523 lines
18 KiB
Python
523 lines
18 KiB
Python
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# Authors: Gilles Louppe, Mathieu Blondel, Maheshakya Wijewardena
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# License: BSD 3 clause
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from copy import deepcopy
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from numbers import Integral, Real
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import numpy as np
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from ..base import BaseEstimator, MetaEstimatorMixin, _fit_context, clone
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from ..exceptions import NotFittedError
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from ..utils._param_validation import HasMethods, Interval, Options
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from ..utils._tags import _safe_tags
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from ..utils.metadata_routing import (
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MetadataRouter,
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MethodMapping,
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_routing_enabled,
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process_routing,
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)
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from ..utils.metaestimators import available_if
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from ..utils.validation import _num_features, check_is_fitted, check_scalar
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from ._base import SelectorMixin, _get_feature_importances
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def _calculate_threshold(estimator, importances, threshold):
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"""Interpret the threshold value"""
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if threshold is None:
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# determine default from estimator
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est_name = estimator.__class__.__name__
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is_l1_penalized = hasattr(estimator, "penalty") and estimator.penalty == "l1"
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is_lasso = "Lasso" in est_name
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is_elasticnet_l1_penalized = "ElasticNet" in est_name and (
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(hasattr(estimator, "l1_ratio_") and np.isclose(estimator.l1_ratio_, 1.0))
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or (hasattr(estimator, "l1_ratio") and np.isclose(estimator.l1_ratio, 1.0))
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)
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if is_l1_penalized or is_lasso or is_elasticnet_l1_penalized:
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# the natural default threshold is 0 when l1 penalty was used
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threshold = 1e-5
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else:
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threshold = "mean"
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if isinstance(threshold, str):
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if "*" in threshold:
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scale, reference = threshold.split("*")
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scale = float(scale.strip())
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reference = reference.strip()
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if reference == "median":
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reference = np.median(importances)
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elif reference == "mean":
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reference = np.mean(importances)
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else:
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raise ValueError("Unknown reference: " + reference)
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threshold = scale * reference
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elif threshold == "median":
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threshold = np.median(importances)
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elif threshold == "mean":
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threshold = np.mean(importances)
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else:
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raise ValueError(
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"Expected threshold='mean' or threshold='median' got %s" % threshold
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)
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else:
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threshold = float(threshold)
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return threshold
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def _estimator_has(attr):
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"""Check if we can delegate a method to the underlying estimator.
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First, we check the fitted `estimator_` if available, otherwise we check the
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unfitted `estimator`. We raise the original `AttributeError` if `attr` does
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not exist. This function is used together with `available_if`.
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"""
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def check(self):
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if hasattr(self, "estimator_"):
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getattr(self.estimator_, attr)
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else:
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getattr(self.estimator, attr)
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return True
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return check
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class SelectFromModel(MetaEstimatorMixin, SelectorMixin, BaseEstimator):
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"""Meta-transformer for selecting features based on importance weights.
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.. versionadded:: 0.17
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Read more in the :ref:`User Guide <select_from_model>`.
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Parameters
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----------
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estimator : object
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The base estimator from which the transformer is built.
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This can be both a fitted (if ``prefit`` is set to True)
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or a non-fitted estimator. The estimator should have a
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``feature_importances_`` or ``coef_`` attribute after fitting.
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Otherwise, the ``importance_getter`` parameter should be used.
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threshold : str or float, default=None
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The threshold value to use for feature selection. Features whose
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absolute importance value is greater or equal are kept while the others
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are discarded. If "median" (resp. "mean"), then the ``threshold`` value
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is the median (resp. the mean) of the feature importances. A scaling
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factor (e.g., "1.25*mean") may also be used. If None and if the
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estimator has a parameter penalty set to l1, either explicitly
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or implicitly (e.g, Lasso), the threshold used is 1e-5.
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Otherwise, "mean" is used by default.
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prefit : bool, default=False
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Whether a prefit model is expected to be passed into the constructor
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directly or not.
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If `True`, `estimator` must be a fitted estimator.
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If `False`, `estimator` is fitted and updated by calling
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`fit` and `partial_fit`, respectively.
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norm_order : non-zero int, inf, -inf, default=1
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Order of the norm used to filter the vectors of coefficients below
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``threshold`` in the case where the ``coef_`` attribute of the
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estimator is of dimension 2.
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max_features : int, callable, default=None
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The maximum number of features to select.
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- If an integer, then it specifies the maximum number of features to
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allow.
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- If a callable, then it specifies how to calculate the maximum number of
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features allowed by using the output of `max_features(X)`.
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- If `None`, then all features are kept.
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To only select based on ``max_features``, set ``threshold=-np.inf``.
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.. versionadded:: 0.20
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.. versionchanged:: 1.1
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`max_features` accepts a callable.
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importance_getter : str or callable, default='auto'
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If 'auto', uses the feature importance either through a ``coef_``
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attribute or ``feature_importances_`` attribute of estimator.
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Also accepts a string that specifies an attribute name/path
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for extracting feature importance (implemented with `attrgetter`).
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For example, give `regressor_.coef_` in case of
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:class:`~sklearn.compose.TransformedTargetRegressor` or
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`named_steps.clf.feature_importances_` in case of
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:class:`~sklearn.pipeline.Pipeline` with its last step named `clf`.
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If `callable`, overrides the default feature importance getter.
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The callable is passed with the fitted estimator and it should
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return importance for each feature.
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.. versionadded:: 0.24
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Attributes
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----------
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estimator_ : estimator
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The base estimator from which the transformer is built. This attribute
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exist only when `fit` has been called.
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- If `prefit=True`, it is a deep copy of `estimator`.
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- If `prefit=False`, it is a clone of `estimator` and fit on the data
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passed to `fit` or `partial_fit`.
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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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max_features_ : int
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Maximum number of features calculated during :term:`fit`. Only defined
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if the ``max_features`` is not `None`.
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- If `max_features` is an `int`, then `max_features_ = max_features`.
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- If `max_features` is a callable, then `max_features_ = max_features(X)`.
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.. versionadded:: 1.1
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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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threshold_ : float
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The threshold value used for feature selection.
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See Also
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--------
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RFE : Recursive feature elimination based on importance weights.
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RFECV : Recursive feature elimination with built-in cross-validated
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selection of the best number of features.
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SequentialFeatureSelector : Sequential cross-validation based feature
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selection. Does not rely on importance weights.
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Notes
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-----
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Allows NaN/Inf in the input if the underlying estimator does as well.
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Examples
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--------
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>>> from sklearn.feature_selection import SelectFromModel
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>>> from sklearn.linear_model import LogisticRegression
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>>> X = [[ 0.87, -1.34, 0.31 ],
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... [-2.79, -0.02, -0.85 ],
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... [-1.34, -0.48, -2.55 ],
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... [ 1.92, 1.48, 0.65 ]]
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>>> y = [0, 1, 0, 1]
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>>> selector = SelectFromModel(estimator=LogisticRegression()).fit(X, y)
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>>> selector.estimator_.coef_
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array([[-0.3252..., 0.8345..., 0.4976...]])
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>>> selector.threshold_
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0.55249...
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>>> selector.get_support()
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array([False, True, False])
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>>> selector.transform(X)
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array([[-1.34],
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[-0.02],
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[-0.48],
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[ 1.48]])
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Using a callable to create a selector that can use no more than half
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of the input features.
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>>> def half_callable(X):
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... return round(len(X[0]) / 2)
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>>> half_selector = SelectFromModel(estimator=LogisticRegression(),
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... max_features=half_callable)
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>>> _ = half_selector.fit(X, y)
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>>> half_selector.max_features_
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2
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"""
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_parameter_constraints: dict = {
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"estimator": [HasMethods("fit")],
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"threshold": [Interval(Real, None, None, closed="both"), str, None],
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"prefit": ["boolean"],
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"norm_order": [
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Interval(Integral, None, -1, closed="right"),
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Interval(Integral, 1, None, closed="left"),
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Options(Real, {np.inf, -np.inf}),
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],
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"max_features": [Interval(Integral, 0, None, closed="left"), callable, None],
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"importance_getter": [str, callable],
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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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threshold=None,
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prefit=False,
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norm_order=1,
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max_features=None,
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importance_getter="auto",
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):
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self.estimator = estimator
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self.threshold = threshold
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self.prefit = prefit
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self.importance_getter = importance_getter
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self.norm_order = norm_order
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self.max_features = max_features
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def _get_support_mask(self):
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estimator = getattr(self, "estimator_", self.estimator)
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max_features = getattr(self, "max_features_", self.max_features)
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if self.prefit:
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try:
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check_is_fitted(self.estimator)
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except NotFittedError as exc:
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raise NotFittedError(
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"When `prefit=True`, `estimator` is expected to be a fitted "
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"estimator."
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) from exc
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if callable(max_features):
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# This branch is executed when `transform` is called directly and thus
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# `max_features_` is not set and we fallback using `self.max_features`
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# that is not validated
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raise NotFittedError(
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"When `prefit=True` and `max_features` is a callable, call `fit` "
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"before calling `transform`."
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)
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elif max_features is not None and not isinstance(max_features, Integral):
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raise ValueError(
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f"`max_features` must be an integer. Got `max_features={max_features}` "
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"instead."
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)
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scores = _get_feature_importances(
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estimator=estimator,
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getter=self.importance_getter,
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transform_func="norm",
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norm_order=self.norm_order,
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)
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threshold = _calculate_threshold(estimator, scores, self.threshold)
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if self.max_features is not None:
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mask = np.zeros_like(scores, dtype=bool)
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candidate_indices = np.argsort(-scores, kind="mergesort")[:max_features]
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mask[candidate_indices] = True
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else:
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mask = np.ones_like(scores, dtype=bool)
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mask[scores < threshold] = False
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return mask
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def _check_max_features(self, X):
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if self.max_features is not None:
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n_features = _num_features(X)
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if callable(self.max_features):
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max_features = self.max_features(X)
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else: # int
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max_features = self.max_features
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check_scalar(
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max_features,
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"max_features",
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Integral,
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min_val=0,
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max_val=n_features,
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)
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self.max_features_ = max_features
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@_fit_context(
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# SelectFromModel.estimator is not validated yet
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prefer_skip_nested_validation=False
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)
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def fit(self, X, y=None, **fit_params):
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"""Fit the SelectFromModel meta-transformer.
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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 training input samples.
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y : array-like of shape (n_samples,), default=None
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The target values (integers that correspond to classes in
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classification, real numbers in regression).
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**fit_params : dict
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- If `enable_metadata_routing=False` (default):
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Parameters directly passed to the `fit` method of the
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sub-estimator. They are ignored if `prefit=True`.
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- If `enable_metadata_routing=True`:
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Parameters safely routed to the `fit` method of the
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sub-estimator. They are ignored if `prefit=True`.
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.. versionchanged:: 1.4
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See :ref:`Metadata Routing User Guide <metadata_routing>` for
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more details.
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Returns
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-------
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self : object
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Fitted estimator.
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"""
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self._check_max_features(X)
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if self.prefit:
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try:
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check_is_fitted(self.estimator)
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except NotFittedError as exc:
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raise NotFittedError(
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"When `prefit=True`, `estimator` is expected to be a fitted "
|
||
|
|
"estimator."
|
||
|
|
) from exc
|
||
|
|
self.estimator_ = deepcopy(self.estimator)
|
||
|
|
else:
|
||
|
|
if _routing_enabled():
|
||
|
|
routed_params = process_routing(self, "fit", **fit_params)
|
||
|
|
self.estimator_ = clone(self.estimator)
|
||
|
|
self.estimator_.fit(X, y, **routed_params.estimator.fit)
|
||
|
|
else:
|
||
|
|
# TODO(SLEP6): remove when metadata routing cannot be disabled.
|
||
|
|
self.estimator_ = clone(self.estimator)
|
||
|
|
self.estimator_.fit(X, y, **fit_params)
|
||
|
|
|
||
|
|
if hasattr(self.estimator_, "feature_names_in_"):
|
||
|
|
self.feature_names_in_ = self.estimator_.feature_names_in_
|
||
|
|
else:
|
||
|
|
self._check_feature_names(X, reset=True)
|
||
|
|
|
||
|
|
return self
|
||
|
|
|
||
|
|
@property
|
||
|
|
def threshold_(self):
|
||
|
|
"""Threshold value used for feature selection."""
|
||
|
|
scores = _get_feature_importances(
|
||
|
|
estimator=self.estimator_,
|
||
|
|
getter=self.importance_getter,
|
||
|
|
transform_func="norm",
|
||
|
|
norm_order=self.norm_order,
|
||
|
|
)
|
||
|
|
return _calculate_threshold(self.estimator, scores, self.threshold)
|
||
|
|
|
||
|
|
@available_if(_estimator_has("partial_fit"))
|
||
|
|
@_fit_context(
|
||
|
|
# SelectFromModel.estimator is not validated yet
|
||
|
|
prefer_skip_nested_validation=False
|
||
|
|
)
|
||
|
|
def partial_fit(self, X, y=None, **partial_fit_params):
|
||
|
|
"""Fit the SelectFromModel meta-transformer only once.
|
||
|
|
|
||
|
|
Parameters
|
||
|
|
----------
|
||
|
|
X : array-like of shape (n_samples, n_features)
|
||
|
|
The training input samples.
|
||
|
|
|
||
|
|
y : array-like of shape (n_samples,), default=None
|
||
|
|
The target values (integers that correspond to classes in
|
||
|
|
classification, real numbers in regression).
|
||
|
|
|
||
|
|
**partial_fit_params : dict
|
||
|
|
- If `enable_metadata_routing=False` (default):
|
||
|
|
|
||
|
|
Parameters directly passed to the `partial_fit` method of the
|
||
|
|
sub-estimator.
|
||
|
|
|
||
|
|
- If `enable_metadata_routing=True`:
|
||
|
|
|
||
|
|
Parameters passed to the `partial_fit` method of the
|
||
|
|
sub-estimator. They are ignored if `prefit=True`.
|
||
|
|
|
||
|
|
.. versionchanged:: 1.4
|
||
|
|
`**partial_fit_params` are routed to the sub-estimator, if
|
||
|
|
`enable_metadata_routing=True` is set via
|
||
|
|
:func:`~sklearn.set_config`, which allows for aliasing.
|
||
|
|
|
||
|
|
See :ref:`Metadata Routing User Guide <metadata_routing>` for
|
||
|
|
more details.
|
||
|
|
|
||
|
|
Returns
|
||
|
|
-------
|
||
|
|
self : object
|
||
|
|
Fitted estimator.
|
||
|
|
"""
|
||
|
|
first_call = not hasattr(self, "estimator_")
|
||
|
|
|
||
|
|
if first_call:
|
||
|
|
self._check_max_features(X)
|
||
|
|
|
||
|
|
if self.prefit:
|
||
|
|
if first_call:
|
||
|
|
try:
|
||
|
|
check_is_fitted(self.estimator)
|
||
|
|
except NotFittedError as exc:
|
||
|
|
raise NotFittedError(
|
||
|
|
"When `prefit=True`, `estimator` is expected to be a fitted "
|
||
|
|
"estimator."
|
||
|
|
) from exc
|
||
|
|
self.estimator_ = deepcopy(self.estimator)
|
||
|
|
return self
|
||
|
|
|
||
|
|
if first_call:
|
||
|
|
self.estimator_ = clone(self.estimator)
|
||
|
|
if _routing_enabled():
|
||
|
|
routed_params = process_routing(self, "partial_fit", **partial_fit_params)
|
||
|
|
self.estimator_ = clone(self.estimator)
|
||
|
|
self.estimator_.partial_fit(X, y, **routed_params.estimator.partial_fit)
|
||
|
|
else:
|
||
|
|
# TODO(SLEP6): remove when metadata routing cannot be disabled.
|
||
|
|
self.estimator_.partial_fit(X, y, **partial_fit_params)
|
||
|
|
|
||
|
|
if hasattr(self.estimator_, "feature_names_in_"):
|
||
|
|
self.feature_names_in_ = self.estimator_.feature_names_in_
|
||
|
|
else:
|
||
|
|
self._check_feature_names(X, reset=first_call)
|
||
|
|
|
||
|
|
return self
|
||
|
|
|
||
|
|
@property
|
||
|
|
def n_features_in_(self):
|
||
|
|
"""Number of features seen during `fit`."""
|
||
|
|
# For consistency with other estimators we raise a AttributeError so
|
||
|
|
# that hasattr() fails if the estimator isn't fitted.
|
||
|
|
try:
|
||
|
|
check_is_fitted(self)
|
||
|
|
except NotFittedError as nfe:
|
||
|
|
raise AttributeError(
|
||
|
|
"{} object has no n_features_in_ attribute.".format(
|
||
|
|
self.__class__.__name__
|
||
|
|
)
|
||
|
|
) from nfe
|
||
|
|
|
||
|
|
return self.estimator_.n_features_in_
|
||
|
|
|
||
|
|
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:: 1.4
|
||
|
|
|
||
|
|
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="partial_fit", callee="partial_fit")
|
||
|
|
.add(caller="fit", callee="fit"),
|
||
|
|
)
|
||
|
|
return router
|
||
|
|
|
||
|
|
def _more_tags(self):
|
||
|
|
return {"allow_nan": _safe_tags(self.estimator, key="allow_nan")}
|