Merge branch 'AICGijon-devel2' into devel

merged IFCB dataset

examples/ifcb_experiments.py

@@ -6,6 +6,7 @@ from quapy.evaluation import evaluation_report
 def newLR():
     return LogisticRegression(n_jobs=-1)
 
+<<<<<<< HEAD
 
 quantifiers = [
     ('CC', qp.method.aggregative.CC(newLR())),
@@ -18,6 +19,17 @@ quantifiers = [
 
 
 for quant_name, quantifier in quantifiers:
+=======
+quantifiers = {'CC':qp.method.aggregative.CC(newLR()),
+               'ACC':qp.method.aggregative.ACC(newLR()),
+               'PCC':qp.method.aggregative.PCC(newLR()),
+               'PACC':qp.method.aggregative.PACC(newLR()),
+               'HDy':qp.method.aggregative.DistributionMatching(newLR()),
+               'EMQ':qp.method.aggregative.EMQ(newLR())
+               }
+
+for quant_name, quantifier in quantifiers.items():
+>>>>>>> 5566e0c97ae1b49b30874b6610d7f5b062009271
     print("Experiment with "+quant_name)
 
     train, test_gen = qp.datasets.fetch_IFCB()

quapy/data/_ifcb.py

@@ -1,5 +1,6 @@
 import os
 import pandas as pd
+<<<<<<< HEAD
 from quapy.protocol import AbstractProtocol
 
 class IFCBTrainSamplesFromDir(AbstractProtocol):
@@ -11,6 +12,55 @@ class IFCBTrainSamplesFromDir(AbstractProtocol):
         for filename in os.listdir(path_dir):
             if filename.endswith('.csv'):
                 self.samples.append(filename)
+=======
+import math
+from quapy.protocol import AbstractProtocol
+from pathlib import Path
+
+def get_sample_list(path_dir):
+    """Gets a sample list finding the csv files in a directory
+
+    Args:
+        path_dir (_type_): directory to look for samples
+
+    Returns:
+        _type_: list of samples
+    """
+    samples = []
+    for filename in sorted(os.listdir(path_dir)):
+        if filename.endswith('.csv'):
+            samples.append(filename)
+    return samples
+
+def generate_modelselection_split(samples, split=0.3):
+    """This function generates a train/test split for model selection
+    without the use of random numbers so the split is always the same
+
+    Args:
+        samples (_type_): list of samples
+        split (float, optional): percentage saved for test. Defaults to 0.3.
+
+    Returns:
+        _type_: list of samples to use as train and list of samples to use as test
+    """
+    num_items_to_pick = math.ceil(len(samples) * split)
+    step_size = math.floor(len(samples) / num_items_to_pick)
+    test_indices = [i * step_size for i in range(num_items_to_pick)]
+    test = [samples[i] for i in test_indices]
+    train = [item for i, item in enumerate(samples) if i not in test_indices]
+    return train, test
+
+class IFCBTrainSamplesFromDir(AbstractProtocol):
+
+    def __init__(self, path_dir:str, classes: list, samples: list = None):
+        self.path_dir = path_dir
+        self.classes = classes
+        self.samples = []
+        if samples is not None:
+            self.samples = samples
+        else:
+            self.samples = get_sample_list(path_dir)
+>>>>>>> 5566e0c97ae1b49b30874b6610d7f5b062009271
 
     def __call__(self):
         for sample in self.samples:
@@ -28,6 +78,7 @@ class IFCBTrainSamplesFromDir(AbstractProtocol):
         """
         return len(self.samples)
 
+<<<<<<< HEAD
 
 class IFCBTestSamples(AbstractProtocol):
 
@@ -40,12 +91,43 @@ class IFCBTestSamples(AbstractProtocol):
             #Load the sample from disk
             X = pd.read_csv(os.path.join(self.path_dir,test_sample['sample']+'.csv')).to_numpy()
             prevalences = test_sample.iloc[1:].to_numpy().astype(float)
+=======
+class IFCBTestSamples(AbstractProtocol):
+
+    def __init__(self, path_dir:str, test_prevalences: pd.DataFrame, samples: list = None, classes: list=None):
+        self.path_dir = path_dir
+        self.test_prevalences = test_prevalences
+        self.classes = classes
+        if samples is not None:
+            self.samples = samples
+        else:
+            self.samples = get_sample_list(path_dir)
+
+    def __call__(self):
+        for test_sample in self.samples:
+            s = pd.read_csv(os.path.join(self.path_dir,test_sample))
+            if self.test_prevalences is not None:
+                X = s
+                # If we are working with the test samples, we have a dataframe with the prevalences and no labels for the test
+                prevalences = self.test_prevalences.loc[self.test_prevalences['sample']==Path(test_sample).stem].to_numpy()[:,1:].flatten().astype(float)
+            else:
+                X = s.iloc[:, 1:].to_numpy()
+                y = s.iloc[:,0]
+                # In this case we compute the sample prevalences from the labels
+                prevalences = y[y.isin(self.classes)].value_counts().reindex(self.classes, fill_value=0).to_numpy()/len(s)
+>>>>>>> 5566e0c97ae1b49b30874b6610d7f5b062009271
             yield X, prevalences
 
     def total(self):
         """
         Returns the total number of samples that the protocol generates.
 
+<<<<<<< HEAD
         :return: The number of test samples to generate.
         """
-        return len(self.test_prevalences.index)
+        return len(self.test_prevalences.index)
+=======
+        :return: The number of training samples to generate.
+        """
+        return len(self.samples)
+>>>>>>> 5566e0c97ae1b49b30874b6610d7f5b062009271

quapy/data/datasets.py

@@ -734,8 +734,7 @@ def fetch_lequa2022(task, data_home=None):
 
     return train, val_gen, test_gen
 
-
+def fetch_IFCB(single_sample_train=True, for_model_selection=False, data_home=None):
-def fetch_IFCB(single_sample_train=True, data_home=None):
     """
     Loads the IFCB dataset for quantification <https://zenodo.org/records/10036244>`. For more
     information on this dataset check the zenodo site.
@@ -746,21 +745,21 @@ def fetch_IFCB(single_sample_train=True, data_home=None):
 
     The datasets are downloaded only once, and stored for fast reuse.
 
-    :param single_sample_train: boolean. If True (default), it returns the train dataset as an instance of
+    :param single_sample_train: a boolean. If true, it will return the train dataset as a
         :class:`quapy.data.base.LabelledCollection` (all examples together).
-        If False, a generator of training samples will be returned.
+        If false, a generator of training samples will be returned. Each example in the training set has an individual label.
-        Each example in the training set has an individual class label.
+    :param for_model_selection: if True, then returns a split 30% of the training set (86 out of 286 samples) to be used for model selection; 
+        if False, then returns the full training set as training set and the test set as the test set
     :param data_home: specify the quapy home directory where collections will be dumped (leave empty to use the default
         ~/quay_data/ directory)
     :return: a tuple `(train, test_gen)` where `train` is an instance of
-        :class:`quapy.data.base.LabelledCollection`, if `single_sample_train` is True or
+        :class:`quapy.data.base.LabelledCollection`, if `single_sample_train` is true or
-        :class:`quapy.data._ifcb.IFCBTrainSamplesFromDir` otherwise, i.e. a sampling protocol that
+        :class:`quapy.data._ifcb.IFCBTrainSamplesFromDir`, i.e. a sampling protocol that returns a series of samples
-        returns a series of samples labelled example by example.
+        labelled example by example. test_gen will be a :class:`quapy.data._ifcb.IFCBTestSamples`, 
-        test_gen is an instance of  :class:`quapy.data._ifcb.IFCBTestSamples`,
         i.e., a sampling protocol that returns a series of samples labelled by prevalence.
     """
 
-    from quapy.data._ifcb import IFCBTrainSamplesFromDir, IFCBTestSamples
+    from quapy.data._ifcb import IFCBTrainSamplesFromDir, IFCBTestSamples, get_sample_list, generate_modelselection_split
 
     if data_home is None:
         data_home = get_quapy_home()
@@ -791,25 +790,35 @@ def fetch_IFCB(single_sample_train=True, data_home=None):
     test_true_prev = pd.read_csv(test_true_prev_path)
     classes = test_true_prev.columns[1:]
 
-    #Load train samples
+    #Load train and test samples
     train_samples_path = join(ifcb_dir,'train')
-    train_gen = IFCBTrainSamplesFromDir(path_dir=train_samples_path, classes=classes)
-
-    #Load test samples
     test_samples_path = join(ifcb_dir,'test')
-    test_gen = IFCBTestSamples(path_dir=test_samples_path, test_prevalences_path=test_true_prev_path)
+
+    if for_model_selection:
+        # In this case, return 70% of training data as the training set and 30% as the test set
+        samples = get_sample_list(train_samples_path)
+        train, test = generate_modelselection_split(samples, split=0.3)
+        train_gen = IFCBTrainSamplesFromDir(path_dir=train_samples_path, classes=classes, samples=train)
+
+        # Test prevalence is computed from class labels
+        test_gen = IFCBTestSamples(path_dir=train_samples_path, test_prevalences=None, samples=test, classes=classes)
+    else:
+        # In this case, we use all training samples as the training set and the test samples as the test set
+        train_gen = IFCBTrainSamplesFromDir(path_dir=train_samples_path, classes=classes)
+        test_gen = IFCBTestSamples(path_dir=test_samples_path, test_prevalences=test_true_prev)
 
     # In the case the user wants it, join all the train samples in one LabelledCollection
     if single_sample_train:
-        X = []
+        X, y = [], []
-        y = []
         for X_, y_ in train_gen():
             X.append(X_)
             y.append(y_)   
 
         X = np.vstack(X)
         y = np.concatenate(y)
-        train = LabelledCollection(X,y, classes=classes)
+        train = LabelledCollection(X, y, classes = classes)
+        
         return train, test_gen
+
     else:
         return train_gen, test_gen

quapy/method/_threshold_optim.py

@@ -0,0 +1,261 @@
+from abc import abstractmethod
+
+import numpy as np
+from sklearn.base import BaseEstimator
+import quapy as qp
+import quapy.functional as F
+from quapy.data import LabelledCollection
+from quapy.method.aggregative import BinaryAggregativeQuantifier
+
+
+class ThresholdOptimization(BinaryAggregativeQuantifier):
+    """
+    Abstract class of Threshold Optimization variants for :class:`ACC` as proposed by
+    `Forman 2006 <https://dl.acm.org/doi/abs/10.1145/1150402.1150423>`_ and
+    `Forman 2008 <https://link.springer.com/article/10.1007/s10618-008-0097-y>`_.
+    The goal is to bring improved stability to the denominator of the adjustment.
+    The different variants are based on different heuristics for choosing a decision threshold
+    that would allow for more true positives and many more false positives, on the grounds this
+    would deliver larger denominators.
+
+    :param classifier: a sklearn's Estimator that generates a classifier
+    :param val_split: indicates the proportion of data to be used as a stratified held-out validation set in which the
+        misclassification rates are to be estimated.
+        This parameter can be indicated as a real value (between 0 and 1), representing a proportion of
+        validation data, or as an integer, indicating that the misclassification rates should be estimated via
+        `k`-fold cross validation (this integer stands for the number of folds `k`, defaults 5), or as a
+        :class:`quapy.data.base.LabelledCollection` (the split itself).
+    """
+
+    def __init__(self, classifier: BaseEstimator, val_split=5, n_jobs=None):
+        self.classifier = classifier
+        self.val_split = val_split
+        self.n_jobs = qp._get_njobs(n_jobs)
+
+    @abstractmethod
+    def condition(self, tpr, fpr) -> float:
+        """
+        Implements the criterion according to which the threshold should be selected.
+        This function should return the (float) score to be minimized.
+
+        :param tpr: float, true positive rate
+        :param fpr: float, false positive rate
+        :return: float, a score for the given `tpr` and `fpr`
+        """
+        ...
+
+    def discard(self, tpr, fpr) -> bool:
+        """
+        Indicates whether a combination of tpr and fpr should be discarded
+
+        :param tpr: float, true positive rate
+        :param fpr: float, false positive rate
+        :return: true if the combination is to be discarded, false otherwise
+        """
+        return (tpr - fpr) == 0
+
+
+    def _eval_candidate_thresholds(self, decision_scores, y):
+        """
+        Seeks for the best `tpr` and `fpr` according to the score obtained at different
+        decision thresholds. The scoring function is implemented in function `_condition`.
+
+        :param decision_scores: array-like with the classification scores
+        :param y: predicted labels for the validation set (or for the training set via `k`-fold cross validation)
+        :return: best `tpr` and `fpr` and `threshold` according to `_condition`
+        """
+        candidate_thresholds = np.unique(decision_scores)
+
+        candidates = []
+        scores = []
+        for candidate_threshold in candidate_thresholds:
+            y_ = self.classes_[1 * (decision_scores >= candidate_threshold)]
+            TP, FP, FN, TN = self._compute_table(y, y_)
+            tpr = self._compute_tpr(TP, FN)
+            fpr = self._compute_fpr(FP, TN)
+            if not self.discard(tpr, fpr):
+                candidate_score = self.condition(tpr, fpr)
+                candidates.append([tpr, fpr, candidate_threshold])
+                scores.append(candidate_score)
+
+        if len(candidates) == 0:
+            # if no candidate gives rise to a valid combination of tpr and fpr, this method defaults to the standard
+            # classify & count; this is akin to assign tpr=1, fpr=0, threshold=0
+            tpr, fpr, threshold = 1, 0, 0
+            candidates.append([tpr, fpr, threshold])
+            scores.append(0)
+
+        candidates = np.asarray(candidates)
+        candidates = candidates[np.argsort(scores)]  # sort candidates by candidate_score
+
+        return candidates
+
+    def aggregate_with_threshold(self, classif_predictions, tprs, fprs, thresholds):
+        # This function performs the adjusted count for given tpr, fpr, and threshold.
+        # Note that, due to broadcasting, tprs, fprs, and thresholds could be arrays of length > 1
+        prevs_estims = np.mean(classif_predictions[:, None] >= thresholds, axis=0)
+        prevs_estims = (prevs_estims - fprs) / (tprs - fprs)
+        prevs_estims = F.as_binary_prevalence(prevs_estims, clip_if_necessary=True)
+        return prevs_estims.squeeze()
+
+    def _compute_table(self, y, y_):
+        TP = np.logical_and(y == y_, y == self.pos_label).sum()
+        FP = np.logical_and(y != y_, y == self.neg_label).sum()
+        FN = np.logical_and(y != y_, y == self.pos_label).sum()
+        TN = np.logical_and(y == y_, y == self.neg_label).sum()
+        return TP, FP, FN, TN
+
+    def _compute_tpr(self, TP, FP):
+        if TP + FP == 0:
+            return 1
+        return TP / (TP + FP)
+
+    def _compute_fpr(self, FP, TN):
+        if FP + TN == 0:
+            return 0
+        return FP / (FP + TN)
+
+    def aggregation_fit(self, classif_predictions: LabelledCollection, data: LabelledCollection):
+        decision_scores, y = classif_predictions.Xy
+        # the standard behavior is to keep the best threshold only
+        self.tpr, self.fpr, self.threshold = self._eval_candidate_thresholds(decision_scores, y)[0]
+        return self
+
+    def aggregate(self, classif_predictions: np.ndarray):
+        # the standard behavior is to compute the adjusted count using the best threshold found
+        return self.aggregate_with_threshold(classif_predictions, self.tpr, self.fpr, self.threshold)
+
+
+class T50(ThresholdOptimization):
+    """
+    Threshold Optimization variant for :class:`ACC` as proposed by
+    `Forman 2006 <https://dl.acm.org/doi/abs/10.1145/1150402.1150423>`_ and
+    `Forman 2008 <https://link.springer.com/article/10.1007/s10618-008-0097-y>`_ that looks
+    for the threshold that makes `tpr` closest to 0.5.
+    The goal is to bring improved stability to the denominator of the adjustment.
+
+    :param classifier: a sklearn's Estimator that generates a classifier
+    :param val_split: indicates the proportion of data to be used as a stratified held-out validation set in which the
+        misclassification rates are to be estimated.
+        This parameter can be indicated as a real value (between 0 and 1), representing a proportion of
+        validation data, or as an integer, indicating that the misclassification rates should be estimated via
+        `k`-fold cross validation (this integer stands for the number of folds `k`, defaults 5), or as a
+        :class:`quapy.data.base.LabelledCollection` (the split itself).
+    """
+
+    def __init__(self, classifier: BaseEstimator, val_split=5):
+        super().__init__(classifier, val_split)
+
+    def condition(self, tpr, fpr) -> float:
+        return abs(tpr - 0.5)
+
+
+class MAX(ThresholdOptimization):
+    """
+    Threshold Optimization variant for :class:`ACC` as proposed by
+    `Forman 2006 <https://dl.acm.org/doi/abs/10.1145/1150402.1150423>`_ and
+    `Forman 2008 <https://link.springer.com/article/10.1007/s10618-008-0097-y>`_ that looks
+    for the threshold that maximizes `tpr-fpr`.
+    The goal is to bring improved stability to the denominator of the adjustment.
+
+    :param classifier: a sklearn's Estimator that generates a classifier
+    :param val_split: indicates the proportion of data to be used as a stratified held-out validation set in which the
+        misclassification rates are to be estimated.
+        This parameter can be indicated as a real value (between 0 and 1), representing a proportion of
+        validation data, or as an integer, indicating that the misclassification rates should be estimated via
+        `k`-fold cross validation (this integer stands for the number of folds `k`, defaults 5), or as a
+        :class:`quapy.data.base.LabelledCollection` (the split itself).
+    """
+
+    def __init__(self, classifier: BaseEstimator, val_split=5):
+        super().__init__(classifier, val_split)
+
+    def condition(self, tpr, fpr) -> float:
+        # MAX strives to maximize (tpr - fpr), which is equivalent to minimize (fpr - tpr)
+        return (fpr - tpr)
+
+
+class X(ThresholdOptimization):
+    """
+    Threshold Optimization variant for :class:`ACC` as proposed by
+    `Forman 2006 <https://dl.acm.org/doi/abs/10.1145/1150402.1150423>`_ and
+    `Forman 2008 <https://link.springer.com/article/10.1007/s10618-008-0097-y>`_ that looks
+    for the threshold that yields `tpr=1-fpr`.
+    The goal is to bring improved stability to the denominator of the adjustment.
+
+    :param classifier: a sklearn's Estimator that generates a classifier
+    :param val_split: indicates the proportion of data to be used as a stratified held-out validation set in which the
+        misclassification rates are to be estimated.
+        This parameter can be indicated as a real value (between 0 and 1), representing a proportion of
+        validation data, or as an integer, indicating that the misclassification rates should be estimated via
+        `k`-fold cross validation (this integer stands for the number of folds `k`, defaults 5), or as a
+        :class:`quapy.data.base.LabelledCollection` (the split itself).
+    """
+
+    def __init__(self, classifier: BaseEstimator, val_split=5):
+        super().__init__(classifier, val_split)
+
+    def condition(self, tpr, fpr) -> float:
+        return abs(1 - (tpr + fpr))
+
+
+class MS(ThresholdOptimization):
+    """
+    Median Sweep. Threshold Optimization variant for :class:`ACC` as proposed by
+    `Forman 2006 <https://dl.acm.org/doi/abs/10.1145/1150402.1150423>`_ and
+    `Forman 2008 <https://link.springer.com/article/10.1007/s10618-008-0097-y>`_ that generates
+    class prevalence estimates for all decision thresholds and returns the median of them all.
+    The goal is to bring improved stability to the denominator of the adjustment.
+
+    :param classifier: a sklearn's Estimator that generates a classifier
+    :param val_split: indicates the proportion of data to be used as a stratified held-out validation set in which the
+        misclassification rates are to be estimated.
+        This parameter can be indicated as a real value (between 0 and 1), representing a proportion of
+        validation data, or as an integer, indicating that the misclassification rates should be estimated via
+        `k`-fold cross validation (this integer stands for the number of folds `k`, defaults 5), or as a
+        :class:`quapy.data.base.LabelledCollection` (the split itself).
+    """
+    def __init__(self, classifier: BaseEstimator, val_split=5):
+        super().__init__(classifier, val_split)
+
+    def condition(self, tpr, fpr) -> float:
+        return 1
+
+    def aggregation_fit(self, classif_predictions: LabelledCollection, data: LabelledCollection):
+        decision_scores, y = classif_predictions.Xy
+        # keeps all candidates
+        tprs_fprs_thresholds = self._eval_candidate_thresholds(decision_scores, y)
+        self.tprs = tprs_fprs_thresholds[:, 0]
+        self.fprs = tprs_fprs_thresholds[:, 1]
+        self.thresholds = tprs_fprs_thresholds[:, 2]
+        return self
+
+    def aggregate(self, classif_predictions: np.ndarray):
+        prevalences = self.aggregate_with_threshold(classif_predictions, self.tprs, self.fprs, self.thresholds)
+        if prevalences.ndim==2:
+            prevalences = np.median(prevalences, axis=0)
+        return prevalences
+
+
+class MS2(MS):
+    """
+    Median Sweep 2. Threshold Optimization variant for :class:`ACC` as proposed by
+    `Forman 2006 <https://dl.acm.org/doi/abs/10.1145/1150402.1150423>`_ and
+    `Forman 2008 <https://link.springer.com/article/10.1007/s10618-008-0097-y>`_ that generates
+    class prevalence estimates for all decision thresholds and returns the median of for cases in
+    which `tpr-fpr>0.25`
+    The goal is to bring improved stability to the denominator of the adjustment.
+
+    :param classifier: a sklearn's Estimator that generates a classifier
+    :param val_split: indicates the proportion of data to be used as a stratified held-out validation set in which the
+        misclassification rates are to be estimated.
+        This parameter can be indicated as a real value (between 0 and 1), representing a proportion of
+        validation data, or as an integer, indicating that the misclassification rates should be estimated via
+        `k`-fold cross validation (this integer stands for the number of folds `k`, defaults 5), or as a
+        :class:`quapy.data.base.LabelledCollection` (the split itself).
+    """
+    def __init__(self, classifier: BaseEstimator, val_split=5):
+        super().__init__(classifier, val_split)
+
+    def discard(self, tpr, fpr) -> bool:
+        return (tpr-fpr) <= 0.25