| |
| |
|
|
| """Recursive feature elimination for feature ranking""" |
|
|
| import warnings |
| from copy import deepcopy |
| from numbers import Integral |
|
|
| import numpy as np |
| from joblib import effective_n_jobs |
|
|
| from ..base import BaseEstimator, MetaEstimatorMixin, _fit_context, clone, is_classifier |
| from ..metrics import get_scorer |
| from ..model_selection import check_cv |
| from ..model_selection._validation import _score |
| from ..utils import Bunch, metadata_routing |
| from ..utils._metadata_requests import ( |
| MetadataRouter, |
| MethodMapping, |
| _raise_for_params, |
| _routing_enabled, |
| process_routing, |
| ) |
| from ..utils._param_validation import HasMethods, Interval, RealNotInt |
| from ..utils._tags import get_tags |
| from ..utils.metaestimators import _safe_split, available_if |
| from ..utils.parallel import Parallel, delayed |
| from ..utils.validation import ( |
| _check_method_params, |
| _deprecate_positional_args, |
| _estimator_has, |
| check_is_fitted, |
| validate_data, |
| ) |
| from ._base import SelectorMixin, _get_feature_importances |
|
|
|
|
| def _rfe_single_fit(rfe, estimator, X, y, train, test, scorer, routed_params): |
| """ |
| Return the score and n_features per step for a fit across one fold. |
| """ |
| X_train, y_train = _safe_split(estimator, X, y, train) |
| X_test, y_test = _safe_split(estimator, X, y, test, train) |
| fit_params = _check_method_params( |
| X, params=routed_params.estimator.fit, indices=train |
| ) |
| score_params = _check_method_params( |
| X=X, params=routed_params.scorer.score, indices=test |
| ) |
|
|
| rfe._fit( |
| X_train, |
| y_train, |
| lambda estimator, features: _score( |
| estimator, |
| X_test[:, features], |
| y_test, |
| scorer, |
| score_params=score_params, |
| ), |
| **fit_params, |
| ) |
|
|
| return rfe.step_scores_, rfe.step_n_features_ |
|
|
|
|
| class RFE(SelectorMixin, MetaEstimatorMixin, BaseEstimator): |
| """Feature ranking with recursive feature elimination. |
| |
| Given an external estimator that assigns weights to features (e.g., the |
| coefficients of a linear model), the goal of recursive feature elimination |
| (RFE) is to select features by recursively considering smaller and smaller |
| sets of features. First, the estimator is trained on the initial set of |
| features and the importance of each feature is obtained either through |
| any specific attribute or callable. |
| Then, the least important features are pruned from current set of features. |
| That procedure is recursively repeated on the pruned set until the desired |
| number of features to select is eventually reached. |
| |
| Read more in the :ref:`User Guide <rfe>`. |
| |
| Parameters |
| ---------- |
| estimator : ``Estimator`` instance |
| A supervised learning estimator with a ``fit`` method that provides |
| information about feature importance |
| (e.g. `coef_`, `feature_importances_`). |
| |
| n_features_to_select : int or float, default=None |
| The number of features to select. If `None`, half of the features are |
| selected. If integer, the parameter is the absolute number of features |
| to select. If float between 0 and 1, it is the fraction of features to |
| select. |
| |
| .. versionchanged:: 0.24 |
| Added float values for fractions. |
| |
| step : int or float, default=1 |
| If greater than or equal to 1, then ``step`` corresponds to the |
| (integer) number of features to remove at each iteration. |
| If within (0.0, 1.0), then ``step`` corresponds to the percentage |
| (rounded down) of features to remove at each iteration. |
| |
| verbose : int, default=0 |
| Controls verbosity of output. |
| |
| importance_getter : str or callable, default='auto' |
| If 'auto', uses the feature importance either through a `coef_` |
| or `feature_importances_` attributes of estimator. |
| |
| Also accepts a string that specifies an attribute name/path |
| for extracting feature importance (implemented with `attrgetter`). |
| For example, give `regressor_.coef_` in case of |
| :class:`~sklearn.compose.TransformedTargetRegressor` or |
| `named_steps.clf.feature_importances_` in case of |
| class:`~sklearn.pipeline.Pipeline` with its last step named `clf`. |
| |
| If `callable`, overrides the default feature importance getter. |
| The callable is passed with the fitted estimator and it should |
| return importance for each feature. |
| |
| .. versionadded:: 0.24 |
| |
| Attributes |
| ---------- |
| classes_ : ndarray of shape (n_classes,) |
| The classes labels. Only available when `estimator` is a classifier. |
| |
| estimator_ : ``Estimator`` instance |
| The fitted estimator used to select features. |
| |
| n_features_ : int |
| The number of selected features. |
| |
| n_features_in_ : int |
| Number of features seen during :term:`fit`. Only defined if the |
| underlying estimator exposes such an attribute when fit. |
| |
| .. versionadded:: 0.24 |
| |
| feature_names_in_ : ndarray of shape (`n_features_in_`,) |
| Names of features seen during :term:`fit`. Defined only when `X` |
| has feature names that are all strings. |
| |
| .. versionadded:: 1.0 |
| |
| ranking_ : ndarray of shape (n_features,) |
| The feature ranking, such that ``ranking_[i]`` corresponds to the |
| ranking position of the i-th feature. Selected (i.e., estimated |
| best) features are assigned rank 1. |
| |
| support_ : ndarray of shape (n_features,) |
| The mask of selected features. |
| |
| See Also |
| -------- |
| RFECV : Recursive feature elimination with built-in cross-validated |
| selection of the best number of features. |
| SelectFromModel : Feature selection based on thresholds of importance |
| weights. |
| SequentialFeatureSelector : Sequential cross-validation based feature |
| selection. Does not rely on importance weights. |
| |
| Notes |
| ----- |
| Allows NaN/Inf in the input if the underlying estimator does as well. |
| |
| References |
| ---------- |
| |
| .. [1] Guyon, I., Weston, J., Barnhill, S., & Vapnik, V., "Gene selection |
| for cancer classification using support vector machines", |
| Mach. Learn., 46(1-3), 389--422, 2002. |
| |
| Examples |
| -------- |
| The following example shows how to retrieve the 5 most informative |
| features in the Friedman #1 dataset. |
| |
| >>> from sklearn.datasets import make_friedman1 |
| >>> from sklearn.feature_selection import RFE |
| >>> from sklearn.svm import SVR |
| >>> X, y = make_friedman1(n_samples=50, n_features=10, random_state=0) |
| >>> estimator = SVR(kernel="linear") |
| >>> selector = RFE(estimator, n_features_to_select=5, step=1) |
| >>> selector = selector.fit(X, y) |
| >>> selector.support_ |
| array([ True, True, True, True, True, False, False, False, False, |
| False]) |
| >>> selector.ranking_ |
| array([1, 1, 1, 1, 1, 6, 4, 3, 2, 5]) |
| """ |
|
|
| _parameter_constraints: dict = { |
| "estimator": [HasMethods(["fit"])], |
| "n_features_to_select": [ |
| None, |
| Interval(RealNotInt, 0, 1, closed="right"), |
| Interval(Integral, 0, None, closed="neither"), |
| ], |
| "step": [ |
| Interval(Integral, 0, None, closed="neither"), |
| Interval(RealNotInt, 0, 1, closed="neither"), |
| ], |
| "verbose": ["verbose"], |
| "importance_getter": [str, callable], |
| } |
|
|
| def __init__( |
| self, |
| estimator, |
| *, |
| n_features_to_select=None, |
| step=1, |
| verbose=0, |
| importance_getter="auto", |
| ): |
| self.estimator = estimator |
| self.n_features_to_select = n_features_to_select |
| self.step = step |
| self.importance_getter = importance_getter |
| self.verbose = verbose |
|
|
| |
| @property |
| def _estimator_type(self): |
| return self.estimator._estimator_type |
|
|
| @property |
| def classes_(self): |
| """Classes labels available when `estimator` is a classifier. |
| |
| Returns |
| ------- |
| ndarray of shape (n_classes,) |
| """ |
| return self.estimator_.classes_ |
|
|
| @_fit_context( |
| |
| prefer_skip_nested_validation=False |
| ) |
| def fit(self, X, y, **fit_params): |
| """Fit the RFE model and then the underlying estimator on the selected features. |
| |
| Parameters |
| ---------- |
| X : {array-like, sparse matrix} of shape (n_samples, n_features) |
| The training input samples. |
| |
| y : array-like of shape (n_samples,) |
| The target values. |
| |
| **fit_params : dict |
| - If `enable_metadata_routing=False` (default): Parameters directly passed |
| to the ``fit`` method of the underlying estimator. |
| |
| - If `enable_metadata_routing=True`: Parameters safely routed to the ``fit`` |
| method of the underlying estimator. |
| |
| .. versionchanged:: 1.6 |
| See :ref:`Metadata Routing User Guide <metadata_routing>` |
| for more details. |
| |
| Returns |
| ------- |
| self : object |
| Fitted estimator. |
| """ |
| if _routing_enabled(): |
| routed_params = process_routing(self, "fit", **fit_params) |
| else: |
| routed_params = Bunch(estimator=Bunch(fit=fit_params)) |
|
|
| return self._fit(X, y, **routed_params.estimator.fit) |
|
|
| def _fit(self, X, y, step_score=None, **fit_params): |
| |
| |
| |
|
|
| X, y = validate_data( |
| self, |
| X, |
| y, |
| accept_sparse="csc", |
| ensure_min_features=2, |
| ensure_all_finite=False, |
| multi_output=True, |
| ) |
|
|
| |
| n_features = X.shape[1] |
| if self.n_features_to_select is None: |
| n_features_to_select = n_features // 2 |
| elif isinstance(self.n_features_to_select, Integral): |
| n_features_to_select = self.n_features_to_select |
| if n_features_to_select > n_features: |
| warnings.warn( |
| ( |
| f"Found {n_features_to_select=} > {n_features=}. There will be" |
| " no feature selection and all features will be kept." |
| ), |
| UserWarning, |
| ) |
| else: |
| n_features_to_select = int(n_features * self.n_features_to_select) |
|
|
| if 0.0 < self.step < 1.0: |
| step = int(max(1, self.step * n_features)) |
| else: |
| step = int(self.step) |
|
|
| support_ = np.ones(n_features, dtype=bool) |
| ranking_ = np.ones(n_features, dtype=int) |
|
|
| if step_score: |
| self.step_n_features_ = [] |
| self.step_scores_ = [] |
|
|
| |
| while np.sum(support_) > n_features_to_select: |
| |
| features = np.arange(n_features)[support_] |
|
|
| |
| estimator = clone(self.estimator) |
| if self.verbose > 0: |
| print("Fitting estimator with %d features." % np.sum(support_)) |
|
|
| estimator.fit(X[:, features], y, **fit_params) |
|
|
| |
| importances = _get_feature_importances( |
| estimator, |
| self.importance_getter, |
| transform_func="square", |
| ) |
| ranks = np.argsort(importances) |
|
|
| |
| ranks = np.ravel(ranks) |
|
|
| |
| threshold = min(step, np.sum(support_) - n_features_to_select) |
|
|
| |
| |
| |
| if step_score: |
| self.step_n_features_.append(len(features)) |
| self.step_scores_.append(step_score(estimator, features)) |
| support_[features[ranks][:threshold]] = False |
| ranking_[np.logical_not(support_)] += 1 |
|
|
| |
| features = np.arange(n_features)[support_] |
| self.estimator_ = clone(self.estimator) |
| self.estimator_.fit(X[:, features], y, **fit_params) |
|
|
| |
| if step_score: |
| self.step_n_features_.append(len(features)) |
| self.step_scores_.append(step_score(self.estimator_, features)) |
| self.n_features_ = support_.sum() |
| self.support_ = support_ |
| self.ranking_ = ranking_ |
|
|
| return self |
|
|
| @available_if(_estimator_has("predict")) |
| def predict(self, X, **predict_params): |
| """Reduce X to the selected features and predict using the estimator. |
| |
| Parameters |
| ---------- |
| X : array of shape [n_samples, n_features] |
| The input samples. |
| |
| **predict_params : dict |
| Parameters to route to the ``predict`` method of the |
| underlying estimator. |
| |
| .. versionadded:: 1.6 |
| Only available if `enable_metadata_routing=True`, |
| which can be set by using |
| ``sklearn.set_config(enable_metadata_routing=True)``. |
| See :ref:`Metadata Routing User Guide <metadata_routing>` |
| for more details. |
| |
| Returns |
| ------- |
| y : array of shape [n_samples] |
| The predicted target values. |
| """ |
| _raise_for_params(predict_params, self, "predict") |
| check_is_fitted(self) |
| if _routing_enabled(): |
| routed_params = process_routing(self, "predict", **predict_params) |
| else: |
| routed_params = Bunch(estimator=Bunch(predict={})) |
|
|
| return self.estimator_.predict( |
| self.transform(X), **routed_params.estimator.predict |
| ) |
|
|
| @available_if(_estimator_has("score")) |
| def score(self, X, y, **score_params): |
| """Reduce X to the selected features and return the score of the estimator. |
| |
| Parameters |
| ---------- |
| X : array of shape [n_samples, n_features] |
| The input samples. |
| |
| y : array of shape [n_samples] |
| The target values. |
| |
| **score_params : dict |
| - If `enable_metadata_routing=False` (default): Parameters directly passed |
| to the ``score`` method of the underlying estimator. |
| |
| - If `enable_metadata_routing=True`: Parameters safely routed to the `score` |
| method of the underlying estimator. |
| |
| .. versionadded:: 1.0 |
| |
| .. versionchanged:: 1.6 |
| See :ref:`Metadata Routing User Guide <metadata_routing>` |
| for more details. |
| |
| Returns |
| ------- |
| score : float |
| Score of the underlying base estimator computed with the selected |
| features returned by `rfe.transform(X)` and `y`. |
| """ |
| check_is_fitted(self) |
| if _routing_enabled(): |
| routed_params = process_routing(self, "score", **score_params) |
| else: |
| routed_params = Bunch(estimator=Bunch(score=score_params)) |
|
|
| return self.estimator_.score( |
| self.transform(X), y, **routed_params.estimator.score |
| ) |
|
|
| def _get_support_mask(self): |
| check_is_fitted(self) |
| return self.support_ |
|
|
| @available_if(_estimator_has("decision_function")) |
| def decision_function(self, X): |
| """Compute the decision function of ``X``. |
| |
| Parameters |
| ---------- |
| X : {array-like or sparse matrix} of shape (n_samples, n_features) |
| The input samples. Internally, it will be converted to |
| ``dtype=np.float32`` and if a sparse matrix is provided |
| to a sparse ``csr_matrix``. |
| |
| Returns |
| ------- |
| score : array, shape = [n_samples, n_classes] or [n_samples] |
| The decision function of the input samples. The order of the |
| classes corresponds to that in the attribute :term:`classes_`. |
| Regression and binary classification produce an array of shape |
| [n_samples]. |
| """ |
| check_is_fitted(self) |
| return self.estimator_.decision_function(self.transform(X)) |
|
|
| @available_if(_estimator_has("predict_proba")) |
| def predict_proba(self, X): |
| """Predict class probabilities for X. |
| |
| Parameters |
| ---------- |
| X : {array-like or sparse matrix} of shape (n_samples, n_features) |
| The input samples. Internally, it will be converted to |
| ``dtype=np.float32`` and if a sparse matrix is provided |
| to a sparse ``csr_matrix``. |
| |
| Returns |
| ------- |
| p : array of shape (n_samples, n_classes) |
| The class probabilities of the input samples. The order of the |
| classes corresponds to that in the attribute :term:`classes_`. |
| """ |
| check_is_fitted(self) |
| return self.estimator_.predict_proba(self.transform(X)) |
|
|
| @available_if(_estimator_has("predict_log_proba")) |
| def predict_log_proba(self, X): |
| """Predict class log-probabilities for X. |
| |
| Parameters |
| ---------- |
| X : array of shape [n_samples, n_features] |
| The input samples. |
| |
| Returns |
| ------- |
| p : array of shape (n_samples, n_classes) |
| The class log-probabilities of the input samples. The order of the |
| classes corresponds to that in the attribute :term:`classes_`. |
| """ |
| check_is_fitted(self) |
| return self.estimator_.predict_log_proba(self.transform(X)) |
|
|
| def __sklearn_tags__(self): |
| tags = super().__sklearn_tags__() |
| sub_estimator_tags = get_tags(self.estimator) |
| tags.estimator_type = sub_estimator_tags.estimator_type |
| tags.classifier_tags = deepcopy(sub_estimator_tags.classifier_tags) |
| tags.regressor_tags = deepcopy(sub_estimator_tags.regressor_tags) |
| if tags.classifier_tags is not None: |
| tags.classifier_tags.poor_score = True |
| if tags.regressor_tags is not None: |
| tags.regressor_tags.poor_score = True |
| tags.target_tags.required = True |
| tags.input_tags.sparse = sub_estimator_tags.input_tags.sparse |
| tags.input_tags.allow_nan = sub_estimator_tags.input_tags.allow_nan |
| return tags |
|
|
| def get_metadata_routing(self): |
| """Get metadata routing of this object. |
| |
| Please check :ref:`User Guide <metadata_routing>` on how the routing |
| mechanism works. |
| |
| .. versionadded:: 1.6 |
| |
| Returns |
| ------- |
| routing : MetadataRouter |
| A :class:`~sklearn.utils.metadata_routing.MetadataRouter` encapsulating |
| routing information. |
| """ |
| router = MetadataRouter(owner=self.__class__.__name__).add( |
| estimator=self.estimator, |
| method_mapping=MethodMapping() |
| .add(caller="fit", callee="fit") |
| .add(caller="predict", callee="predict") |
| .add(caller="score", callee="score"), |
| ) |
| return router |
|
|
|
|
| class RFECV(RFE): |
| """Recursive feature elimination with cross-validation to select features. |
| |
| The number of features selected is tuned automatically by fitting an :class:`RFE` |
| selector on the different cross-validation splits (provided by the `cv` parameter). |
| The performance of the :class:`RFE` selector are evaluated using `scorer` for |
| different number of selected features and aggregated together. Finally, the scores |
| are averaged across folds and the number of features selected is set to the number |
| of features that maximize the cross-validation score. |
| See glossary entry for :term:`cross-validation estimator`. |
| |
| Read more in the :ref:`User Guide <rfe>`. |
| |
| Parameters |
| ---------- |
| estimator : ``Estimator`` instance |
| A supervised learning estimator with a ``fit`` method that provides |
| information about feature importance either through a ``coef_`` |
| attribute or through a ``feature_importances_`` attribute. |
| |
| step : int or float, default=1 |
| If greater than or equal to 1, then ``step`` corresponds to the |
| (integer) number of features to remove at each iteration. |
| If within (0.0, 1.0), then ``step`` corresponds to the percentage |
| (rounded down) of features to remove at each iteration. |
| Note that the last iteration may remove fewer than ``step`` features in |
| order to reach ``min_features_to_select``. |
| |
| min_features_to_select : int, default=1 |
| The minimum number of features to be selected. This number of features |
| will always be scored, even if the difference between the original |
| feature count and ``min_features_to_select`` isn't divisible by |
| ``step``. |
| |
| .. versionadded:: 0.20 |
| |
| cv : int, cross-validation generator or an iterable, default=None |
| Determines the cross-validation splitting strategy. |
| Possible inputs for cv are: |
| |
| - None, to use the default 5-fold cross-validation, |
| - integer, to specify the number of folds. |
| - :term:`CV splitter`, |
| - An iterable yielding (train, test) splits as arrays of indices. |
| |
| For integer/None inputs, if ``y`` is binary or multiclass, |
| :class:`~sklearn.model_selection.StratifiedKFold` is used. If the |
| estimator is not a classifier or if ``y`` is neither binary nor multiclass, |
| :class:`~sklearn.model_selection.KFold` is used. |
| |
| Refer :ref:`User Guide <cross_validation>` for the various |
| cross-validation strategies that can be used here. |
| |
| .. versionchanged:: 0.22 |
| ``cv`` default value of None changed from 3-fold to 5-fold. |
| |
| scoring : str, callable or None, default=None |
| A string (see :ref:`scoring_parameter`) or |
| a scorer callable object / function with signature |
| ``scorer(estimator, X, y)``. |
| |
| verbose : int, default=0 |
| Controls verbosity of output. |
| |
| n_jobs : int or None, default=None |
| Number of cores to run in parallel while fitting across folds. |
| ``None`` means 1 unless in a :obj:`joblib.parallel_backend` context. |
| ``-1`` means using all processors. See :term:`Glossary <n_jobs>` |
| for more details. |
| |
| .. versionadded:: 0.18 |
| |
| importance_getter : str or callable, default='auto' |
| If 'auto', uses the feature importance either through a `coef_` |
| or `feature_importances_` attributes of estimator. |
| |
| Also accepts a string that specifies an attribute name/path |
| for extracting feature importance. |
| For example, give `regressor_.coef_` in case of |
| :class:`~sklearn.compose.TransformedTargetRegressor` or |
| `named_steps.clf.feature_importances_` in case of |
| :class:`~sklearn.pipeline.Pipeline` with its last step named `clf`. |
| |
| If `callable`, overrides the default feature importance getter. |
| The callable is passed with the fitted estimator and it should |
| return importance for each feature. |
| |
| .. versionadded:: 0.24 |
| |
| Attributes |
| ---------- |
| classes_ : ndarray of shape (n_classes,) |
| The classes labels. Only available when `estimator` is a classifier. |
| |
| estimator_ : ``Estimator`` instance |
| The fitted estimator used to select features. |
| |
| cv_results_ : dict of ndarrays |
| All arrays (values of the dictionary) are sorted in ascending order |
| by the number of features used (i.e., the first element of the array |
| represents the models that used the least number of features, while the |
| last element represents the models that used all available features). |
| |
| .. versionadded:: 1.0 |
| |
| This dictionary contains the following keys: |
| |
| split(k)_test_score : ndarray of shape (n_subsets_of_features,) |
| The cross-validation scores across (k)th fold. |
| |
| mean_test_score : ndarray of shape (n_subsets_of_features,) |
| Mean of scores over the folds. |
| |
| std_test_score : ndarray of shape (n_subsets_of_features,) |
| Standard deviation of scores over the folds. |
| |
| n_features : ndarray of shape (n_subsets_of_features,) |
| Number of features used at each step. |
| |
| .. versionadded:: 1.5 |
| |
| n_features_ : int |
| The number of selected features with cross-validation. |
| |
| n_features_in_ : int |
| Number of features seen during :term:`fit`. Only defined if the |
| underlying estimator exposes such an attribute when fit. |
| |
| .. versionadded:: 0.24 |
| |
| feature_names_in_ : ndarray of shape (`n_features_in_`,) |
| Names of features seen during :term:`fit`. Defined only when `X` |
| has feature names that are all strings. |
| |
| .. versionadded:: 1.0 |
| |
| ranking_ : narray of shape (n_features,) |
| The feature ranking, such that `ranking_[i]` |
| corresponds to the ranking |
| position of the i-th feature. |
| Selected (i.e., estimated best) |
| features are assigned rank 1. |
| |
| support_ : ndarray of shape (n_features,) |
| The mask of selected features. |
| |
| See Also |
| -------- |
| RFE : Recursive feature elimination. |
| |
| Notes |
| ----- |
| The size of all values in ``cv_results_`` is equal to |
| ``ceil((n_features - min_features_to_select) / step) + 1``, |
| where step is the number of features removed at each iteration. |
| |
| Allows NaN/Inf in the input if the underlying estimator does as well. |
| |
| References |
| ---------- |
| |
| .. [1] Guyon, I., Weston, J., Barnhill, S., & Vapnik, V., "Gene selection |
| for cancer classification using support vector machines", |
| Mach. Learn., 46(1-3), 389--422, 2002. |
| |
| Examples |
| -------- |
| The following example shows how to retrieve the a-priori not known 5 |
| informative features in the Friedman #1 dataset. |
| |
| >>> from sklearn.datasets import make_friedman1 |
| >>> from sklearn.feature_selection import RFECV |
| >>> from sklearn.svm import SVR |
| >>> X, y = make_friedman1(n_samples=50, n_features=10, random_state=0) |
| >>> estimator = SVR(kernel="linear") |
| >>> selector = RFECV(estimator, step=1, cv=5) |
| >>> selector = selector.fit(X, y) |
| >>> selector.support_ |
| array([ True, True, True, True, True, False, False, False, False, |
| False]) |
| >>> selector.ranking_ |
| array([1, 1, 1, 1, 1, 6, 4, 3, 2, 5]) |
| """ |
|
|
| _parameter_constraints: dict = { |
| **RFE._parameter_constraints, |
| "min_features_to_select": [Interval(Integral, 0, None, closed="neither")], |
| "cv": ["cv_object"], |
| "scoring": [None, str, callable], |
| "n_jobs": [None, Integral], |
| } |
| _parameter_constraints.pop("n_features_to_select") |
| __metadata_request__fit = {"groups": metadata_routing.UNUSED} |
|
|
| def __init__( |
| self, |
| estimator, |
| *, |
| step=1, |
| min_features_to_select=1, |
| cv=None, |
| scoring=None, |
| verbose=0, |
| n_jobs=None, |
| importance_getter="auto", |
| ): |
| self.estimator = estimator |
| self.step = step |
| self.importance_getter = importance_getter |
| self.cv = cv |
| self.scoring = scoring |
| self.verbose = verbose |
| self.n_jobs = n_jobs |
| self.min_features_to_select = min_features_to_select |
|
|
| |
| @_deprecate_positional_args(version="1.8") |
| @_fit_context( |
| |
| prefer_skip_nested_validation=False |
| ) |
| def fit(self, X, y, *, groups=None, **params): |
| """Fit the RFE model and automatically tune the number of selected features. |
| |
| Parameters |
| ---------- |
| X : {array-like, sparse matrix} of shape (n_samples, n_features) |
| Training vector, where `n_samples` is the number of samples and |
| `n_features` is the total number of features. |
| |
| y : array-like of shape (n_samples,) |
| Target values (integers for classification, real numbers for |
| regression). |
| |
| groups : array-like of shape (n_samples,) or None, default=None |
| Group labels for the samples used while splitting the dataset into |
| train/test set. Only used in conjunction with a "Group" :term:`cv` |
| instance (e.g., :class:`~sklearn.model_selection.GroupKFold`). |
| |
| .. versionadded:: 0.20 |
| |
| **params : dict of str -> object |
| Parameters passed to the ``fit`` method of the estimator, |
| the scorer, and the CV splitter. |
| |
| .. versionadded:: 1.6 |
| Only available if `enable_metadata_routing=True`, |
| which can be set by using |
| ``sklearn.set_config(enable_metadata_routing=True)``. |
| See :ref:`Metadata Routing User Guide <metadata_routing>` |
| for more details. |
| |
| Returns |
| ------- |
| self : object |
| Fitted estimator. |
| """ |
| _raise_for_params(params, self, "fit") |
| X, y = validate_data( |
| self, |
| X, |
| y, |
| accept_sparse="csr", |
| ensure_min_features=2, |
| ensure_all_finite=False, |
| multi_output=True, |
| ) |
|
|
| if _routing_enabled(): |
| if groups is not None: |
| params.update({"groups": groups}) |
| routed_params = process_routing(self, "fit", **params) |
| else: |
| routed_params = Bunch( |
| estimator=Bunch(fit={}), |
| splitter=Bunch(split={"groups": groups}), |
| scorer=Bunch(score={}), |
| ) |
|
|
| |
| cv = check_cv(self.cv, y, classifier=is_classifier(self.estimator)) |
| scorer = self._get_scorer() |
|
|
| |
| |
| n_features = X.shape[1] |
| if self.min_features_to_select > n_features: |
| warnings.warn( |
| ( |
| f"Found min_features_to_select={self.min_features_to_select} > " |
| f"{n_features=}. There will be no feature selection and all " |
| "features will be kept." |
| ), |
| UserWarning, |
| ) |
| rfe = RFE( |
| estimator=self.estimator, |
| n_features_to_select=min(self.min_features_to_select, n_features), |
| importance_getter=self.importance_getter, |
| step=self.step, |
| verbose=self.verbose, |
| ) |
|
|
| |
| |
| |
|
|
| |
| |
| |
| |
| |
| |
| |
|
|
| if effective_n_jobs(self.n_jobs) == 1: |
| parallel, func = list, _rfe_single_fit |
| else: |
| parallel = Parallel(n_jobs=self.n_jobs) |
| func = delayed(_rfe_single_fit) |
|
|
| scores_features = parallel( |
| func(clone(rfe), self.estimator, X, y, train, test, scorer, routed_params) |
| for train, test in cv.split(X, y, **routed_params.splitter.split) |
| ) |
| scores, step_n_features = zip(*scores_features) |
|
|
| step_n_features_rev = np.array(step_n_features[0])[::-1] |
| scores = np.array(scores) |
|
|
| |
| scores_sum_rev = np.sum(scores, axis=0)[::-1] |
| n_features_to_select = step_n_features_rev[np.argmax(scores_sum_rev)] |
|
|
| |
| rfe = RFE( |
| estimator=self.estimator, |
| n_features_to_select=n_features_to_select, |
| step=self.step, |
| importance_getter=self.importance_getter, |
| verbose=self.verbose, |
| ) |
|
|
| rfe.fit(X, y, **routed_params.estimator.fit) |
|
|
| |
| self.support_ = rfe.support_ |
| self.n_features_ = rfe.n_features_ |
| self.ranking_ = rfe.ranking_ |
| self.estimator_ = clone(self.estimator) |
| self.estimator_.fit(self._transform(X), y, **routed_params.estimator.fit) |
|
|
| |
| scores_rev = scores[:, ::-1] |
| self.cv_results_ = { |
| "mean_test_score": np.mean(scores_rev, axis=0), |
| "std_test_score": np.std(scores_rev, axis=0), |
| **{f"split{i}_test_score": scores_rev[i] for i in range(scores.shape[0])}, |
| "n_features": step_n_features_rev, |
| } |
| return self |
|
|
| def score(self, X, y, **score_params): |
| """Score using the `scoring` option on the given test data and labels. |
| |
| Parameters |
| ---------- |
| X : array-like of shape (n_samples, n_features) |
| Test samples. |
| |
| y : array-like of shape (n_samples,) |
| True labels for X. |
| |
| **score_params : dict |
| Parameters to pass to the `score` method of the underlying scorer. |
| |
| .. versionadded:: 1.6 |
| Only available if `enable_metadata_routing=True`, |
| which can be set by using |
| ``sklearn.set_config(enable_metadata_routing=True)``. |
| See :ref:`Metadata Routing User Guide <metadata_routing>` |
| for more details. |
| |
| Returns |
| ------- |
| score : float |
| Score of self.predict(X) w.r.t. y defined by `scoring`. |
| """ |
| _raise_for_params(score_params, self, "score") |
| scoring = self._get_scorer() |
| if _routing_enabled(): |
| routed_params = process_routing(self, "score", **score_params) |
| else: |
| routed_params = Bunch() |
| routed_params.scorer = Bunch(score={}) |
|
|
| return scoring(self, X, y, **routed_params.scorer.score) |
|
|
| def get_metadata_routing(self): |
| """Get metadata routing of this object. |
| |
| Please check :ref:`User Guide <metadata_routing>` on how the routing |
| mechanism works. |
| |
| .. versionadded:: 1.6 |
| |
| Returns |
| ------- |
| routing : MetadataRouter |
| A :class:`~sklearn.utils.metadata_routing.MetadataRouter` encapsulating |
| routing information. |
| """ |
| router = MetadataRouter(owner=self.__class__.__name__) |
| router.add( |
| estimator=self.estimator, |
| method_mapping=MethodMapping().add(caller="fit", callee="fit"), |
| ) |
| router.add( |
| splitter=check_cv(self.cv), |
| method_mapping=MethodMapping().add( |
| caller="fit", |
| callee="split", |
| ), |
| ) |
| router.add( |
| scorer=self._get_scorer(), |
| method_mapping=MethodMapping() |
| .add(caller="fit", callee="score") |
| .add(caller="score", callee="score"), |
| ) |
|
|
| return router |
|
|
| def _get_scorer(self): |
| if self.scoring is None: |
| scoring = "accuracy" if is_classifier(self.estimator) else "r2" |
| else: |
| scoring = self.scoring |
| return get_scorer(scoring) |
|
|