729 lines
26 KiB
Python
729 lines
26 KiB
Python
"""Calibration of predicted probabilities."""
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# Author: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
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# Balazs Kegl <balazs.kegl@gmail.com>
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# Jan Hendrik Metzen <jhm@informatik.uni-bremen.de>
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# Mathieu Blondel <mathieu@mblondel.org>
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#
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# License: BSD 3 clause
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import warnings
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from inspect import signature
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from contextlib import suppress
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from math import log
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import numpy as np
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from joblib import Parallel
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from scipy.special import expit
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from scipy.special import xlogy
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from scipy.optimize import fmin_bfgs
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from .preprocessing import LabelEncoder
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from .base import (BaseEstimator, ClassifierMixin, RegressorMixin, clone,
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MetaEstimatorMixin)
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from .preprocessing import label_binarize, LabelBinarizer
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from .utils import check_array, indexable, column_or_1d
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from .utils.fixes import delayed
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from .utils.validation import check_is_fitted, check_consistent_length
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from .utils.validation import _check_sample_weight
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from .pipeline import Pipeline
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from .isotonic import IsotonicRegression
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from .svm import LinearSVC
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from .model_selection import check_cv
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from .utils.validation import _deprecate_positional_args
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def _fit_calibrated_classifer(estimator, X, y, train, test, supports_sw,
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method, classes, sample_weight=None):
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"""Fit calibrated classifier for a given dataset split.
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Returns
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-------
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calibrated_classifier : estimator object
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The calibrated estimator.
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"""
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if sample_weight is not None and supports_sw:
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estimator.fit(X[train], y[train],
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sample_weight=sample_weight[train])
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else:
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estimator.fit(X[train], y[train])
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calibrated_classifier = _CalibratedClassifier(estimator,
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method=method,
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classes=classes)
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sw = None if sample_weight is None else sample_weight[test]
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calibrated_classifier.fit(X[test], y[test], sample_weight=sw)
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return calibrated_classifier
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class CalibratedClassifierCV(ClassifierMixin,
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MetaEstimatorMixin,
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BaseEstimator):
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"""Probability calibration with isotonic regression or logistic regression.
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This class uses cross-validation to both estimate the parameters of a
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classifier and subsequently calibrate a classifier. For each cv split it
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fits a copy of the base estimator to the training folds, and calibrates it
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using the testing fold. For prediction, predicted probabilities are
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averaged across these individual calibrated classifiers.
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Already fitted classifiers can be calibrated via the parameter cv="prefit".
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In this case, no cross-validation is used and all provided data is used
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for calibration. The user has to take care manually that data for model
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fitting and calibration are disjoint.
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The calibration is based on the :term:`decision_function` method of the
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`base_estimator` if it exists, else on :term:`predict_proba`.
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Read more in the :ref:`User Guide <calibration>`.
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Parameters
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----------
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base_estimator : estimator instance, default=None
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The classifier whose output need to be calibrated to provide more
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accurate `predict_proba` outputs. The default classifier is
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a :class:`~sklearn.svm.LinearSVC`.
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method : {'sigmoid', 'isotonic'}, default='sigmoid'
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The method to use for calibration. Can be 'sigmoid' which
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corresponds to Platt's method (i.e. a logistic regression model) or
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'isotonic' which is a non-parametric approach. It is not advised to
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use isotonic calibration with too few calibration samples
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``(<<1000)`` since it tends to overfit.
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cv : int, cross-validation generator, iterable or "prefit", \
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default=None
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Determines the cross-validation splitting strategy.
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Possible inputs for cv are:
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- None, to use the default 5-fold cross-validation,
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- integer, to specify the number of folds.
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- :term:`CV splitter`,
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- An iterable yielding (train, test) splits as arrays of indices.
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For integer/None inputs, if ``y`` is binary or multiclass,
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:class:`~sklearn.model_selection.StratifiedKFold` is used. If ``y`` is
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neither binary nor multiclass, :class:`~sklearn.model_selection.KFold`
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is used.
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Refer to the :ref:`User Guide <cross_validation>` for the various
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cross-validation strategies that can be used here.
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If "prefit" is passed, it is assumed that `base_estimator` has been
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fitted already and all data is used for calibration.
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.. versionchanged:: 0.22
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``cv`` default value if None changed from 3-fold to 5-fold.
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n_jobs : int, default=None
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Number of jobs to run in parallel.
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``None`` means 1 unless in a :obj:`joblib.parallel_backend` context.
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``-1`` means using all processors.
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Base estimator clones are fitted in parallel across cross-validation
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iterations. Therefore parallelism happens only when cv != "prefit".
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See :term:`Glossary <n_jobs>` for more details.
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.. versionadded:: 0.24
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Attributes
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----------
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classes_ : ndarray of shape (n_classes,)
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The class labels.
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calibrated_classifiers_ : list (len() equal to cv or 1 if cv == "prefit")
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The list of calibrated classifiers, one for each cross-validation
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split, which has been fitted on training folds and
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calibrated on the testing fold.
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Examples
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--------
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>>> from sklearn.datasets import make_classification
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>>> from sklearn.naive_bayes import GaussianNB
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>>> from sklearn.calibration import CalibratedClassifierCV
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>>> X, y = make_classification(n_samples=100, n_features=2,
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... n_redundant=0, random_state=42)
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>>> base_clf = GaussianNB()
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>>> calibrated_clf = CalibratedClassifierCV(base_estimator=base_clf, cv=3)
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>>> calibrated_clf.fit(X, y)
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CalibratedClassifierCV(base_estimator=GaussianNB(), cv=3)
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>>> len(calibrated_clf.calibrated_classifiers_)
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3
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>>> calibrated_clf.predict_proba(X)[:5, :]
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array([[0.110..., 0.889...],
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[0.072..., 0.927...],
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[0.928..., 0.071...],
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[0.928..., 0.071...],
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[0.071..., 0.928...]])
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>>> from sklearn.model_selection import train_test_split
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>>> X, y = make_classification(n_samples=100, n_features=2,
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... n_redundant=0, random_state=42)
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>>> X_train, X_calib, y_train, y_calib = train_test_split(
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... X, y, random_state=42
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... )
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>>> base_clf = GaussianNB()
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>>> base_clf.fit(X_train, y_train)
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GaussianNB()
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>>> calibrated_clf = CalibratedClassifierCV(
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... base_estimator=base_clf,
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... cv="prefit"
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... )
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>>> calibrated_clf.fit(X_calib, y_calib)
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CalibratedClassifierCV(base_estimator=GaussianNB(), cv='prefit')
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>>> len(calibrated_clf.calibrated_classifiers_)
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1
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>>> calibrated_clf.predict_proba([[-0.5, 0.5]])
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array([[0.936..., 0.063...]])
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References
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----------
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.. [1] Obtaining calibrated probability estimates from decision trees
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and naive Bayesian classifiers, B. Zadrozny & C. Elkan, ICML 2001
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.. [2] Transforming Classifier Scores into Accurate Multiclass
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Probability Estimates, B. Zadrozny & C. Elkan, (KDD 2002)
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.. [3] Probabilistic Outputs for Support Vector Machines and Comparisons to
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Regularized Likelihood Methods, J. Platt, (1999)
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.. [4] Predicting Good Probabilities with Supervised Learning,
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A. Niculescu-Mizil & R. Caruana, ICML 2005
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"""
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@_deprecate_positional_args
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def __init__(self, base_estimator=None, *, method='sigmoid',
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cv=None, n_jobs=None):
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self.base_estimator = base_estimator
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self.method = method
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self.cv = cv
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self.n_jobs = n_jobs
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def fit(self, X, y, sample_weight=None):
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"""Fit the calibrated model
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Parameters
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----------
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X : array-like of shape (n_samples, n_features)
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Training data.
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y : array-like of shape (n_samples,)
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Target values.
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sample_weight : array-like of shape (n_samples,), default=None
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Sample weights. If None, then samples are equally weighted.
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Returns
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-------
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self : object
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Returns an instance of self.
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"""
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X, y = indexable(X, y)
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self.calibrated_classifiers_ = []
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if self.base_estimator is None:
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# we want all classifiers that don't expose a random_state
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# to be deterministic (and we don't want to expose this one).
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base_estimator = LinearSVC(random_state=0)
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else:
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base_estimator = self.base_estimator
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if self.cv == "prefit":
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# Set `n_features_in_` attribute
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if isinstance(self.base_estimator, Pipeline):
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check_is_fitted(self.base_estimator[-1])
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else:
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check_is_fitted(self.base_estimator)
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with suppress(AttributeError):
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self.n_features_in_ = base_estimator.n_features_in_
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self.classes_ = self.base_estimator.classes_
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calibrated_classifier = _CalibratedClassifier(
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base_estimator, method=self.method)
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calibrated_classifier.fit(X, y, sample_weight)
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self.calibrated_classifiers_.append(calibrated_classifier)
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else:
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X, y = self._validate_data(
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X, y, accept_sparse=['csc', 'csr', 'coo'],
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force_all_finite=False, allow_nd=True
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)
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le = LabelBinarizer().fit(y)
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self.classes_ = le.classes_
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# Check that each cross-validation fold can have at least one
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# example per class
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if isinstance(self.cv, int):
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n_folds = self.cv
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elif hasattr(self.cv, "n_splits"):
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n_folds = self.cv.n_splits
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else:
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n_folds = None
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if n_folds and np.any([np.sum(y == class_) < n_folds
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for class_ in self.classes_]):
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raise ValueError(f"Requesting {n_folds}-fold cross-validation "
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f"but provided less than {n_folds} examples "
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"for at least one class.")
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cv = check_cv(self.cv, y, classifier=True)
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fit_parameters = signature(base_estimator.fit).parameters
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supports_sw = "sample_weight" in fit_parameters
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if sample_weight is not None:
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sample_weight = _check_sample_weight(sample_weight, X)
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if not supports_sw:
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estimator_name = type(base_estimator).__name__
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warnings.warn("Since %s does not support sample_weights, "
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"sample weights will only be used for the "
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"calibration itself." % estimator_name)
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parallel = Parallel(n_jobs=self.n_jobs)
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self.calibrated_classifiers_ = parallel(delayed(
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_fit_calibrated_classifer)(clone(base_estimator),
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X, y,
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train=train, test=test,
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method=self.method,
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classes=self.classes_,
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supports_sw=supports_sw,
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sample_weight=sample_weight)
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for train, test
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in cv.split(X, y))
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return self
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def predict_proba(self, X):
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"""Posterior probabilities of classification
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This function returns posterior probabilities of classification
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according to each class on an array of test vectors X.
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Parameters
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----------
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X : array-like of shape (n_samples, n_features)
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The samples.
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Returns
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-------
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C : ndarray of shape (n_samples, n_classes)
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The predicted probas.
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"""
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check_is_fitted(self)
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X = check_array(X, accept_sparse=['csc', 'csr', 'coo'],
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force_all_finite=False)
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# Compute the arithmetic mean of the predictions of the calibrated
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# classifiers
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mean_proba = np.zeros((X.shape[0], len(self.classes_)))
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for calibrated_classifier in self.calibrated_classifiers_:
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proba = calibrated_classifier.predict_proba(X)
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mean_proba += proba
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mean_proba /= len(self.calibrated_classifiers_)
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return mean_proba
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def predict(self, X):
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"""Predict the target of new samples. The predicted class is the
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class that has the highest probability, and can thus be different
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from the prediction of the uncalibrated classifier.
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Parameters
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----------
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X : array-like of shape (n_samples, n_features)
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The samples.
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Returns
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-------
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C : ndarray of shape (n_samples,)
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The predicted class.
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"""
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check_is_fitted(self)
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return self.classes_[np.argmax(self.predict_proba(X), axis=1)]
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def _more_tags(self):
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return {
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'_xfail_checks': {
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'check_sample_weights_invariance':
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'zero sample_weight is not equivalent to removing samples',
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}
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}
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class _CalibratedClassifier:
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"""Probability calibration with isotonic regression or sigmoid.
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It assumes that base_estimator has already been fit, and trains the
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calibration on the input set of the fit function. Note that this class
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should not be used as an estimator directly. Use CalibratedClassifierCV
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with cv="prefit" instead.
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Parameters
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----------
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base_estimator : instance BaseEstimator
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The classifier whose output decision function needs to be calibrated
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to offer more accurate predict_proba outputs. No default value since
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it has to be an already fitted estimator.
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method : {'sigmoid', 'isotonic'}, default='sigmoid'
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The method to use for calibration. Can be 'sigmoid' which
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corresponds to Platt's method or 'isotonic' which is a
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non-parametric approach based on isotonic regression.
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classes : array-like of shape (n_classes,), default=None
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Contains unique classes used to fit the base estimator.
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if None, then classes is extracted from the given target values
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in fit().
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See Also
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--------
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CalibratedClassifierCV
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References
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----------
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.. [1] Obtaining calibrated probability estimates from decision trees
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and naive Bayesian classifiers, B. Zadrozny & C. Elkan, ICML 2001
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.. [2] Transforming Classifier Scores into Accurate Multiclass
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Probability Estimates, B. Zadrozny & C. Elkan, (KDD 2002)
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.. [3] Probabilistic Outputs for Support Vector Machines and Comparisons to
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Regularized Likelihood Methods, J. Platt, (1999)
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.. [4] Predicting Good Probabilities with Supervised Learning,
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A. Niculescu-Mizil & R. Caruana, ICML 2005
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"""
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@_deprecate_positional_args
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def __init__(self, base_estimator, *, method='sigmoid', classes=None):
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self.base_estimator = base_estimator
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self.method = method
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self.classes = classes
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def _preproc(self, X):
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n_classes = len(self.classes_)
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if hasattr(self.base_estimator, "decision_function"):
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df = self.base_estimator.decision_function(X)
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if df.ndim == 1:
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df = df[:, np.newaxis]
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elif hasattr(self.base_estimator, "predict_proba"):
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df = self.base_estimator.predict_proba(X)
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if n_classes == 2:
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df = df[:, 1:]
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else:
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raise RuntimeError('classifier has no decision_function or '
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'predict_proba method.')
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idx_pos_class = self.label_encoder_.\
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transform(self.base_estimator.classes_)
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return df, idx_pos_class
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def fit(self, X, y, sample_weight=None):
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"""Calibrate the fitted model
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Parameters
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----------
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X : array-like of shape (n_samples, n_features)
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Training data.
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y : array-like of shape (n_samples,)
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Target values.
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sample_weight : array-like of shape (n_samples,), default=None
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Sample weights. If None, then samples are equally weighted.
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Returns
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-------
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self : object
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Returns an instance of self.
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"""
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self.label_encoder_ = LabelEncoder()
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if self.classes is None:
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self.label_encoder_.fit(y)
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else:
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self.label_encoder_.fit(self.classes)
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self.classes_ = self.label_encoder_.classes_
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Y = label_binarize(y, classes=self.classes_)
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df, idx_pos_class = self._preproc(X)
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self.calibrators_ = []
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for k, this_df in zip(idx_pos_class, df.T):
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if self.method == 'isotonic':
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calibrator = IsotonicRegression(out_of_bounds='clip')
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elif self.method == 'sigmoid':
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calibrator = _SigmoidCalibration()
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else:
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raise ValueError('method should be "sigmoid" or '
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'"isotonic". Got %s.' % self.method)
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calibrator.fit(this_df, Y[:, k], sample_weight)
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self.calibrators_.append(calibrator)
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return self
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def predict_proba(self, X):
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"""Posterior probabilities of classification
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This function returns posterior probabilities of classification
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according to each class on an array of test vectors X.
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Parameters
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----------
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X : array-like of shape (n_samples, n_features)
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The samples.
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Returns
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-------
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C : ndarray of shape (n_samples, n_classes)
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The predicted probas. Can be exact zeros.
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"""
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n_classes = len(self.classes_)
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proba = np.zeros((X.shape[0], n_classes))
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df, idx_pos_class = self._preproc(X)
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for k, this_df, calibrator in \
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zip(idx_pos_class, df.T, self.calibrators_):
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if n_classes == 2:
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k += 1
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proba[:, k] = calibrator.predict(this_df)
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# Normalize the probabilities
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if n_classes == 2:
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proba[:, 0] = 1. - proba[:, 1]
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else:
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proba /= np.sum(proba, axis=1)[:, np.newaxis]
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# XXX : for some reason all probas can be 0
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proba[np.isnan(proba)] = 1. / n_classes
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# Deal with cases where the predicted probability minimally exceeds 1.0
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proba[(1.0 < proba) & (proba <= 1.0 + 1e-5)] = 1.0
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return proba
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def _sigmoid_calibration(df, y, sample_weight=None):
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|
"""Probability Calibration with sigmoid method (Platt 2000)
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|
|
|
Parameters
|
|
----------
|
|
df : ndarray of shape (n_samples,)
|
|
The decision function or predict proba for the samples.
|
|
|
|
y : ndarray of shape (n_samples,)
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|
The targets.
|
|
|
|
sample_weight : array-like of shape (n_samples,), default=None
|
|
Sample weights. If None, then samples are equally weighted.
|
|
|
|
Returns
|
|
-------
|
|
a : float
|
|
The slope.
|
|
|
|
b : float
|
|
The intercept.
|
|
|
|
References
|
|
----------
|
|
Platt, "Probabilistic Outputs for Support Vector Machines"
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|
"""
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|
df = column_or_1d(df)
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|
y = column_or_1d(y)
|
|
|
|
F = df # F follows Platt's notations
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|
|
|
# Bayesian priors (see Platt end of section 2.2)
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prior0 = float(np.sum(y <= 0))
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prior1 = y.shape[0] - prior0
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T = np.zeros(y.shape)
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T[y > 0] = (prior1 + 1.) / (prior1 + 2.)
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|
T[y <= 0] = 1. / (prior0 + 2.)
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|
T1 = 1. - T
|
|
|
|
def objective(AB):
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|
# From Platt (beginning of Section 2.2)
|
|
P = expit(-(AB[0] * F + AB[1]))
|
|
loss = -(xlogy(T, P) + xlogy(T1, 1. - P))
|
|
if sample_weight is not None:
|
|
return (sample_weight * loss).sum()
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|
else:
|
|
return loss.sum()
|
|
|
|
def grad(AB):
|
|
# gradient of the objective function
|
|
P = expit(-(AB[0] * F + AB[1]))
|
|
TEP_minus_T1P = T - P
|
|
if sample_weight is not None:
|
|
TEP_minus_T1P *= sample_weight
|
|
dA = np.dot(TEP_minus_T1P, F)
|
|
dB = np.sum(TEP_minus_T1P)
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|
return np.array([dA, dB])
|
|
|
|
AB0 = np.array([0., log((prior0 + 1.) / (prior1 + 1.))])
|
|
AB_ = fmin_bfgs(objective, AB0, fprime=grad, disp=False)
|
|
return AB_[0], AB_[1]
|
|
|
|
|
|
class _SigmoidCalibration(RegressorMixin, BaseEstimator):
|
|
"""Sigmoid regression model.
|
|
|
|
Attributes
|
|
----------
|
|
a_ : float
|
|
The slope.
|
|
|
|
b_ : float
|
|
The intercept.
|
|
"""
|
|
def fit(self, X, y, sample_weight=None):
|
|
"""Fit the model using X, y as training data.
|
|
|
|
Parameters
|
|
----------
|
|
X : array-like of shape (n_samples,)
|
|
Training data.
|
|
|
|
y : array-like of shape (n_samples,)
|
|
Training target.
|
|
|
|
sample_weight : array-like of shape (n_samples,), default=None
|
|
Sample weights. If None, then samples are equally weighted.
|
|
|
|
Returns
|
|
-------
|
|
self : object
|
|
Returns an instance of self.
|
|
"""
|
|
X = column_or_1d(X)
|
|
y = column_or_1d(y)
|
|
X, y = indexable(X, y)
|
|
|
|
self.a_, self.b_ = _sigmoid_calibration(X, y, sample_weight)
|
|
return self
|
|
|
|
def predict(self, T):
|
|
"""Predict new data by linear interpolation.
|
|
|
|
Parameters
|
|
----------
|
|
T : array-like of shape (n_samples,)
|
|
Data to predict from.
|
|
|
|
Returns
|
|
-------
|
|
T_ : ndarray of shape (n_samples,)
|
|
The predicted data.
|
|
"""
|
|
T = column_or_1d(T)
|
|
return expit(-(self.a_ * T + self.b_))
|
|
|
|
|
|
@_deprecate_positional_args
|
|
def calibration_curve(y_true, y_prob, *, normalize=False, n_bins=5,
|
|
strategy='uniform'):
|
|
"""Compute true and predicted probabilities for a calibration curve.
|
|
|
|
The method assumes the inputs come from a binary classifier, and
|
|
discretize the [0, 1] interval into bins.
|
|
|
|
Calibration curves may also be referred to as reliability diagrams.
|
|
|
|
Read more in the :ref:`User Guide <calibration>`.
|
|
|
|
Parameters
|
|
----------
|
|
y_true : array-like of shape (n_samples,)
|
|
True targets.
|
|
|
|
y_prob : array-like of shape (n_samples,)
|
|
Probabilities of the positive class.
|
|
|
|
normalize : bool, default=False
|
|
Whether y_prob needs to be normalized into the [0, 1] interval, i.e.
|
|
is not a proper probability. If True, the smallest value in y_prob
|
|
is linearly mapped onto 0 and the largest one onto 1.
|
|
|
|
n_bins : int, default=5
|
|
Number of bins to discretize the [0, 1] interval. A bigger number
|
|
requires more data. Bins with no samples (i.e. without
|
|
corresponding values in `y_prob`) will not be returned, thus the
|
|
returned arrays may have less than `n_bins` values.
|
|
|
|
strategy : {'uniform', 'quantile'}, default='uniform'
|
|
Strategy used to define the widths of the bins.
|
|
|
|
uniform
|
|
The bins have identical widths.
|
|
quantile
|
|
The bins have the same number of samples and depend on `y_prob`.
|
|
|
|
Returns
|
|
-------
|
|
prob_true : ndarray of shape (n_bins,) or smaller
|
|
The proportion of samples whose class is the positive class, in each
|
|
bin (fraction of positives).
|
|
|
|
prob_pred : ndarray of shape (n_bins,) or smaller
|
|
The mean predicted probability in each bin.
|
|
|
|
References
|
|
----------
|
|
Alexandru Niculescu-Mizil and Rich Caruana (2005) Predicting Good
|
|
Probabilities With Supervised Learning, in Proceedings of the 22nd
|
|
International Conference on Machine Learning (ICML).
|
|
See section 4 (Qualitative Analysis of Predictions).
|
|
|
|
Examples
|
|
--------
|
|
>>> import numpy as np
|
|
>>> from sklearn.calibration import calibration_curve
|
|
>>> y_true = np.array([0, 0, 0, 0, 1, 1, 1, 1, 1])
|
|
>>> y_pred = np.array([0.1, 0.2, 0.3, 0.4, 0.65, 0.7, 0.8, 0.9, 1.])
|
|
>>> prob_true, prob_pred = calibration_curve(y_true, y_pred, n_bins=3)
|
|
>>> prob_true
|
|
array([0. , 0.5, 1. ])
|
|
>>> prob_pred
|
|
array([0.2 , 0.525, 0.85 ])
|
|
"""
|
|
y_true = column_or_1d(y_true)
|
|
y_prob = column_or_1d(y_prob)
|
|
check_consistent_length(y_true, y_prob)
|
|
|
|
if normalize: # Normalize predicted values into interval [0, 1]
|
|
y_prob = (y_prob - y_prob.min()) / (y_prob.max() - y_prob.min())
|
|
elif y_prob.min() < 0 or y_prob.max() > 1:
|
|
raise ValueError("y_prob has values outside [0, 1] and normalize is "
|
|
"set to False.")
|
|
|
|
labels = np.unique(y_true)
|
|
if len(labels) > 2:
|
|
raise ValueError("Only binary classification is supported. "
|
|
"Provided labels %s." % labels)
|
|
y_true = label_binarize(y_true, classes=labels)[:, 0]
|
|
|
|
if strategy == 'quantile': # Determine bin edges by distribution of data
|
|
quantiles = np.linspace(0, 1, n_bins + 1)
|
|
bins = np.percentile(y_prob, quantiles * 100)
|
|
bins[-1] = bins[-1] + 1e-8
|
|
elif strategy == 'uniform':
|
|
bins = np.linspace(0., 1. + 1e-8, n_bins + 1)
|
|
else:
|
|
raise ValueError("Invalid entry to 'strategy' input. Strategy "
|
|
"must be either 'quantile' or 'uniform'.")
|
|
|
|
binids = np.digitize(y_prob, bins) - 1
|
|
|
|
bin_sums = np.bincount(binids, weights=y_prob, minlength=len(bins))
|
|
bin_true = np.bincount(binids, weights=y_true, minlength=len(bins))
|
|
bin_total = np.bincount(binids, minlength=len(bins))
|
|
|
|
nonzero = bin_total != 0
|
|
prob_true = bin_true[nonzero] / bin_total[nonzero]
|
|
prob_pred = bin_sums[nonzero] / bin_total[nonzero]
|
|
|
|
return prob_true, prob_pred
|