forked from moreo/QuaPy
adapting new format
This commit is contained in:
parent
8e15678c36
commit
8368c467dc
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@ -14,10 +14,10 @@ import constants
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def baselines():
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yield CC(LR(n_jobs=-1)), "CC"
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yield ACC(LR(n_jobs=-1)), "ACC"
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yield PCC(LR(n_jobs=-1)), "PCC"
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yield PACC(LR(n_jobs=-1)), "PACC"
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yield EMQ(CalibratedClassifierCV(LR(), n_jobs=-1)), "SLD"
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# yield ACC(LR(n_jobs=-1)), "ACC"
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# yield PCC(LR(n_jobs=-1)), "PCC"
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# yield PACC(LR(n_jobs=-1)), "PACC"
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# yield EMQ(CalibratedClassifierCV(LR(), n_jobs=-1)), "SLD"
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# yield HDy(LR(n_jobs=-1)) if args.task == 'T1A' else OneVsAll(HDy(LR()), n_jobs=-1), "HDy"
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# yield MLPE(), "MLPE"
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@ -28,7 +28,7 @@ def main(args):
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path_dev_vectors = os.path.join(args.datadir, 'dev_vectors')
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path_dev_prevs = os.path.join(args.datadir, 'dev_prevalences.csv')
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path_train = os.path.join(args.datadir, 'training_vectors.txt')
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path_train = os.path.join(args.datadir, 'training_vectors.csv')
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qp.environ['SAMPLE_SIZE'] = constants.SAMPLE_SIZE[args.task]
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@ -46,13 +46,15 @@ def main(args):
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# }
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param_grid = {
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'C': [1],
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'C': [0.01],
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'class_weight': ['balanced']
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}
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target_metric = qp.error.mrae
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def gen_samples():
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return gen_load_samples(path_dev_vectors, ground_truth_path=path_dev_prevs, return_id=False,
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load_fn=load_vector_documents, nF=nF)
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load_fn=load_vector_documents, ext='csv')
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for quantifier, q_name in baselines():
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print(f'{q_name}: Model selection')
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@ -61,12 +63,12 @@ def main(args):
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param_grid,
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sample_size=None,
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protocol='gen',
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error=qp.error.mae,
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error=target_metric, #qp.error.mae,
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refit=False,
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verbose=True
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).fit(train, gen_samples)
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print(f'{q_name} got MAE={quantifier.best_score_:.3f} (hyper-params: {quantifier.best_params_})')
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print(f'{q_name} got MRAE={quantifier.best_score_:.5f} (hyper-params: {quantifier.best_params_})')
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model_path = os.path.join(models_path, q_name+'.pkl')
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print(f'saving model in {model_path}')
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@ -91,8 +93,8 @@ if __name__ == '__main__':
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raise ValueError(f'path {args.datadir} is not a valid directory')
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if not os.path.exists(os.path.join(args.datadir, "dev_prevalences.csv")):
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raise FileNotFoundError(f'path {args.datadir} does not contain "dev_prevalences.csv" file')
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if not os.path.exists(os.path.join(args.datadir, "training_vectors.txt")):
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raise FileNotFoundError(f'path {args.datadir} does not contain "training_vectors.txt" file')
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if not os.path.exists(os.path.join(args.datadir, "training_vectors.csv")):
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raise FileNotFoundError(f'path {args.datadir} does not contain "training_vectors.csv" file')
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if not os.path.exists(os.path.join(args.datadir, "dev_vectors")):
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raise FileNotFoundError(f'path {args.datadir} does not contain "dev_vectors" folder')
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@ -1,8 +1,14 @@
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import argparse
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import pickle
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from sklearn.decomposition import TruncatedSVD
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from sklearn.feature_extraction.text import TfidfVectorizer
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from sklearn.linear_model import LogisticRegression as LR
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from sklearn.pipeline import Pipeline
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from sklearn.preprocessing import StandardScaler
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from LeQua2022.pretrained_embeddings import TfidfWordEmbeddingTransformer, WordEmbeddingAverageTransformer
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from LeQua2022.word_class_embeddings import WordClassEmbeddingsTransformer, ConcatenateEmbeddingsTransformer
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from quapy.method.aggregative import *
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from quapy.method.non_aggregative import MaximumLikelihoodPrevalenceEstimation as MLPE
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import quapy.functional as F
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@ -20,7 +26,7 @@ def baselines():
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yield PCC(LR(n_jobs=-1)), "PCC"
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yield PACC(LR(n_jobs=-1)), "PACC"
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yield EMQ(CalibratedClassifierCV(LR(), n_jobs=-1)), "SLD"
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yield HDy(LR(n_jobs=-1)) if args.task == 'T2A' else OneVsAll(HDy(LR()), n_jobs=-1), "HDy"
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# yield HDy(LR(n_jobs=-1)) if args.task == 'T2A' else OneVsAll(HDy(LR()), n_jobs=-1), "HDy"
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# yield MLPE(), "MLPE"
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@ -35,9 +41,69 @@ def main(args):
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qp.environ['SAMPLE_SIZE'] = constants.SAMPLE_SIZE[args.task]
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train = LabelledCollection.load(path_train, load_raw_documents)
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tfidf = TfidfVectorizer(lowercase=True, stop_words='english', min_df=4) # TfidfVectorizer(min_df=5)
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train.instances = tfidf.fit_transform(train.instances)
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nF = train.instances.shape[1]
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if args.mode == 'tfidf1':
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tfidf = TfidfVectorizer(min_df=5, sublinear_tf=True)
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if args.mode == 'tfidf2':
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tfidf = TfidfVectorizer(min_df=5, sublinear_tf=True, ngram_range=(1,2))
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if args.mode == 'tfidf3':
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tfidf = Pipeline([
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('tfidf', TfidfVectorizer(min_df=5, sublinear_tf=True)),
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('svd', TruncatedSVD(n_components=300))
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])
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if args.mode == 'tfidf4':
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tfidf = Pipeline([
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('tfidf', TfidfVectorizer(min_df=5, sublinear_tf=True, ngram_range=(1,2))),
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('svd', TruncatedSVD(n_components=300))
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])
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if args.mode == 'glove1':
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tfidf = Pipeline([
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('glove-ave', WordEmbeddingAverageTransformer(wordset_name='glove', path='/mnt/1T/Datasets/GloVe')),
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('zscore', StandardScaler())
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])
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if args.mode == 'glove2':
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tfidf = WordEmbeddingAverageTransformer(wordset_name='glove', path='/mnt/1T/Datasets/GloVe')
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if args.mode == 'glove3':
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vect = TfidfVectorizer(min_df=5, sublinear_tf=True)
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tfidf = Pipeline([
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('tfidf', vect),
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('embedding', TfidfWordEmbeddingTransformer(
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wordset_name='glove',
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features_call=vect.get_feature_names_out,
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path='/mnt/1T/Datasets/GloVe')),
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('zscore', StandardScaler())
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])
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if args.mode == 'glove4':
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vect = TfidfVectorizer(min_df=5, sublinear_tf=True)
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tfidf = Pipeline([
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('tfidf', vect),
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('embedding', TfidfWordEmbeddingTransformer(
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wordset_name='glove',
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features_call=vect.get_feature_names_out,
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path='/mnt/1T/Datasets/GloVe'))
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])
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if args.mode == 'wce1':
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tfidf = WordClassEmbeddingsTransformer()
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if args.mode == 'wce2':
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glove = Pipeline([
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('glove-ave', WordEmbeddingAverageTransformer(wordset_name='glove', path='/mnt/1T/Datasets/GloVe')),
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('zscore', StandardScaler())
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])
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wce = WordClassEmbeddingsTransformer()
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tfidf = ConcatenateEmbeddingsTransformer([glove, wce])
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if args.mode == 'wce3':
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glove = Pipeline([
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('glove-ave', WordEmbeddingAverageTransformer(wordset_name='glove', path='/mnt/1T/Datasets/GloVe')),
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('zscore', StandardScaler())
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])
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wce = WordClassEmbeddingsTransformer()
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tfidf = Pipeline([
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('glove-wce', ConcatenateEmbeddingsTransformer([glove, wce])),
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('svd', TruncatedSVD(n_components=300))
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])
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target_metric = qp.error.mrae
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train.instances = tfidf.fit_transform(*train.Xy)
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print(f'number of classes: {len(train.classes_)}')
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print(f'number of training documents: {len(train)}')
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@ -58,6 +124,7 @@ def main(args):
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return gen_load_samples(path_dev_vectors, ground_truth_path=path_dev_prevs, return_id=False,
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load_fn=load_raw_unlabelled_documents, vectorizer=tfidf)
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outs = []
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for quantifier, q_name in baselines():
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print(f'{q_name}: Model selection')
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quantifier = qp.model_selection.GridSearchQ(
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@ -65,17 +132,25 @@ def main(args):
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param_grid,
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sample_size=None,
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protocol='gen',
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error=qp.error.mae,
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error=target_metric, #qp.error.mae,
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refit=False,
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verbose=True
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).fit(train, gen_samples)
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print(f'{q_name} got MAE={quantifier.best_score_:.3f} (hyper-params: {quantifier.best_params_})')
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print(f'{q_name} got MAE={quantifier.best_score_:.5f} (hyper-params: {quantifier.best_params_})')
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outs.append(f'{q_name} got MAE={quantifier.best_score_:.5f} (hyper-params: {quantifier.best_params_})')
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model_path = os.path.join(models_path, q_name+'.'+args.task+'.pkl')
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print(f'saving model in {model_path}')
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pickle.dump(quantifier.best_model(), open(model_path, 'wb'), protocol=pickle.HIGHEST_PROTOCOL)
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print(tfidf)
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print(args.mode)
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print(outs)
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with open(f'{args.mode}.{args.task}.txt', 'wt') as foo:
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for line in outs:
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foo.write(f'{line}\n')
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if __name__ == '__main__':
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parser = argparse.ArgumentParser(description='LeQua2022 Task T2A/T2B baselines')
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@ -87,6 +162,8 @@ if __name__ == '__main__':
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parser.add_argument('modeldir', metavar='MODEL-PATH', type=str,
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help='Path where to save the models. '
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'A subdirectory named <task> will be automatically created.')
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parser.add_argument('mode', metavar='PREPROCESSMODE', type=str,
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help='modality of preprocessing')
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args = parser.parse_args()
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if not os.path.exists(args.datadir):
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@ -34,33 +34,42 @@ def load_raw_unlabelled_documents(path, vectorizer=None):
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return documents, None
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def load_vector_documents(path, nF=None):
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X, y = sklearn.datasets.load_svmlight_file(path, n_features=nF)
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y = y.astype(int)
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# def load_vector_documents(path, nF=None):
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# X, y = sklearn.datasets.load_svmlight_file(path, n_features=nF, zero_based=True)
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# y = y.astype(int)
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# return X, y
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def load_vector_documents(path):
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D = pd.read_csv(path).to_numpy(dtype=np.float)
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labelled = D.shape[1] == 301
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if labelled:
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X, y = D[:,:300], D[:,-1].astype(np.int).flatten()
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else:
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X, y = D, None
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return X, y
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def __gen_load_samples_with_groudtruth(path_dir:str, return_id:bool, ground_truth_path:str, load_fn, **load_kwargs):
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def __gen_load_samples_with_groudtruth(path_dir:str, return_id:bool, ground_truth_path:str, ext:str, load_fn, **load_kwargs):
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true_prevs = ResultSubmission.load(ground_truth_path)
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for id, prevalence in true_prevs.iterrows():
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sample, _ = load_fn(os.path.join(path_dir, f'{id}.txt'), **load_kwargs)
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sample, _ = load_fn(os.path.join(path_dir, f'{id}.{ext}'), **load_kwargs)
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yield (id, sample, prevalence) if return_id else (sample, prevalence)
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def __gen_load_samples_without_groudtruth(path_dir:str, return_id:bool, load_fn, **load_kwargs):
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nsamples = len(glob(os.path.join(path_dir, '*.txt')))
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def __gen_load_samples_without_groudtruth(path_dir:str, return_id:bool, ext:str, load_fn, **load_kwargs):
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nsamples = len(glob(os.path.join(path_dir, f'*.{ext}')))
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for id in range(nsamples):
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sample, _ = load_fn(os.path.join(path_dir, f'{id}.txt'), **load_kwargs)
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sample, _ = load_fn(os.path.join(path_dir, f'{id}.{ext}'), **load_kwargs)
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yield (id, sample) if return_id else sample
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def gen_load_samples(path_dir:str, ground_truth_path:str = None, return_id=True, load_fn=load_vector_documents, **load_kwargs):
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def gen_load_samples(path_dir:str, ground_truth_path:str = None, return_id=True, ext='txt', load_fn=load_vector_documents, **load_kwargs):
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if ground_truth_path is None:
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# the generator function returns tuples (docid:str, sample:csr_matrix or str)
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gen_fn = __gen_load_samples_without_groudtruth(path_dir, return_id, load_fn, **load_kwargs)
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gen_fn = __gen_load_samples_without_groudtruth(path_dir, return_id, ext, load_fn, **load_kwargs)
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else:
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# the generator function returns tuples (docid:str, sample:csr_matrix or str, prevalence:ndarray)
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gen_fn = __gen_load_samples_with_groudtruth(path_dir, return_id, ground_truth_path, load_fn, **load_kwargs)
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gen_fn = __gen_load_samples_with_groudtruth(path_dir, return_id, ground_truth_path, ext, load_fn, **load_kwargs)
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for r in gen_fn:
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yield r
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@ -139,7 +148,11 @@ class ResultSubmission:
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@classmethod
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def check_file_format(cls, path) -> Union[pd.DataFrame, Tuple[pd.DataFrame, str]]:
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df = pd.read_csv(path, index_col=0)
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try:
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df = pd.read_csv(path, index_col=0)
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except Exception as e:
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print(f'the file {path} does not seem to be a valid csv file. ')
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print(e)
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return ResultSubmission.check_dataframe_format(df, path=path)
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@classmethod
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@ -24,6 +24,7 @@ def artificial_prevalence_prediction(
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verbose=False):
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"""
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Performs the predictions for all samples generated according to the artificial sampling protocol.
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:param model: the model in charge of generating the class prevalence estimations
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:param test: the test set on which to perform arificial sampling
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:param sample_size: the size of the samples
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@ -3,6 +3,8 @@ import signal
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from copy import deepcopy
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from typing import Union, Callable
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import numpy as np
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import quapy as qp
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from quapy.data.base import LabelledCollection
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from quapy.evaluation import artificial_prevalence_prediction, natural_prevalence_prediction, gen_prevalence_prediction
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@ -190,6 +192,7 @@ class GridSearchQ(BaseQuantifier):
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model.fit(training)
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true_prevalences, estim_prevalences = self.__generate_predictions(model, val_split)
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score = self.error(true_prevalences, estim_prevalences)
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self._sout(f'checking hyperparams={params} got {self.error.__name__} score {score:.5f}')
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if self.best_score_ is None or score < self.best_score_:
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self.best_score_ = score
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