Source code for eli5.permutation_importance

A module for computing feature importances by measuring how score decreases
when a feature is not available. It contains basic building blocks;
there is a full-featured sklearn-compatible implementation
in :class:`~.PermutationImportance`.

A similar method is described in Breiman, "Random Forests", Machine Learning,
45(1), 5-32, 2001 (available online at, with an
application to random forests. It is known in literature as
"Mean Decrease Accuracy (MDA)" or "permutation importance".
from __future__ import absolute_import
from typing import Tuple, List, Callable, Any

import numpy as np
from sklearn.utils import check_random_state

[docs]def iter_shuffled(X, columns_to_shuffle=None, pre_shuffle=False, random_state=None): """ Return an iterator of X matrices which have one or more columns shuffled. After each iteration yielded matrix is mutated inplace, so if you want to use multiple of them at the same time, make copies. ``columns_to_shuffle`` is a sequence of column numbers to shuffle. By default, all columns are shuffled once, i.e. columns_to_shuffle is ``range(X.shape[1])``. If ``pre_shuffle`` is True, a copy of ``X`` is shuffled once, and then result takes shuffled columns from this copy. If it is False, columns are shuffled on fly. ``pre_shuffle = True`` can be faster if there is a lot of columns, or if columns are used multiple times. """ rng = check_random_state(random_state) if columns_to_shuffle is None: columns_to_shuffle = range(X.shape[1]) if pre_shuffle: X_shuffled = X.copy() rng.shuffle(X_shuffled) X_res = X.copy() for columns in columns_to_shuffle: if pre_shuffle: X_res[:, columns] = X_shuffled[:, columns] else: rng.shuffle(X_res[:, columns]) yield X_res X_res[:, columns] = X[:, columns]
[docs]def get_score_importances( score_func, # type: Callable[[Any, Any], float] X, y, n_iter=5, # type: int columns_to_shuffle=None, random_state=None ): # type: (...) -> Tuple[float, List[np.ndarray]] """ Return ``(base_score, score_decreases)`` tuple with the base score and score decreases when a feature is not available. ``base_score`` is ``score_func(X, y)``; ``score_decreases`` is a list of length ``n_iter`` with feature importance arrays (each array is of shape ``n_features``); feature importances are computed as score decrease when a feature is not available. ``n_iter`` iterations of the basic algorithm is done, each iteration starting from a different random seed. If you just want feature importances, you can take a mean of the result:: import numpy as np from eli5.permutation_importance import get_score_importances base_score, score_decreases = get_score_importances(score_func, X, y) feature_importances = np.mean(score_decreases, axis=0) """ rng = check_random_state(random_state) base_score = score_func(X, y) scores_decreases = [] for i in range(n_iter): scores_shuffled = _get_scores_shufled( score_func, X, y, columns_to_shuffle=columns_to_shuffle, random_state=rng ) scores_decreases.append(-scores_shuffled + base_score) return base_score, scores_decreases
def _get_scores_shufled(score_func, X, y, columns_to_shuffle=None, random_state=None): Xs = iter_shuffled(X, columns_to_shuffle, random_state=random_state) return np.array([score_func(X_shuffled, y) for X_shuffled in Xs])