721 lines
27 KiB
Python
721 lines
27 KiB
Python
"""
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Testing for the partial dependence module.
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"""
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import numpy as np
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import pytest
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import sklearn
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from sklearn.inspection import partial_dependence
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from sklearn.inspection._partial_dependence import (
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_grid_from_X,
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_partial_dependence_brute,
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_partial_dependence_recursion
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)
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from sklearn.ensemble import GradientBoostingClassifier
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from sklearn.ensemble import GradientBoostingRegressor
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from sklearn.ensemble import RandomForestRegressor
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from sklearn.experimental import enable_hist_gradient_boosting # noqa
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from sklearn.ensemble import HistGradientBoostingClassifier
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from sklearn.ensemble import HistGradientBoostingRegressor
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from sklearn.linear_model import LinearRegression
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from sklearn.linear_model import LogisticRegression
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from sklearn.linear_model import MultiTaskLasso
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from sklearn.tree import DecisionTreeRegressor
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from sklearn.datasets import load_iris
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from sklearn.datasets import make_classification, make_regression
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from sklearn.cluster import KMeans
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from sklearn.compose import make_column_transformer
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from sklearn.metrics import r2_score
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from sklearn.preprocessing import PolynomialFeatures
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from sklearn.preprocessing import StandardScaler
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from sklearn.preprocessing import RobustScaler
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from sklearn.preprocessing import scale
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from sklearn.pipeline import make_pipeline
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from sklearn.dummy import DummyClassifier
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from sklearn.base import BaseEstimator, ClassifierMixin, clone
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from sklearn.exceptions import NotFittedError
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from sklearn.utils._testing import assert_allclose
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from sklearn.utils._testing import assert_array_equal
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from sklearn.utils import _IS_32BIT
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from sklearn.utils.validation import check_random_state
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from sklearn.tree.tests.test_tree import assert_is_subtree
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# toy sample
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X = [[-2, -1], [-1, -1], [-1, -2], [1, 1], [1, 2], [2, 1]]
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y = [-1, -1, -1, 1, 1, 1]
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# (X, y), n_targets <-- as expected in the output of partial_dep()
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binary_classification_data = (make_classification(n_samples=50,
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random_state=0), 1)
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multiclass_classification_data = (make_classification(n_samples=50,
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n_classes=3,
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n_clusters_per_class=1,
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random_state=0), 3)
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regression_data = (make_regression(n_samples=50, random_state=0), 1)
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multioutput_regression_data = (make_regression(n_samples=50, n_targets=2,
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random_state=0), 2)
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# iris
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iris = load_iris()
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@pytest.mark.filterwarnings("ignore:A Bunch will be returned")
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@pytest.mark.parametrize('Estimator, method, data', [
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(GradientBoostingClassifier, 'auto', binary_classification_data),
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(GradientBoostingClassifier, 'auto', multiclass_classification_data),
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(GradientBoostingClassifier, 'brute', binary_classification_data),
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(GradientBoostingClassifier, 'brute', multiclass_classification_data),
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(GradientBoostingRegressor, 'auto', regression_data),
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(GradientBoostingRegressor, 'brute', regression_data),
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(DecisionTreeRegressor, 'brute', regression_data),
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(LinearRegression, 'brute', regression_data),
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(LinearRegression, 'brute', multioutput_regression_data),
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(LogisticRegression, 'brute', binary_classification_data),
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(LogisticRegression, 'brute', multiclass_classification_data),
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(MultiTaskLasso, 'brute', multioutput_regression_data),
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])
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@pytest.mark.parametrize('grid_resolution', (5, 10))
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@pytest.mark.parametrize('features', ([1], [1, 2]))
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@pytest.mark.parametrize('kind', ('legacy', 'average', 'individual', 'both'))
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def test_output_shape(Estimator, method, data, grid_resolution,
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features, kind):
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# Check that partial_dependence has consistent output shape for different
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# kinds of estimators:
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# - classifiers with binary and multiclass settings
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# - regressors
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# - multi-task regressors
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est = Estimator()
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# n_target corresponds to the number of classes (1 for binary classif) or
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# the number of tasks / outputs in multi task settings. It's equal to 1 for
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# classical regression_data.
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(X, y), n_targets = data
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n_instances = X.shape[0]
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est.fit(X, y)
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result = partial_dependence(
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est, X=X, features=features, method=method, kind=kind,
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grid_resolution=grid_resolution
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)
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# FIXME: Remove 'legacy' support in 1.1
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pdp, axes = result if kind == 'legacy' else (result, result["values"])
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expected_pdp_shape = (n_targets,
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*[grid_resolution for _ in range(len(features))])
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expected_ice_shape = (n_targets, n_instances,
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*[grid_resolution for _ in range(len(features))])
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if kind == 'legacy':
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assert pdp.shape == expected_pdp_shape
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elif kind == 'average':
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assert pdp.average.shape == expected_pdp_shape
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elif kind == 'individual':
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assert pdp.individual.shape == expected_ice_shape
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else: # 'both'
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assert pdp.average.shape == expected_pdp_shape
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assert pdp.individual.shape == expected_ice_shape
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expected_axes_shape = (len(features), grid_resolution)
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assert axes is not None
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assert np.asarray(axes).shape == expected_axes_shape
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def test_grid_from_X():
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# tests for _grid_from_X: sanity check for output, and for shapes.
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# Make sure that the grid is a cartesian product of the input (it will use
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# the unique values instead of the percentiles)
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percentiles = (.05, .95)
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grid_resolution = 100
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X = np.asarray([[1, 2],
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[3, 4]])
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grid, axes = _grid_from_X(X, percentiles, grid_resolution)
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assert_array_equal(grid, [[1, 2],
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[1, 4],
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[3, 2],
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[3, 4]])
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assert_array_equal(axes, X.T)
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# test shapes of returned objects depending on the number of unique values
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# for a feature.
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rng = np.random.RandomState(0)
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grid_resolution = 15
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# n_unique_values > grid_resolution
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X = rng.normal(size=(20, 2))
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grid, axes = _grid_from_X(X, percentiles, grid_resolution=grid_resolution)
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assert grid.shape == (grid_resolution * grid_resolution, X.shape[1])
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assert np.asarray(axes).shape == (2, grid_resolution)
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# n_unique_values < grid_resolution, will use actual values
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n_unique_values = 12
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X[n_unique_values - 1:, 0] = 12345
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rng.shuffle(X) # just to make sure the order is irrelevant
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grid, axes = _grid_from_X(X, percentiles, grid_resolution=grid_resolution)
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assert grid.shape == (n_unique_values * grid_resolution, X.shape[1])
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# axes is a list of arrays of different shapes
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assert axes[0].shape == (n_unique_values,)
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assert axes[1].shape == (grid_resolution,)
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@pytest.mark.parametrize(
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"grid_resolution, percentiles, err_msg",
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[(2, (0, 0.0001), "percentiles are too close"),
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(100, (1, 2, 3, 4), "'percentiles' must be a sequence of 2 elements"),
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(100, 12345, "'percentiles' must be a sequence of 2 elements"),
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(100, (-1, .95), r"'percentiles' values must be in \[0, 1\]"),
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(100, (.05, 2), r"'percentiles' values must be in \[0, 1\]"),
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(100, (.9, .1), r"percentiles\[0\] must be strictly less than"),
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(1, (0.05, 0.95), "'grid_resolution' must be strictly greater than 1")]
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)
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def test_grid_from_X_error(grid_resolution, percentiles, err_msg):
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X = np.asarray([[1, 2], [3, 4]])
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with pytest.raises(ValueError, match=err_msg):
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_grid_from_X(
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X, grid_resolution=grid_resolution, percentiles=percentiles
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)
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@pytest.mark.parametrize('target_feature', range(5))
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@pytest.mark.parametrize('est, method', [
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(LinearRegression(), 'brute'),
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(GradientBoostingRegressor(random_state=0), 'brute'),
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(GradientBoostingRegressor(random_state=0), 'recursion'),
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(HistGradientBoostingRegressor(random_state=0), 'brute'),
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(HistGradientBoostingRegressor(random_state=0), 'recursion')]
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)
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def test_partial_dependence_helpers(est, method, target_feature):
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# Check that what is returned by _partial_dependence_brute or
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# _partial_dependence_recursion is equivalent to manually setting a target
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# feature to a given value, and computing the average prediction over all
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# samples.
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# This also checks that the brute and recursion methods give the same
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# output.
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# Note that even on the trainset, the brute and the recursion methods
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# aren't always strictly equivalent, in particular when the slow method
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# generates unrealistic samples that have low mass in the joint
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# distribution of the input features, and when some of the features are
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# dependent. Hence the high tolerance on the checks.
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X, y = make_regression(random_state=0, n_features=5, n_informative=5)
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# The 'init' estimator for GBDT (here the average prediction) isn't taken
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# into account with the recursion method, for technical reasons. We set
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# the mean to 0 to that this 'bug' doesn't have any effect.
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y = y - y.mean()
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est.fit(X, y)
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# target feature will be set to .5 and then to 123
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features = np.array([target_feature], dtype=np.int32)
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grid = np.array([[.5],
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[123]])
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if method == 'brute':
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pdp, predictions = _partial_dependence_brute(est, grid, features, X,
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response_method='auto')
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else:
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pdp = _partial_dependence_recursion(est, grid, features)
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mean_predictions = []
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for val in (.5, 123):
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X_ = X.copy()
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X_[:, target_feature] = val
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mean_predictions.append(est.predict(X_).mean())
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pdp = pdp[0] # (shape is (1, 2) so make it (2,))
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# allow for greater margin for error with recursion method
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rtol = 1e-1 if method == 'recursion' else 1e-3
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assert np.allclose(pdp, mean_predictions, rtol=rtol)
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@pytest.mark.parametrize('seed', range(1))
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def test_recursion_decision_tree_vs_forest_and_gbdt(seed):
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# Make sure that the recursion method gives the same results on a
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# DecisionTreeRegressor and a GradientBoostingRegressor or a
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# RandomForestRegressor with 1 tree and equivalent parameters.
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rng = np.random.RandomState(seed)
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# Purely random dataset to avoid correlated features
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n_samples = 1000
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n_features = 5
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X = rng.randn(n_samples, n_features)
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y = rng.randn(n_samples) * 10
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# The 'init' estimator for GBDT (here the average prediction) isn't taken
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# into account with the recursion method, for technical reasons. We set
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# the mean to 0 to that this 'bug' doesn't have any effect.
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y = y - y.mean()
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# set max_depth not too high to avoid splits with same gain but different
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# features
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max_depth = 5
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tree_seed = 0
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forest = RandomForestRegressor(n_estimators=1, max_features=None,
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bootstrap=False, max_depth=max_depth,
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random_state=tree_seed)
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# The forest will use ensemble.base._set_random_states to set the
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# random_state of the tree sub-estimator. We simulate this here to have
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# equivalent estimators.
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equiv_random_state = check_random_state(tree_seed).randint(
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np.iinfo(np.int32).max)
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gbdt = GradientBoostingRegressor(n_estimators=1, learning_rate=1,
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criterion='mse', max_depth=max_depth,
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random_state=equiv_random_state)
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tree = DecisionTreeRegressor(max_depth=max_depth,
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random_state=equiv_random_state)
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forest.fit(X, y)
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gbdt.fit(X, y)
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tree.fit(X, y)
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# sanity check: if the trees aren't the same, the PD values won't be equal
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try:
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assert_is_subtree(tree.tree_, gbdt[0, 0].tree_)
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assert_is_subtree(tree.tree_, forest[0].tree_)
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except AssertionError:
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# For some reason the trees aren't exactly equal on 32bits, so the PDs
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# cannot be equal either. See
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# https://github.com/scikit-learn/scikit-learn/issues/8853
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assert _IS_32BIT, "this should only fail on 32 bit platforms"
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return
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grid = rng.randn(50).reshape(-1, 1)
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for f in range(n_features):
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features = np.array([f], dtype=np.int32)
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pdp_forest = _partial_dependence_recursion(forest, grid, features)
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pdp_gbdt = _partial_dependence_recursion(gbdt, grid, features)
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pdp_tree = _partial_dependence_recursion(tree, grid, features)
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np.testing.assert_allclose(pdp_gbdt, pdp_tree)
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np.testing.assert_allclose(pdp_forest, pdp_tree)
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@pytest.mark.parametrize('est', (
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GradientBoostingClassifier(random_state=0),
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HistGradientBoostingClassifier(random_state=0),
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))
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@pytest.mark.parametrize('target_feature', (0, 1, 2, 3, 4, 5))
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def test_recursion_decision_function(est, target_feature):
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# Make sure the recursion method (implicitly uses decision_function) has
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# the same result as using brute method with
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# response_method=decision_function
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X, y = make_classification(n_classes=2, n_clusters_per_class=1,
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random_state=1)
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assert np.mean(y) == .5 # make sure the init estimator predicts 0 anyway
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est.fit(X, y)
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preds_1 = partial_dependence(
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est, X, [target_feature], response_method='decision_function',
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method='recursion', kind='average'
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)
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preds_2 = partial_dependence(
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est, X, [target_feature], response_method='decision_function',
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method='brute', kind='average'
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)
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assert_allclose(preds_1['average'], preds_2['average'], atol=1e-7)
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@pytest.mark.parametrize('est', (
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LinearRegression(),
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GradientBoostingRegressor(random_state=0),
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HistGradientBoostingRegressor(random_state=0, min_samples_leaf=1,
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max_leaf_nodes=None, max_iter=1),
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DecisionTreeRegressor(random_state=0),
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))
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@pytest.mark.parametrize('power', (1, 2))
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def test_partial_dependence_easy_target(est, power):
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# If the target y only depends on one feature in an obvious way (linear or
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# quadratic) then the partial dependence for that feature should reflect
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# it.
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# We here fit a linear regression_data model (with polynomial features if
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# needed) and compute r_squared to check that the partial dependence
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# correctly reflects the target.
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rng = np.random.RandomState(0)
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n_samples = 200
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target_variable = 2
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X = rng.normal(size=(n_samples, 5))
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y = X[:, target_variable]**power
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est.fit(X, y)
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pdp = partial_dependence(
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est, features=[target_variable], X=X, grid_resolution=1000,
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kind='average'
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)
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new_X = pdp["values"][0].reshape(-1, 1)
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new_y = pdp['average'][0]
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# add polynomial features if needed
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new_X = PolynomialFeatures(degree=power).fit_transform(new_X)
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lr = LinearRegression().fit(new_X, new_y)
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r2 = r2_score(new_y, lr.predict(new_X))
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assert r2 > .99
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|
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@pytest.mark.parametrize('Estimator',
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(sklearn.tree.DecisionTreeClassifier,
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sklearn.tree.ExtraTreeClassifier,
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|
sklearn.ensemble.ExtraTreesClassifier,
|
|
sklearn.neighbors.KNeighborsClassifier,
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sklearn.neighbors.RadiusNeighborsClassifier,
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sklearn.ensemble.RandomForestClassifier))
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def test_multiclass_multioutput(Estimator):
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# Make sure error is raised for multiclass-multioutput classifiers
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# make multiclass-multioutput dataset
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X, y = make_classification(n_classes=3, n_clusters_per_class=1,
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random_state=0)
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y = np.array([y, y]).T
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est = Estimator()
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est.fit(X, y)
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with pytest.raises(
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|
ValueError,
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|
match="Multiclass-multioutput estimators are not supported"):
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partial_dependence(est, X, [0])
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|
|
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class NoPredictProbaNoDecisionFunction(ClassifierMixin, BaseEstimator):
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def fit(self, X, y):
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# simulate that we have some classes
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self.classes_ = [0, 1]
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return self
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|
|
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@pytest.mark.filterwarnings("ignore:A Bunch will be returned")
|
|
@pytest.mark.parametrize(
|
|
"estimator, params, err_msg",
|
|
[(KMeans(),
|
|
{'features': [0]},
|
|
"'estimator' must be a fitted regressor or classifier"),
|
|
(LinearRegression(),
|
|
{'features': [0], 'response_method': 'predict_proba'},
|
|
'The response_method parameter is ignored for regressors'),
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|
(GradientBoostingClassifier(random_state=0),
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|
{'features': [0], 'response_method': 'predict_proba',
|
|
'method': 'recursion'},
|
|
"'recursion' method, the response_method must be 'decision_function'"),
|
|
(GradientBoostingClassifier(random_state=0),
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|
{'features': [0], 'response_method': 'predict_proba', 'method': 'auto'},
|
|
"'recursion' method, the response_method must be 'decision_function'"),
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|
(GradientBoostingClassifier(random_state=0),
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{'features': [0], 'response_method': 'blahblah'},
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|
'response_method blahblah is invalid. Accepted response_method'),
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|
(NoPredictProbaNoDecisionFunction(),
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|
{'features': [0], 'response_method': 'auto'},
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'The estimator has no predict_proba and no decision_function method'),
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|
(NoPredictProbaNoDecisionFunction(),
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{'features': [0], 'response_method': 'predict_proba'},
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|
'The estimator has no predict_proba method.'),
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|
(NoPredictProbaNoDecisionFunction(),
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|
{'features': [0], 'response_method': 'decision_function'},
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|
'The estimator has no decision_function method.'),
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|
(LinearRegression(),
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|
{'features': [0], 'method': 'blahblah'},
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|
'blahblah is invalid. Accepted method names are brute, recursion, auto'),
|
|
(LinearRegression(),
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|
{'features': [0], 'method': 'recursion', 'kind': 'individual'},
|
|
"The 'recursion' method only applies when 'kind' is set to 'average'"),
|
|
(LinearRegression(),
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|
{'features': [0], 'method': 'recursion', 'kind': 'both'},
|
|
"The 'recursion' method only applies when 'kind' is set to 'average'"),
|
|
(LinearRegression(),
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|
{'features': [0], 'method': 'recursion'},
|
|
"Only the following estimators support the 'recursion' method:")]
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|
)
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def test_partial_dependence_error(estimator, params, err_msg):
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|
X, y = make_classification(random_state=0)
|
|
estimator.fit(X, y)
|
|
|
|
with pytest.raises(ValueError, match=err_msg):
|
|
partial_dependence(estimator, X, **params)
|
|
|
|
|
|
@pytest.mark.parametrize(
|
|
"with_dataframe, err_msg",
|
|
[(True, "Only array-like or scalar are supported"),
|
|
(False, "Only array-like or scalar are supported")]
|
|
)
|
|
def test_partial_dependence_slice_error(with_dataframe, err_msg):
|
|
X, y = make_classification(random_state=0)
|
|
if with_dataframe:
|
|
pd = pytest.importorskip('pandas')
|
|
X = pd.DataFrame(X)
|
|
estimator = LogisticRegression().fit(X, y)
|
|
|
|
with pytest.raises(TypeError, match=err_msg):
|
|
partial_dependence(estimator, X, features=slice(0, 2, 1))
|
|
|
|
|
|
@pytest.mark.parametrize(
|
|
'estimator',
|
|
[LinearRegression(), GradientBoostingClassifier(random_state=0)]
|
|
)
|
|
@pytest.mark.parametrize('features', [-1, 10000])
|
|
def test_partial_dependence_unknown_feature_indices(estimator, features):
|
|
X, y = make_classification(random_state=0)
|
|
estimator.fit(X, y)
|
|
|
|
err_msg = 'all features must be in'
|
|
with pytest.raises(ValueError, match=err_msg):
|
|
partial_dependence(estimator, X, [features])
|
|
|
|
|
|
@pytest.mark.parametrize(
|
|
'estimator',
|
|
[LinearRegression(), GradientBoostingClassifier(random_state=0)]
|
|
)
|
|
def test_partial_dependence_unknown_feature_string(estimator):
|
|
pd = pytest.importorskip("pandas")
|
|
X, y = make_classification(random_state=0)
|
|
df = pd.DataFrame(X)
|
|
estimator.fit(df, y)
|
|
|
|
features = ['random']
|
|
err_msg = 'A given column is not a column of the dataframe'
|
|
with pytest.raises(ValueError, match=err_msg):
|
|
partial_dependence(estimator, df, features)
|
|
|
|
|
|
@pytest.mark.parametrize(
|
|
'estimator',
|
|
[LinearRegression(), GradientBoostingClassifier(random_state=0)]
|
|
)
|
|
def test_partial_dependence_X_list(estimator):
|
|
# check that array-like objects are accepted
|
|
X, y = make_classification(random_state=0)
|
|
estimator.fit(X, y)
|
|
partial_dependence(estimator, list(X), [0], kind='average')
|
|
|
|
|
|
def test_warning_recursion_non_constant_init():
|
|
# make sure that passing a non-constant init parameter to a GBDT and using
|
|
# recursion method yields a warning.
|
|
|
|
gbc = GradientBoostingClassifier(init=DummyClassifier(), random_state=0)
|
|
gbc.fit(X, y)
|
|
|
|
with pytest.warns(
|
|
UserWarning,
|
|
match='Using recursion method with a non-constant init predictor'):
|
|
partial_dependence(gbc, X, [0], method='recursion', kind='average')
|
|
|
|
with pytest.warns(
|
|
UserWarning,
|
|
match='Using recursion method with a non-constant init predictor'):
|
|
partial_dependence(gbc, X, [0], method='recursion', kind='average')
|
|
|
|
|
|
def test_partial_dependence_sample_weight():
|
|
# Test near perfect correlation between partial dependence and diagonal
|
|
# when sample weights emphasize y = x predictions
|
|
# non-regression test for #13193
|
|
# TODO: extend to HistGradientBoosting once sample_weight is supported
|
|
N = 1000
|
|
rng = np.random.RandomState(123456)
|
|
mask = rng.randint(2, size=N, dtype=bool)
|
|
|
|
x = rng.rand(N)
|
|
# set y = x on mask and y = -x outside
|
|
y = x.copy()
|
|
y[~mask] = -y[~mask]
|
|
X = np.c_[mask, x]
|
|
# sample weights to emphasize data points where y = x
|
|
sample_weight = np.ones(N)
|
|
sample_weight[mask] = 1000.
|
|
|
|
clf = GradientBoostingRegressor(n_estimators=10, random_state=1)
|
|
clf.fit(X, y, sample_weight=sample_weight)
|
|
|
|
pdp = partial_dependence(clf, X, features=[1], kind='average')
|
|
|
|
assert np.corrcoef(pdp['average'], pdp["values"])[0, 1] > 0.99
|
|
|
|
|
|
def test_hist_gbdt_sw_not_supported():
|
|
# TODO: remove/fix when PDP supports HGBT with sample weights
|
|
clf = HistGradientBoostingRegressor(random_state=1)
|
|
clf.fit(X, y, sample_weight=np.ones(len(X)))
|
|
|
|
with pytest.raises(NotImplementedError,
|
|
match="does not support partial dependence"):
|
|
partial_dependence(clf, X, features=[1])
|
|
|
|
|
|
def test_partial_dependence_pipeline():
|
|
# check that the partial dependence support pipeline
|
|
iris = load_iris()
|
|
|
|
scaler = StandardScaler()
|
|
clf = DummyClassifier(random_state=42)
|
|
pipe = make_pipeline(scaler, clf)
|
|
|
|
clf.fit(scaler.fit_transform(iris.data), iris.target)
|
|
pipe.fit(iris.data, iris.target)
|
|
|
|
features = 0
|
|
pdp_pipe = partial_dependence(
|
|
pipe, iris.data, features=[features], grid_resolution=10,
|
|
kind='average'
|
|
)
|
|
pdp_clf = partial_dependence(
|
|
clf, scaler.transform(iris.data), features=[features],
|
|
grid_resolution=10, kind='average'
|
|
)
|
|
assert_allclose(pdp_pipe['average'], pdp_clf['average'])
|
|
assert_allclose(
|
|
pdp_pipe["values"][0],
|
|
pdp_clf["values"][0] * scaler.scale_[features] + scaler.mean_[features]
|
|
)
|
|
|
|
|
|
@pytest.mark.parametrize(
|
|
"estimator",
|
|
[LogisticRegression(max_iter=1000, random_state=0),
|
|
GradientBoostingClassifier(random_state=0, n_estimators=5)],
|
|
ids=['estimator-brute', 'estimator-recursion']
|
|
)
|
|
@pytest.mark.parametrize(
|
|
"preprocessor",
|
|
[None,
|
|
make_column_transformer(
|
|
(StandardScaler(), [iris.feature_names[i] for i in (0, 2)]),
|
|
(RobustScaler(), [iris.feature_names[i] for i in (1, 3)])),
|
|
make_column_transformer(
|
|
(StandardScaler(), [iris.feature_names[i] for i in (0, 2)]),
|
|
remainder='passthrough')],
|
|
ids=['None', 'column-transformer', 'column-transformer-passthrough']
|
|
)
|
|
@pytest.mark.parametrize(
|
|
"features",
|
|
[[0, 2], [iris.feature_names[i] for i in (0, 2)]],
|
|
ids=['features-integer', 'features-string']
|
|
)
|
|
def test_partial_dependence_dataframe(estimator, preprocessor, features):
|
|
# check that the partial dependence support dataframe and pipeline
|
|
# including a column transformer
|
|
pd = pytest.importorskip("pandas")
|
|
df = pd.DataFrame(scale(iris.data), columns=iris.feature_names)
|
|
|
|
pipe = make_pipeline(preprocessor, estimator)
|
|
pipe.fit(df, iris.target)
|
|
pdp_pipe = partial_dependence(
|
|
pipe, df, features=features, grid_resolution=10, kind='average'
|
|
)
|
|
|
|
# the column transformer will reorder the column when transforming
|
|
# we mixed the index to be sure that we are computing the partial
|
|
# dependence of the right columns
|
|
if preprocessor is not None:
|
|
X_proc = clone(preprocessor).fit_transform(df)
|
|
features_clf = [0, 1]
|
|
else:
|
|
X_proc = df
|
|
features_clf = [0, 2]
|
|
|
|
clf = clone(estimator).fit(X_proc, iris.target)
|
|
pdp_clf = partial_dependence(
|
|
clf, X_proc, features=features_clf, method='brute', grid_resolution=10,
|
|
kind='average'
|
|
)
|
|
|
|
assert_allclose(pdp_pipe['average'], pdp_clf['average'])
|
|
if preprocessor is not None:
|
|
scaler = preprocessor.named_transformers_['standardscaler']
|
|
assert_allclose(
|
|
pdp_pipe["values"][1],
|
|
pdp_clf["values"][1] * scaler.scale_[1] + scaler.mean_[1]
|
|
)
|
|
else:
|
|
assert_allclose(pdp_pipe["values"][1], pdp_clf["values"][1])
|
|
|
|
|
|
@pytest.mark.parametrize(
|
|
"features, expected_pd_shape",
|
|
[(0, (3, 10)),
|
|
(iris.feature_names[0], (3, 10)),
|
|
([0, 2], (3, 10, 10)),
|
|
([iris.feature_names[i] for i in (0, 2)], (3, 10, 10)),
|
|
([True, False, True, False], (3, 10, 10))],
|
|
ids=['scalar-int', 'scalar-str', 'list-int', 'list-str', 'mask']
|
|
)
|
|
def test_partial_dependence_feature_type(features, expected_pd_shape):
|
|
# check all possible features type supported in PDP
|
|
pd = pytest.importorskip("pandas")
|
|
df = pd.DataFrame(iris.data, columns=iris.feature_names)
|
|
|
|
preprocessor = make_column_transformer(
|
|
(StandardScaler(), [iris.feature_names[i] for i in (0, 2)]),
|
|
(RobustScaler(), [iris.feature_names[i] for i in (1, 3)])
|
|
)
|
|
pipe = make_pipeline(
|
|
preprocessor, LogisticRegression(max_iter=1000, random_state=0)
|
|
)
|
|
pipe.fit(df, iris.target)
|
|
pdp_pipe = partial_dependence(
|
|
pipe, df, features=features, grid_resolution=10, kind='average'
|
|
)
|
|
assert pdp_pipe['average'].shape == expected_pd_shape
|
|
assert len(pdp_pipe["values"]) == len(pdp_pipe['average'].shape) - 1
|
|
|
|
|
|
@pytest.mark.parametrize(
|
|
"estimator", [LinearRegression(), LogisticRegression(),
|
|
GradientBoostingRegressor(), GradientBoostingClassifier()]
|
|
)
|
|
def test_partial_dependence_unfitted(estimator):
|
|
X = iris.data
|
|
preprocessor = make_column_transformer(
|
|
(StandardScaler(), [0, 2]), (RobustScaler(), [1, 3])
|
|
)
|
|
pipe = make_pipeline(preprocessor, estimator)
|
|
with pytest.raises(NotFittedError, match="is not fitted yet"):
|
|
partial_dependence(pipe, X, features=[0, 2], grid_resolution=10)
|
|
with pytest.raises(NotFittedError, match="is not fitted yet"):
|
|
partial_dependence(estimator, X, features=[0, 2], grid_resolution=10)
|
|
|
|
|
|
@pytest.mark.parametrize('Estimator, data', [
|
|
(LinearRegression, multioutput_regression_data),
|
|
(LogisticRegression, binary_classification_data)])
|
|
def test_kind_average_and_average_of_individual(Estimator, data):
|
|
est = Estimator()
|
|
(X, y), n_targets = data
|
|
est.fit(X, y)
|
|
|
|
pdp_avg = partial_dependence(
|
|
est, X=X, features=[1, 2], kind='average'
|
|
)
|
|
pdp_ind = partial_dependence(
|
|
est, X=X, features=[1, 2], kind='individual'
|
|
)
|
|
avg_ind = np.mean(pdp_ind['individual'], axis=1)
|
|
assert_allclose(avg_ind, pdp_avg['average'])
|
|
|
|
|
|
def test_warning_for_kind_legacy():
|
|
est = LogisticRegression()
|
|
(X, y), n_targets = binary_classification_data
|
|
est.fit(X, y)
|
|
|
|
err_msg = ("A Bunch will be returned in place of 'predictions' from "
|
|
"version 1.1")
|
|
with pytest.warns(FutureWarning, match=err_msg):
|
|
partial_dependence(est, X=X, features=[1, 2])
|
|
|
|
with pytest.warns(FutureWarning, match=err_msg):
|
|
partial_dependence(est, X=X, features=[1, 2], kind='legacy')
|