adding non aggregative methods experimental

experimental_non_aggregative/custom_vectorizers.py

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+from scipy.sparse import csc_matrix, csr_matrix
+from sklearn.base import BaseEstimator, TransformerMixin
+from sklearn.feature_extraction.text import TfidfTransformer, TfidfVectorizer, CountVectorizer
+import numpy as np
+from joblib import Parallel, delayed
+import sklearn
+import math
+from scipy.stats import t
+
+
+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 __ig_factor(p_tc, p_t, p_c):
+    den = p_t * p_c
+    if den != 0.0 and p_tc != 0:
+        return p_tc * math.log(p_tc / den, 2)
+    else:
+        return 0.0
+
+
+def information_gain(cell):
+    return __ig_factor(cell.p_tp(), cell.p_f(), cell.p_c()) + \
+           __ig_factor(cell.p_fp(), cell.p_f(), cell.p_not_c()) +\
+           __ig_factor(cell.p_fn(), cell.p_not_f(), cell.p_c()) + \
+           __ig_factor(cell.p_tn(), cell.p_not_f(), cell.p_not_c())
+
+
+def squared_information_gain(cell):
+    return information_gain(cell)**2
+
+
+def posneg_information_gain(cell):
+    ig = information_gain(cell)
+    if cell.tpr() < cell.fpr():
+        return -ig
+    else:
+        return ig
+
+
+def pos_information_gain(cell):
+    if cell.tpr() < cell.fpr():
+        return 0
+    else:
+        return information_gain(cell)
+
+def pointwise_mutual_information(cell):
+    return __ig_factor(cell.p_tp(), cell.p_f(), cell.p_c())
+
+
+def gss(cell):
+    return cell.p_tp()*cell.p_tn() - cell.p_fp()*cell.p_fn()
+
+
+def chi_square(cell):
+    den = cell.p_f() * cell.p_not_f() * cell.p_c() * cell.p_not_c()
+    if den==0.0: return 0.0
+    num = gss(cell)**2
+    return num / den
+
+
+def conf_interval(xt, n):
+    if n>30:
+        z2 = 3.84145882069 # norm.ppf(0.5+0.95/2.0)**2
+    else:
+        z2 = t.ppf(0.5 + 0.95 / 2.0, df=max(n-1,1)) ** 2
+    p = (xt + 0.5 * z2) / (n + z2)
+    amplitude = 0.5 * z2 * math.sqrt((p * (1.0 - p)) / (n + z2))
+    return p, amplitude
+
+
+def strength(minPosRelFreq, minPos, maxNeg):
+    if minPos > maxNeg:
+        return math.log(2.0 * minPosRelFreq, 2.0)
+    else:
+        return 0.0
+
+
+#set cancel_features=True to allow some features to be weighted as 0 (as in the original article)
+#however, for some extremely imbalanced dataset caused all documents to be 0
+def conf_weight(cell, cancel_features=False):
+    c = cell.get_c()
+    not_c = cell.get_not_c()
+    tp = cell.tp
+    fp = cell.fp
+
+    pos_p, pos_amp = conf_interval(tp, c)
+    neg_p, neg_amp = conf_interval(fp, not_c)
+
+    min_pos = pos_p-pos_amp
+    max_neg = neg_p+neg_amp
+    den = (min_pos + max_neg)
+    minpos_relfreq = min_pos / (den if den != 0 else 1)
+
+    str_tplus = strength(minpos_relfreq, min_pos, max_neg);
+
+    if str_tplus == 0 and not cancel_features:
+        return 1e-20
+
+    return str_tplus
+
+
+def get_tsr_matrix(cell_matrix, tsr_score_funtion):
+    nC = len(cell_matrix)
+    nF = len(cell_matrix[0])
+    tsr_matrix = [[tsr_score_funtion(cell_matrix[c,f]) for f in range(nF)] for c in range(nC)]
+    return np.array(tsr_matrix)
+
+
+def feature_label_contingency_table(positive_document_indexes, feature_document_indexes, nD):
+    tp_ = len(positive_document_indexes & feature_document_indexes)
+    fp_ = len(feature_document_indexes - positive_document_indexes)
+    fn_ = len(positive_document_indexes - feature_document_indexes)
+    tn_ = nD - (tp_ + fp_ + fn_)
+    return ContTable(tp=tp_, tn=tn_, fp=fp_, fn=fn_)
+
+
+def category_tables(feature_sets, category_sets, c, nD, nF):
+    return [feature_label_contingency_table(category_sets[c], feature_sets[f], nD) for f in range(nF)]
+
+
+def get_supervised_matrix(coocurrence_matrix, label_matrix, n_jobs=-1):
+    """
+    Computes the nC x nF supervised matrix M where Mcf is the 4-cell contingency table for feature f and class c.
+    Efficiency O(nF x nC x log(S)) where S is the sparse factor
+    """
+
+    nD, nF = coocurrence_matrix.shape
+    nD2, nC = label_matrix.shape
+
+    if nD != nD2:
+        raise ValueError('Number of rows in coocurrence matrix shape %s and label matrix shape %s is not consistent' %
+                         (coocurrence_matrix.shape,label_matrix.shape))
+
+    def nonzero_set(matrix, col):
+        return set(matrix[:, col].nonzero()[0])
+
+    if isinstance(coocurrence_matrix, csr_matrix):
+        coocurrence_matrix = csc_matrix(coocurrence_matrix)
+    feature_sets = [nonzero_set(coocurrence_matrix, f) for f in range(nF)]
+    category_sets = [nonzero_set(label_matrix, c) for c in range(nC)]
+    cell_matrix = Parallel(n_jobs=n_jobs, backend="threading")(
+        delayed(category_tables)(feature_sets, category_sets, c, nD, nF) for c in range(nC)
+    )
+    return np.array(cell_matrix)
+
+
+class TSRweighting(BaseEstimator,TransformerMixin):
+    """
+    Supervised Term Weighting function based on any Term Selection Reduction (TSR) function (e.g., information gain,
+    chi-square, etc.) or, more generally, on any function that could be computed on the 4-cell contingency table for
+    each category-feature pair.
+    The supervised_4cell_matrix is a `(n_classes, n_words)` matrix containing the 4-cell contingency tables
+    for each class-word pair, and can be pre-computed (e.g., during the feature selection phase) and passed as an
+    argument.
+    When `n_classes>1`, i.e., in multiclass scenarios, a global_policy is used in order to determine a
+    single feature-score which informs about its relevance. Accepted policies include "max" (takes the max score
+    across categories), "ave" and "wave" (take the average, or weighted average, across all categories -- weights
+    correspond to the class prevalence), and "sum" (which sums all category scores).
+    """
+
+    def __init__(self, tsr_function, global_policy='max', supervised_4cell_matrix=None, sublinear_tf=True, norm='l2', min_df=3, n_jobs=-1):
+        if global_policy not in ['max', 'ave', 'wave', 'sum']: raise ValueError('Global policy should be in {"max", "ave", "wave", "sum"}')
+        self.tsr_function = tsr_function
+        self.global_policy = global_policy
+        self.supervised_4cell_matrix = supervised_4cell_matrix
+        self.sublinear_tf = sublinear_tf
+        self.norm = norm
+        self.min_df = min_df
+        self.n_jobs = n_jobs
+
+    def fit(self, X, y):
+        self.count_vectorizer = CountVectorizer(min_df=self.min_df)
+        X = self.count_vectorizer.fit_transform(X)
+
+        self.tf_vectorizer = TfidfTransformer(
+            norm=None, use_idf=False, smooth_idf=False, sublinear_tf=self.sublinear_tf
+        ).fit(X)
+
+        if len(y.shape) == 1:
+            y = np.expand_dims(y, axis=1)
+
+        nD, nC = y.shape
+        nF = len(self.tf_vectorizer.get_feature_names_out())
+
+        if self.supervised_4cell_matrix is None:
+            self.supervised_4cell_matrix = get_supervised_matrix(X, y, n_jobs=self.n_jobs)
+        else:
+            if self.supervised_4cell_matrix.shape != (nC, nF):
+                raise ValueError("Shape of supervised information matrix is inconsistent with X and y")
+
+        tsr_matrix = get_tsr_matrix(self.supervised_4cell_matrix, self.tsr_function)
+
+        if self.global_policy == 'ave':
+            self.global_tsr_vector = np.average(tsr_matrix, axis=0)
+        elif self.global_policy == 'wave':
+            category_prevalences = [sum(y[:,c])*1.0/nD for c in range(nC)]
+            self.global_tsr_vector = np.average(tsr_matrix, axis=0, weights=category_prevalences)
+        elif self.global_policy == 'sum':
+            self.global_tsr_vector = np.sum(tsr_matrix, axis=0)
+        elif self.global_policy == 'max':
+            self.global_tsr_vector = np.amax(tsr_matrix, axis=0)
+        return self
+
+    def fit_transform(self, X, y):
+        return self.fit(X,y).transform(X)
+
+    def transform(self, X):
+        if not hasattr(self, 'global_tsr_vector'): raise NameError('TSRweighting: transform method called before fit.')
+        X = self.count_vectorizer.transform(X)
+        tf_X = self.tf_vectorizer.transform(X).toarray()
+        weighted_X = np.multiply(tf_X, self.global_tsr_vector)
+        if self.norm is not None and self.norm!='none':
+            weighted_X = sklearn.preprocessing.normalize(weighted_X, norm=self.norm, axis=1, copy=False)
+        return csr_matrix(weighted_X)

experimental_non_aggregative/method_dxs.py

@@ -0,0 +1,148 @@
+from sklearn.feature_extraction.text import TfidfVectorizer, CountVectorizer
+from sklearn.linear_model import LogisticRegression
+
+import quapy as qp
+from data import LabelledCollection
+import numpy as np
+
+from experimental_non_aggregative.custom_vectorizers import *
+from protocol import APP
+from quapy.method.aggregative import _get_divergence, HDy, DistributionMatching
+from quapy.method.base import BaseQuantifier
+from scipy import optimize
+import pandas as pd
+
+
+# TODO: explore the bernoulli (term presence/absence) variant
+# TODO: explore the multinomial (term frequency) variant
+# TODO: explore the multinomial + length normalization variant
+# TODO: consolidate the TSR-variant (e.g., using information gain) variant;
+#   - works better with the idf?
+#   - works better with length normalization?
+#   - etc
+
+class DxS(BaseQuantifier):
+    def __init__(self, vectorizer=None, divergence='topsoe'):
+        self.vectorizer = vectorizer
+        self.divergence = divergence
+
+    # def __as_distribution(self, instances):
+    #     return np.asarray(instances.sum(axis=0) / instances.sum()).flatten()
+
+    def __as_distribution(self, instances):
+        dist = instances.sum(axis=0) / instances.sum()
+        return np.asarray(dist).flatten()
+
+    def fit(self, data: LabelledCollection):
+
+        text_instances, labels = data.Xy
+
+        if self.vectorizer is not None:
+            text_instances = self.vectorizer.fit_transform(text_instances, y=labels)
+
+        distributions = []
+        for class_i in data.classes_:
+            distributions.append(self.__as_distribution(text_instances[labels == class_i]))
+        self.validation_distribution = np.asarray(distributions)
+        return self
+
+    def quantify(self, text_instances):
+        if self.vectorizer is not None:
+            text_instances = self.vectorizer.transform(text_instances)
+
+        test_distribution = self.__as_distribution(text_instances)
+        divergence = _get_divergence(self.divergence)
+        n_classes, n_feats = self.validation_distribution.shape
+
+        def match(prev):
+            prev = np.expand_dims(prev, axis=0)
+            mixture_distribution = (prev @ self.validation_distribution).flatten()
+            return divergence(test_distribution, mixture_distribution)
+
+        # the initial point is set as the uniform distribution
+        uniform_distribution = np.full(fill_value=1 / n_classes, shape=(n_classes,))
+
+        # solutions are bounded to those contained in the unit-simplex
+        bounds = tuple((0, 1) for x in range(n_classes))  # values in [0,1]
+        constraints = ({'type': 'eq', 'fun': lambda x: 1 - sum(x)})  # values summing up to 1
+        r = optimize.minimize(match, x0=uniform_distribution, method='SLSQP', bounds=bounds, constraints=constraints)
+        return r.x
+
+
+
+if __name__ == '__main__':
+
+    qp.environ['SAMPLE_SIZE'] = 250
+    qp.environ['N_JOBS'] = -1
+    min_df = 10
+    # dataset = 'imdb'
+    repeats = 10
+    error = 'mae'
+
+    div = 'topsoe'
+
+    # generates tuples (dataset, method, method_name)
+    # (the dataset is needed for methods that process the dataset differently)
+    def gen_methods():
+
+        for dataset in qp.datasets.REVIEWS_SENTIMENT_DATASETS:
+
+            data = qp.datasets.fetch_reviews(dataset, tfidf=False)
+
+            bernoulli_vectorizer = CountVectorizer(min_df=min_df, binary=True)
+            dxs = DxS(divergence=div, vectorizer=bernoulli_vectorizer)
+            yield data, dxs, 'DxS-Bernoulli'
+
+            multinomial_vectorizer = CountVectorizer(min_df=min_df, binary=False)
+            dxs = DxS(divergence=div, vectorizer=multinomial_vectorizer)
+            yield data, dxs, 'DxS-multinomial'
+
+            tf_vectorizer = TfidfVectorizer(sublinear_tf=False, use_idf=False, min_df=min_df, norm=None)
+            dxs = DxS(divergence=div, vectorizer=tf_vectorizer)
+            yield data, dxs, 'DxS-TF'
+
+            logtf_vectorizer = TfidfVectorizer(sublinear_tf=True, use_idf=False, min_df=min_df, norm=None)
+            dxs = DxS(divergence=div, vectorizer=logtf_vectorizer)
+            yield data, dxs, 'DxS-logTF'
+
+            tfidf_vectorizer = TfidfVectorizer(use_idf=True, min_df=min_df, norm=None)
+            dxs = DxS(divergence=div, vectorizer=tfidf_vectorizer)
+            yield data, dxs, 'DxS-TFIDF'
+
+            tfidf_vectorizer = TfidfVectorizer(use_idf=True, min_df=min_df, norm='l2')
+            dxs = DxS(divergence=div, vectorizer=tfidf_vectorizer)
+            yield data, dxs, 'DxS-TFIDF-l2'
+
+            tsr_vectorizer = TSRweighting(tsr_function=information_gain, min_df=min_df, norm='l2')
+            dxs = DxS(divergence=div, vectorizer=tsr_vectorizer)
+            yield data, dxs, 'DxS-TFTSR-l2'
+
+            data = qp.datasets.fetch_reviews(dataset, tfidf=True, min_df=min_df)
+            hdy = HDy(LogisticRegression())
+            yield data, hdy, 'HDy'
+
+            dm = DistributionMatching(LogisticRegression(), divergence=div, nbins=5)
+            yield data, dm, 'DM-5b'
+
+            dm = DistributionMatching(LogisticRegression(), divergence=div, nbins=10)
+            yield data, dm, 'DM-10b'
+
+
+    result_path = 'results.csv'
+    with open(result_path, 'wt') as csv:
+        csv.write(f'Method\tDataset\tMAE\tMRAE\n')
+        for data, quantifier, quant_name in gen_methods():
+            quantifier.fit(data.training)
+            report = qp.evaluation.evaluation_report(quantifier, APP(data.test, repeats=repeats), error_metrics=['mae','mrae'], verbose=True)
+            means = report.mean()
+            csv.write(f'{quant_name}\t{data.name}\t{means["mae"]:.5f}\t{means["mrae"]:.5f}\n')
+
+    df = pd.read_csv(result_path, sep='\t')
+    # print(df)
+
+    pv = df.pivot_table(index='Method', columns="Dataset", values=["MAE", "MRAE"])
+    print(pv)
+
+
+
+