837 lines
28 KiB
Python
837 lines
28 KiB
Python
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import re
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import numpy as np
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import pytest
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from joblib import cpu_count
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from sklearn import datasets
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from sklearn.base import ClassifierMixin, clone
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from sklearn.datasets import (
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load_linnerud,
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make_classification,
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make_multilabel_classification,
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make_regression,
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)
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from sklearn.dummy import DummyClassifier, DummyRegressor
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from sklearn.ensemble import (
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GradientBoostingRegressor,
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RandomForestClassifier,
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StackingRegressor,
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)
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from sklearn.exceptions import NotFittedError
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from sklearn.impute import SimpleImputer
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from sklearn.linear_model import (
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Lasso,
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LinearRegression,
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LogisticRegression,
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OrthogonalMatchingPursuit,
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PassiveAggressiveClassifier,
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Ridge,
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SGDClassifier,
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SGDRegressor,
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)
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from sklearn.metrics import jaccard_score, mean_squared_error
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from sklearn.model_selection import GridSearchCV, train_test_split
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from sklearn.multiclass import OneVsRestClassifier
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from sklearn.multioutput import (
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ClassifierChain,
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MultiOutputClassifier,
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MultiOutputRegressor,
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RegressorChain,
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)
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from sklearn.pipeline import make_pipeline
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from sklearn.svm import LinearSVC
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from sklearn.tree import DecisionTreeClassifier
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from sklearn.utils import shuffle
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from sklearn.utils._testing import (
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assert_almost_equal,
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assert_array_almost_equal,
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assert_array_equal,
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)
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from sklearn.utils.fixes import (
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BSR_CONTAINERS,
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COO_CONTAINERS,
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CSC_CONTAINERS,
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CSR_CONTAINERS,
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DOK_CONTAINERS,
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LIL_CONTAINERS,
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)
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def test_multi_target_regression():
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X, y = datasets.make_regression(n_targets=3, random_state=0)
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X_train, y_train = X[:50], y[:50]
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X_test, y_test = X[50:], y[50:]
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references = np.zeros_like(y_test)
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for n in range(3):
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rgr = GradientBoostingRegressor(random_state=0)
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rgr.fit(X_train, y_train[:, n])
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references[:, n] = rgr.predict(X_test)
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rgr = MultiOutputRegressor(GradientBoostingRegressor(random_state=0))
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rgr.fit(X_train, y_train)
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y_pred = rgr.predict(X_test)
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assert_almost_equal(references, y_pred)
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def test_multi_target_regression_partial_fit():
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X, y = datasets.make_regression(n_targets=3, random_state=0)
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X_train, y_train = X[:50], y[:50]
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X_test, y_test = X[50:], y[50:]
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references = np.zeros_like(y_test)
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half_index = 25
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for n in range(3):
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sgr = SGDRegressor(random_state=0, max_iter=5)
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sgr.partial_fit(X_train[:half_index], y_train[:half_index, n])
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sgr.partial_fit(X_train[half_index:], y_train[half_index:, n])
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references[:, n] = sgr.predict(X_test)
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sgr = MultiOutputRegressor(SGDRegressor(random_state=0, max_iter=5))
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sgr.partial_fit(X_train[:half_index], y_train[:half_index])
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sgr.partial_fit(X_train[half_index:], y_train[half_index:])
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y_pred = sgr.predict(X_test)
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assert_almost_equal(references, y_pred)
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assert not hasattr(MultiOutputRegressor(Lasso), "partial_fit")
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def test_multi_target_regression_one_target():
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# Test multi target regression raises
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X, y = datasets.make_regression(n_targets=1, random_state=0)
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rgr = MultiOutputRegressor(GradientBoostingRegressor(random_state=0))
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msg = "at least two dimensions"
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with pytest.raises(ValueError, match=msg):
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rgr.fit(X, y)
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@pytest.mark.parametrize(
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"sparse_container",
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CSR_CONTAINERS
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+ CSC_CONTAINERS
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+ COO_CONTAINERS
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+ LIL_CONTAINERS
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+ DOK_CONTAINERS
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+ BSR_CONTAINERS,
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)
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def test_multi_target_sparse_regression(sparse_container):
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X, y = datasets.make_regression(n_targets=3, random_state=0)
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X_train, y_train = X[:50], y[:50]
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X_test = X[50:]
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rgr = MultiOutputRegressor(Lasso(random_state=0))
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rgr_sparse = MultiOutputRegressor(Lasso(random_state=0))
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rgr.fit(X_train, y_train)
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rgr_sparse.fit(sparse_container(X_train), y_train)
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assert_almost_equal(
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rgr.predict(X_test), rgr_sparse.predict(sparse_container(X_test))
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)
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def test_multi_target_sample_weights_api():
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X = [[1, 2, 3], [4, 5, 6]]
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y = [[3.141, 2.718], [2.718, 3.141]]
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w = [0.8, 0.6]
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rgr = MultiOutputRegressor(OrthogonalMatchingPursuit())
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msg = "does not support sample weights"
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with pytest.raises(ValueError, match=msg):
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rgr.fit(X, y, w)
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# no exception should be raised if the base estimator supports weights
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rgr = MultiOutputRegressor(GradientBoostingRegressor(random_state=0))
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rgr.fit(X, y, w)
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def test_multi_target_sample_weight_partial_fit():
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# weighted regressor
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X = [[1, 2, 3], [4, 5, 6]]
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y = [[3.141, 2.718], [2.718, 3.141]]
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w = [2.0, 1.0]
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rgr_w = MultiOutputRegressor(SGDRegressor(random_state=0, max_iter=5))
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rgr_w.partial_fit(X, y, w)
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# weighted with different weights
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w = [2.0, 2.0]
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rgr = MultiOutputRegressor(SGDRegressor(random_state=0, max_iter=5))
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rgr.partial_fit(X, y, w)
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assert rgr.predict(X)[0][0] != rgr_w.predict(X)[0][0]
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def test_multi_target_sample_weights():
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# weighted regressor
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Xw = [[1, 2, 3], [4, 5, 6]]
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yw = [[3.141, 2.718], [2.718, 3.141]]
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w = [2.0, 1.0]
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rgr_w = MultiOutputRegressor(GradientBoostingRegressor(random_state=0))
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rgr_w.fit(Xw, yw, w)
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# unweighted, but with repeated samples
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X = [[1, 2, 3], [1, 2, 3], [4, 5, 6]]
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y = [[3.141, 2.718], [3.141, 2.718], [2.718, 3.141]]
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rgr = MultiOutputRegressor(GradientBoostingRegressor(random_state=0))
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rgr.fit(X, y)
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X_test = [[1.5, 2.5, 3.5], [3.5, 4.5, 5.5]]
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assert_almost_equal(rgr.predict(X_test), rgr_w.predict(X_test))
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# Import the data
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iris = datasets.load_iris()
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# create a multiple targets by randomized shuffling and concatenating y.
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X = iris.data
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y1 = iris.target
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y2 = shuffle(y1, random_state=1)
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y3 = shuffle(y1, random_state=2)
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y = np.column_stack((y1, y2, y3))
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n_samples, n_features = X.shape
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n_outputs = y.shape[1]
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n_classes = len(np.unique(y1))
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classes = list(map(np.unique, (y1, y2, y3)))
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def test_multi_output_classification_partial_fit_parallelism():
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sgd_linear_clf = SGDClassifier(loss="log_loss", random_state=1, max_iter=5)
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mor = MultiOutputClassifier(sgd_linear_clf, n_jobs=4)
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mor.partial_fit(X, y, classes)
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est1 = mor.estimators_[0]
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mor.partial_fit(X, y)
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est2 = mor.estimators_[0]
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if cpu_count() > 1:
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# parallelism requires this to be the case for a sane implementation
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assert est1 is not est2
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# check multioutput has predict_proba
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def test_hasattr_multi_output_predict_proba():
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# default SGDClassifier has loss='hinge'
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# which does not expose a predict_proba method
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sgd_linear_clf = SGDClassifier(random_state=1, max_iter=5)
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multi_target_linear = MultiOutputClassifier(sgd_linear_clf)
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multi_target_linear.fit(X, y)
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assert not hasattr(multi_target_linear, "predict_proba")
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# case where predict_proba attribute exists
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sgd_linear_clf = SGDClassifier(loss="log_loss", random_state=1, max_iter=5)
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multi_target_linear = MultiOutputClassifier(sgd_linear_clf)
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multi_target_linear.fit(X, y)
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assert hasattr(multi_target_linear, "predict_proba")
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# check predict_proba passes
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def test_multi_output_predict_proba():
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sgd_linear_clf = SGDClassifier(random_state=1, max_iter=5)
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param = {"loss": ("hinge", "log_loss", "modified_huber")}
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# inner function for custom scoring
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def custom_scorer(estimator, X, y):
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if hasattr(estimator, "predict_proba"):
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return 1.0
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else:
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return 0.0
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grid_clf = GridSearchCV(
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sgd_linear_clf,
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param_grid=param,
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scoring=custom_scorer,
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cv=3,
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error_score="raise",
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)
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multi_target_linear = MultiOutputClassifier(grid_clf)
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multi_target_linear.fit(X, y)
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multi_target_linear.predict_proba(X)
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# SGDClassifier defaults to loss='hinge' which is not a probabilistic
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# loss function; therefore it does not expose a predict_proba method
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sgd_linear_clf = SGDClassifier(random_state=1, max_iter=5)
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multi_target_linear = MultiOutputClassifier(sgd_linear_clf)
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multi_target_linear.fit(X, y)
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inner2_msg = "probability estimates are not available for loss='hinge'"
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inner1_msg = "'SGDClassifier' has no attribute 'predict_proba'"
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outer_msg = "'MultiOutputClassifier' has no attribute 'predict_proba'"
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with pytest.raises(AttributeError, match=outer_msg) as exec_info:
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multi_target_linear.predict_proba(X)
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assert isinstance(exec_info.value.__cause__, AttributeError)
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assert inner1_msg in str(exec_info.value.__cause__)
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assert isinstance(exec_info.value.__cause__.__cause__, AttributeError)
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assert inner2_msg in str(exec_info.value.__cause__.__cause__)
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def test_multi_output_classification_partial_fit():
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# test if multi_target initializes correctly with base estimator and fit
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# assert predictions work as expected for predict
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sgd_linear_clf = SGDClassifier(loss="log_loss", random_state=1, max_iter=5)
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multi_target_linear = MultiOutputClassifier(sgd_linear_clf)
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# train the multi_target_linear and also get the predictions.
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half_index = X.shape[0] // 2
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multi_target_linear.partial_fit(X[:half_index], y[:half_index], classes=classes)
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first_predictions = multi_target_linear.predict(X)
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assert (n_samples, n_outputs) == first_predictions.shape
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multi_target_linear.partial_fit(X[half_index:], y[half_index:])
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second_predictions = multi_target_linear.predict(X)
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assert (n_samples, n_outputs) == second_predictions.shape
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# train the linear classification with each column and assert that
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# predictions are equal after first partial_fit and second partial_fit
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for i in range(3):
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# create a clone with the same state
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sgd_linear_clf = clone(sgd_linear_clf)
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sgd_linear_clf.partial_fit(
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X[:half_index], y[:half_index, i], classes=classes[i]
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)
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assert_array_equal(sgd_linear_clf.predict(X), first_predictions[:, i])
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sgd_linear_clf.partial_fit(X[half_index:], y[half_index:, i])
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assert_array_equal(sgd_linear_clf.predict(X), second_predictions[:, i])
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def test_multi_output_classification_partial_fit_no_first_classes_exception():
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sgd_linear_clf = SGDClassifier(loss="log_loss", random_state=1, max_iter=5)
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multi_target_linear = MultiOutputClassifier(sgd_linear_clf)
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msg = "classes must be passed on the first call to partial_fit."
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with pytest.raises(ValueError, match=msg):
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multi_target_linear.partial_fit(X, y)
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def test_multi_output_classification():
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# test if multi_target initializes correctly with base estimator and fit
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# assert predictions work as expected for predict, prodict_proba and score
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forest = RandomForestClassifier(n_estimators=10, random_state=1)
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multi_target_forest = MultiOutputClassifier(forest)
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# train the multi_target_forest and also get the predictions.
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multi_target_forest.fit(X, y)
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predictions = multi_target_forest.predict(X)
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assert (n_samples, n_outputs) == predictions.shape
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predict_proba = multi_target_forest.predict_proba(X)
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assert len(predict_proba) == n_outputs
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for class_probabilities in predict_proba:
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assert (n_samples, n_classes) == class_probabilities.shape
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assert_array_equal(np.argmax(np.dstack(predict_proba), axis=1), predictions)
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# train the forest with each column and assert that predictions are equal
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for i in range(3):
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forest_ = clone(forest) # create a clone with the same state
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forest_.fit(X, y[:, i])
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assert list(forest_.predict(X)) == list(predictions[:, i])
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assert_array_equal(list(forest_.predict_proba(X)), list(predict_proba[i]))
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def test_multiclass_multioutput_estimator():
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# test to check meta of meta estimators
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||
|
|
svc = LinearSVC(dual="auto", random_state=0)
|
||
|
|
multi_class_svc = OneVsRestClassifier(svc)
|
||
|
|
multi_target_svc = MultiOutputClassifier(multi_class_svc)
|
||
|
|
|
||
|
|
multi_target_svc.fit(X, y)
|
||
|
|
|
||
|
|
predictions = multi_target_svc.predict(X)
|
||
|
|
assert (n_samples, n_outputs) == predictions.shape
|
||
|
|
|
||
|
|
# train the forest with each column and assert that predictions are equal
|
||
|
|
for i in range(3):
|
||
|
|
multi_class_svc_ = clone(multi_class_svc) # create a clone
|
||
|
|
multi_class_svc_.fit(X, y[:, i])
|
||
|
|
assert list(multi_class_svc_.predict(X)) == list(predictions[:, i])
|
||
|
|
|
||
|
|
|
||
|
|
def test_multiclass_multioutput_estimator_predict_proba():
|
||
|
|
seed = 542
|
||
|
|
|
||
|
|
# make test deterministic
|
||
|
|
rng = np.random.RandomState(seed)
|
||
|
|
|
||
|
|
# random features
|
||
|
|
X = rng.normal(size=(5, 5))
|
||
|
|
|
||
|
|
# random labels
|
||
|
|
y1 = np.array(["b", "a", "a", "b", "a"]).reshape(5, 1) # 2 classes
|
||
|
|
y2 = np.array(["d", "e", "f", "e", "d"]).reshape(5, 1) # 3 classes
|
||
|
|
|
||
|
|
Y = np.concatenate([y1, y2], axis=1)
|
||
|
|
|
||
|
|
clf = MultiOutputClassifier(
|
||
|
|
LogisticRegression(solver="liblinear", random_state=seed)
|
||
|
|
)
|
||
|
|
|
||
|
|
clf.fit(X, Y)
|
||
|
|
|
||
|
|
y_result = clf.predict_proba(X)
|
||
|
|
y_actual = [
|
||
|
|
np.array(
|
||
|
|
[
|
||
|
|
[0.23481764, 0.76518236],
|
||
|
|
[0.67196072, 0.32803928],
|
||
|
|
[0.54681448, 0.45318552],
|
||
|
|
[0.34883923, 0.65116077],
|
||
|
|
[0.73687069, 0.26312931],
|
||
|
|
]
|
||
|
|
),
|
||
|
|
np.array(
|
||
|
|
[
|
||
|
|
[0.5171785, 0.23878628, 0.24403522],
|
||
|
|
[0.22141451, 0.64102704, 0.13755846],
|
||
|
|
[0.16751315, 0.18256843, 0.64991843],
|
||
|
|
[0.27357372, 0.55201592, 0.17441036],
|
||
|
|
[0.65745193, 0.26062899, 0.08191907],
|
||
|
|
]
|
||
|
|
),
|
||
|
|
]
|
||
|
|
|
||
|
|
for i in range(len(y_actual)):
|
||
|
|
assert_almost_equal(y_result[i], y_actual[i])
|
||
|
|
|
||
|
|
|
||
|
|
def test_multi_output_classification_sample_weights():
|
||
|
|
# weighted classifier
|
||
|
|
Xw = [[1, 2, 3], [4, 5, 6]]
|
||
|
|
yw = [[3, 2], [2, 3]]
|
||
|
|
w = np.asarray([2.0, 1.0])
|
||
|
|
forest = RandomForestClassifier(n_estimators=10, random_state=1)
|
||
|
|
clf_w = MultiOutputClassifier(forest)
|
||
|
|
clf_w.fit(Xw, yw, w)
|
||
|
|
|
||
|
|
# unweighted, but with repeated samples
|
||
|
|
X = [[1, 2, 3], [1, 2, 3], [4, 5, 6]]
|
||
|
|
y = [[3, 2], [3, 2], [2, 3]]
|
||
|
|
forest = RandomForestClassifier(n_estimators=10, random_state=1)
|
||
|
|
clf = MultiOutputClassifier(forest)
|
||
|
|
clf.fit(X, y)
|
||
|
|
|
||
|
|
X_test = [[1.5, 2.5, 3.5], [3.5, 4.5, 5.5]]
|
||
|
|
assert_almost_equal(clf.predict(X_test), clf_w.predict(X_test))
|
||
|
|
|
||
|
|
|
||
|
|
def test_multi_output_classification_partial_fit_sample_weights():
|
||
|
|
# weighted classifier
|
||
|
|
Xw = [[1, 2, 3], [4, 5, 6], [1.5, 2.5, 3.5]]
|
||
|
|
yw = [[3, 2], [2, 3], [3, 2]]
|
||
|
|
w = np.asarray([2.0, 1.0, 1.0])
|
||
|
|
sgd_linear_clf = SGDClassifier(random_state=1, max_iter=20)
|
||
|
|
clf_w = MultiOutputClassifier(sgd_linear_clf)
|
||
|
|
clf_w.fit(Xw, yw, w)
|
||
|
|
|
||
|
|
# unweighted, but with repeated samples
|
||
|
|
X = [[1, 2, 3], [1, 2, 3], [4, 5, 6], [1.5, 2.5, 3.5]]
|
||
|
|
y = [[3, 2], [3, 2], [2, 3], [3, 2]]
|
||
|
|
sgd_linear_clf = SGDClassifier(random_state=1, max_iter=20)
|
||
|
|
clf = MultiOutputClassifier(sgd_linear_clf)
|
||
|
|
clf.fit(X, y)
|
||
|
|
X_test = [[1.5, 2.5, 3.5]]
|
||
|
|
assert_array_almost_equal(clf.predict(X_test), clf_w.predict(X_test))
|
||
|
|
|
||
|
|
|
||
|
|
def test_multi_output_exceptions():
|
||
|
|
# NotFittedError when fit is not done but score, predict and
|
||
|
|
# and predict_proba are called
|
||
|
|
moc = MultiOutputClassifier(LinearSVC(dual="auto", random_state=0))
|
||
|
|
with pytest.raises(NotFittedError):
|
||
|
|
moc.score(X, y)
|
||
|
|
|
||
|
|
# ValueError when number of outputs is different
|
||
|
|
# for fit and score
|
||
|
|
y_new = np.column_stack((y1, y2))
|
||
|
|
moc.fit(X, y)
|
||
|
|
with pytest.raises(ValueError):
|
||
|
|
moc.score(X, y_new)
|
||
|
|
|
||
|
|
# ValueError when y is continuous
|
||
|
|
msg = "Unknown label type"
|
||
|
|
with pytest.raises(ValueError, match=msg):
|
||
|
|
moc.fit(X, X[:, 1])
|
||
|
|
|
||
|
|
|
||
|
|
@pytest.mark.parametrize("response_method", ["predict_proba", "predict"])
|
||
|
|
def test_multi_output_not_fitted_error(response_method):
|
||
|
|
"""Check that we raise the proper error when the estimator is not fitted"""
|
||
|
|
moc = MultiOutputClassifier(LogisticRegression())
|
||
|
|
with pytest.raises(NotFittedError):
|
||
|
|
getattr(moc, response_method)(X)
|
||
|
|
|
||
|
|
|
||
|
|
def test_multi_output_delegate_predict_proba():
|
||
|
|
"""Check the behavior for the delegation of predict_proba to the underlying
|
||
|
|
estimator"""
|
||
|
|
|
||
|
|
# A base estimator with `predict_proba`should expose the method even before fit
|
||
|
|
moc = MultiOutputClassifier(LogisticRegression())
|
||
|
|
assert hasattr(moc, "predict_proba")
|
||
|
|
moc.fit(X, y)
|
||
|
|
assert hasattr(moc, "predict_proba")
|
||
|
|
|
||
|
|
# A base estimator without `predict_proba` should raise an AttributeError
|
||
|
|
moc = MultiOutputClassifier(LinearSVC(dual="auto"))
|
||
|
|
assert not hasattr(moc, "predict_proba")
|
||
|
|
|
||
|
|
outer_msg = "'MultiOutputClassifier' has no attribute 'predict_proba'"
|
||
|
|
inner_msg = "'LinearSVC' object has no attribute 'predict_proba'"
|
||
|
|
with pytest.raises(AttributeError, match=outer_msg) as exec_info:
|
||
|
|
moc.predict_proba(X)
|
||
|
|
assert isinstance(exec_info.value.__cause__, AttributeError)
|
||
|
|
assert inner_msg == str(exec_info.value.__cause__)
|
||
|
|
|
||
|
|
moc.fit(X, y)
|
||
|
|
assert not hasattr(moc, "predict_proba")
|
||
|
|
with pytest.raises(AttributeError, match=outer_msg) as exec_info:
|
||
|
|
moc.predict_proba(X)
|
||
|
|
assert isinstance(exec_info.value.__cause__, AttributeError)
|
||
|
|
assert inner_msg == str(exec_info.value.__cause__)
|
||
|
|
|
||
|
|
|
||
|
|
def generate_multilabel_dataset_with_correlations():
|
||
|
|
# Generate a multilabel data set from a multiclass dataset as a way of
|
||
|
|
# by representing the integer number of the original class using a binary
|
||
|
|
# encoding.
|
||
|
|
X, y = make_classification(
|
||
|
|
n_samples=1000, n_features=100, n_classes=16, n_informative=10, random_state=0
|
||
|
|
)
|
||
|
|
|
||
|
|
Y_multi = np.array([[int(yyy) for yyy in format(yy, "#06b")[2:]] for yy in y])
|
||
|
|
return X, Y_multi
|
||
|
|
|
||
|
|
|
||
|
|
def test_classifier_chain_fit_and_predict_with_linear_svc():
|
||
|
|
# Fit classifier chain and verify predict performance using LinearSVC
|
||
|
|
X, Y = generate_multilabel_dataset_with_correlations()
|
||
|
|
classifier_chain = ClassifierChain(LinearSVC(dual="auto"))
|
||
|
|
classifier_chain.fit(X, Y)
|
||
|
|
|
||
|
|
Y_pred = classifier_chain.predict(X)
|
||
|
|
assert Y_pred.shape == Y.shape
|
||
|
|
|
||
|
|
Y_decision = classifier_chain.decision_function(X)
|
||
|
|
|
||
|
|
Y_binary = Y_decision >= 0
|
||
|
|
assert_array_equal(Y_binary, Y_pred)
|
||
|
|
assert not hasattr(classifier_chain, "predict_proba")
|
||
|
|
|
||
|
|
|
||
|
|
@pytest.mark.parametrize("csr_container", CSR_CONTAINERS)
|
||
|
|
def test_classifier_chain_fit_and_predict_with_sparse_data(csr_container):
|
||
|
|
# Fit classifier chain with sparse data
|
||
|
|
X, Y = generate_multilabel_dataset_with_correlations()
|
||
|
|
X_sparse = csr_container(X)
|
||
|
|
|
||
|
|
classifier_chain = ClassifierChain(LogisticRegression())
|
||
|
|
classifier_chain.fit(X_sparse, Y)
|
||
|
|
Y_pred_sparse = classifier_chain.predict(X_sparse)
|
||
|
|
|
||
|
|
classifier_chain = ClassifierChain(LogisticRegression())
|
||
|
|
classifier_chain.fit(X, Y)
|
||
|
|
Y_pred_dense = classifier_chain.predict(X)
|
||
|
|
|
||
|
|
assert_array_equal(Y_pred_sparse, Y_pred_dense)
|
||
|
|
|
||
|
|
|
||
|
|
def test_classifier_chain_vs_independent_models():
|
||
|
|
# Verify that an ensemble of classifier chains (each of length
|
||
|
|
# N) can achieve a higher Jaccard similarity score than N independent
|
||
|
|
# models
|
||
|
|
X, Y = generate_multilabel_dataset_with_correlations()
|
||
|
|
X_train = X[:600, :]
|
||
|
|
X_test = X[600:, :]
|
||
|
|
Y_train = Y[:600, :]
|
||
|
|
Y_test = Y[600:, :]
|
||
|
|
|
||
|
|
ovr = OneVsRestClassifier(LogisticRegression())
|
||
|
|
ovr.fit(X_train, Y_train)
|
||
|
|
Y_pred_ovr = ovr.predict(X_test)
|
||
|
|
|
||
|
|
chain = ClassifierChain(LogisticRegression())
|
||
|
|
chain.fit(X_train, Y_train)
|
||
|
|
Y_pred_chain = chain.predict(X_test)
|
||
|
|
|
||
|
|
assert jaccard_score(Y_test, Y_pred_chain, average="samples") > jaccard_score(
|
||
|
|
Y_test, Y_pred_ovr, average="samples"
|
||
|
|
)
|
||
|
|
|
||
|
|
|
||
|
|
@pytest.mark.parametrize("response_method", ["predict_proba", "predict_log_proba"])
|
||
|
|
def test_base_chain_fit_and_predict(response_method):
|
||
|
|
# Fit base chain and verify predict performance
|
||
|
|
X, Y = generate_multilabel_dataset_with_correlations()
|
||
|
|
chains = [RegressorChain(Ridge()), ClassifierChain(LogisticRegression())]
|
||
|
|
for chain in chains:
|
||
|
|
chain.fit(X, Y)
|
||
|
|
Y_pred = chain.predict(X)
|
||
|
|
assert Y_pred.shape == Y.shape
|
||
|
|
assert [c.coef_.size for c in chain.estimators_] == list(
|
||
|
|
range(X.shape[1], X.shape[1] + Y.shape[1])
|
||
|
|
)
|
||
|
|
|
||
|
|
Y_prob = getattr(chains[1], response_method)(X)
|
||
|
|
if response_method == "predict_log_proba":
|
||
|
|
Y_prob = np.exp(Y_prob)
|
||
|
|
Y_binary = Y_prob >= 0.5
|
||
|
|
assert_array_equal(Y_binary, Y_pred)
|
||
|
|
|
||
|
|
assert isinstance(chains[1], ClassifierMixin)
|
||
|
|
|
||
|
|
|
||
|
|
@pytest.mark.parametrize("csr_container", CSR_CONTAINERS)
|
||
|
|
def test_base_chain_fit_and_predict_with_sparse_data_and_cv(csr_container):
|
||
|
|
# Fit base chain with sparse data cross_val_predict
|
||
|
|
X, Y = generate_multilabel_dataset_with_correlations()
|
||
|
|
X_sparse = csr_container(X)
|
||
|
|
base_chains = [
|
||
|
|
ClassifierChain(LogisticRegression(), cv=3),
|
||
|
|
RegressorChain(Ridge(), cv=3),
|
||
|
|
]
|
||
|
|
for chain in base_chains:
|
||
|
|
chain.fit(X_sparse, Y)
|
||
|
|
Y_pred = chain.predict(X_sparse)
|
||
|
|
assert Y_pred.shape == Y.shape
|
||
|
|
|
||
|
|
|
||
|
|
def test_base_chain_random_order():
|
||
|
|
# Fit base chain with random order
|
||
|
|
X, Y = generate_multilabel_dataset_with_correlations()
|
||
|
|
for chain in [ClassifierChain(LogisticRegression()), RegressorChain(Ridge())]:
|
||
|
|
chain_random = clone(chain).set_params(order="random", random_state=42)
|
||
|
|
chain_random.fit(X, Y)
|
||
|
|
chain_fixed = clone(chain).set_params(order=chain_random.order_)
|
||
|
|
chain_fixed.fit(X, Y)
|
||
|
|
assert_array_equal(chain_fixed.order_, chain_random.order_)
|
||
|
|
assert list(chain_random.order) != list(range(4))
|
||
|
|
assert len(chain_random.order_) == 4
|
||
|
|
assert len(set(chain_random.order_)) == 4
|
||
|
|
# Randomly ordered chain should behave identically to a fixed order
|
||
|
|
# chain with the same order.
|
||
|
|
for est1, est2 in zip(chain_random.estimators_, chain_fixed.estimators_):
|
||
|
|
assert_array_almost_equal(est1.coef_, est2.coef_)
|
||
|
|
|
||
|
|
|
||
|
|
def test_base_chain_crossval_fit_and_predict():
|
||
|
|
# Fit chain with cross_val_predict and verify predict
|
||
|
|
# performance
|
||
|
|
X, Y = generate_multilabel_dataset_with_correlations()
|
||
|
|
|
||
|
|
for chain in [ClassifierChain(LogisticRegression()), RegressorChain(Ridge())]:
|
||
|
|
chain.fit(X, Y)
|
||
|
|
chain_cv = clone(chain).set_params(cv=3)
|
||
|
|
chain_cv.fit(X, Y)
|
||
|
|
Y_pred_cv = chain_cv.predict(X)
|
||
|
|
Y_pred = chain.predict(X)
|
||
|
|
|
||
|
|
assert Y_pred_cv.shape == Y_pred.shape
|
||
|
|
assert not np.all(Y_pred == Y_pred_cv)
|
||
|
|
if isinstance(chain, ClassifierChain):
|
||
|
|
assert jaccard_score(Y, Y_pred_cv, average="samples") > 0.4
|
||
|
|
else:
|
||
|
|
assert mean_squared_error(Y, Y_pred_cv) < 0.25
|
||
|
|
|
||
|
|
|
||
|
|
@pytest.mark.parametrize(
|
||
|
|
"estimator",
|
||
|
|
[
|
||
|
|
RandomForestClassifier(n_estimators=2),
|
||
|
|
MultiOutputClassifier(RandomForestClassifier(n_estimators=2)),
|
||
|
|
ClassifierChain(RandomForestClassifier(n_estimators=2)),
|
||
|
|
],
|
||
|
|
)
|
||
|
|
def test_multi_output_classes_(estimator):
|
||
|
|
# Tests classes_ attribute of multioutput classifiers
|
||
|
|
# RandomForestClassifier supports multioutput out-of-the-box
|
||
|
|
estimator.fit(X, y)
|
||
|
|
assert isinstance(estimator.classes_, list)
|
||
|
|
assert len(estimator.classes_) == n_outputs
|
||
|
|
for estimator_classes, expected_classes in zip(classes, estimator.classes_):
|
||
|
|
assert_array_equal(estimator_classes, expected_classes)
|
||
|
|
|
||
|
|
|
||
|
|
class DummyRegressorWithFitParams(DummyRegressor):
|
||
|
|
def fit(self, X, y, sample_weight=None, **fit_params):
|
||
|
|
self._fit_params = fit_params
|
||
|
|
return super().fit(X, y, sample_weight)
|
||
|
|
|
||
|
|
|
||
|
|
class DummyClassifierWithFitParams(DummyClassifier):
|
||
|
|
def fit(self, X, y, sample_weight=None, **fit_params):
|
||
|
|
self._fit_params = fit_params
|
||
|
|
return super().fit(X, y, sample_weight)
|
||
|
|
|
||
|
|
|
||
|
|
@pytest.mark.filterwarnings("ignore:`n_features_in_` is deprecated")
|
||
|
|
@pytest.mark.parametrize(
|
||
|
|
"estimator, dataset",
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|
|
[
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||
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|
(
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||
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|
MultiOutputClassifier(DummyClassifierWithFitParams(strategy="prior")),
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||
|
|
datasets.make_multilabel_classification(),
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||
|
|
),
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||
|
|
(
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||
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|
MultiOutputRegressor(DummyRegressorWithFitParams()),
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||
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|
datasets.make_regression(n_targets=3, random_state=0),
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|
),
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||
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|
],
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|
)
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|
def test_multioutput_estimator_with_fit_params(estimator, dataset):
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|
X, y = dataset
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|
some_param = np.zeros_like(X)
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|
estimator.fit(X, y, some_param=some_param)
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|
for dummy_estimator in estimator.estimators_:
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|
assert "some_param" in dummy_estimator._fit_params
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|
|
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||
|
|
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||
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|
def test_regressor_chain_w_fit_params():
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|
# Make sure fit_params are properly propagated to the sub-estimators
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|
rng = np.random.RandomState(0)
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|
X, y = datasets.make_regression(n_targets=3, random_state=0)
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|
weight = rng.rand(y.shape[0])
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|
|
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||
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|
class MySGD(SGDRegressor):
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|
def fit(self, X, y, **fit_params):
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|
self.sample_weight_ = fit_params["sample_weight"]
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|
super().fit(X, y, **fit_params)
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|
|
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||
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|
model = RegressorChain(MySGD())
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|
|
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||
|
|
# Fitting with params
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|
|
fit_param = {"sample_weight": weight}
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|
model.fit(X, y, **fit_param)
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||
|
|
|
||
|
|
for est in model.estimators_:
|
||
|
|
assert est.sample_weight_ is weight
|
||
|
|
|
||
|
|
|
||
|
|
@pytest.mark.parametrize(
|
||
|
|
"MultiOutputEstimator, Estimator",
|
||
|
|
[(MultiOutputClassifier, LogisticRegression), (MultiOutputRegressor, Ridge)],
|
||
|
|
)
|
||
|
|
# FIXME: we should move this test in `estimator_checks` once we are able
|
||
|
|
# to construct meta-estimator instances
|
||
|
|
def test_support_missing_values(MultiOutputEstimator, Estimator):
|
||
|
|
# smoke test to check that pipeline MultioutputEstimators are letting
|
||
|
|
# the validation of missing values to
|
||
|
|
# the underlying pipeline, regressor or classifier
|
||
|
|
rng = np.random.RandomState(42)
|
||
|
|
X, y = rng.randn(50, 2), rng.binomial(1, 0.5, (50, 3))
|
||
|
|
mask = rng.choice([1, 0], X.shape, p=[0.01, 0.99]).astype(bool)
|
||
|
|
X[mask] = np.nan
|
||
|
|
|
||
|
|
pipe = make_pipeline(SimpleImputer(), Estimator())
|
||
|
|
MultiOutputEstimator(pipe).fit(X, y).score(X, y)
|
||
|
|
|
||
|
|
|
||
|
|
@pytest.mark.parametrize("order_type", [list, np.array, tuple])
|
||
|
|
def test_classifier_chain_tuple_order(order_type):
|
||
|
|
X = [[1, 2, 3], [4, 5, 6], [1.5, 2.5, 3.5]]
|
||
|
|
y = [[3, 2], [2, 3], [3, 2]]
|
||
|
|
order = order_type([1, 0])
|
||
|
|
|
||
|
|
chain = ClassifierChain(RandomForestClassifier(), order=order)
|
||
|
|
|
||
|
|
chain.fit(X, y)
|
||
|
|
X_test = [[1.5, 2.5, 3.5]]
|
||
|
|
y_test = [[3, 2]]
|
||
|
|
assert_array_almost_equal(chain.predict(X_test), y_test)
|
||
|
|
|
||
|
|
|
||
|
|
def test_classifier_chain_tuple_invalid_order():
|
||
|
|
X = [[1, 2, 3], [4, 5, 6], [1.5, 2.5, 3.5]]
|
||
|
|
y = [[3, 2], [2, 3], [3, 2]]
|
||
|
|
order = tuple([1, 2])
|
||
|
|
|
||
|
|
chain = ClassifierChain(RandomForestClassifier(), order=order)
|
||
|
|
|
||
|
|
with pytest.raises(ValueError, match="invalid order"):
|
||
|
|
chain.fit(X, y)
|
||
|
|
|
||
|
|
|
||
|
|
def test_classifier_chain_verbose(capsys):
|
||
|
|
X, y = make_multilabel_classification(
|
||
|
|
n_samples=100, n_features=5, n_classes=3, n_labels=3, random_state=0
|
||
|
|
)
|
||
|
|
X_train, X_test, y_train, y_test = train_test_split(X, y, random_state=0)
|
||
|
|
|
||
|
|
pattern = (
|
||
|
|
r"\[Chain\].*\(1 of 3\) Processing order 0, total=.*\n"
|
||
|
|
r"\[Chain\].*\(2 of 3\) Processing order 1, total=.*\n"
|
||
|
|
r"\[Chain\].*\(3 of 3\) Processing order 2, total=.*\n$"
|
||
|
|
)
|
||
|
|
|
||
|
|
classifier = ClassifierChain(
|
||
|
|
DecisionTreeClassifier(),
|
||
|
|
order=[0, 1, 2],
|
||
|
|
random_state=0,
|
||
|
|
verbose=True,
|
||
|
|
)
|
||
|
|
classifier.fit(X_train, y_train)
|
||
|
|
assert re.match(pattern, capsys.readouterr()[0])
|
||
|
|
|
||
|
|
|
||
|
|
def test_regressor_chain_verbose(capsys):
|
||
|
|
X, y = make_regression(n_samples=125, n_targets=3, random_state=0)
|
||
|
|
X_train, X_test, y_train, y_test = train_test_split(X, y, random_state=0)
|
||
|
|
|
||
|
|
pattern = (
|
||
|
|
r"\[Chain\].*\(1 of 3\) Processing order 1, total=.*\n"
|
||
|
|
r"\[Chain\].*\(2 of 3\) Processing order 0, total=.*\n"
|
||
|
|
r"\[Chain\].*\(3 of 3\) Processing order 2, total=.*\n$"
|
||
|
|
)
|
||
|
|
regressor = RegressorChain(
|
||
|
|
LinearRegression(),
|
||
|
|
order=[1, 0, 2],
|
||
|
|
random_state=0,
|
||
|
|
verbose=True,
|
||
|
|
)
|
||
|
|
regressor.fit(X_train, y_train)
|
||
|
|
assert re.match(pattern, capsys.readouterr()[0])
|
||
|
|
|
||
|
|
|
||
|
|
def test_multioutputregressor_ducktypes_fitted_estimator():
|
||
|
|
"""Test that MultiOutputRegressor checks the fitted estimator for
|
||
|
|
predict. Non-regression test for #16549."""
|
||
|
|
X, y = load_linnerud(return_X_y=True)
|
||
|
|
stacker = StackingRegressor(
|
||
|
|
estimators=[("sgd", SGDRegressor(random_state=1))],
|
||
|
|
final_estimator=Ridge(),
|
||
|
|
cv=2,
|
||
|
|
)
|
||
|
|
|
||
|
|
reg = MultiOutputRegressor(estimator=stacker).fit(X, y)
|
||
|
|
|
||
|
|
# Does not raise
|
||
|
|
reg.predict(X)
|
||
|
|
|
||
|
|
|
||
|
|
@pytest.mark.parametrize(
|
||
|
|
"Cls, method", [(ClassifierChain, "fit"), (MultiOutputClassifier, "partial_fit")]
|
||
|
|
)
|
||
|
|
def test_fit_params_no_routing(Cls, method):
|
||
|
|
"""Check that we raise an error when passing metadata not requested by the
|
||
|
|
underlying classifier.
|
||
|
|
"""
|
||
|
|
X, y = make_classification(n_samples=50)
|
||
|
|
clf = Cls(PassiveAggressiveClassifier())
|
||
|
|
|
||
|
|
with pytest.raises(ValueError, match="is only supported if"):
|
||
|
|
getattr(clf, method)(X, y, test=1)
|
||
|
|
|
||
|
|
|
||
|
|
def test_multioutput_regressor_has_partial_fit():
|
||
|
|
# Test that an unfitted MultiOutputRegressor handles available_if for
|
||
|
|
# partial_fit correctly
|
||
|
|
est = MultiOutputRegressor(LinearRegression())
|
||
|
|
msg = "This 'MultiOutputRegressor' has no attribute 'partial_fit'"
|
||
|
|
with pytest.raises(AttributeError, match=msg):
|
||
|
|
getattr(est, "partial_fit")
|