nb">type</span><span class="p">(</span><span class="n">model</span><span class="p">)</span><span class="si">}</span><span class="s1"> on non-binary dataset </span><span class="si">{</span><span class="n">dataset</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="k">return</span>
<span class="n">model</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="n">dataset</span><span class="o">.</span><span class="n">training</span><span class="p">)</span>
<span class="n">estim_prevalences</span> <span class="o">=</span> <span class="n">model</span><span class="o">.</span><span class="n">quantify</span><span class="p">(</span><span class="n">dataset</span><span class="o">.</span><span class="n">test</span><span class="o">.</span><span class="n">instances</span><span class="p">)</span>
<span class="n">true_prevalences</span> <span class="o">=</span> <span class="n">dataset</span><span class="o">.</span><span class="n">test</span><span class="o">.</span><span class="n">prevalence</span><span class="p">()</span>
<span class="n">error</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">error</span><span class="o">.</span><span class="n">mae</span><span class="p">(</span><span class="n">true_prevalences</span><span class="p">,</span> <span class="n">estim_prevalences</span><span class="p">)</span>
<span class="k">assert</span> <span class="nb">type</span><span class="p">(</span><span class="n">error</span><span class="p">)</span> <span class="o">==</span> <span class="n">np</span><span class="o">.</span><span class="n">float64</span></div>
<div class="viewcode-block" id="test_non_aggregative_methods">
<a class="viewcode-back" href="../../../quapy.tests.html#quapy.tests.test_methods.test_non_aggregative_methods">[docs]</a>
<span class="nd">@pytest</span><span class="o">.</span><span class="n">mark</span><span class="o">.</span><span class="n">parametrize</span><span class="p">(</span><span class="s1">&#39;dataset&#39;</span><span class="p">,</span> <span class="n">tinydatasets</span><span class="p">)</span>
<span class="nd">@pytest</span><span class="o">.</span><span class="n">mark</span><span class="o">.</span><span class="n">parametrize</span><span class="p">(</span><span class="s1">&#39;non_aggregative_method&#39;</span><span class="p">,</span> <span class="n">NON_AGGREGATIVE_METHODS</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">test_non_aggregative_methods</span><span class="p">(</span><span class="n">dataset</span><span class="p">:</span> <span class="n">Dataset</span><span class="p">,</span> <span class="n">non_aggregative_method</span><span class="p">):</span>
<span class="n">model</span> <span class="o">=</span> <span class="n">non_aggregative_method</span><span class="p">()</span>
<span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="n">BinaryQuantifier</span><span class="p">)</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">dataset</span><span class="o">.</span><span class="n">binary</span><span class="p">:</span>
<span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;skipping the test of binary model </span><span class="si">{</span><span class="n">model</span><span class="si">}</span><span class="s1"> on non-binary dataset </span><span class="si">{</span><span class="n">dataset</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="k">return</span>
<span class="n">model</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="n">dataset</span><span class="o">.</span><span class="n">training</span><span class="p">)</span>
<span class="n">estim_prevalences</span> <span class="o">=</span> <span class="n">model</span><span class="o">.</span><span class="n">quantify</span><span class="p">(</span><span class="n">dataset</span><span class="o">.</span><span class="n">test</span><span class="o">.</span><span class="n">instances</span><span class="p">)</span>
<span class="n">true_prevalences</span> <span class="o">=</span> <span class="n">dataset</span><span class="o">.</span><span class="n">test</span><span class="o">.</span><span class="n">prevalence</span><span class="p">()</span>
<span class="n">error</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">error</span><span class="o">.</span><span class="n">mae</span><span class="p">(</span><span class="n">true_prevalences</span><span class="p">,</span> <span class="n">estim_prevalences</span><span class="p">)</span>
<span class="k">assert</span> <span class="nb">type</span><span class="p">(</span><span class="n">error</span><span class="p">)</span> <span class="o">==</span> <span class="n">np</span><span class="o">.</span><span class="n">float64</span></div>
<div class="viewcode-block" id="test_ensemble_method">
<a class="viewcode-back" href="../../../quapy.tests.html#quapy.tests.test_methods.test_ensemble_method">[docs]</a>
<span class="nd">@pytest</span><span class="o">.</span><span class="n">mark</span><span class="o">.</span><span class="n">parametrize</span><span class="p">(</span><span class="s1">&#39;base_method&#39;</span><span class="p">,</span> <span class="p">[</span><span class="n">method</span><span class="o">.</span><span class="n">aggregative</span><span class="o">.</span><span class="n">ACC</span><span class="p">,</span> <span class="n">method</span><span class="o">.</span><span class="n">aggregative</span><span class="o">.</span><span class="n">PACC</span><span class="p">])</span>
<span class="nd">@pytest</span><span class="o">.</span><span class="n">mark</span><span class="o">.</span><span class="n">parametrize</span><span class="p">(</span><span class="s1">&#39;learner&#39;</span><span class="p">,</span> <span class="p">[</span><span class="n">LogisticRegression</span><span class="p">])</span>
<span class="nd">@pytest</span><span class="o">.</span><span class="n">mark</span><span class="o">.</span><span class="n">parametrize</span><span class="p">(</span><span class="s1">&#39;dataset&#39;</span><span class="p">,</span> <span class="n">tinydatasets</span><span class="p">)</span>
<span class="nd">@pytest</span><span class="o">.</span><span class="n">mark</span><span class="o">.</span><span class="n">parametrize</span><span class="p">(</span><span class="s1">&#39;policy&#39;</span><span class="p">,</span> <span class="n">Ensemble</span><span class="o">.</span><span class="n">VALID_POLICIES</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">test_ensemble_method</span><span class="p">(</span><span class="n">base_method</span><span class="p">,</span> <span class="n">learner</span><span class="p">,</span> <span class="n">dataset</span><span class="p">:</span> <span class="n">Dataset</span><span class="p">,</span> <span class="n">policy</span><span class="p">):</span>
<span class="n">qp</span><span class="o">.</span><span class="n">environ</span><span class="p">[</span><span class="s1">&#39;SAMPLE_SIZE&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="mi">20</span>
<span class="n">base_quantifier</span><span class="o">=</span><span class="n">base_method</span><span class="p">(</span><span class="n">learner</span><span class="p">())</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">dataset</span><span class="o">.</span><span class="n">binary</span> <span class="ow">and</span> <span class="n">policy</span><span class="o">==</span><span class="s1">&#39;ds&#39;</span><span class="p">:</span>
<span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;skipping the test of binary policy ds on non-binary dataset </span><span class="si">{</span><span class="n">dataset</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="k">return</span>
<span class="n">model</span> <span class="o">=</span> <span class="n">Ensemble</span><span class="p">(</span><span class="n">quantifier</span><span class="o">=</span><span class="n">base_quantifier</span><span class="p">,</span> <span class="n">size</span><span class="o">=</span><span class="mi">3</span><span class="p">,</span> <span class="n">policy</span><span class="o">=</span><span class="n">policy</span><span class="p">,</span> <span class="n">n_jobs</span><span class="o">=-</span><span class="mi">1</span><span class="p">)</span>
<span class="n">model</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="n">dataset</span><span class="o">.</span><span class="n">training</span><span class="p">)</span>
<span class="n">estim_prevalences</span> <span class="o">=</span> <span class="n">model</span><span class="o">.</span><span class="n">quantify</span><span class="p">(</span><span class="n">dataset</span><span class="o">.</span><span class="n">test</span><span class="o">.</span><span class="n">instances</span><span class="p">)</span>
<span class="n">true_prevalences</span> <span class="o">=</span> <span class="n">dataset</span><span class="o">.</span><span class="n">test</span><span class="o">.</span><span class="n">prevalence</span><span class="p">()</span>
<span class="n">error</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">error</span><span class="o">.</span><span class="n">mae</span><span class="p">(</span><span class="n">true_prevalences</span><span class="p">,</span> <span class="n">estim_prevalences</span><span class="p">)</span>
<span class="k">assert</span> <span class="nb">type</span><span class="p">(</span><span class="n">error</span><span class="p">)</span> <span class="o">==</span> <span class="n">np</span><span class="o">.</span><span class="n">float64</span></div>
<div class="viewcode-block" id="test_quanet_method">
<a class="viewcode-back" href="../../../quapy.tests.html#quapy.tests.test_methods.test_quanet_method">[docs]</a>
<span class="k">def</span> <span class="nf">test_quanet_method</span><span class="p">():</span>
<span class="k">try</span><span class="p">:</span>
<span class="kn">import</span> <span class="nn">quapy.classification.neural</span>
<span class="k">except</span> <span class="ne">ModuleNotFoundError</span><span class="p">:</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">&#39;skipping QuaNet test due to missing torch package&#39;</span><span class="p">)</span>
<span class="k">return</span>
<span class="n">qp</span><span class="o">.</span><span class="n">environ</span><span class="p">[</span><span class="s1">&#39;SAMPLE_SIZE&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="mi">100</span>
<span class="c1"># load the kindle dataset as text, and convert words to numerical indexes</span>
<span class="n">dataset</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">datasets</span><span class="o">.</span><span class="n">fetch_reviews</span><span class="p">(</span><span class="s1">&#39;kindle&#39;</span><span class="p">,</span> <span class="n">pickle</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span><span class="o">.</span><span class="n">reduce</span><span class="p">(</span><span class="mi">200</span><span class="p">,</span> <span class="mi">200</span><span class="p">)</span>
<span class="n">qp</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">preprocessing</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="n">dataset</span><span class="p">,</span> <span class="n">min_df</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="kn">from</span> <span class="nn">quapy.classification.neural</span> <span class="kn">import</span> <span class="n">CNNnet</span>
<span class="n">cnn</span> <span class="o">=</span> <span class="n">CNNnet</span><span class="p">(</span><span class="n">dataset</span><span class="o">.</span><span class="n">vocabulary_size</span><span class="p">,</span> <span class="n">dataset</span><span class="o">.</span><span class="n">n_classes</span><span class="p">)</span>
<span class="kn">from</span> <span class="nn">quapy.classification.neural</span> <span class="kn">import</span> <span class="n">NeuralClassifierTrainer</span>
<span class="n">learner</span> <span class="o">=</span> <span class="n">NeuralClassifierTrainer</span><span class="p">(</span><span class="n">cnn</span><span class="p">,</span> <span class="n">device</span><span class="o">=</span><span class="s1">&#39;cuda&#39;</span><span class="p">)</span>
<span class="kn">from</span> <span class="nn">quapy.method.meta</span> <span class="kn">import</span> <span class="n">QuaNet</span>
<span class="n">model</span> <span class="o">=</span> <span class="n">QuaNet</span><span class="p">(</span><span class="n">learner</span><span class="p">,</span> <span class="n">device</span><span class="o">=</span><span class="s1">&#39;cuda&#39;</span><span class="p">)</span>
<span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="n">BinaryQuantifier</span><span class="p">)</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">dataset</span><span class="o">.</span><span class="n">binary</span><span class="p">:</span>
<span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;skipping the test of binary model </span><span class="si">{</span><span class="n">model</span><span class="si">}</span><span class="s1"> on non-binary dataset </span><span class="si">{</span><span class="n">dataset</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="k">return</span>
<span class="n">model</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="n">dataset</span><span class="o">.</span><span class="n">training</span><span class="p">)</span>
<span class="n">estim_prevalences</span> <span class="o">=</span> <span class="n">model</span><span class="o">.</span><span class="n">quantify</span><span class="p">(</span><span class="n">dataset</span><span class="o">.</span><span class="n">test</span><span class="o">.</span><span class="n">instances</span><span class="p">)</span>
<span class="n">true_prevalences</span> <span class="o">=</span> <span class="n">dataset</span><span class="o">.</span><span class="n">test</span><span class="o">.</span><span class="n">prevalence</span><span class="p">()</span>
<span class="n">error</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">error</span><span class="o">.</span><span class="n">mae</span><span class="p">(</span><span class="n">true_prevalences</span><span class="p">,</span> <span class="n">estim_prevalences</span><span class="p">)</span>
<span class="k">assert</span> <span class="nb">type</span><span class="p">(</span><span class="n">error</span><span class="p">)</span> <span class="o">==</span> <span class="n">np</span><span class="o">.</span><span class="n">float64</span></div>
<div class="viewcode-block" id="test_str_label_names">
<a class="viewcode-back" href="../../../quapy.tests.html#quapy.tests.test_methods.test_str_label_names">[docs]</a>
<span class="k">def</span> <span class="nf">test_str_label_names</span><span class="p">():</span>
<span class="n">model</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">method</span><span class="o">.</span><span class="n">aggregative</span><span class="o">.</span><span class="n">CC</span><span class="p">(</span><span class="n">LogisticRegression</span><span class="p">())</span>
<span class="n">dataset</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">datasets</span><span class="o">.</span><span class="n">fetch_reviews</span><span class="p">(</span><span class="s1">&#39;imdb&#39;</span><span class="p">,</span> <span class="n">pickle</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="n">dataset</span> <span class="o">=</span> <span class="n">Dataset</span><span class="p">(</span><span class="n">dataset</span><span class="o">.</span><span class="n">training</span><span class="o">.</span><span class="n">sampling</span><span class="p">(</span><span class="mi">1000</span><span class="p">,</span> <span class="o">*</span><span class="n">dataset</span><span class="o">.</span><span class="n">training</span><span class="o">.</span><span class="n">prevalence</span><span class="p">()),</span>
<span class="n">dataset</span><span class="o">.</span><span class="n">test</span><span class="o">.</span><span class="n">sampling</span><span class="p">(</span><span class="mi">1000</span><span class="p">,</span> <span class="mf">0.25</span><span class="p">,</span> <span class="mf">0.75</span><span class="p">))</span>
<span class="n">qp</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">preprocessing</span><span class="o">.</span><span class="n">text2tfidf</span><span class="p">(</span><span class="n">dataset</span><span class="p">,</span> <span class="n">min_df</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">seed</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
<span class="n">model</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="n">dataset</span><span class="o">.</span><span class="n">training</span><span class="p">)</span>
<span class="n">int_estim_prevalences</span> <span class="o">=</span> <span class="n">model</span><span class="o">.</span><span class="n">quantify</span><span class="p">(</span><span class="n">dataset</span><span class="o">.</span><span class="n">test</span><span class="o">.</span><span class="n">instances</span><span class="p">)</span>
<span class="n">true_prevalences</span> <span class="o">=</span> <span class="n">dataset</span><span class="o">.</span><span class="n">test</span><span class="o">.</span><span class="n">prevalence</span><span class="p">()</span>
<span class="n">error</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">error</span><span class="o">.</span><span class="n">mae</span><span class="p">(</span><span class="n">true_prevalences</span><span class="p">,</span> <span class="n">int_estim_prevalences</span><span class="p">)</span>
<span class="k">assert</span> <span class="nb">type</span><span class="p">(</span><span class="n">error</span><span class="p">)</span> <span class="o">==</span> <span class="n">np</span><span class="o">.</span><span class="n">float64</span>
<span class="n">dataset_str</span> <span class="o">=</span> <span class="n">Dataset</span><span class="p">(</span><span class="n">LabelledCollection</span><span class="p">(</span><span class="n">dataset</span><span class="o">.</span><span class="n">training</span><span class="o">.</span><span class="n">instances</span><span class="p">,</span>
<span class="p">[</span><span class="s1">&#39;one&#39;</span> <span class="k">if</span> <span class="n">label</span> <span class="o">==</span> <span class="mi">1</span> <span class="k">else</span> <span class="s1">&#39;zero&#39;</span> <span class="k">for</span> <span class="n">label</span> <span class="ow">in</span> <span class="n">dataset</span><span class="o">.</span><span class="n">training</span><span class="o">.</span><span class="n">labels</span><span class="p">]),</span>
<span class="n">LabelledCollection</span><span class="p">(</span><span class="n">dataset</span><span class="o">.</span><span class="n">test</span><span class="o">.</span><span class="n">instances</span><span class="p">,</span>
<span class="p">[</span><span class="s1">&#39;one&#39;</span> <span class="k">if</span> <span class="n">label</span> <span class="o">==</span> <span class="mi">1</span> <span class="k">else</span> <span class="s1">&#39;zero&#39;</span> <span class="k">for</span> <span class="n">label</span> <span class="ow">in</span> <span class="n">dataset</span><span class="o">.</span><span class="n">test</span><span class="o">.</span><span class="n">labels</span><span class="p">]))</span>
<span class="k">assert</span> <span class="nb">all</span><span class="p">(</span><span class="n">dataset_str</span><span class="o">.</span><span class="n">training</span><span class="o">.</span><span class="n">classes_</span> <span class="o">==</span> <span class="n">dataset_str</span><span class="o">.</span><span class="n">test</span><span class="o">.</span><span class="n">classes_</span><span class="p">),</span> <span class="s1">&#39;wrong indexation&#39;</span>
<span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">seed</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
<span class="n">model</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="n">dataset_str</span><span class="o">.</span><span class="n">training</span><span class="p">)</span>
<span class="n">str_estim_prevalences</span> <span class="o">=</span> <span class="n">model</span><span class="o">.</span><span class="n">quantify</span><span class="p">(</span><span class="n">dataset_str</span><span class="o">.</span><span class="n">test</span><span class="o">.</span><span class="n">instances</span><span class="p">)</span>
<span class="n">true_prevalences</span> <span class="o">=</span> <span class="n">dataset_str</span><span class="o">.</span><span class="n">test</span><span class="o">.</span><span class="n">prevalence</span><span class="p">()</span>
<span class="n">error</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">error</span><span class="o">.</span><span class="n">mae</span><span class="p">(</span><span class="n">true_prevalences</span><span class="p">,</span> <span class="n">str_estim_prevalences</span><span class="p">)</span>
<span class="k">assert</span> <span class="nb">type</span><span class="p">(</span><span class="n">error</span><span class="p">)</span> <span class="o">==</span> <span class="n">np</span><span class="o">.</span><span class="n">float64</span>
<span class="nb">print</span><span class="p">(</span><span class="n">true_prevalences</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">int_estim_prevalences</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">str_estim_prevalences</span><span class="p">)</span>
<span class="n">np</span><span class="o">.</span><span class="n">testing</span><span class="o">.</span><span class="n">assert_almost_equal</span><span class="p">(</span><span class="n">int_estim_prevalences</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
<span class="n">str_estim_prevalences</span><span class="p">[</span><span class="nb">list</span><span class="p">(</span><span class="n">model</span><span class="o">.</span><span class="n">classes_</span><span class="p">)</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="s1">&#39;one&#39;</span><span class="p">)])</span></div>
<span class="c1"># helper</span>
<span class="k">def</span> <span class="nf">__fit_test</span><span class="p">(</span><span class="n">quantifier</span><span class="p">,</span> <span class="n">train</span><span class="p">,</span> <span class="n">test</span><span class="p">):</span>
<span class="n">quantifier</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="n">train</span><span class="p">)</span>
<span class="n">test_samples</span> <span class="o">=</span> <span class="n">APP</span><span class="p">(</span><span class="n">test</span><span class="p">)</span>
<span class="n">true_prevs</span><span class="p">,</span> <span class="n">estim_prevs</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">evaluation</span><span class="o">.</span><span class="n">prediction</span><span class="p">(</span><span class="n">quantifier</span><span class="p">,</span> <span class="n">test_samples</span><span class="p">)</span>
<span class="k">return</span> <span class="n">qp</span><span class="o">.</span><span class="n">error</span><span class="o">.</span><span class="n">mae</span><span class="p">(</span><span class="n">true_prevs</span><span class="p">,</span> <span class="n">estim_prevs</span><span class="p">),</span> <span class="n">estim_prevs</span>
<div class="viewcode-block" id="test_median_meta">
<a class="viewcode-back" href="../../../quapy.tests.html#quapy.tests.test_methods.test_median_meta">[docs]</a>
<span class="k">def</span> <span class="nf">test_median_meta</span><span class="p">():</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> This test compares the performance of the MedianQuantifier with respect to computing the median of the predictions</span>
<span class="sd"> of a differently parameterized quantifier. We use the DistributionMatching base quantifier and the median is</span>
<span class="sd"> computed across different values of nbins</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">qp</span><span class="o">.</span><span class="n">environ</span><span class="p">[</span><span class="s1">&#39;SAMPLE_SIZE&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="mi">100</span>
<span class="c1"># grid of values</span>
<span class="n">nbins_grid</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">range</span><span class="p">(</span><span class="mi">2</span><span class="p">,</span> <span class="mi">11</span><span class="p">))</span>
<span class="n">dataset</span> <span class="o">=</span> <span class="s1">&#39;kindle&#39;</span>
<span class="n">train</span><span class="p">,</span> <span class="n">test</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">datasets</span><span class="o">.</span><span class="n">fetch_reviews</span><span class="p">(</span><span class="n">dataset</span><span class="p">,</span> <span class="n">tfidf</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">min_df</span><span class="o">=</span><span class="mi">10</span><span class="p">)</span><span class="o">.</span><span class="n">train_test</span>
<span class="n">prevs</span> <span class="o">=</span> <span class="p">[]</span>
<span class="n">errors</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">nbins</span> <span class="ow">in</span> <span class="n">nbins_grid</span><span class="p">:</span>
<span class="k">with</span> <span class="n">qp</span><span class="o">.</span><span class="n">util</span><span class="o">.</span><span class="n">temp_seed</span><span class="p">(</span><span class="mi">0</span><span class="p">):</span>
<span class="n">q</span> <span class="o">=</span> <span class="n">DMy</span><span class="p">(</span><span class="n">LogisticRegression</span><span class="p">(),</span> <span class="n">nbins</span><span class="o">=</span><span class="n">nbins</span><span class="p">)</span>
<span class="n">mae</span><span class="p">,</span> <span class="n">estim_prevs</span> <span class="o">=</span> <span class="n">__fit_test</span><span class="p">(</span><span class="n">q</span><span class="p">,</span> <span class="n">train</span><span class="p">,</span> <span class="n">test</span><span class="p">)</span>
<span class="n">prevs</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">estim_prevs</span><span class="p">)</span>
<span class="n">errors</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">mae</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">dataset</span><span class="si">}</span><span class="s1"> DistributionMatching(nbins=</span><span class="si">{</span><span class="n">nbins</span><span class="si">}</span><span class="s1">) got MAE </span><span class="si">{</span><span class="n">mae</span><span class="si">:</span><span class="s1">.4f</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="n">prevs</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">prevs</span><span class="p">)</span>
<span class="n">mae</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">errors</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">MAE=</span><span class="si">{</span><span class="n">mae</span><span class="si">:</span><span class="s1">.4f</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="n">q</span> <span class="o">=</span> <span class="n">DMy</span><span class="p">(</span><span class="n">LogisticRegression</span><span class="p">())</span>
<span class="n">q</span> <span class="o">=</span> <span class="n">MedianEstimator</span><span class="p">(</span><span class="n">q</span><span class="p">,</span> <span class="n">param_grid</span><span class="o">=</span><span class="p">{</span><span class="s1">&#39;nbins&#39;</span><span class="p">:</span> <span class="n">nbins_grid</span><span class="p">},</span> <span class="n">random_state</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">n_jobs</span><span class="o">=-</span><span class="mi">1</span><span class="p">)</span>
<span class="n">median_mae</span><span class="p">,</span> <span class="n">prev</span> <span class="o">=</span> <span class="n">__fit_test</span><span class="p">(</span><span class="n">q</span><span class="p">,</span> <span class="n">train</span><span class="p">,</span> <span class="n">test</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">MAE=</span><span class="si">{</span><span class="n">median_mae</span><span class="si">:</span><span class="s1">.4f</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="n">np</span><span class="o">.</span><span class="n">testing</span><span class="o">.</span><span class="n">assert_almost_equal</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">median</span><span class="p">(</span><span class="n">prevs</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">),</span> <span class="n">prev</span><span class="p">)</span>
<span class="k">assert</span> <span class="n">median_mae</span> <span class="o">&lt;</span> <span class="n">mae</span><span class="p">,</span> <span class="s1">&#39;the median-based quantifier provided a higher error...&#39;</span></div>
<div class="viewcode-block" id="test_median_meta_modsel">
<a class="viewcode-back" href="../../../quapy.tests.html#quapy.tests.test_methods.test_median_meta_modsel">[docs]</a>
<span class="k">def</span> <span class="nf">test_median_meta_modsel</span><span class="p">():</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> This test checks the median-meta quantifier with model selection</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">qp</span><span class="o">.</span><span class="n">environ</span><span class="p">[</span><span class="s1">&#39;SAMPLE_SIZE&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="mi">100</span>
<span class="n">dataset</span> <span class="o">=</span> <span class="s1">&#39;kindle&#39;</span>
<span class="n">train</span><span class="p">,</span> <span class="n">test</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">datasets</span><span class="o">.</span><span class="n">fetch_reviews</span><span class="p">(</span><span class="n">dataset</span><span class="p">,</span> <span class="n">tfidf</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">min_df</span><span class="o">=</span><span class="mi">10</span><span class="p">)</span><span class="o">.</span><span class="n">train_test</span>
<span class="n">train</span><span class="p">,</span> <span class="n">val</span> <span class="o">=</span> <span class="n">train</span><span class="o">.</span><span class="n">split_stratified</span><span class="p">(</span><span class="n">random_state</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
<span class="n">nbins_grid</span> <span class="o">=</span> <span class="p">[</span><span class="mi">2</span><span class="p">,</span> <span class="mi">4</span><span class="p">,</span> <span class="mi">5</span><span class="p">,</span> <span class="mi">10</span><span class="p">,</span> <span class="mi">15</span><span class="p">]</span>
<span class="n">q</span> <span class="o">=</span> <span class="n">DMy</span><span class="p">(</span><span class="n">LogisticRegression</span><span class="p">())</span>
<span class="n">q</span> <span class="o">=</span> <span class="n">MedianEstimator</span><span class="p">(</span><span class="n">q</span><span class="p">,</span> <span class="n">param_grid</span><span class="o">=</span><span class="p">{</span><span class="s1">&#39;nbins&#39;</span><span class="p">:</span> <span class="n">nbins_grid</span><span class="p">},</span> <span class="n">random_state</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">n_jobs</span><span class="o">=-</span><span class="mi">1</span><span class="p">)</span>
<span class="n">median_mae</span><span class="p">,</span> <span class="n">_</span> <span class="o">=</span> <span class="n">__fit_test</span><span class="p">(</span><span class="n">q</span><span class="p">,</span> <span class="n">train</span><span class="p">,</span> <span class="n">test</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">MAE=</span><span class="si">{</span><span class="n">median_mae</span><span class="si">:</span><span class="s1">.4f</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="n">q</span> <span class="o">=</span> <span class="n">DMy</span><span class="p">(</span><span class="n">LogisticRegression</span><span class="p">())</span>
<span class="n">lr_params</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;classifier__C&#39;</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">logspace</span><span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">3</span><span class="p">)}</span>
<span class="n">q</span> <span class="o">=</span> <span class="n">MedianEstimator</span><span class="p">(</span><span class="n">q</span><span class="p">,</span> <span class="n">param_grid</span><span class="o">=</span><span class="p">{</span><span class="s1">&#39;nbins&#39;</span><span class="p">:</span> <span class="n">nbins_grid</span><span class="p">},</span> <span class="n">random_state</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">n_jobs</span><span class="o">=-</span><span class="mi">1</span><span class="p">)</span>
<span class="n">q</span> <span class="o">=</span> <span class="n">GridSearchQ</span><span class="p">(</span><span class="n">q</span><span class="p">,</span> <span class="n">param_grid</span><span class="o">=</span><span class="n">lr_params</span><span class="p">,</span> <span class="n">protocol</span><span class="o">=</span><span class="n">APP</span><span class="p">(</span><span class="n">val</span><span class="p">),</span> <span class="n">n_jobs</span><span class="o">=-</span><span class="mi">1</span><span class="p">)</span>
<span class="n">optimized_median_ave</span><span class="p">,</span> <span class="n">_</span> <span class="o">=</span> <span class="n">__fit_test</span><span class="p">(</span><span class="n">q</span><span class="p">,</span> <span class="n">train</span><span class="p">,</span> <span class="n">test</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">MAE=</span><span class="si">{</span><span class="n">optimized_median_ave</span><span class="si">:</span><span class="s1">.4f</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="k">assert</span> <span class="n">optimized_median_ave</span> <span class="o">&lt;</span> <span class="n">median_mae</span><span class="p">,</span> <span class="s2">&quot;the optimized method yielded worse performance...&quot;</span></div>
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<h1>Source code for quapy.tests.test_modsel</h1><div class="highlight"><pre>
<span></span><span class="kn">import</span> <span class="nn">unittest</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
<span class="kn">from</span> <span class="nn">sklearn.linear_model</span> <span class="kn">import</span> <span class="n">LogisticRegression</span>
<span class="kn">from</span> <span class="nn">sklearn.svm</span> <span class="kn">import</span> <span class="n">SVC</span>
<span class="kn">import</span> <span class="nn">quapy</span> <span class="k">as</span> <span class="nn">qp</span>
<span class="kn">from</span> <span class="nn">quapy.method.aggregative</span> <span class="kn">import</span> <span class="n">PACC</span>
<span class="kn">from</span> <span class="nn">quapy.model_selection</span> <span class="kn">import</span> <span class="n">GridSearchQ</span>
<span class="kn">from</span> <span class="nn">quapy.protocol</span> <span class="kn">import</span> <span class="n">APP</span>
<span class="kn">import</span> <span class="nn">time</span>
<div class="viewcode-block" id="ModselTestCase">
<a class="viewcode-back" href="../../../quapy.tests.html#quapy.tests.test_modsel.ModselTestCase">[docs]</a>
<span class="k">class</span> <span class="nc">ModselTestCase</span><span class="p">(</span><span class="n">unittest</span><span class="o">.</span><span class="n">TestCase</span><span class="p">):</span>
<div class="viewcode-block" id="ModselTestCase.test_modsel">
<a class="viewcode-back" href="../../../quapy.tests.html#quapy.tests.test_modsel.ModselTestCase.test_modsel">[docs]</a>
<span class="k">def</span> <span class="nf">test_modsel</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="n">q</span> <span class="o">=</span> <span class="n">PACC</span><span class="p">(</span><span class="n">LogisticRegression</span><span class="p">(</span><span class="n">random_state</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">max_iter</span><span class="o">=</span><span class="mi">5000</span><span class="p">))</span>
<span class="n">data</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">datasets</span><span class="o">.</span><span class="n">fetch_reviews</span><span class="p">(</span><span class="s1">&#39;imdb&#39;</span><span class="p">,</span> <span class="n">tfidf</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">min_df</span><span class="o">=</span><span class="mi">10</span><span class="p">)</span>
<span class="n">training</span><span class="p">,</span> <span class="n">validation</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">training</span><span class="o">.</span><span class="n">split_stratified</span><span class="p">(</span><span class="mf">0.7</span><span class="p">,</span> <span class="n">random_state</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="n">param_grid</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;classifier__C&#39;</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">logspace</span><span class="p">(</span><span class="o">-</span><span class="mi">3</span><span class="p">,</span><span class="mi">3</span><span class="p">,</span><span class="mi">7</span><span class="p">)}</span>
<span class="n">app</span> <span class="o">=</span> <span class="n">APP</span><span class="p">(</span><span class="n">validation</span><span class="p">,</span> <span class="n">sample_size</span><span class="o">=</span><span class="mi">100</span><span class="p">,</span> <span class="n">random_state</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="n">q</span> <span class="o">=</span> <span class="n">GridSearchQ</span><span class="p">(</span>
<span class="n">q</span><span class="p">,</span> <span class="n">param_grid</span><span class="p">,</span> <span class="n">protocol</span><span class="o">=</span><span class="n">app</span><span class="p">,</span> <span class="n">error</span><span class="o">=</span><span class="s1">&#39;mae&#39;</span><span class="p">,</span> <span class="n">refit</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">timeout</span><span class="o">=-</span><span class="mi">1</span><span class="p">,</span> <span class="n">verbose</span><span class="o">=</span><span class="kc">True</span>
<span class="p">)</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="n">training</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">&#39;best params&#39;</span><span class="p">,</span> <span class="n">q</span><span class="o">.</span><span class="n">best_params_</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">&#39;best score&#39;</span><span class="p">,</span> <span class="n">q</span><span class="o">.</span><span class="n">best_score_</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertEqual</span><span class="p">(</span><span class="n">q</span><span class="o">.</span><span class="n">best_params_</span><span class="p">[</span><span class="s1">&#39;classifier__C&#39;</span><span class="p">],</span> <span class="mf">10.0</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertEqual</span><span class="p">(</span><span class="n">q</span><span class="o">.</span><span class="n">best_model</span><span class="p">()</span><span class="o">.</span><span class="n">get_params</span><span class="p">()[</span><span class="s1">&#39;classifier__C&#39;</span><span class="p">],</span> <span class="mf">10.0</span><span class="p">)</span></div>
<div class="viewcode-block" id="ModselTestCase.test_modsel_parallel">
<a class="viewcode-back" href="../../../quapy.tests.html#quapy.tests.test_modsel.ModselTestCase.test_modsel_parallel">[docs]</a>
<span class="k">def</span> <span class="nf">test_modsel_parallel</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="n">q</span> <span class="o">=</span> <span class="n">PACC</span><span class="p">(</span><span class="n">LogisticRegression</span><span class="p">(</span><span class="n">random_state</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">max_iter</span><span class="o">=</span><span class="mi">5000</span><span class="p">))</span>
<span class="n">data</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">datasets</span><span class="o">.</span><span class="n">fetch_reviews</span><span class="p">(</span><span class="s1">&#39;imdb&#39;</span><span class="p">,</span> <span class="n">tfidf</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">min_df</span><span class="o">=</span><span class="mi">10</span><span class="p">)</span>
<span class="n">training</span><span class="p">,</span> <span class="n">validation</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">training</span><span class="o">.</span><span class="n">split_stratified</span><span class="p">(</span><span class="mf">0.7</span><span class="p">,</span> <span class="n">random_state</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="c1"># test = data.test</span>
<span class="n">param_grid</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;classifier__C&#39;</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">logspace</span><span class="p">(</span><span class="o">-</span><span class="mi">3</span><span class="p">,</span><span class="mi">3</span><span class="p">,</span><span class="mi">7</span><span class="p">)}</span>
<span class="n">app</span> <span class="o">=</span> <span class="n">APP</span><span class="p">(</span><span class="n">validation</span><span class="p">,</span> <span class="n">sample_size</span><span class="o">=</span><span class="mi">100</span><span class="p">,</span> <span class="n">random_state</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="n">q</span> <span class="o">=</span> <span class="n">GridSearchQ</span><span class="p">(</span>
<span class="n">q</span><span class="p">,</span> <span class="n">param_grid</span><span class="p">,</span> <span class="n">protocol</span><span class="o">=</span><span class="n">app</span><span class="p">,</span> <span class="n">error</span><span class="o">=</span><span class="s1">&#39;mae&#39;</span><span class="p">,</span> <span class="n">refit</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">timeout</span><span class="o">=-</span><span class="mi">1</span><span class="p">,</span> <span class="n">n_jobs</span><span class="o">=-</span><span class="mi">1</span><span class="p">,</span> <span class="n">verbose</span><span class="o">=</span><span class="kc">True</span>
<span class="p">)</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="n">training</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">&#39;best params&#39;</span><span class="p">,</span> <span class="n">q</span><span class="o">.</span><span class="n">best_params_</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">&#39;best score&#39;</span><span class="p">,</span> <span class="n">q</span><span class="o">.</span><span class="n">best_score_</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertEqual</span><span class="p">(</span><span class="n">q</span><span class="o">.</span><span class="n">best_params_</span><span class="p">[</span><span class="s1">&#39;classifier__C&#39;</span><span class="p">],</span> <span class="mf">10.0</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertEqual</span><span class="p">(</span><span class="n">q</span><span class="o">.</span><span class="n">best_model</span><span class="p">()</span><span class="o">.</span><span class="n">get_params</span><span class="p">()[</span><span class="s1">&#39;classifier__C&#39;</span><span class="p">],</span> <span class="mf">10.0</span><span class="p">)</span></div>
<div class="viewcode-block" id="ModselTestCase.test_modsel_parallel_speedup">
<a class="viewcode-back" href="../../../quapy.tests.html#quapy.tests.test_modsel.ModselTestCase.test_modsel_parallel_speedup">[docs]</a>
<span class="k">def</span> <span class="nf">test_modsel_parallel_speedup</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">class</span> <span class="nc">SlowLR</span><span class="p">(</span><span class="n">LogisticRegression</span><span class="p">):</span>
<span class="k">def</span> <span class="nf">fit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">sample_weight</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<span class="n">time</span><span class="o">.</span><span class="n">sleep</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span>
<span class="k">return</span> <span class="nb">super</span><span class="p">(</span><span class="n">SlowLR</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="n">X</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">sample_weight</span><span class="p">)</span>
<span class="n">q</span> <span class="o">=</span> <span class="n">PACC</span><span class="p">(</span><span class="n">SlowLR</span><span class="p">(</span><span class="n">random_state</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">max_iter</span><span class="o">=</span><span class="mi">5000</span><span class="p">))</span>
<span class="n">data</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">datasets</span><span class="o">.</span><span class="n">fetch_reviews</span><span class="p">(</span><span class="s1">&#39;imdb&#39;</span><span class="p">,</span> <span class="n">tfidf</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">min_df</span><span class="o">=</span><span class="mi">10</span><span class="p">)</span>
<span class="n">training</span><span class="p">,</span> <span class="n">validation</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">training</span><span class="o">.</span><span class="n">split_stratified</span><span class="p">(</span><span class="mf">0.7</span><span class="p">,</span> <span class="n">random_state</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="n">param_grid</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;classifier__C&#39;</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">logspace</span><span class="p">(</span><span class="o">-</span><span class="mi">3</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">7</span><span class="p">)}</span>
<span class="n">app</span> <span class="o">=</span> <span class="n">APP</span><span class="p">(</span><span class="n">validation</span><span class="p">,</span> <span class="n">sample_size</span><span class="o">=</span><span class="mi">100</span><span class="p">,</span> <span class="n">random_state</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="n">tinit</span> <span class="o">=</span> <span class="n">time</span><span class="o">.</span><span class="n">time</span><span class="p">()</span>
<span class="n">GridSearchQ</span><span class="p">(</span>
<span class="n">q</span><span class="p">,</span> <span class="n">param_grid</span><span class="p">,</span> <span class="n">protocol</span><span class="o">=</span><span class="n">app</span><span class="p">,</span> <span class="n">error</span><span class="o">=</span><span class="s1">&#39;mae&#39;</span><span class="p">,</span> <span class="n">refit</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">timeout</span><span class="o">=-</span><span class="mi">1</span><span class="p">,</span> <span class="n">n_jobs</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">verbose</span><span class="o">=</span><span class="kc">True</span>
<span class="p">)</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="n">training</span><span class="p">)</span>
<span class="n">tend_nooptim</span> <span class="o">=</span> <span class="n">time</span><span class="o">.</span><span class="n">time</span><span class="p">()</span><span class="o">-</span><span class="n">tinit</span>
<span class="n">tinit</span> <span class="o">=</span> <span class="n">time</span><span class="o">.</span><span class="n">time</span><span class="p">()</span>
<span class="n">GridSearchQ</span><span class="p">(</span>
<span class="n">q</span><span class="p">,</span> <span class="n">param_grid</span><span class="p">,</span> <span class="n">protocol</span><span class="o">=</span><span class="n">app</span><span class="p">,</span> <span class="n">error</span><span class="o">=</span><span class="s1">&#39;mae&#39;</span><span class="p">,</span> <span class="n">refit</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">timeout</span><span class="o">=-</span><span class="mi">1</span><span class="p">,</span> <span class="n">n_jobs</span><span class="o">=-</span><span class="mi">1</span><span class="p">,</span> <span class="n">verbose</span><span class="o">=</span><span class="kc">True</span>
<span class="p">)</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="n">training</span><span class="p">)</span>
<span class="n">tend_optim</span> <span class="o">=</span> <span class="n">time</span><span class="o">.</span><span class="n">time</span><span class="p">()</span> <span class="o">-</span> <span class="n">tinit</span>
<span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;parallel training took </span><span class="si">{</span><span class="n">tend_optim</span><span class="si">:</span><span class="s1">.4f</span><span class="si">}</span><span class="s1">s&#39;</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;sequential training took </span><span class="si">{</span><span class="n">tend_nooptim</span><span class="si">:</span><span class="s1">.4f</span><span class="si">}</span><span class="s1">s&#39;</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertEqual</span><span class="p">(</span><span class="n">tend_optim</span> <span class="o">&lt;</span> <span class="p">(</span><span class="mf">0.5</span><span class="o">*</span><span class="n">tend_nooptim</span><span class="p">),</span> <span class="kc">True</span><span class="p">)</span></div>
<div class="viewcode-block" id="ModselTestCase.test_modsel_timeout">
<a class="viewcode-back" href="../../../quapy.tests.html#quapy.tests.test_modsel.ModselTestCase.test_modsel_timeout">[docs]</a>
<span class="k">def</span> <span class="nf">test_modsel_timeout</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">class</span> <span class="nc">SlowLR</span><span class="p">(</span><span class="n">LogisticRegression</span><span class="p">):</span>
<span class="k">def</span> <span class="nf">fit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">X</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">sample_weight</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<span class="kn">import</span> <span class="nn">time</span>
<span class="n">time</span><span class="o">.</span><span class="n">sleep</span><span class="p">(</span><span class="mi">10</span><span class="p">)</span>
<span class="nb">super</span><span class="p">(</span><span class="n">SlowLR</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="n">X</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">sample_weight</span><span class="p">)</span>
<span class="n">q</span> <span class="o">=</span> <span class="n">PACC</span><span class="p">(</span><span class="n">SlowLR</span><span class="p">())</span>
<span class="n">data</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">datasets</span><span class="o">.</span><span class="n">fetch_reviews</span><span class="p">(</span><span class="s1">&#39;imdb&#39;</span><span class="p">,</span> <span class="n">tfidf</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">min_df</span><span class="o">=</span><span class="mi">10</span><span class="p">)</span>
<span class="n">training</span><span class="p">,</span> <span class="n">validation</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">training</span><span class="o">.</span><span class="n">split_stratified</span><span class="p">(</span><span class="mf">0.7</span><span class="p">,</span> <span class="n">random_state</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="c1"># test = data.test</span>
<span class="n">param_grid</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;classifier__C&#39;</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">logspace</span><span class="p">(</span><span class="o">-</span><span class="mi">3</span><span class="p">,</span><span class="mi">3</span><span class="p">,</span><span class="mi">7</span><span class="p">)}</span>
<span class="n">app</span> <span class="o">=</span> <span class="n">APP</span><span class="p">(</span><span class="n">validation</span><span class="p">,</span> <span class="n">sample_size</span><span class="o">=</span><span class="mi">100</span><span class="p">,</span> <span class="n">random_state</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="n">q</span> <span class="o">=</span> <span class="n">GridSearchQ</span><span class="p">(</span>
<span class="n">q</span><span class="p">,</span> <span class="n">param_grid</span><span class="p">,</span> <span class="n">protocol</span><span class="o">=</span><span class="n">app</span><span class="p">,</span> <span class="n">error</span><span class="o">=</span><span class="s1">&#39;mae&#39;</span><span class="p">,</span> <span class="n">refit</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">timeout</span><span class="o">=</span><span class="mi">3</span><span class="p">,</span> <span class="n">n_jobs</span><span class="o">=-</span><span class="mi">1</span><span class="p">,</span> <span class="n">verbose</span><span class="o">=</span><span class="kc">True</span>
<span class="p">)</span>
<span class="k">with</span> <span class="bp">self</span><span class="o">.</span><span class="n">assertRaises</span><span class="p">(</span><span class="ne">TimeoutError</span><span class="p">):</span>
<span class="n">q</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="n">training</span><span class="p">)</span></div>
</div>
<span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s1">&#39;__main__&#39;</span><span class="p">:</span>
<span class="n">unittest</span><span class="o">.</span><span class="n">main</span><span class="p">()</span>
</pre></div>
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<h1>Source code for quapy.tests.test_protocols</h1><div class="highlight"><pre>
<span></span><span class="kn">import</span> <span class="nn">unittest</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
<span class="kn">import</span> <span class="nn">quapy.functional</span>
<span class="kn">from</span> <span class="nn">quapy.data</span> <span class="kn">import</span> <span class="n">LabelledCollection</span>
<span class="kn">from</span> <span class="nn">quapy.protocol</span> <span class="kn">import</span> <span class="n">APP</span><span class="p">,</span> <span class="n">NPP</span><span class="p">,</span> <span class="n">UPP</span><span class="p">,</span> <span class="n">DomainMixer</span><span class="p">,</span> <span class="n">AbstractStochasticSeededProtocol</span>
<div class="viewcode-block" id="mock_labelled_collection">
<a class="viewcode-back" href="../../../quapy.tests.html#quapy.tests.test_protocols.mock_labelled_collection">[docs]</a>
<span class="k">def</span> <span class="nf">mock_labelled_collection</span><span class="p">(</span><span class="n">prefix</span><span class="o">=</span><span class="s1">&#39;&#39;</span><span class="p">):</span>
<span class="n">y</span> <span class="o">=</span> <span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">*</span> <span class="mi">250</span> <span class="o">+</span> <span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">*</span> <span class="mi">250</span> <span class="o">+</span> <span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">*</span> <span class="mi">250</span> <span class="o">+</span> <span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">*</span> <span class="mi">250</span>
<span class="n">X</span> <span class="o">=</span> <span class="p">[</span><span class="n">prefix</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="o">+</span> <span class="s1">&#39;-&#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">yi</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">yi</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">y</span><span class="p">)]</span>
<span class="k">return</span> <span class="n">LabelledCollection</span><span class="p">(</span><span class="n">X</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">classes</span><span class="o">=</span><span class="nb">sorted</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">unique</span><span class="p">(</span><span class="n">y</span><span class="p">)))</span></div>
<div class="viewcode-block" id="samples_to_str">
<a class="viewcode-back" href="../../../quapy.tests.html#quapy.tests.test_protocols.samples_to_str">[docs]</a>
<span class="k">def</span> <span class="nf">samples_to_str</span><span class="p">(</span><span class="n">protocol</span><span class="p">):</span>
<span class="n">samples_str</span> <span class="o">=</span> <span class="s2">&quot;&quot;</span>
<span class="k">for</span> <span class="n">instances</span><span class="p">,</span> <span class="n">prev</span> <span class="ow">in</span> <span class="n">protocol</span><span class="p">():</span>
<span class="n">samples_str</span> <span class="o">+=</span> <span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">instances</span><span class="si">}</span><span class="se">\t</span><span class="si">{</span><span class="n">prev</span><span class="si">}</span><span class="se">\n</span><span class="s1">&#39;</span>
<span class="k">return</span> <span class="n">samples_str</span></div>
<div class="viewcode-block" id="TestProtocols">
<a class="viewcode-back" href="../../../quapy.tests.html#quapy.tests.test_protocols.TestProtocols">[docs]</a>
<span class="k">class</span> <span class="nc">TestProtocols</span><span class="p">(</span><span class="n">unittest</span><span class="o">.</span><span class="n">TestCase</span><span class="p">):</span>
<div class="viewcode-block" id="TestProtocols.test_app_sanity_check">
<a class="viewcode-back" href="../../../quapy.tests.html#quapy.tests.test_protocols.TestProtocols.test_app_sanity_check">[docs]</a>
<span class="k">def</span> <span class="nf">test_app_sanity_check</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="n">data</span> <span class="o">=</span> <span class="n">mock_labelled_collection</span><span class="p">()</span>
<span class="n">n_prevpoints</span> <span class="o">=</span> <span class="mi">101</span>
<span class="n">repeats</span> <span class="o">=</span> <span class="mi">10</span>
<span class="k">with</span> <span class="bp">self</span><span class="o">.</span><span class="n">assertRaises</span><span class="p">(</span><span class="ne">RuntimeError</span><span class="p">):</span>
<span class="n">p</span> <span class="o">=</span> <span class="n">APP</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">sample_size</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">n_prevalences</span><span class="o">=</span><span class="n">n_prevpoints</span><span class="p">,</span> <span class="n">repeats</span><span class="o">=</span><span class="n">repeats</span><span class="p">,</span> <span class="n">random_state</span><span class="o">=</span><span class="mi">42</span><span class="p">)</span>
<span class="n">n_combinations</span> <span class="o">=</span> \
<span class="n">quapy</span><span class="o">.</span><span class="n">functional</span><span class="o">.</span><span class="n">num_prevalence_combinations</span><span class="p">(</span><span class="n">n_prevpoints</span><span class="p">,</span> <span class="n">n_classes</span><span class="o">=</span><span class="n">data</span><span class="o">.</span><span class="n">n_classes</span><span class="p">,</span> <span class="n">n_repeats</span><span class="o">=</span><span class="n">repeats</span><span class="p">)</span>
<span class="n">p</span> <span class="o">=</span> <span class="n">APP</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">sample_size</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">n_prevalences</span><span class="o">=</span><span class="n">n_prevpoints</span><span class="p">,</span> <span class="n">random_state</span><span class="o">=</span><span class="mi">42</span><span class="p">,</span> <span class="n">sanity_check</span><span class="o">=</span><span class="n">n_combinations</span><span class="p">)</span>
<span class="n">p</span> <span class="o">=</span> <span class="n">APP</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">sample_size</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">n_prevalences</span><span class="o">=</span><span class="n">n_prevpoints</span><span class="p">,</span> <span class="n">random_state</span><span class="o">=</span><span class="mi">42</span><span class="p">,</span> <span class="n">sanity_check</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span></div>
<div class="viewcode-block" id="TestProtocols.test_app_replicate">
<a class="viewcode-back" href="../../../quapy.tests.html#quapy.tests.test_protocols.TestProtocols.test_app_replicate">[docs]</a>
<span class="k">def</span> <span class="nf">test_app_replicate</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="n">data</span> <span class="o">=</span> <span class="n">mock_labelled_collection</span><span class="p">()</span>
<span class="n">p</span> <span class="o">=</span> <span class="n">APP</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">sample_size</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">n_prevalences</span><span class="o">=</span><span class="mi">11</span><span class="p">,</span> <span class="n">random_state</span><span class="o">=</span><span class="mi">42</span><span class="p">)</span>
<span class="n">samples1</span> <span class="o">=</span> <span class="n">samples_to_str</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>
<span class="n">samples2</span> <span class="o">=</span> <span class="n">samples_to_str</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertEqual</span><span class="p">(</span><span class="n">samples1</span><span class="p">,</span> <span class="n">samples2</span><span class="p">)</span>
<span class="n">p</span> <span class="o">=</span> <span class="n">APP</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">sample_size</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">n_prevalences</span><span class="o">=</span><span class="mi">11</span><span class="p">)</span> <span class="c1"># &lt;- random_state is by default set to 0</span>
<span class="n">samples1</span> <span class="o">=</span> <span class="n">samples_to_str</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>
<span class="n">samples2</span> <span class="o">=</span> <span class="n">samples_to_str</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertEqual</span><span class="p">(</span><span class="n">samples1</span><span class="p">,</span> <span class="n">samples2</span><span class="p">)</span></div>
<div class="viewcode-block" id="TestProtocols.test_app_not_replicate">
<a class="viewcode-back" href="../../../quapy.tests.html#quapy.tests.test_protocols.TestProtocols.test_app_not_replicate">[docs]</a>
<span class="k">def</span> <span class="nf">test_app_not_replicate</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="n">data</span> <span class="o">=</span> <span class="n">mock_labelled_collection</span><span class="p">()</span>
<span class="n">p</span> <span class="o">=</span> <span class="n">APP</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">sample_size</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">n_prevalences</span><span class="o">=</span><span class="mi">11</span><span class="p">,</span> <span class="n">random_state</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span>
<span class="n">samples1</span> <span class="o">=</span> <span class="n">samples_to_str</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>
<span class="n">samples2</span> <span class="o">=</span> <span class="n">samples_to_str</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertNotEqual</span><span class="p">(</span><span class="n">samples1</span><span class="p">,</span> <span class="n">samples2</span><span class="p">)</span>
<span class="n">p</span> <span class="o">=</span> <span class="n">APP</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">sample_size</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">n_prevalences</span><span class="o">=</span><span class="mi">11</span><span class="p">,</span> <span class="n">random_state</span><span class="o">=</span><span class="mi">42</span><span class="p">)</span>
<span class="n">samples1</span> <span class="o">=</span> <span class="n">samples_to_str</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>
<span class="n">p</span> <span class="o">=</span> <span class="n">APP</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">sample_size</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">n_prevalences</span><span class="o">=</span><span class="mi">11</span><span class="p">,</span> <span class="n">random_state</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
<span class="n">samples2</span> <span class="o">=</span> <span class="n">samples_to_str</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertNotEqual</span><span class="p">(</span><span class="n">samples1</span><span class="p">,</span> <span class="n">samples2</span><span class="p">)</span></div>
<div class="viewcode-block" id="TestProtocols.test_app_number">
<a class="viewcode-back" href="../../../quapy.tests.html#quapy.tests.test_protocols.TestProtocols.test_app_number">[docs]</a>
<span class="k">def</span> <span class="nf">test_app_number</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="n">data</span> <span class="o">=</span> <span class="n">mock_labelled_collection</span><span class="p">()</span>
<span class="n">p</span> <span class="o">=</span> <span class="n">APP</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">sample_size</span><span class="o">=</span><span class="mi">100</span><span class="p">,</span> <span class="n">n_prevalences</span><span class="o">=</span><span class="mi">10</span><span class="p">,</span> <span class="n">repeats</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="c1"># surprisingly enough, for some n_prevalences the test fails, notwithstanding</span>
<span class="c1"># everything is correct. The problem is that in function APP.prevalence_grid()</span>
<span class="c1"># there is sometimes one rounding error that gets cumulated and</span>
<span class="c1"># surpasses 1.0 (by a very small float value, 0.0000000000002 or sthe like)</span>
<span class="c1"># so these tuples are mistakenly removed... I have tried with np.close, and</span>
<span class="c1"># other workarounds, but eventually happens that there is some negative probability</span>
<span class="c1"># in the sampling function...</span>
<span class="n">count</span> <span class="o">=</span> <span class="mi">0</span>
<span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="n">p</span><span class="p">():</span>
<span class="n">count</span><span class="o">+=</span><span class="mi">1</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertEqual</span><span class="p">(</span><span class="n">count</span><span class="p">,</span> <span class="n">p</span><span class="o">.</span><span class="n">total</span><span class="p">())</span></div>
<div class="viewcode-block" id="TestProtocols.test_npp_replicate">
<a class="viewcode-back" href="../../../quapy.tests.html#quapy.tests.test_protocols.TestProtocols.test_npp_replicate">[docs]</a>
<span class="k">def</span> <span class="nf">test_npp_replicate</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="n">data</span> <span class="o">=</span> <span class="n">mock_labelled_collection</span><span class="p">()</span>
<span class="n">p</span> <span class="o">=</span> <span class="n">NPP</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">sample_size</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">repeats</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">random_state</span><span class="o">=</span><span class="mi">42</span><span class="p">)</span>
<span class="n">samples1</span> <span class="o">=</span> <span class="n">samples_to_str</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>
<span class="n">samples2</span> <span class="o">=</span> <span class="n">samples_to_str</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertEqual</span><span class="p">(</span><span class="n">samples1</span><span class="p">,</span> <span class="n">samples2</span><span class="p">)</span>
<span class="n">p</span> <span class="o">=</span> <span class="n">NPP</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">sample_size</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">repeats</span><span class="o">=</span><span class="mi">5</span><span class="p">)</span> <span class="c1"># &lt;- random_state is by default set to 0</span>
<span class="n">samples1</span> <span class="o">=</span> <span class="n">samples_to_str</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>
<span class="n">samples2</span> <span class="o">=</span> <span class="n">samples_to_str</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertEqual</span><span class="p">(</span><span class="n">samples1</span><span class="p">,</span> <span class="n">samples2</span><span class="p">)</span></div>
<div class="viewcode-block" id="TestProtocols.test_npp_not_replicate">
<a class="viewcode-back" href="../../../quapy.tests.html#quapy.tests.test_protocols.TestProtocols.test_npp_not_replicate">[docs]</a>
<span class="k">def</span> <span class="nf">test_npp_not_replicate</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="n">data</span> <span class="o">=</span> <span class="n">mock_labelled_collection</span><span class="p">()</span>
<span class="n">p</span> <span class="o">=</span> <span class="n">NPP</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">sample_size</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">repeats</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">random_state</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span>
<span class="n">samples1</span> <span class="o">=</span> <span class="n">samples_to_str</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>
<span class="n">samples2</span> <span class="o">=</span> <span class="n">samples_to_str</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertNotEqual</span><span class="p">(</span><span class="n">samples1</span><span class="p">,</span> <span class="n">samples2</span><span class="p">)</span>
<span class="n">p</span> <span class="o">=</span> <span class="n">NPP</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">sample_size</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">repeats</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">random_state</span><span class="o">=</span><span class="mi">42</span><span class="p">)</span>
<span class="n">samples1</span> <span class="o">=</span> <span class="n">samples_to_str</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>
<span class="n">p</span> <span class="o">=</span> <span class="n">NPP</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">sample_size</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">repeats</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">random_state</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
<span class="n">samples2</span> <span class="o">=</span> <span class="n">samples_to_str</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertNotEqual</span><span class="p">(</span><span class="n">samples1</span><span class="p">,</span> <span class="n">samples2</span><span class="p">)</span></div>
<div class="viewcode-block" id="TestProtocols.test_kraemer_replicate">
<a class="viewcode-back" href="../../../quapy.tests.html#quapy.tests.test_protocols.TestProtocols.test_kraemer_replicate">[docs]</a>
<span class="k">def</span> <span class="nf">test_kraemer_replicate</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="n">data</span> <span class="o">=</span> <span class="n">mock_labelled_collection</span><span class="p">()</span>
<span class="n">p</span> <span class="o">=</span> <span class="n">UPP</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">sample_size</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">repeats</span><span class="o">=</span><span class="mi">10</span><span class="p">,</span> <span class="n">random_state</span><span class="o">=</span><span class="mi">42</span><span class="p">)</span>
<span class="n">samples1</span> <span class="o">=</span> <span class="n">samples_to_str</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>
<span class="n">samples2</span> <span class="o">=</span> <span class="n">samples_to_str</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertEqual</span><span class="p">(</span><span class="n">samples1</span><span class="p">,</span> <span class="n">samples2</span><span class="p">)</span>
<span class="n">p</span> <span class="o">=</span> <span class="n">UPP</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">sample_size</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">repeats</span><span class="o">=</span><span class="mi">10</span><span class="p">)</span> <span class="c1"># &lt;- random_state is by default set to 0</span>
<span class="n">samples1</span> <span class="o">=</span> <span class="n">samples_to_str</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>
<span class="n">samples2</span> <span class="o">=</span> <span class="n">samples_to_str</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertEqual</span><span class="p">(</span><span class="n">samples1</span><span class="p">,</span> <span class="n">samples2</span><span class="p">)</span></div>
<div class="viewcode-block" id="TestProtocols.test_kraemer_not_replicate">
<a class="viewcode-back" href="../../../quapy.tests.html#quapy.tests.test_protocols.TestProtocols.test_kraemer_not_replicate">[docs]</a>
<span class="k">def</span> <span class="nf">test_kraemer_not_replicate</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="n">data</span> <span class="o">=</span> <span class="n">mock_labelled_collection</span><span class="p">()</span>
<span class="n">p</span> <span class="o">=</span> <span class="n">UPP</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">sample_size</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">repeats</span><span class="o">=</span><span class="mi">10</span><span class="p">,</span> <span class="n">random_state</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span>
<span class="n">samples1</span> <span class="o">=</span> <span class="n">samples_to_str</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>
<span class="n">samples2</span> <span class="o">=</span> <span class="n">samples_to_str</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertNotEqual</span><span class="p">(</span><span class="n">samples1</span><span class="p">,</span> <span class="n">samples2</span><span class="p">)</span></div>
<div class="viewcode-block" id="TestProtocols.test_covariate_shift_replicate">
<a class="viewcode-back" href="../../../quapy.tests.html#quapy.tests.test_protocols.TestProtocols.test_covariate_shift_replicate">[docs]</a>
<span class="k">def</span> <span class="nf">test_covariate_shift_replicate</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="n">dataA</span> <span class="o">=</span> <span class="n">mock_labelled_collection</span><span class="p">(</span><span class="s1">&#39;domA&#39;</span><span class="p">)</span>
<span class="n">dataB</span> <span class="o">=</span> <span class="n">mock_labelled_collection</span><span class="p">(</span><span class="s1">&#39;domB&#39;</span><span class="p">)</span>
<span class="n">p</span> <span class="o">=</span> <span class="n">DomainMixer</span><span class="p">(</span><span class="n">dataA</span><span class="p">,</span> <span class="n">dataB</span><span class="p">,</span> <span class="n">sample_size</span><span class="o">=</span><span class="mi">10</span><span class="p">,</span> <span class="n">mixture_points</span><span class="o">=</span><span class="mi">11</span><span class="p">,</span> <span class="n">random_state</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="n">samples1</span> <span class="o">=</span> <span class="n">samples_to_str</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>
<span class="n">samples2</span> <span class="o">=</span> <span class="n">samples_to_str</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertEqual</span><span class="p">(</span><span class="n">samples1</span><span class="p">,</span> <span class="n">samples2</span><span class="p">)</span>
<span class="n">p</span> <span class="o">=</span> <span class="n">DomainMixer</span><span class="p">(</span><span class="n">dataA</span><span class="p">,</span> <span class="n">dataB</span><span class="p">,</span> <span class="n">sample_size</span><span class="o">=</span><span class="mi">10</span><span class="p">,</span> <span class="n">mixture_points</span><span class="o">=</span><span class="mi">11</span><span class="p">)</span> <span class="c1"># &lt;- random_state is by default set to 0</span>
<span class="n">samples1</span> <span class="o">=</span> <span class="n">samples_to_str</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>
<span class="n">samples2</span> <span class="o">=</span> <span class="n">samples_to_str</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertEqual</span><span class="p">(</span><span class="n">samples1</span><span class="p">,</span> <span class="n">samples2</span><span class="p">)</span></div>
<div class="viewcode-block" id="TestProtocols.test_covariate_shift_not_replicate">
<a class="viewcode-back" href="../../../quapy.tests.html#quapy.tests.test_protocols.TestProtocols.test_covariate_shift_not_replicate">[docs]</a>
<span class="k">def</span> <span class="nf">test_covariate_shift_not_replicate</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="n">dataA</span> <span class="o">=</span> <span class="n">mock_labelled_collection</span><span class="p">(</span><span class="s1">&#39;domA&#39;</span><span class="p">)</span>
<span class="n">dataB</span> <span class="o">=</span> <span class="n">mock_labelled_collection</span><span class="p">(</span><span class="s1">&#39;domB&#39;</span><span class="p">)</span>
<span class="n">p</span> <span class="o">=</span> <span class="n">DomainMixer</span><span class="p">(</span><span class="n">dataA</span><span class="p">,</span> <span class="n">dataB</span><span class="p">,</span> <span class="n">sample_size</span><span class="o">=</span><span class="mi">10</span><span class="p">,</span> <span class="n">mixture_points</span><span class="o">=</span><span class="mi">11</span><span class="p">,</span> <span class="n">random_state</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span>
<span class="n">samples1</span> <span class="o">=</span> <span class="n">samples_to_str</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>
<span class="n">samples2</span> <span class="o">=</span> <span class="n">samples_to_str</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertNotEqual</span><span class="p">(</span><span class="n">samples1</span><span class="p">,</span> <span class="n">samples2</span><span class="p">)</span></div>
<div class="viewcode-block" id="TestProtocols.test_no_seed_init">
<a class="viewcode-back" href="../../../quapy.tests.html#quapy.tests.test_protocols.TestProtocols.test_no_seed_init">[docs]</a>
<span class="k">def</span> <span class="nf">test_no_seed_init</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">class</span> <span class="nc">NoSeedInit</span><span class="p">(</span><span class="n">AbstractStochasticSeededProtocol</span><span class="p">):</span>
<span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">data</span> <span class="o">=</span> <span class="n">mock_labelled_collection</span><span class="p">()</span>
<span class="k">def</span> <span class="nf">samples_parameters</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="c1"># return a matrix containing sampling indexes in the rows</span>
<span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">randint</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">),</span> <span class="mi">10</span><span class="o">*</span><span class="mi">10</span><span class="p">)</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="mi">10</span><span class="p">,</span> <span class="mi">10</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">sample</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">params</span><span class="p">):</span>
<span class="n">index</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">unique</span><span class="p">(</span><span class="n">params</span><span class="p">)</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">sampling_from_index</span><span class="p">(</span><span class="n">index</span><span class="p">)</span>
<span class="n">p</span> <span class="o">=</span> <span class="n">NoSeedInit</span><span class="p">()</span>
<span class="c1"># this should raise a ValueError, since the class is said to be AbstractStochasticSeededProtocol but the</span>
<span class="c1"># random_seed has never been passed to super(NoSeedInit, self).__init__(random_seed)</span>
<span class="k">with</span> <span class="bp">self</span><span class="o">.</span><span class="n">assertRaises</span><span class="p">(</span><span class="ne">ValueError</span><span class="p">):</span>
<span class="k">for</span> <span class="n">sample</span> <span class="ow">in</span> <span class="n">p</span><span class="p">():</span>
<span class="k">pass</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">&#39;done&#39;</span><span class="p">)</span></div>
</div>
<span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s1">&#39;__main__&#39;</span><span class="p">:</span>
<span class="n">unittest</span><span class="o">.</span><span class="n">main</span><span class="p">()</span>
</pre></div>
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<h1>Source code for quapy.tests.test_replicability</h1><div class="highlight"><pre>
<span></span><span class="kn">import</span> <span class="nn">unittest</span>
<span class="kn">import</span> <span class="nn">quapy</span> <span class="k">as</span> <span class="nn">qp</span>
<span class="kn">from</span> <span class="nn">quapy.data</span> <span class="kn">import</span> <span class="n">LabelledCollection</span>
<span class="kn">from</span> <span class="nn">quapy.functional</span> <span class="kn">import</span> <span class="n">strprev</span>
<span class="kn">from</span> <span class="nn">sklearn.linear_model</span> <span class="kn">import</span> <span class="n">LogisticRegression</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
<span class="kn">from</span> <span class="nn">quapy.method.aggregative</span> <span class="kn">import</span> <span class="n">PACC</span>
<span class="kn">import</span> <span class="nn">quapy.functional</span> <span class="k">as</span> <span class="nn">F</span>
<div class="viewcode-block" id="MyTestCase">
<a class="viewcode-back" href="../../../quapy.tests.html#quapy.tests.test_replicability.MyTestCase">[docs]</a>
<span class="k">class</span> <span class="nc">MyTestCase</span><span class="p">(</span><span class="n">unittest</span><span class="o">.</span><span class="n">TestCase</span><span class="p">):</span>
<div class="viewcode-block" id="MyTestCase.test_prediction_replicability">
<a class="viewcode-back" href="../../../quapy.tests.html#quapy.tests.test_replicability.MyTestCase.test_prediction_replicability">[docs]</a>
<span class="k">def</span> <span class="nf">test_prediction_replicability</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="n">dataset</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">datasets</span><span class="o">.</span><span class="n">fetch_UCIBinaryDataset</span><span class="p">(</span><span class="s1">&#39;yeast&#39;</span><span class="p">)</span>
<span class="k">with</span> <span class="n">qp</span><span class="o">.</span><span class="n">util</span><span class="o">.</span><span class="n">temp_seed</span><span class="p">(</span><span class="mi">0</span><span class="p">):</span>
<span class="n">lr</span> <span class="o">=</span> <span class="n">LogisticRegression</span><span class="p">(</span><span class="n">random_state</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">max_iter</span><span class="o">=</span><span class="mi">10000</span><span class="p">)</span>
<span class="n">pacc</span> <span class="o">=</span> <span class="n">PACC</span><span class="p">(</span><span class="n">lr</span><span class="p">)</span>
<span class="n">prev</span> <span class="o">=</span> <span class="n">pacc</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="n">dataset</span><span class="o">.</span><span class="n">training</span><span class="p">)</span><span class="o">.</span><span class="n">quantify</span><span class="p">(</span><span class="n">dataset</span><span class="o">.</span><span class="n">test</span><span class="o">.</span><span class="n">X</span><span class="p">)</span>
<span class="n">str_prev1</span> <span class="o">=</span> <span class="n">strprev</span><span class="p">(</span><span class="n">prev</span><span class="p">,</span> <span class="n">prec</span><span class="o">=</span><span class="mi">5</span><span class="p">)</span>
<span class="k">with</span> <span class="n">qp</span><span class="o">.</span><span class="n">util</span><span class="o">.</span><span class="n">temp_seed</span><span class="p">(</span><span class="mi">0</span><span class="p">):</span>
<span class="n">lr</span> <span class="o">=</span> <span class="n">LogisticRegression</span><span class="p">(</span><span class="n">random_state</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">max_iter</span><span class="o">=</span><span class="mi">10000</span><span class="p">)</span>
<span class="n">pacc</span> <span class="o">=</span> <span class="n">PACC</span><span class="p">(</span><span class="n">lr</span><span class="p">)</span>
<span class="n">prev2</span> <span class="o">=</span> <span class="n">pacc</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="n">dataset</span><span class="o">.</span><span class="n">training</span><span class="p">)</span><span class="o">.</span><span class="n">quantify</span><span class="p">(</span><span class="n">dataset</span><span class="o">.</span><span class="n">test</span><span class="o">.</span><span class="n">X</span><span class="p">)</span>
<span class="n">str_prev2</span> <span class="o">=</span> <span class="n">strprev</span><span class="p">(</span><span class="n">prev2</span><span class="p">,</span> <span class="n">prec</span><span class="o">=</span><span class="mi">5</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertEqual</span><span class="p">(</span><span class="n">str_prev1</span><span class="p">,</span> <span class="n">str_prev2</span><span class="p">)</span> <span class="c1"># add assertion here</span></div>
<div class="viewcode-block" id="MyTestCase.test_samping_replicability">
<a class="viewcode-back" href="../../../quapy.tests.html#quapy.tests.test_replicability.MyTestCase.test_samping_replicability">[docs]</a>
<span class="k">def</span> <span class="nf">test_samping_replicability</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">def</span> <span class="nf">equal_collections</span><span class="p">(</span><span class="n">c1</span><span class="p">,</span> <span class="n">c2</span><span class="p">,</span> <span class="n">value</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertEqual</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">all</span><span class="p">(</span><span class="n">c1</span><span class="o">.</span><span class="n">Xtr</span> <span class="o">==</span> <span class="n">c2</span><span class="o">.</span><span class="n">Xtr</span><span class="p">),</span> <span class="n">value</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertEqual</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">all</span><span class="p">(</span><span class="n">c1</span><span class="o">.</span><span class="n">ytr</span> <span class="o">==</span> <span class="n">c2</span><span class="o">.</span><span class="n">ytr</span><span class="p">),</span> <span class="n">value</span><span class="p">)</span>
<span class="k">if</span> <span class="n">value</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertEqual</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">all</span><span class="p">(</span><span class="n">c1</span><span class="o">.</span><span class="n">classes_</span> <span class="o">==</span> <span class="n">c2</span><span class="o">.</span><span class="n">classes_</span><span class="p">),</span> <span class="n">value</span><span class="p">)</span>
<span class="n">X</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="nb">str</span><span class="p">,</span> <span class="nb">range</span><span class="p">(</span><span class="mi">100</span><span class="p">)))</span>
<span class="n">y</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">randint</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">100</span><span class="p">)</span>
<span class="n">data</span> <span class="o">=</span> <span class="n">LabelledCollection</span><span class="p">(</span><span class="n">instances</span><span class="o">=</span><span class="n">X</span><span class="p">,</span> <span class="n">labels</span><span class="o">=</span><span class="n">y</span><span class="p">)</span>
<span class="n">sample1</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">sampling</span><span class="p">(</span><span class="mi">50</span><span class="p">)</span>
<span class="n">sample2</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">sampling</span><span class="p">(</span><span class="mi">50</span><span class="p">)</span>
<span class="n">equal_collections</span><span class="p">(</span><span class="n">sample1</span><span class="p">,</span> <span class="n">sample2</span><span class="p">,</span> <span class="kc">False</span><span class="p">)</span>
<span class="n">sample1</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">sampling</span><span class="p">(</span><span class="mi">50</span><span class="p">,</span> <span class="n">random_state</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
<span class="n">sample2</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">sampling</span><span class="p">(</span><span class="mi">50</span><span class="p">,</span> <span class="n">random_state</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
<span class="n">equal_collections</span><span class="p">(</span><span class="n">sample1</span><span class="p">,</span> <span class="n">sample2</span><span class="p">,</span> <span class="kc">True</span><span class="p">)</span>
<span class="n">sample1</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">sampling</span><span class="p">(</span><span class="mi">50</span><span class="p">,</span> <span class="o">*</span><span class="p">[</span><span class="mf">0.7</span><span class="p">,</span> <span class="mf">0.3</span><span class="p">],</span> <span class="n">random_state</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
<span class="n">sample2</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">sampling</span><span class="p">(</span><span class="mi">50</span><span class="p">,</span> <span class="o">*</span><span class="p">[</span><span class="mf">0.7</span><span class="p">,</span> <span class="mf">0.3</span><span class="p">],</span> <span class="n">random_state</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
<span class="n">equal_collections</span><span class="p">(</span><span class="n">sample1</span><span class="p">,</span> <span class="n">sample2</span><span class="p">,</span> <span class="kc">True</span><span class="p">)</span>
<span class="k">with</span> <span class="n">qp</span><span class="o">.</span><span class="n">util</span><span class="o">.</span><span class="n">temp_seed</span><span class="p">(</span><span class="mi">0</span><span class="p">):</span>
<span class="n">sample1</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">sampling</span><span class="p">(</span><span class="mi">50</span><span class="p">,</span> <span class="o">*</span><span class="p">[</span><span class="mf">0.7</span><span class="p">,</span> <span class="mf">0.3</span><span class="p">])</span>
<span class="k">with</span> <span class="n">qp</span><span class="o">.</span><span class="n">util</span><span class="o">.</span><span class="n">temp_seed</span><span class="p">(</span><span class="mi">0</span><span class="p">):</span>
<span class="n">sample2</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">sampling</span><span class="p">(</span><span class="mi">50</span><span class="p">,</span> <span class="o">*</span><span class="p">[</span><span class="mf">0.7</span><span class="p">,</span> <span class="mf">0.3</span><span class="p">])</span>
<span class="n">equal_collections</span><span class="p">(</span><span class="n">sample1</span><span class="p">,</span> <span class="n">sample2</span><span class="p">,</span> <span class="kc">True</span><span class="p">)</span>
<span class="n">sample1</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">sampling</span><span class="p">(</span><span class="mi">50</span><span class="p">,</span> <span class="o">*</span><span class="p">[</span><span class="mf">0.7</span><span class="p">,</span> <span class="mf">0.3</span><span class="p">],</span> <span class="n">random_state</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
<span class="n">sample2</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">sampling</span><span class="p">(</span><span class="mi">50</span><span class="p">,</span> <span class="o">*</span><span class="p">[</span><span class="mf">0.7</span><span class="p">,</span> <span class="mf">0.3</span><span class="p">],</span> <span class="n">random_state</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
<span class="n">equal_collections</span><span class="p">(</span><span class="n">sample1</span><span class="p">,</span> <span class="n">sample2</span><span class="p">,</span> <span class="kc">True</span><span class="p">)</span>
<span class="n">sample1_tr</span><span class="p">,</span> <span class="n">sample1_te</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">split_stratified</span><span class="p">(</span><span class="n">train_prop</span><span class="o">=</span><span class="mf">0.7</span><span class="p">,</span> <span class="n">random_state</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
<span class="n">sample2_tr</span><span class="p">,</span> <span class="n">sample2_te</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">split_stratified</span><span class="p">(</span><span class="n">train_prop</span><span class="o">=</span><span class="mf">0.7</span><span class="p">,</span> <span class="n">random_state</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
<span class="n">equal_collections</span><span class="p">(</span><span class="n">sample1_tr</span><span class="p">,</span> <span class="n">sample2_tr</span><span class="p">,</span> <span class="kc">True</span><span class="p">)</span>
<span class="n">equal_collections</span><span class="p">(</span><span class="n">sample1_te</span><span class="p">,</span> <span class="n">sample2_te</span><span class="p">,</span> <span class="kc">True</span><span class="p">)</span>
<span class="k">with</span> <span class="n">qp</span><span class="o">.</span><span class="n">util</span><span class="o">.</span><span class="n">temp_seed</span><span class="p">(</span><span class="mi">0</span><span class="p">):</span>
<span class="n">sample1_tr</span><span class="p">,</span> <span class="n">sample1_te</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">split_stratified</span><span class="p">(</span><span class="n">train_prop</span><span class="o">=</span><span class="mf">0.7</span><span class="p">)</span>
<span class="k">with</span> <span class="n">qp</span><span class="o">.</span><span class="n">util</span><span class="o">.</span><span class="n">temp_seed</span><span class="p">(</span><span class="mi">0</span><span class="p">):</span>
<span class="n">sample2_tr</span><span class="p">,</span> <span class="n">sample2_te</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">split_stratified</span><span class="p">(</span><span class="n">train_prop</span><span class="o">=</span><span class="mf">0.7</span><span class="p">)</span>
<span class="n">equal_collections</span><span class="p">(</span><span class="n">sample1_tr</span><span class="p">,</span> <span class="n">sample2_tr</span><span class="p">,</span> <span class="kc">True</span><span class="p">)</span>
<span class="n">equal_collections</span><span class="p">(</span><span class="n">sample1_te</span><span class="p">,</span> <span class="n">sample2_te</span><span class="p">,</span> <span class="kc">True</span><span class="p">)</span></div>
<div class="viewcode-block" id="MyTestCase.test_parallel_replicability">
<a class="viewcode-back" href="../../../quapy.tests.html#quapy.tests.test_replicability.MyTestCase.test_parallel_replicability">[docs]</a>
<span class="k">def</span> <span class="nf">test_parallel_replicability</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="n">train</span><span class="p">,</span> <span class="n">test</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">datasets</span><span class="o">.</span><span class="n">fetch_UCIMulticlassDataset</span><span class="p">(</span><span class="s1">&#39;dry-bean&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">train_test</span>
<span class="n">test</span> <span class="o">=</span> <span class="n">test</span><span class="o">.</span><span class="n">sampling</span><span class="p">(</span><span class="mi">500</span><span class="p">,</span> <span class="o">*</span><span class="p">[</span><span class="mf">0.1</span><span class="p">,</span> <span class="mf">0.0</span><span class="p">,</span> <span class="mf">0.1</span><span class="p">,</span> <span class="mf">0.1</span><span class="p">,</span> <span class="mf">0.2</span><span class="p">,</span> <span class="mf">0.5</span><span class="p">,</span> <span class="mf">0.0</span><span class="p">])</span>
<span class="k">with</span> <span class="n">qp</span><span class="o">.</span><span class="n">util</span><span class="o">.</span><span class="n">temp_seed</span><span class="p">(</span><span class="mi">10</span><span class="p">):</span>
<span class="n">pacc</span> <span class="o">=</span> <span class="n">PACC</span><span class="p">(</span><span class="n">LogisticRegression</span><span class="p">(),</span> <span class="n">val_split</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">n_jobs</span><span class="o">=</span><span class="mi">2</span><span class="p">)</span>
<span class="n">pacc</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="n">train</span><span class="p">,</span> <span class="n">val_split</span><span class="o">=</span><span class="mf">0.5</span><span class="p">)</span>
<span class="n">prev1</span> <span class="o">=</span> <span class="n">F</span><span class="o">.</span><span class="n">strprev</span><span class="p">(</span><span class="n">pacc</span><span class="o">.</span><span class="n">quantify</span><span class="p">(</span><span class="n">test</span><span class="o">.</span><span class="n">instances</span><span class="p">))</span>
<span class="k">with</span> <span class="n">qp</span><span class="o">.</span><span class="n">util</span><span class="o">.</span><span class="n">temp_seed</span><span class="p">(</span><span class="mi">0</span><span class="p">):</span>
<span class="n">pacc</span> <span class="o">=</span> <span class="n">PACC</span><span class="p">(</span><span class="n">LogisticRegression</span><span class="p">(),</span> <span class="n">val_split</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">n_jobs</span><span class="o">=</span><span class="mi">2</span><span class="p">)</span>
<span class="n">pacc</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="n">train</span><span class="p">,</span> <span class="n">val_split</span><span class="o">=</span><span class="mf">0.5</span><span class="p">)</span>
<span class="n">prev2</span> <span class="o">=</span> <span class="n">F</span><span class="o">.</span><span class="n">strprev</span><span class="p">(</span><span class="n">pacc</span><span class="o">.</span><span class="n">quantify</span><span class="p">(</span><span class="n">test</span><span class="o">.</span><span class="n">instances</span><span class="p">))</span>
<span class="k">with</span> <span class="n">qp</span><span class="o">.</span><span class="n">util</span><span class="o">.</span><span class="n">temp_seed</span><span class="p">(</span><span class="mi">0</span><span class="p">):</span>
<span class="n">pacc</span> <span class="o">=</span> <span class="n">PACC</span><span class="p">(</span><span class="n">LogisticRegression</span><span class="p">(),</span> <span class="n">val_split</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">n_jobs</span><span class="o">=</span><span class="mi">2</span><span class="p">)</span>
<span class="n">pacc</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="n">train</span><span class="p">,</span> <span class="n">val_split</span><span class="o">=</span><span class="mf">0.5</span><span class="p">)</span>
<span class="n">prev3</span> <span class="o">=</span> <span class="n">F</span><span class="o">.</span><span class="n">strprev</span><span class="p">(</span><span class="n">pacc</span><span class="o">.</span><span class="n">quantify</span><span class="p">(</span><span class="n">test</span><span class="o">.</span><span class="n">instances</span><span class="p">))</span>
<span class="nb">print</span><span class="p">(</span><span class="n">prev1</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">prev2</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">prev3</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertNotEqual</span><span class="p">(</span><span class="n">prev1</span><span class="p">,</span> <span class="n">prev2</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertEqual</span><span class="p">(</span><span class="n">prev2</span><span class="p">,</span> <span class="n">prev3</span><span class="p">)</span></div>
</div>
<span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s1">&#39;__main__&#39;</span><span class="p">:</span>
<span class="n">unittest</span><span class="o">.</span><span class="n">main</span><span class="p">()</span>
</pre></div>
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<h1>Source code for quapy.util</h1><div class="highlight"><pre>
<span></span><span class="kn">import</span><span class="w"> </span><span class="nn">contextlib</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">itertools</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">multiprocessing</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">os</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">pickle</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">urllib</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">pathlib</span><span class="w"> </span><span class="kn">import</span> <span class="n">Path</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">contextlib</span><span class="w"> </span><span class="kn">import</span> <span class="n">ExitStack</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">pandas</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">pd</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">quapy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">qp</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">joblib</span><span class="w"> </span><span class="kn">import</span> <span class="n">Parallel</span><span class="p">,</span> <span class="n">delayed</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">time</span><span class="w"> </span><span class="kn">import</span> <span class="n">time</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">signal</span>
<span class="k">def</span><span class="w"> </span><span class="nf">_get_parallel_slices</span><span class="p">(</span><span class="n">n_tasks</span><span class="p">,</span> <span class="n">n_jobs</span><span class="p">):</span>
<span class="k">if</span> <span class="n">n_jobs</span> <span class="o">==</span> <span class="o">-</span><span class="mi">1</span><span class="p">:</span>
<span class="n">n_jobs</span> <span class="o">=</span> <span class="n">multiprocessing</span><span class="o">.</span><span class="n">cpu_count</span><span class="p">()</span>
<span class="n">batch</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">n_tasks</span> <span class="o">/</span> <span class="n">n_jobs</span><span class="p">)</span>
<span class="n">remainder</span> <span class="o">=</span> <span class="n">n_tasks</span> <span class="o">%</span> <span class="n">n_jobs</span>
<span class="k">return</span> <span class="p">[</span><span class="nb">slice</span><span class="p">(</span><span class="n">job</span> <span class="o">*</span> <span class="n">batch</span><span class="p">,</span> <span class="p">(</span><span class="n">job</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span> <span class="o">*</span> <span class="n">batch</span> <span class="o">+</span> <span class="p">(</span><span class="n">remainder</span> <span class="k">if</span> <span class="n">job</span> <span class="o">==</span> <span class="n">n_jobs</span> <span class="o">-</span> <span class="mi">1</span> <span class="k">else</span> <span class="mi">0</span><span class="p">))</span> <span class="k">for</span> <span class="n">job</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">n_jobs</span><span class="p">)]</span>
<div class="viewcode-block" id="map_parallel">
<a class="viewcode-back" href="../../quapy.html#quapy.util.map_parallel">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">map_parallel</span><span class="p">(</span><span class="n">func</span><span class="p">,</span> <span class="n">args</span><span class="p">,</span> <span class="n">n_jobs</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Applies func to n_jobs slices of args. E.g., if args is an array of 99 items and n_jobs=2, then</span>
<span class="sd"> func is applied in two parallel processes to args[0:50] and to args[50:99]. func is a function</span>
<span class="sd"> that already works with a list of arguments.</span>
<span class="sd"> :param func: function to be parallelized</span>
<span class="sd"> :param args: array-like of arguments to be passed to the function in different parallel calls</span>
<span class="sd"> :param n_jobs: the number of workers</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">args</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">args</span><span class="p">)</span>
<span class="n">slices</span> <span class="o">=</span> <span class="n">_get_parallel_slices</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">args</span><span class="p">),</span> <span class="n">n_jobs</span><span class="p">)</span>
<span class="n">results</span> <span class="o">=</span> <span class="n">Parallel</span><span class="p">(</span><span class="n">n_jobs</span><span class="o">=</span><span class="n">n_jobs</span><span class="p">)(</span>
<span class="n">delayed</span><span class="p">(</span><span class="n">func</span><span class="p">)(</span><span class="n">args</span><span class="p">[</span><span class="n">slice_i</span><span class="p">])</span> <span class="k">for</span> <span class="n">slice_i</span> <span class="ow">in</span> <span class="n">slices</span>
<span class="p">)</span>
<span class="k">return</span> <span class="nb">list</span><span class="p">(</span><span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="o">.</span><span class="n">from_iterable</span><span class="p">(</span><span class="n">results</span><span class="p">))</span></div>
<div class="viewcode-block" id="parallel">
<a class="viewcode-back" href="../../quapy.html#quapy.util.parallel">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">parallel</span><span class="p">(</span><span class="n">func</span><span class="p">,</span> <span class="n">args</span><span class="p">,</span> <span class="n">n_jobs</span><span class="p">,</span> <span class="n">seed</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">asarray</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">backend</span><span class="o">=</span><span class="s1">&#39;loky&#39;</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> A wrapper of multiprocessing:</span>
<span class="sd"> &gt;&gt;&gt; Parallel(n_jobs=n_jobs)(</span>
<span class="sd"> &gt;&gt;&gt; delayed(func)(args_i) for args_i in args</span>
<span class="sd"> &gt;&gt;&gt; )</span>
<span class="sd"> that takes the `quapy.environ` variable as input silently.</span>
<span class="sd"> Seeds the child processes to ensure reproducibility when n_jobs&gt;1.</span>
<span class="sd"> :param func: callable</span>
<span class="sd"> :param args: args of func</span>
<span class="sd"> :param seed: the numeric seed</span>
<span class="sd"> :param asarray: set to True to return a np.ndarray instead of a list</span>
<span class="sd"> :param backend: indicates the backend used for handling parallel works</span>
<span class="sd"> :param open_args: if True, then the delayed function is called on *args_i, instead of on args_i</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">def</span><span class="w"> </span><span class="nf">func_dec</span><span class="p">(</span><span class="n">environ</span><span class="p">,</span> <span class="n">seed</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span>
<span class="n">qp</span><span class="o">.</span><span class="n">environ</span> <span class="o">=</span> <span class="n">environ</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
<span class="n">qp</span><span class="o">.</span><span class="n">environ</span><span class="p">[</span><span class="s1">&#39;N_JOBS&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="mi">1</span>
<span class="c1">#set a context with a temporal seed to ensure results are reproducibles in parallel</span>
<span class="k">with</span> <span class="n">ExitStack</span><span class="p">()</span> <span class="k">as</span> <span class="n">stack</span><span class="p">:</span>
<span class="k">if</span> <span class="n">seed</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
<span class="n">stack</span><span class="o">.</span><span class="n">enter_context</span><span class="p">(</span><span class="n">qp</span><span class="o">.</span><span class="n">util</span><span class="o">.</span><span class="n">temp_seed</span><span class="p">(</span><span class="n">seed</span><span class="p">))</span>
<span class="k">return</span> <span class="n">func</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">)</span>
<span class="n">out</span> <span class="o">=</span> <span class="n">Parallel</span><span class="p">(</span><span class="n">n_jobs</span><span class="o">=</span><span class="n">n_jobs</span><span class="p">,</span> <span class="n">backend</span><span class="o">=</span><span class="n">backend</span><span class="p">)(</span>
<span class="n">delayed</span><span class="p">(</span><span class="n">func_dec</span><span class="p">)(</span><span class="n">qp</span><span class="o">.</span><span class="n">environ</span><span class="p">,</span> <span class="kc">None</span> <span class="k">if</span> <span class="n">seed</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="n">seed</span><span class="o">+</span><span class="n">i</span><span class="p">,</span> <span class="n">args_i</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">args_i</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">args</span><span class="p">)</span>
<span class="p">)</span>
<span class="k">if</span> <span class="n">asarray</span><span class="p">:</span>
<span class="n">out</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">out</span><span class="p">)</span>
<span class="k">return</span> <span class="n">out</span></div>
<div class="viewcode-block" id="parallel_unpack">
<a class="viewcode-back" href="../../quapy.html#quapy.util.parallel_unpack">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">parallel_unpack</span><span class="p">(</span><span class="n">func</span><span class="p">,</span> <span class="n">args</span><span class="p">,</span> <span class="n">n_jobs</span><span class="p">,</span> <span class="n">seed</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">asarray</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">backend</span><span class="o">=</span><span class="s1">&#39;loky&#39;</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> A wrapper of multiprocessing:</span>
<span class="sd"> &gt;&gt;&gt; Parallel(n_jobs=n_jobs)(</span>
<span class="sd"> &gt;&gt;&gt; delayed(func)(*args_i) for args_i in args</span>
<span class="sd"> &gt;&gt;&gt; )</span>
<span class="sd"> that takes the `quapy.environ` variable as input silently.</span>
<span class="sd"> Seeds the child processes to ensure reproducibility when n_jobs&gt;1.</span>
<span class="sd"> :param func: callable</span>
<span class="sd"> :param args: args of func</span>
<span class="sd"> :param seed: the numeric seed</span>
<span class="sd"> :param asarray: set to True to return a np.ndarray instead of a list</span>
<span class="sd"> :param backend: indicates the backend used for handling parallel works</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">def</span><span class="w"> </span><span class="nf">func_dec</span><span class="p">(</span><span class="n">environ</span><span class="p">,</span> <span class="n">seed</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span>
<span class="n">qp</span><span class="o">.</span><span class="n">environ</span> <span class="o">=</span> <span class="n">environ</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
<span class="n">qp</span><span class="o">.</span><span class="n">environ</span><span class="p">[</span><span class="s1">&#39;N_JOBS&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="mi">1</span>
<span class="c1"># set a context with a temporal seed to ensure results are reproducibles in parallel</span>
<span class="k">with</span> <span class="n">ExitStack</span><span class="p">()</span> <span class="k">as</span> <span class="n">stack</span><span class="p">:</span>
<span class="k">if</span> <span class="n">seed</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
<span class="n">stack</span><span class="o">.</span><span class="n">enter_context</span><span class="p">(</span><span class="n">qp</span><span class="o">.</span><span class="n">util</span><span class="o">.</span><span class="n">temp_seed</span><span class="p">(</span><span class="n">seed</span><span class="p">))</span>
<span class="k">return</span> <span class="n">func</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">)</span>
<span class="n">out</span> <span class="o">=</span> <span class="n">Parallel</span><span class="p">(</span><span class="n">n_jobs</span><span class="o">=</span><span class="n">n_jobs</span><span class="p">,</span> <span class="n">backend</span><span class="o">=</span><span class="n">backend</span><span class="p">)(</span>
<span class="n">delayed</span><span class="p">(</span><span class="n">func_dec</span><span class="p">)(</span><span class="n">qp</span><span class="o">.</span><span class="n">environ</span><span class="p">,</span> <span class="kc">None</span> <span class="k">if</span> <span class="n">seed</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="n">seed</span> <span class="o">+</span> <span class="n">i</span><span class="p">,</span> <span class="o">*</span><span class="n">args_i</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">args_i</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">args</span><span class="p">)</span>
<span class="p">)</span>
<span class="k">if</span> <span class="n">asarray</span><span class="p">:</span>
<span class="n">out</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">out</span><span class="p">)</span>
<span class="k">return</span> <span class="n">out</span></div>
<div class="viewcode-block" id="temp_seed">
<a class="viewcode-back" href="../../quapy.html#quapy.util.temp_seed">[docs]</a>
<span class="nd">@contextlib</span><span class="o">.</span><span class="n">contextmanager</span>
<span class="k">def</span><span class="w"> </span><span class="nf">temp_seed</span><span class="p">(</span><span class="n">random_state</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Can be used in a &quot;with&quot; context to set a temporal seed without modifying the outer numpy&#39;s current state. E.g.:</span>
<span class="sd"> &gt;&gt;&gt; with temp_seed(random_seed):</span>
<span class="sd"> &gt;&gt;&gt; pass # do any computation depending on np.random functionality</span>
<span class="sd"> :param random_state: the seed to set within the &quot;with&quot; context</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">if</span> <span class="n">random_state</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
<span class="n">state</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">get_state</span><span class="p">()</span>
<span class="c1">#save the seed just in case is needed (for instance for setting the seed to child processes)</span>
<span class="n">qp</span><span class="o">.</span><span class="n">environ</span><span class="p">[</span><span class="s1">&#39;_R_SEED&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">random_state</span>
<span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">seed</span><span class="p">(</span><span class="n">random_state</span><span class="p">)</span>
<span class="k">try</span><span class="p">:</span>
<span class="k">yield</span>
<span class="k">finally</span><span class="p">:</span>
<span class="k">if</span> <span class="n">random_state</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
<span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">set_state</span><span class="p">(</span><span class="n">state</span><span class="p">)</span></div>
<div class="viewcode-block" id="download_file">
<a class="viewcode-back" href="../../quapy.html#quapy.util.download_file">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">download_file</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">archive_filename</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Downloads a file from a url</span>
<span class="sd"> :param url: the url</span>
<span class="sd"> :param archive_filename: destination filename</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">def</span><span class="w"> </span><span class="nf">progress</span><span class="p">(</span><span class="n">blocknum</span><span class="p">,</span> <span class="n">bs</span><span class="p">,</span> <span class="n">size</span><span class="p">):</span>
<span class="n">total_sz_mb</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%.2f</span><span class="s1"> MB&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">size</span> <span class="o">/</span> <span class="mf">1e6</span><span class="p">)</span>
<span class="n">current_sz_mb</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%.2f</span><span class="s1"> MB&#39;</span> <span class="o">%</span> <span class="p">((</span><span class="n">blocknum</span> <span class="o">*</span> <span class="n">bs</span><span class="p">)</span> <span class="o">/</span> <span class="mf">1e6</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\r</span><span class="s1">downloaded </span><span class="si">%s</span><span class="s1"> / </span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">current_sz_mb</span><span class="p">,</span> <span class="n">total_sz_mb</span><span class="p">),</span> <span class="n">end</span><span class="o">=</span><span class="s1">&#39;&#39;</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Downloading </span><span class="si">%s</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="n">url</span><span class="p">)</span>
<span class="n">urllib</span><span class="o">.</span><span class="n">request</span><span class="o">.</span><span class="n">urlretrieve</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">filename</span><span class="o">=</span><span class="n">archive_filename</span><span class="p">,</span> <span class="n">reporthook</span><span class="o">=</span><span class="n">progress</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">&quot;&quot;</span><span class="p">)</span></div>
<div class="viewcode-block" id="download_file_if_not_exists">
<a class="viewcode-back" href="../../quapy.html#quapy.util.download_file_if_not_exists">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">download_file_if_not_exists</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">archive_filename</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Downloads a file (using :meth:`download_file`) if the file does not exist.</span>
<span class="sd"> :param url: the url</span>
<span class="sd"> :param archive_filename: destination filename</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">archive_filename</span><span class="p">):</span>
<span class="k">return</span>
<span class="n">create_if_not_exist</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="n">archive_filename</span><span class="p">))</span>
<span class="n">download_file</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">archive_filename</span><span class="p">)</span></div>
<div class="viewcode-block" id="create_if_not_exist">
<a class="viewcode-back" href="../../quapy.html#quapy.util.create_if_not_exist">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">create_if_not_exist</span><span class="p">(</span><span class="n">path</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> An alias to `os.makedirs(path, exist_ok=True)` that also returns the path. This is useful in cases like, e.g.:</span>
<span class="sd"> &gt;&gt;&gt; path = create_if_not_exist(os.path.join(dir, subdir, anotherdir))</span>
<span class="sd"> :param path: path to create</span>
<span class="sd"> :return: the path itself</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="k">return</span> <span class="n">path</span></div>
<div class="viewcode-block" id="get_quapy_home">
<a class="viewcode-back" href="../../quapy.html#quapy.util.get_quapy_home">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">get_quapy_home</span><span class="p">():</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Gets the home directory of QuaPy, i.e., the directory where QuaPy saves permanent data, such as dowloaded datasets.</span>
<span class="sd"> This directory is `~/quapy_data`</span>
<span class="sd"> :return: a string representing the path</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">home</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">Path</span><span class="o">.</span><span class="n">home</span><span class="p">()),</span> <span class="s1">&#39;quapy_data&#39;</span><span class="p">)</span>
<span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">home</span><span class="p">,</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="k">return</span> <span class="n">home</span></div>
<div class="viewcode-block" id="create_parent_dir">
<a class="viewcode-back" href="../../quapy.html#quapy.util.create_parent_dir">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">create_parent_dir</span><span class="p">(</span><span class="n">path</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Creates the parent dir (if any) of a given path, if not exists. E.g., for `./path/to/file.txt`, the path `./path/to`</span>
<span class="sd"> is created.</span>
<span class="sd"> :param path: the path</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">parentdir</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">path</span><span class="p">)</span><span class="o">.</span><span class="n">parent</span>
<span class="k">if</span> <span class="n">parentdir</span><span class="p">:</span>
<span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">parentdir</span><span class="p">,</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span></div>
<div class="viewcode-block" id="save_text_file">
<a class="viewcode-back" href="../../quapy.html#quapy.util.save_text_file">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">save_text_file</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">text</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Saves a text file to disk, given its full path, and creates the parent directory if missing.</span>
<span class="sd"> :param path: path where to save the path.</span>
<span class="sd"> :param text: text to save.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">create_parent_dir</span><span class="p">(</span><span class="n">path</span><span class="p">)</span>
<span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="s1">&#39;wt&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fout</span><span class="p">:</span>
<span class="n">fout</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">text</span><span class="p">)</span></div>
<div class="viewcode-block" id="pickled_resource">
<a class="viewcode-back" href="../../quapy.html#quapy.util.pickled_resource">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">pickled_resource</span><span class="p">(</span><span class="n">pickle_path</span><span class="p">:</span><span class="nb">str</span><span class="p">,</span> <span class="n">generation_func</span><span class="p">:</span><span class="nb">callable</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Allows for fast reuse of resources that are generated only once by calling generation_func(\\*args). The next times</span>
<span class="sd"> this function is invoked, it loads the pickled resource. Example:</span>
<span class="sd"> &gt;&gt;&gt; def some_array(n): # a mock resource created with one parameter (`n`)</span>
<span class="sd"> &gt;&gt;&gt; return np.random.rand(n)</span>
<span class="sd"> &gt;&gt;&gt; pickled_resource(&#39;./my_array.pkl&#39;, some_array, 10) # the resource does not exist: it is created by calling some_array(10)</span>
<span class="sd"> &gt;&gt;&gt; pickled_resource(&#39;./my_array.pkl&#39;, some_array, 10) # the resource exists; it is loaded from &#39;./my_array.pkl&#39;</span>
<span class="sd"> :param pickle_path: the path where to save (first time) and load (next times) the resource</span>
<span class="sd"> :param generation_func: the function that generates the resource, in case it does not exist in pickle_path</span>
<span class="sd"> :param args: any arg that generation_func uses for generating the resources</span>
<span class="sd"> :return: the resource</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">if</span> <span class="n">pickle_path</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="k">return</span> <span class="n">generation_func</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">pickle_path</span><span class="p">):</span>
<span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">pickle_path</span><span class="p">,</span> <span class="s1">&#39;rb&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fin</span><span class="p">:</span>
<span class="n">instance</span> <span class="o">=</span> <span class="n">pickle</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">fin</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">instance</span> <span class="o">=</span> <span class="n">generation_func</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">)</span>
<span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">Path</span><span class="p">(</span><span class="n">pickle_path</span><span class="p">)</span><span class="o">.</span><span class="n">parent</span><span class="p">),</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">pickle_path</span><span class="p">,</span> <span class="s1">&#39;wb&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">foo</span><span class="p">:</span>
<span class="n">pickle</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="n">instance</span><span class="p">,</span> <span class="n">foo</span><span class="p">,</span> <span class="n">pickle</span><span class="o">.</span><span class="n">HIGHEST_PROTOCOL</span><span class="p">)</span>
<span class="k">return</span> <span class="n">instance</span></div>
<span class="k">def</span><span class="w"> </span><span class="nf">_check_sample_size</span><span class="p">(</span><span class="n">sample_size</span><span class="p">):</span>
<span class="k">if</span> <span class="n">sample_size</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="k">assert</span> <span class="n">qp</span><span class="o">.</span><span class="n">environ</span><span class="p">[</span><span class="s1">&#39;SAMPLE_SIZE&#39;</span><span class="p">]</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">,</span> \
<span class="s1">&#39;error: sample_size set to None, and cannot be resolved from the environment&#39;</span>
<span class="n">sample_size</span> <span class="o">=</span> <span class="n">qp</span><span class="o">.</span><span class="n">environ</span><span class="p">[</span><span class="s1">&#39;SAMPLE_SIZE&#39;</span><span class="p">]</span>
<span class="k">assert</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">sample_size</span><span class="p">,</span> <span class="nb">int</span><span class="p">)</span> <span class="ow">and</span> <span class="n">sample_size</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">,</span> \
<span class="s1">&#39;error: sample_size is not a positive integer&#39;</span>
<span class="k">return</span> <span class="n">sample_size</span>
<div class="viewcode-block" id="load_report">
<a class="viewcode-back" href="../../quapy.html#quapy.util.load_report">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">load_report</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">as_dict</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
<span class="k">def</span><span class="w"> </span><span class="nf">str2prev_arr</span><span class="p">(</span><span class="n">strprev</span><span class="p">):</span>
<span class="n">within</span> <span class="o">=</span> <span class="n">strprev</span><span class="o">.</span><span class="n">strip</span><span class="p">(</span><span class="s1">&#39;[]&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">split</span><span class="p">()</span>
<span class="n">float_list</span> <span class="o">=</span> <span class="p">[</span><span class="nb">float</span><span class="p">(</span><span class="n">p</span><span class="p">)</span> <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">within</span><span class="p">]</span>
<span class="n">float_list</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="mf">1.</span> <span class="o">-</span> <span class="nb">sum</span><span class="p">(</span><span class="n">float_list</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">])</span>
<span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">float_list</span><span class="p">)</span>
<span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">index_col</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
<span class="n">df</span><span class="p">[</span><span class="s1">&#39;true-prev&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">df</span><span class="p">[</span><span class="s1">&#39;true-prev&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">apply</span><span class="p">(</span><span class="n">str2prev_arr</span><span class="p">)</span>
<span class="n">df</span><span class="p">[</span><span class="s1">&#39;estim-prev&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">df</span><span class="p">[</span><span class="s1">&#39;estim-prev&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">apply</span><span class="p">(</span><span class="n">str2prev_arr</span><span class="p">)</span>
<span class="k">if</span> <span class="n">as_dict</span><span class="p">:</span>
<span class="n">d</span> <span class="o">=</span> <span class="p">{}</span>
<span class="k">for</span> <span class="n">col</span> <span class="ow">in</span> <span class="n">df</span><span class="o">.</span><span class="n">columns</span><span class="o">.</span><span class="n">values</span><span class="p">:</span>
<span class="n">vals</span> <span class="o">=</span> <span class="n">df</span><span class="p">[</span><span class="n">col</span><span class="p">]</span><span class="o">.</span><span class="n">values</span>
<span class="k">if</span> <span class="n">col</span> <span class="ow">in</span> <span class="p">[</span><span class="s1">&#39;true-prev&#39;</span><span class="p">,</span> <span class="s1">&#39;estim-prev&#39;</span><span class="p">]:</span>
<span class="n">vals</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">vstack</span><span class="p">(</span><span class="n">vals</span><span class="p">)</span>
<span class="n">d</span><span class="p">[</span><span class="n">col</span><span class="p">]</span> <span class="o">=</span> <span class="n">vals</span>
<span class="k">return</span> <span class="n">d</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="n">df</span></div>
<div class="viewcode-block" id="EarlyStop">
<a class="viewcode-back" href="../../quapy.html#quapy.util.EarlyStop">[docs]</a>
<span class="k">class</span><span class="w"> </span><span class="nc">EarlyStop</span><span class="p">:</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> A class implementing the early-stopping condition typically used for training neural networks.</span>
<span class="sd"> &gt;&gt;&gt; earlystop = EarlyStop(patience=2, lower_is_better=True)</span>
<span class="sd"> &gt;&gt;&gt; earlystop(0.9, epoch=0)</span>
<span class="sd"> &gt;&gt;&gt; earlystop(0.7, epoch=1)</span>
<span class="sd"> &gt;&gt;&gt; earlystop.IMPROVED # is True</span>
<span class="sd"> &gt;&gt;&gt; earlystop(1.0, epoch=2)</span>
<span class="sd"> &gt;&gt;&gt; earlystop.STOP # is False (patience=1)</span>
<span class="sd"> &gt;&gt;&gt; earlystop(1.0, epoch=3)</span>
<span class="sd"> &gt;&gt;&gt; earlystop.STOP # is True (patience=0)</span>
<span class="sd"> &gt;&gt;&gt; earlystop.best_epoch # is 1</span>
<span class="sd"> &gt;&gt;&gt; earlystop.best_score # is 0.7</span>
<span class="sd"> :param patience: the number of (consecutive) times that a monitored evaluation metric (typically obtaind in a</span>
<span class="sd"> held-out validation split) can be found to be worse than the best one obtained so far, before flagging the</span>
<span class="sd"> stopping condition. An instance of this class is `callable`, and is to be used as follows:</span>
<span class="sd"> :param lower_is_better: if True (default) the metric is to be minimized.</span>
<span class="sd"> :ivar best_score: keeps track of the best value seen so far</span>
<span class="sd"> :ivar best_epoch: keeps track of the epoch in which the best score was set</span>
<span class="sd"> :ivar STOP: flag (boolean) indicating the stopping condition</span>
<span class="sd"> :ivar IMPROVED: flag (boolean) indicating whether there was an improvement in the last call</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">patience</span><span class="p">,</span> <span class="n">lower_is_better</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">PATIENCE_LIMIT</span> <span class="o">=</span> <span class="n">patience</span>
<span class="bp">self</span><span class="o">.</span><span class="n">better</span> <span class="o">=</span> <span class="k">lambda</span> <span class="n">a</span><span class="p">,</span><span class="n">b</span><span class="p">:</span> <span class="n">a</span><span class="o">&lt;</span><span class="n">b</span> <span class="k">if</span> <span class="n">lower_is_better</span> <span class="k">else</span> <span class="n">a</span><span class="o">&gt;</span><span class="n">b</span>
<span class="bp">self</span><span class="o">.</span><span class="n">patience</span> <span class="o">=</span> <span class="n">patience</span>
<span class="bp">self</span><span class="o">.</span><span class="n">best_score</span> <span class="o">=</span> <span class="kc">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">best_epoch</span> <span class="o">=</span> <span class="kc">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">STOP</span> <span class="o">=</span> <span class="kc">False</span>
<span class="bp">self</span><span class="o">.</span><span class="n">IMPROVED</span> <span class="o">=</span> <span class="kc">False</span>
<span class="k">def</span><span class="w"> </span><span class="fm">__call__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">watch_score</span><span class="p">,</span> <span class="n">epoch</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Commits the new score found in epoch `epoch`. If the score improves over the best score found so far, then</span>
<span class="sd"> the patiente counter gets reset. If otherwise, the patience counter is decreased, and in case it reachs 0,</span>
<span class="sd"> the flag STOP becomes True.</span>
<span class="sd"> :param watch_score: the new score</span>
<span class="sd"> :param epoch: the current epoch</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="bp">self</span><span class="o">.</span><span class="n">IMPROVED</span> <span class="o">=</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">best_score</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">better</span><span class="p">(</span><span class="n">watch_score</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">best_score</span><span class="p">))</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">IMPROVED</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">best_score</span> <span class="o">=</span> <span class="n">watch_score</span>
<span class="bp">self</span><span class="o">.</span><span class="n">best_epoch</span> <span class="o">=</span> <span class="n">epoch</span>
<span class="bp">self</span><span class="o">.</span><span class="n">patience</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">PATIENCE_LIMIT</span>
<span class="k">else</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">patience</span> <span class="o">-=</span> <span class="mi">1</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">patience</span> <span class="o">&lt;=</span> <span class="mi">0</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">STOP</span> <span class="o">=</span> <span class="kc">True</span></div>
<div class="viewcode-block" id="timeout">
<a class="viewcode-back" href="../../quapy.html#quapy.util.timeout">[docs]</a>
<span class="nd">@contextlib</span><span class="o">.</span><span class="n">contextmanager</span>
<span class="k">def</span><span class="w"> </span><span class="nf">timeout</span><span class="p">(</span><span class="n">seconds</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Opens a context that will launch an exception if not closed after a given number of seconds</span>
<span class="sd"> &gt;&gt;&gt; def func(start_msg, end_msg):</span>
<span class="sd"> &gt;&gt;&gt; print(start_msg)</span>
<span class="sd"> &gt;&gt;&gt; sleep(2)</span>
<span class="sd"> &gt;&gt;&gt; print(end_msg)</span>
<span class="sd"> &gt;&gt;&gt;</span>
<span class="sd"> &gt;&gt;&gt; with timeout(1):</span>
<span class="sd"> &gt;&gt;&gt; func(&#39;begin function&#39;, &#39;end function&#39;)</span>
<span class="sd"> &gt;&gt;&gt; Out[]</span>
<span class="sd"> &gt;&gt;&gt; begin function</span>
<span class="sd"> &gt;&gt;&gt; TimeoutError</span>
<span class="sd"> :param seconds: number of seconds, set to &lt;=0 to ignore the timer</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">if</span> <span class="n">seconds</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">:</span>
<span class="k">def</span><span class="w"> </span><span class="nf">handler</span><span class="p">(</span><span class="n">signum</span><span class="p">,</span> <span class="n">frame</span><span class="p">):</span>
<span class="k">raise</span> <span class="ne">TimeoutError</span><span class="p">()</span>
<span class="n">signal</span><span class="o">.</span><span class="n">signal</span><span class="p">(</span><span class="n">signal</span><span class="o">.</span><span class="n">SIGALRM</span><span class="p">,</span> <span class="n">handler</span><span class="p">)</span>
<span class="n">signal</span><span class="o">.</span><span class="n">alarm</span><span class="p">(</span><span class="n">seconds</span><span class="p">)</span>
<span class="k">yield</span>
<span class="k">if</span> <span class="n">seconds</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">:</span>
<span class="n">signal</span><span class="o">.</span><span class="n">alarm</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span></div>
</pre></div>
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123
docs/build/html/_static/_sphinx_javascript_frameworks_compat.js vendored
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@ -1,123 +0,0 @@
/* Compatability shim for jQuery and underscores.js.
*
* Copyright Sphinx contributors
* Released under the two clause BSD licence
*/
/**
* small helper function to urldecode strings
*
* See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL
*/
jQuery.urldecode = function(x) {
if (!x) {
return x
}
return decodeURIComponent(x.replace(/\+/g, ' '));
};
/**
* small helper function to urlencode strings
*/
jQuery.urlencode = encodeURIComponent;
/**
* This function returns the parsed url parameters of the
* current request. Multiple values per key are supported,
* it will always return arrays of strings for the value parts.
*/
jQuery.getQueryParameters = function(s) {
if (typeof s === 'undefined')
s = document.location.search;
var parts = s.substr(s.indexOf('?') + 1).split('&');
var result = {};
for (var i = 0; i < parts.length; i++) {
var tmp = parts[i].split('=', 2);
var key = jQuery.urldecode(tmp[0]);
var value = jQuery.urldecode(tmp[1]);
if (key in result)
result[key].push(value);
else
result[key] = [value];
}
return result;
};
/**
* highlight a given string on a jquery object by wrapping it in
* span elements with the given class name.
*/
jQuery.fn.highlightText = function(text, className) {
function highlight(node, addItems) {
if (node.nodeType === 3) {
var val = node.nodeValue;
var pos = val.toLowerCase().indexOf(text);
if (pos >= 0 &&
!jQuery(node.parentNode).hasClass(className) &&
!jQuery(node.parentNode).hasClass("nohighlight")) {
var span;
var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg");
if (isInSVG) {
span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
} else {
span = document.createElement("span");
span.className = className;
}
span.appendChild(document.createTextNode(val.substr(pos, text.length)));
node.parentNode.insertBefore(span, node.parentNode.insertBefore(
document.createTextNode(val.substr(pos + text.length)),
node.nextSibling));
node.nodeValue = val.substr(0, pos);
if (isInSVG) {
var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect");
var bbox = node.parentElement.getBBox();
rect.x.baseVal.value = bbox.x;
rect.y.baseVal.value = bbox.y;
rect.width.baseVal.value = bbox.width;
rect.height.baseVal.value = bbox.height;
rect.setAttribute('class', className);
addItems.push({
"parent": node.parentNode,
"target": rect});
}
}
}
else if (!jQuery(node).is("button, select, textarea")) {
jQuery.each(node.childNodes, function() {
highlight(this, addItems);
});
}
}
var addItems = [];
var result = this.each(function() {
highlight(this, addItems);
});
for (var i = 0; i < addItems.length; ++i) {
jQuery(addItems[i].parent).before(addItems[i].target);
}
return result;
};
/*
* backward compatibility for jQuery.browser
* This will be supported until firefox bug is fixed.
*/
if (!jQuery.browser) {
jQuery.uaMatch = function(ua) {
ua = ua.toLowerCase();
var match = /(chrome)[ \/]([\w.]+)/.exec(ua) ||
/(webkit)[ \/]([\w.]+)/.exec(ua) ||
/(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) ||
/(msie) ([\w.]+)/.exec(ua) ||
ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) ||
[];
return {
browser: match[ 1 ] || "",
version: match[ 2 ] || "0"
};
};
jQuery.browser = {};
jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true;
}

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/**
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/* Highlighting utilities for Sphinx HTML documentation. */
"use strict";
const SPHINX_HIGHLIGHT_ENABLED = true;
/**
* highlight a given string on a node by wrapping it in
* span elements with the given class name.
*/
const _highlight = (node, addItems, text, className) => {
if (node.nodeType === Node.TEXT_NODE) {
const val = node.nodeValue;
const parent = node.parentNode;
const pos = val.toLowerCase().indexOf(text);
if (
pos >= 0
&& !parent.classList.contains(className)
&& !parent.classList.contains("nohighlight")
) {
let span;
const closestNode = parent.closest("body, svg, foreignObject");
const isInSVG = closestNode && closestNode.matches("svg");
if (isInSVG) {
span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
} else {
span = document.createElement("span");
span.classList.add(className);
}
span.appendChild(document.createTextNode(val.substr(pos, text.length)));
const rest = document.createTextNode(val.substr(pos + text.length));
parent.insertBefore(span, parent.insertBefore(rest, node.nextSibling));
node.nodeValue = val.substr(0, pos);
/* There may be more occurrences of search term in this node. So call this
* function recursively on the remaining fragment.
*/
_highlight(rest, addItems, text, className);
if (isInSVG) {
const rect = document.createElementNS(
"http://www.w3.org/2000/svg",
"rect",
);
const bbox = parent.getBBox();
rect.x.baseVal.value = bbox.x;
rect.y.baseVal.value = bbox.y;
rect.width.baseVal.value = bbox.width;
rect.height.baseVal.value = bbox.height;
rect.setAttribute("class", className);
addItems.push({ parent: parent, target: rect });
}
}
} else if (node.matches && !node.matches("button, select, textarea")) {
node.childNodes.forEach((el) => _highlight(el, addItems, text, className));
}
};
const _highlightText = (thisNode, text, className) => {
let addItems = [];
_highlight(thisNode, addItems, text, className);
addItems.forEach((obj) =>
obj.parent.insertAdjacentElement("beforebegin", obj.target),
);
};
/**
* Small JavaScript module for the documentation.
*/
const SphinxHighlight = {
/**
* highlight the search words provided in localstorage in the text
*/
highlightSearchWords: () => {
if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight
// get and clear terms from localstorage
const url = new URL(window.location);
const highlight =
localStorage.getItem("sphinx_highlight_terms")
|| url.searchParams.get("highlight")
|| "";
localStorage.removeItem("sphinx_highlight_terms");
// Update history only if '?highlight' is present; otherwise it
// clears text fragments (not set in window.location by the browser)
if (url.searchParams.has("highlight")) {
url.searchParams.delete("highlight");
window.history.replaceState({}, "", url);
}
// get individual terms from highlight string
const terms = highlight
.toLowerCase()
.split(/\s+/)
.filter((x) => x);
if (terms.length === 0) return; // nothing to do
// There should never be more than one element matching "div.body"
const divBody = document.querySelectorAll("div.body");
const body = divBody.length ? divBody[0] : document.querySelector("body");
window.setTimeout(() => {
terms.forEach((term) => _highlightText(body, term, "highlighted"));
}, 10);
const searchBox = document.getElementById("searchbox");
if (searchBox === null) return;
searchBox.appendChild(
document
.createRange()
.createContextualFragment(
'<p class="highlight-link">'
+ '<a href="javascript:SphinxHighlight.hideSearchWords()">'
+ _("Hide Search Matches")
+ "</a></p>",
),
);
},
/**
* helper function to hide the search marks again
*/
hideSearchWords: () => {
document
.querySelectorAll("#searchbox .highlight-link")
.forEach((el) => el.remove());
document
.querySelectorAll("span.highlighted")
.forEach((el) => el.classList.remove("highlighted"));
localStorage.removeItem("sphinx_highlight_terms");
},
initEscapeListener: () => {
// only install a listener if it is really needed
if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return;
document.addEventListener("keydown", (event) => {
// bail for input elements
if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName))
return;
// bail with special keys
if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey)
return;
if (
DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS
&& event.key === "Escape"
) {
SphinxHighlight.hideSearchWords();
event.preventDefault();
}
});
},
};
_ready(() => {
/* Do not call highlightSearchWords() when we are on the search page.
* It will highlight words from the *previous* search query.
*/
if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords();
SphinxHighlight.initEscapeListener();
});

354
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@ -1,354 +0,0 @@
/*
* sphinxdoc.css_t
* ~~~~~~~~~~~~~~~
*
* Sphinx stylesheet -- sphinxdoc theme. Originally created by
* Armin Ronacher for Werkzeug.
*
* :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
@import url("basic.css");
/* -- page layout ----------------------------------------------------------- */
body {
font-family: 'Lucida Grande', 'Lucida Sans Unicode', 'Geneva',
'Verdana', sans-serif;
font-size: 14px;
letter-spacing: -0.01em;
line-height: 150%;
text-align: center;
background-color: #BFD1D4;
color: black;
padding: 0;
border: 1px solid #aaa;
margin: 0px 80px 0px 80px;
min-width: 740px;
}
div.document {
background-color: white;
text-align: left;
background-image: url(contents.png);
background-repeat: repeat-x;
}
div.documentwrapper {
float: left;
width: 100%;
}
div.bodywrapper {
margin: 0 calc(230px + 10px) 0 0;
border-right: 1px solid #ccc;
}
div.body {
margin: 0;
padding: 0.5em 20px 20px 20px;
}
div.related {
font-size: 1em;
}
div.related ul {
background-image: url(navigation.png);
height: 2em;
border-top: 1px solid #ddd;
border-bottom: 1px solid #ddd;
}
div.related ul li {
margin: 0;
padding: 0;
height: 2em;
float: left;
}
div.related ul li.right {
float: right;
margin-right: 5px;
}
div.related ul li a {
margin: 0;
padding: 0 5px 0 5px;
line-height: 1.75em;
color: #EE9816;
}
div.related ul li a:hover {
color: #3CA8E7;
}
div.sphinxsidebarwrapper {
padding: 0;
}
div.sphinxsidebar {
padding: 0.5em 15px 15px 0;
width: calc(230px - 20px);
float: right;
font-size: 1em;
text-align: left;
}
div.sphinxsidebar h3, div.sphinxsidebar h4 {
margin: 1em 0 0.5em 0;
font-size: 1em;
padding: 0.1em 0 0.1em 0.5em;
color: white;
border: 1px solid #86989B;
background-color: #AFC1C4;
}
div.sphinxsidebar h3 a {
color: white;
}
div.sphinxsidebar ul {
padding-left: 1.5em;
margin-top: 7px;
padding: 0;
line-height: 130%;
}
div.sphinxsidebar ul ul {
margin-left: 20px;
}
div.footer {
background-color: #E3EFF1;
color: #86989B;
padding: 3px 8px 3px 0;
clear: both;
font-size: 0.8em;
text-align: right;
}
div.footer a {
color: #86989B;
text-decoration: underline;
}
/* -- body styles ----------------------------------------------------------- */
p {
margin: 0.8em 0 0.5em 0;
}
a {
color: #CA7900;
text-decoration: none;
}
a:hover {
color: #2491CF;
}
a:visited {
color: #551A8B;
}
div.body a {
text-decoration: underline;
}
h1 {
margin: 0;
padding: 0.7em 0 0.3em 0;
font-size: 1.5em;
color: #11557C;
}
h2 {
margin: 1.3em 0 0.2em 0;
font-size: 1.35em;
padding: 0;
}
h3 {
margin: 1em 0 -0.3em 0;
font-size: 1.2em;
}
div.body h1 a, div.body h2 a, div.body h3 a, div.body h4 a, div.body h5 a, div.body h6 a {
color: black!important;
}
h1 a.anchor, h2 a.anchor, h3 a.anchor, h4 a.anchor, h5 a.anchor, h6 a.anchor {
display: none;
margin: 0 0 0 0.3em;
padding: 0 0.2em 0 0.2em;
color: #aaa!important;
}
h1:hover a.anchor, h2:hover a.anchor, h3:hover a.anchor, h4:hover a.anchor,
h5:hover a.anchor, h6:hover a.anchor {
display: inline;
}
h1 a.anchor:hover, h2 a.anchor:hover, h3 a.anchor:hover, h4 a.anchor:hover,
h5 a.anchor:hover, h6 a.anchor:hover {
color: #777;
background-color: #eee;
}
a.headerlink {
color: #c60f0f!important;
font-size: 1em;
margin-left: 6px;
padding: 0 4px 0 4px;
text-decoration: none!important;
}
a.headerlink:hover {
background-color: #ccc;
color: white!important;
}
cite, code, code {
font-family: 'Consolas', 'Deja Vu Sans Mono',
'Bitstream Vera Sans Mono', monospace;
font-size: 0.95em;
letter-spacing: 0.01em;
}
code {
background-color: #f2f2f2;
border-bottom: 1px solid #ddd;
color: #333;
}
code.descname, code.descclassname, code.xref {
border: 0;
}
hr {
border: 1px solid #abc;
margin: 2em;
}
a code {
border: 0;
color: #CA7900;
}
a code:hover {
color: #2491CF;
}
pre {
font-family: 'Consolas', 'Deja Vu Sans Mono',
'Bitstream Vera Sans Mono', monospace;
font-size: 0.95em;
letter-spacing: 0.015em;
line-height: 120%;
padding: 0.5em;
border: 1px solid #ccc;
}
pre a {
color: inherit;
text-decoration: underline;
}
td.linenos pre {
padding: 0.5em 0;
}
div.quotebar {
background-color: #f8f8f8;
max-width: 250px;
float: right;
padding: 2px 7px;
border: 1px solid #ccc;
}
nav.contents,
aside.topic,
div.topic {
background-color: #f8f8f8;
}
table {
border-collapse: collapse;
margin: 0 -0.5em 0 -0.5em;
}
table td, table th {
padding: 0.2em 0.5em 0.2em 0.5em;
}
div.admonition, div.warning {
font-size: 0.9em;
margin: 1em 0 1em 0;
border: 1px solid #86989B;
background-color: #f7f7f7;
padding: 0;
}
div.admonition p, div.warning p {
margin: 0.5em 1em 0.5em 1em;
padding: 0;
}
div.admonition pre, div.warning pre {
margin: 0.4em 1em 0.4em 1em;
}
div.admonition p.admonition-title,
div.warning p.admonition-title {
margin: 0;
padding: 0.1em 0 0.1em 0.5em;
color: white;
border-bottom: 1px solid #86989B;
font-weight: bold;
background-color: #AFC1C4;
}
div.warning {
border: 1px solid #940000;
}
div.warning p.admonition-title {
background-color: #CF0000;
border-bottom-color: #940000;
}
div.admonition ul, div.admonition ol,
div.warning ul, div.warning ol {
margin: 0.1em 0.5em 0.5em 3em;
padding: 0;
}
div.versioninfo {
margin: 1em 0 0 0;
border: 1px solid #ccc;
background-color: #DDEAF0;
padding: 8px;
line-height: 1.3em;
font-size: 0.9em;
}
.viewcode-back {
font-family: 'Lucida Grande', 'Lucida Sans Unicode', 'Geneva',
'Verdana', sans-serif;
}
div.viewcode-block:target {
background-color: #f4debf;
border-top: 1px solid #ac9;
border-bottom: 1px solid #ac9;
}
div.code-block-caption {
background-color: #ddd;
color: #222;
border: 1px solid #ccc;
}

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<!DOCTYPE html>
<html class="writer-html5" lang="en" data-content_root="./">
<head>
<meta charset="utf-8" /><meta name="generator" content="Docutils 0.19: https://docutils.sourceforge.io/" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>API &mdash; QuaPy: A Python-based open-source framework for quantification 0.1.8 documentation</title>
<link rel="stylesheet" type="text/css" href="_static/pygments.css?v=92fd9be5" />
<link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
<!--[if lt IE 9]>
<script src="_static/js/html5shiv.min.js"></script>
<![endif]-->
<script src="_static/jquery.js?v=5d32c60e"></script>
<script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
<script src="_static/documentation_options.js?v=22607128"></script>
<script src="_static/doctools.js?v=9a2dae69"></script>
<script src="_static/sphinx_highlight.js?v=dc90522c"></script>
<script src="_static/js/theme.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
</head>
<body class="wy-body-for-nav">
<div class="wy-grid-for-nav">
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-scroll">
<div class="wy-side-nav-search" >
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QuaPy: A Python-based open-source framework for quantification
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<input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
<input type="hidden" name="check_keywords" value="yes" />
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</form>
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<div itemprop="articleBody">
<section id="api">
<h1>API<a class="headerlink" href="#api" title="Link to this heading"></a></h1>
<table class="autosummary longtable docutils align-default">
<tbody>
<tr class="row-odd"><td><p><a class="reference internal" href="generated/quapy.html#module-quapy" title="quapy"><code class="xref py py-obj docutils literal notranslate"><span class="pre">quapy</span></code></a></p></td>
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</tr>
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106
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<!DOCTYPE html>
<html class="writer-html5" lang="en" data-content_root="../">
<head>
<meta charset="utf-8" /><meta name="generator" content="Docutils 0.19: https://docutils.sourceforge.io/" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>quapy &mdash; QuaPy: A Python-based open-source framework for quantification 0.1.8 documentation</title>
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<section id="module-quapy">
<span id="quapy"></span><h1>quapy<a class="headerlink" href="#module-quapy" title="Link to this heading"></a></h1>
<p>QuaPy module for quantification</p>
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<section id="quapy-benchmarking-package">
<h1>quapy.benchmarking package<a class="headerlink" href="#quapy-benchmarking-package" title="Link to this heading"></a></h1>
<section id="submodules">
<h2>Submodules<a class="headerlink" href="#submodules" title="Link to this heading"></a></h2>
</section>
<section id="module-quapy.benchmarking.typical">
<span id="quapy-benchmarking-typical-module"></span><h2>quapy.benchmarking.typical module<a class="headerlink" href="#module-quapy.benchmarking.typical" title="Link to this heading"></a></h2>
<dl class="py function">
<dt class="sig sig-object py" id="quapy.benchmarking.typical.wrap_cls_params">
<span class="sig-prename descclassname"><span class="pre">quapy.benchmarking.typical.</span></span><span class="sig-name descname"><span class="pre">wrap_cls_params</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">params</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#quapy.benchmarking.typical.wrap_cls_params" title="Link to this definition"></a></dt>
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Para meter los módulos dentro de doc hay que hacer un
sphinx-apidoc -o docs/source/ quapy/ -P
Eso importa todo lo que haya en quapy/ (incluidos los ficheros _ gracias a -P) en source y crea un rst para cada uno.
Parece que lo del -P no funciona. Hay que meterlos a mano en quapy.method.rst
Luego, simplemente
make html

35
docs/make.bat
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@ECHO OFF
pushd %~dp0
REM Command file for Sphinx documentation
if "%SPHINXBUILD%" == "" (
set SPHINXBUILD=sphinx-build
)
set SOURCEDIR=source
set BUILDDIR=build
%SPHINXBUILD% >NUL 2>NUL
if errorlevel 9009 (
echo.
echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
echo.installed, then set the SPHINXBUILD environment variable to point
echo.to the full path of the 'sphinx-build' executable. Alternatively you
echo.may add the Sphinx directory to PATH.
echo.
echo.If you don't have Sphinx installed, grab it from
echo.https://www.sphinx-doc.org/
exit /b 1
)
if "%1" == "" goto help
%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
goto end
:help
%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
:end
popd

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!*.png

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.navbar-brand.logo .title.logo__title {
display: none;
}
.navbar-brand img {
max-height: 2.2rem;
width: auto;
}
.navbar-brand.logo .title.logo__title {
font-size: 1.05rem;
line-height: 1.15;
white-space: nowrap;
}
@media (max-width: 1200px) {
.bd-header .navbar-header-items {
min-width: 0;
}
.bd-header .navbar-header-items__center {
overflow-x: auto;
}
.bd-header .bd-navbar-elements {
flex-wrap: nowrap;
}
}
.hero-copy {
font-size: 1.15rem;
line-height: 1.7;
max-width: 56rem;
margin: 0 0 1.5rem 0;
}
.landing-grid {
margin: 1.2rem 0 2rem 0;
}
.landing-card {
border-radius: 1rem;
border: 1px solid var(--pst-color-border, #d0d7de);
box-shadow: 0 10px 24px rgba(15, 23, 42, 0.08);
}
.landing-card .sd-card-title {
font-size: 1.1rem;
}
[data-theme="dark"] .landing-card {
box-shadow: 0 10px 24px rgba(0, 0, 0, 0.22);
}

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# Configuration file for the Sphinx documentation builder.
#
# For the full list of built-in configuration values, see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
# -- Project information -----------------------------------------------------
# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
import pathlib
import sys
from os.path import join
quapy_path = join(pathlib.Path(__file__).parents[2].resolve().as_posix(), 'quapy')
wiki_path = join(pathlib.Path(__file__).parents[0].resolve().as_posix(), 'wiki')
source_path = pathlib.Path(__file__).parents[2].resolve().as_posix()
print(f'quapy path={quapy_path}')
print(f'quapy source path={source_path}')
sys.path.insert(0, quapy_path)
sys.path.insert(0, wiki_path)
sys.path.insert(0, source_path)
print(sys.path)
project = 'QuaPy: A Python-based open-source framework for quantification'
copyright = '2024, Alejandro Moreo'
author = 'Alejandro Moreo'
import quapy
release = quapy.__version__
# -- General configuration ---------------------------------------------------
# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
extensions = [
'sphinx.ext.autosectionlabel',
'sphinx.ext.duration',
'sphinx.ext.doctest',
'sphinx.ext.autodoc',
'sphinx.ext.autosummary',
'sphinx.ext.viewcode',
'sphinx.ext.napoleon',
'sphinx.ext.intersphinx',
'myst_parser',
'sphinx_design',
]
autosectionlabel_prefix_document = True
source_suffix = ['.rst', '.md']
myst_enable_extensions = ['colon_fence']
templates_path = ['_templates']
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This pattern also affects html_static_path and html_extra_path.
exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
# -- Options for HTML output -------------------------------------------------
# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
#html_theme = 'sphinx_rtd_theme'
html_theme = 'pydata_sphinx_theme'
# html_theme = 'furo'
# need to be installed: pip install furo (not working...)
html_static_path = ['_static']
html_css_files = ['custom.css']
html_theme_options = {
'logo': {
'image_light': '_static/quapy_logo.png',
'image_dark': '_static/quapy_logo_dark.png',
},
'icon_links': [
{
'name': 'GitHub',
'url': 'https://github.com/HLT-ISTI/QuaPy',
'icon': 'fa-brands fa-github',
'type': 'fontawesome',
},
],
}
# intersphinx configuration
intersphinx_mapping = {
"sklearn": ("https://scikit-learn.org/stable/", None),
}

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```{toctree}
:hidden:
Home <self>
manuals
API <quapy>
```
# QuaPy
```{div} hero-copy
QuaPy is an open-source Python framework for quantification, also known as
supervised prevalence estimation or learning to quantify. It is designed with
research and experimental analysis in mind, and combines datasets, protocols,
evaluation measures, visualization tools, and a broad collection of
quantification methods in a single workflow.
```
`````{grid} 1 1 2 2
:gutter: 3
:class-container: landing-grid
````{grid-item-card} Quickstart
:class-card: landing-card
Install QuaPy and run your first quantifier in a few lines of code.
+++
```{button-link} #installation
:color: primary
Get Started
```
````
````{grid-item-card} Manuals
:class-card: landing-card
Hands-on guides with methodological context, literature pointers, and reproducible workflows.
+++
```{button-ref} manuals
:ref-type: doc
:color: primary
Open Manuals
```
````
````{grid-item-card} API
:class-card: landing-card
Browse the full reference for `quapy`, including methods, datasets, utilities, and research-oriented extensions.
+++
```{button-ref} quapy
:ref-type: doc
:color: primary
Browse API
```
````
````{grid-item-card} GitHub
:class-card: landing-card
Explore the source code, open issues, and current development branch activity.
+++
```{button-link} https://github.com/HLT-ISTI/QuaPy
:color: primary
Open GitHub
```
````
`````
## Installation
```sh
pip install quapy
```
## Why QuaPy
QuaPy is built around the concept of a data sample and supports the main tasks
in the quantification workflow: training quantifiers, generating evaluation
samples, measuring quantification error, selecting models under distribution
shift, and visualizing experimental behaviour. The framework is especially
suited for research settings, where one often needs not only implementations,
but also methodological context, literature links, and reproducible evaluation
procedures.
Some of the main features are:
* Implementation of many popular quantification methods, including Classify & Count and its variants,
Expectation Maximization, HDy, QuaNet, quantification ensembles, and Bayesian extensions.
* Evaluation protocols for generating test samples under prior probability shift.
* A broad set of quantification-oriented evaluation metrics.
* Ready-to-use textual, numeric, and benchmark competition datasets.
* Method documentation that points back to the relevant literature and original papers.
* Native support for binary and single-label multiclass quantification.
* Visualization tools for analysing predictions, drift, confidence regions, and ternary prevalences.
## First Example
The following script fetches a binary dataset, trains an Adjusted Classify & Count quantifier,
and evaluates the resulting prevalence prediction with Mean Absolute Error.
```python
import quapy as qp
training, test = qp.datasets.fetch_UCIBinaryDataset("yeast").train_test
model = qp.method.aggregative.ACC()
Xtr, ytr = training.Xy
model.fit(Xtr, ytr)
estim_prevalence = model.predict(test.X)
true_prevalence = test.prevalence()
error = qp.error.mae(true_prevalence, estim_prevalence)
print(f'Mean Absolute Error (MAE)={error:.3f}')
```
Quantification is especially useful when the class prevalence of the test data
may differ from that of the training data. QuaPy implements protocols that make
it easy to evaluate methods across many such shifts. See the [](./manuals) for
worked examples.
## Citing QuaPy
If you find QuaPy useful, please consider citing the original paper.
```bibtex
@inproceedings{moreo2021quapy,
title={QuaPy: a python-based framework for quantification},
author={Moreo, Alejandro and Esuli, Andrea and Sebastiani, Fabrizio},
booktitle={Proceedings of the 30th ACM International Conference on Information \& Knowledge Management},
pages={4534--4543},
year={2021}
}
```
## Contributing
If you want to contribute improvements to QuaPy, please open a pull request
against the `devel` branch.
## Acknowledgments
```{image} SoBigData.png
:width: 250px
:alt: SoBigData++
```
This work has been supported by the QuaDaSh project
_"Finanziato dall'Unione europea---Next Generation EU,
Missione 4 Componente 2 CUP B53D23026250001"_.

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.. QuaPy: A Python-based open-source framework for quantification documentation master file, created by
sphinx-quickstart on Wed Feb 7 16:26:46 2024.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
Welcome to QuaPy's documentation!
==========================================================================================
QuaPy is a Python-based open-source framework for quantification.
This document contains the API of the modules included in QuaPy.
Installation
------------
`pip install quapy`
GitHub
------------
QuaPy is hosted in GitHub at `https://github.com/HLT-ISTI/QuaPy <https://github.com/HLT-ISTI/QuaPy>`_
.. toctree::
:maxdepth: 2
:caption: Contents:
Contents
--------
.. toctree::
modules
Indices and tables
==================
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`

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