326 lines
12 KiB
Python
326 lines
12 KiB
Python
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"""
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Sequential feature selection
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"""
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from numbers import Integral, Real
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import numpy as np
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import warnings
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from ._base import SelectorMixin
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from ..base import BaseEstimator, MetaEstimatorMixin, clone
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from ..utils._param_validation import HasMethods, Hidden, Interval, StrOptions
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from ..utils._tags import _safe_tags
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from ..utils.validation import check_is_fitted
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from ..model_selection import cross_val_score
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from ..metrics import get_scorer_names
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class SequentialFeatureSelector(SelectorMixin, MetaEstimatorMixin, BaseEstimator):
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"""Transformer that performs Sequential Feature Selection.
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This Sequential Feature Selector adds (forward selection) or
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removes (backward selection) features to form a feature subset in a
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greedy fashion. At each stage, this estimator chooses the best feature to
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add or remove based on the cross-validation score of an estimator. In
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the case of unsupervised learning, this Sequential Feature Selector
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looks only at the features (X), not the desired outputs (y).
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Read more in the :ref:`User Guide <sequential_feature_selection>`.
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.. versionadded:: 0.24
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Parameters
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----------
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estimator : estimator instance
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An unfitted estimator.
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n_features_to_select : "auto", int or float, default='warn'
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If `"auto"`, the behaviour depends on the `tol` parameter:
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- if `tol` is not `None`, then features are selected until the score
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improvement does not exceed `tol`.
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- otherwise, half of the features are selected.
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If integer, the parameter is the absolute number of features to select.
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If float between 0 and 1, it is the fraction of features to select.
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.. versionadded:: 1.1
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The option `"auto"` was added in version 1.1.
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.. deprecated:: 1.1
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The default changed from `None` to `"warn"` in 1.1 and will become
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`"auto"` in 1.3. `None` and `'warn'` will be removed in 1.3.
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To keep the same behaviour as `None`, set
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`n_features_to_select="auto" and `tol=None`.
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tol : float, default=None
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If the score is not incremented by at least `tol` between two
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consecutive feature additions or removals, stop adding or removing.
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`tol` can be negative when removing features using `direction="backward"`.
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It can be useful to reduce the number of features at the cost of a small
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decrease in the score.
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`tol` is enabled only when `n_features_to_select` is `"auto"`.
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.. versionadded:: 1.1
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direction : {'forward', 'backward'}, default='forward'
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Whether to perform forward selection or backward selection.
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scoring : str or callable, default=None
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A single str (see :ref:`scoring_parameter`) or a callable
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(see :ref:`scoring`) to evaluate the predictions on the test set.
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NOTE that when using a custom scorer, it should return a single
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value.
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If None, the estimator's score method is used.
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cv : int, cross-validation generator or an iterable, 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 in a `(Stratified)KFold`,
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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 the estimator is a classifier and ``y`` is
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either binary or multiclass, :class:`StratifiedKFold` is used. In all
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other cases, :class:`KFold` is used. These splitters are instantiated
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with `shuffle=False` so the splits will be the same across calls.
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Refer :ref:`User Guide <cross_validation>` for the various
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cross-validation strategies that can be used here.
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n_jobs : int, default=None
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Number of jobs to run in parallel. When evaluating a new feature to
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add or remove, the cross-validation procedure is parallel over the
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folds.
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``None`` means 1 unless in a :obj:`joblib.parallel_backend` context.
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``-1`` means using all processors. See :term:`Glossary <n_jobs>`
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for more details.
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Attributes
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----------
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n_features_in_ : int
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Number of features seen during :term:`fit`. Only defined if the
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underlying estimator exposes such an attribute when fit.
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.. versionadded:: 0.24
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feature_names_in_ : ndarray of shape (`n_features_in_`,)
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Names of features seen during :term:`fit`. Defined only when `X`
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has feature names that are all strings.
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.. versionadded:: 1.0
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n_features_to_select_ : int
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The number of features that were selected.
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support_ : ndarray of shape (n_features,), dtype=bool
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The mask of selected features.
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See Also
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--------
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GenericUnivariateSelect : Univariate feature selector with configurable
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strategy.
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RFE : Recursive feature elimination based on importance weights.
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RFECV : Recursive feature elimination based on importance weights, with
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automatic selection of the number of features.
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SelectFromModel : Feature selection based on thresholds of importance
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weights.
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Examples
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--------
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>>> from sklearn.feature_selection import SequentialFeatureSelector
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>>> from sklearn.neighbors import KNeighborsClassifier
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>>> from sklearn.datasets import load_iris
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>>> X, y = load_iris(return_X_y=True)
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>>> knn = KNeighborsClassifier(n_neighbors=3)
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>>> sfs = SequentialFeatureSelector(knn, n_features_to_select=3)
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>>> sfs.fit(X, y)
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SequentialFeatureSelector(estimator=KNeighborsClassifier(n_neighbors=3),
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n_features_to_select=3)
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>>> sfs.get_support()
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array([ True, False, True, True])
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>>> sfs.transform(X).shape
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(150, 3)
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"""
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_parameter_constraints: dict = {
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"estimator": [HasMethods(["fit"])],
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"n_features_to_select": [
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StrOptions({"auto", "warn"}, deprecated={"warn"}),
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Interval(Real, 0, 1, closed="right"),
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Interval(Integral, 0, None, closed="neither"),
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Hidden(None),
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],
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"tol": [None, Interval(Real, None, None, closed="neither")],
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"direction": [StrOptions({"forward", "backward"})],
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"scoring": [None, StrOptions(set(get_scorer_names())), callable],
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"cv": ["cv_object"],
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"n_jobs": [None, Integral],
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}
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def __init__(
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self,
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estimator,
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*,
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n_features_to_select="warn",
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tol=None,
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direction="forward",
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scoring=None,
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cv=5,
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n_jobs=None,
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):
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self.estimator = estimator
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self.n_features_to_select = n_features_to_select
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self.tol = tol
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self.direction = direction
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self.scoring = scoring
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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=None):
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"""Learn the features to select from 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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Training vectors, where `n_samples` is the number of samples and
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`n_features` is the number of predictors.
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y : array-like of shape (n_samples,), default=None
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Target values. This parameter may be ignored for
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unsupervised learning.
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Returns
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-------
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self : object
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Returns the instance itself.
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"""
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self._validate_params()
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# FIXME: to be removed in 1.3
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if self.n_features_to_select in ("warn", None):
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# for backwards compatibility
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warnings.warn(
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"Leaving `n_features_to_select` to "
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"None is deprecated in 1.0 and will become 'auto' "
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"in 1.3. To keep the same behaviour as with None "
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"(i.e. select half of the features) and avoid "
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"this warning, you should manually set "
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"`n_features_to_select='auto'` and set tol=None "
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"when creating an instance.",
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FutureWarning,
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)
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tags = self._get_tags()
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X = self._validate_data(
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X,
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accept_sparse="csc",
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ensure_min_features=2,
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force_all_finite=not tags.get("allow_nan", True),
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)
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n_features = X.shape[1]
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# FIXME: to be fixed in 1.3
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error_msg = (
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"n_features_to_select must be either 'auto', 'warn', "
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"None, an integer in [1, n_features - 1] "
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"representing the absolute "
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"number of features, or a float in (0, 1] "
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"representing a percentage of features to "
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f"select. Got {self.n_features_to_select}"
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)
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if self.n_features_to_select in ("warn", None):
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if self.tol is not None:
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raise ValueError("tol is only enabled if `n_features_to_select='auto'`")
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self.n_features_to_select_ = n_features // 2
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elif self.n_features_to_select == "auto":
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if self.tol is not None:
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# With auto feature selection, `n_features_to_select_` will be updated
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# to `support_.sum()` after features are selected.
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self.n_features_to_select_ = n_features - 1
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else:
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self.n_features_to_select_ = n_features // 2
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elif isinstance(self.n_features_to_select, Integral):
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if not 0 < self.n_features_to_select < n_features:
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raise ValueError(error_msg)
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self.n_features_to_select_ = self.n_features_to_select
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elif isinstance(self.n_features_to_select, Real):
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self.n_features_to_select_ = int(n_features * self.n_features_to_select)
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if self.tol is not None and self.tol < 0 and self.direction == "forward":
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raise ValueError("tol must be positive when doing forward selection")
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cloned_estimator = clone(self.estimator)
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# the current mask corresponds to the set of features:
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# - that we have already *selected* if we do forward selection
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# - that we have already *excluded* if we do backward selection
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current_mask = np.zeros(shape=n_features, dtype=bool)
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n_iterations = (
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self.n_features_to_select_
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if self.n_features_to_select == "auto" or self.direction == "forward"
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else n_features - self.n_features_to_select_
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)
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old_score = -np.inf
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is_auto_select = self.tol is not None and self.n_features_to_select == "auto"
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for _ in range(n_iterations):
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new_feature_idx, new_score = self._get_best_new_feature_score(
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cloned_estimator, X, y, current_mask
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)
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if is_auto_select and ((new_score - old_score) < self.tol):
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break
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old_score = new_score
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current_mask[new_feature_idx] = True
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if self.direction == "backward":
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current_mask = ~current_mask
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self.support_ = current_mask
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self.n_features_to_select_ = self.support_.sum()
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return self
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def _get_best_new_feature_score(self, estimator, X, y, current_mask):
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# Return the best new feature and its score to add to the current_mask,
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# i.e. return the best new feature and its score to add (resp. remove)
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# when doing forward selection (resp. backward selection).
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# Feature will be added if the current score and past score are greater
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# than tol when n_feature is auto,
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candidate_feature_indices = np.flatnonzero(~current_mask)
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scores = {}
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for feature_idx in candidate_feature_indices:
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candidate_mask = current_mask.copy()
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candidate_mask[feature_idx] = True
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if self.direction == "backward":
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candidate_mask = ~candidate_mask
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X_new = X[:, candidate_mask]
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scores[feature_idx] = cross_val_score(
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estimator,
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X_new,
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y,
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cv=self.cv,
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scoring=self.scoring,
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n_jobs=self.n_jobs,
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).mean()
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new_feature_idx = max(scores, key=lambda feature_idx: scores[feature_idx])
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return new_feature_idx, scores[new_feature_idx]
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def _get_support_mask(self):
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check_is_fitted(self)
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return self.support_
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def _more_tags(self):
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return {
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"allow_nan": _safe_tags(self.estimator, key="allow_nan"),
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}
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