651 lines
22 KiB
Python
651 lines
22 KiB
Python
"""Testing for the boost module (sklearn.ensemble.boost)."""
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import numpy as np
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import pytest
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import re
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from scipy.sparse import csc_matrix
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from scipy.sparse import csr_matrix
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from scipy.sparse import coo_matrix
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from scipy.sparse import dok_matrix
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from scipy.sparse import lil_matrix
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from sklearn.utils._testing import assert_array_equal, assert_array_less
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from sklearn.utils._testing import assert_array_almost_equal
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from sklearn.base import BaseEstimator
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from sklearn.base import clone
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from sklearn.dummy import DummyClassifier, DummyRegressor
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from sklearn.linear_model import LinearRegression
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from sklearn.model_selection import train_test_split
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from sklearn.model_selection import GridSearchCV
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from sklearn.ensemble import AdaBoostClassifier
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from sklearn.ensemble import AdaBoostRegressor
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from sklearn.ensemble._weight_boosting import _samme_proba
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from sklearn.svm import SVC, SVR
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from sklearn.tree import DecisionTreeClassifier, DecisionTreeRegressor
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from sklearn.utils import shuffle
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from sklearn.utils._mocking import NoSampleWeightWrapper
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from sklearn import datasets
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# Common random state
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rng = np.random.RandomState(0)
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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_class = ["foo", "foo", "foo", 1, 1, 1] # test string class labels
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y_regr = [-1, -1, -1, 1, 1, 1]
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T = [[-1, -1], [2, 2], [3, 2]]
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y_t_class = ["foo", 1, 1]
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y_t_regr = [-1, 1, 1]
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# Load the iris dataset and randomly permute it
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iris = datasets.load_iris()
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perm = rng.permutation(iris.target.size)
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iris.data, iris.target = shuffle(iris.data, iris.target, random_state=rng)
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# Load the diabetes dataset and randomly permute it
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diabetes = datasets.load_diabetes()
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diabetes.data, diabetes.target = shuffle(
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diabetes.data, diabetes.target, random_state=rng
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)
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def test_samme_proba():
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# Test the `_samme_proba` helper function.
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# Define some example (bad) `predict_proba` output.
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probs = np.array(
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[[1, 1e-6, 0], [0.19, 0.6, 0.2], [-999, 0.51, 0.5], [1e-6, 1, 1e-9]]
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)
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probs /= np.abs(probs.sum(axis=1))[:, np.newaxis]
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# _samme_proba calls estimator.predict_proba.
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# Make a mock object so I can control what gets returned.
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class MockEstimator:
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def predict_proba(self, X):
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assert_array_equal(X.shape, probs.shape)
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return probs
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mock = MockEstimator()
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samme_proba = _samme_proba(mock, 3, np.ones_like(probs))
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assert_array_equal(samme_proba.shape, probs.shape)
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assert np.isfinite(samme_proba).all()
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# Make sure that the correct elements come out as smallest --
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# `_samme_proba` should preserve the ordering in each example.
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assert_array_equal(np.argmin(samme_proba, axis=1), [2, 0, 0, 2])
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assert_array_equal(np.argmax(samme_proba, axis=1), [0, 1, 1, 1])
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def test_oneclass_adaboost_proba():
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# Test predict_proba robustness for one class label input.
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# In response to issue #7501
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# https://github.com/scikit-learn/scikit-learn/issues/7501
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y_t = np.ones(len(X))
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clf = AdaBoostClassifier().fit(X, y_t)
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assert_array_almost_equal(clf.predict_proba(X), np.ones((len(X), 1)))
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@pytest.mark.parametrize("algorithm", ["SAMME", "SAMME.R"])
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def test_classification_toy(algorithm):
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# Check classification on a toy dataset.
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clf = AdaBoostClassifier(algorithm=algorithm, random_state=0)
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clf.fit(X, y_class)
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assert_array_equal(clf.predict(T), y_t_class)
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assert_array_equal(np.unique(np.asarray(y_t_class)), clf.classes_)
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assert clf.predict_proba(T).shape == (len(T), 2)
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assert clf.decision_function(T).shape == (len(T),)
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def test_regression_toy():
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# Check classification on a toy dataset.
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clf = AdaBoostRegressor(random_state=0)
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clf.fit(X, y_regr)
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assert_array_equal(clf.predict(T), y_t_regr)
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def test_iris():
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# Check consistency on dataset iris.
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classes = np.unique(iris.target)
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clf_samme = prob_samme = None
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for alg in ["SAMME", "SAMME.R"]:
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clf = AdaBoostClassifier(algorithm=alg)
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clf.fit(iris.data, iris.target)
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assert_array_equal(classes, clf.classes_)
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proba = clf.predict_proba(iris.data)
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if alg == "SAMME":
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clf_samme = clf
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prob_samme = proba
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assert proba.shape[1] == len(classes)
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assert clf.decision_function(iris.data).shape[1] == len(classes)
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score = clf.score(iris.data, iris.target)
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assert score > 0.9, "Failed with algorithm %s and score = %f" % (alg, score)
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# Check we used multiple estimators
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assert len(clf.estimators_) > 1
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# Check for distinct random states (see issue #7408)
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assert len(set(est.random_state for est in clf.estimators_)) == len(
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clf.estimators_
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)
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# Somewhat hacky regression test: prior to
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# ae7adc880d624615a34bafdb1d75ef67051b8200,
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# predict_proba returned SAMME.R values for SAMME.
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clf_samme.algorithm = "SAMME.R"
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assert_array_less(0, np.abs(clf_samme.predict_proba(iris.data) - prob_samme))
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@pytest.mark.parametrize("loss", ["linear", "square", "exponential"])
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def test_diabetes(loss):
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# Check consistency on dataset diabetes.
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reg = AdaBoostRegressor(loss=loss, random_state=0)
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reg.fit(diabetes.data, diabetes.target)
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score = reg.score(diabetes.data, diabetes.target)
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assert score > 0.55
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# Check we used multiple estimators
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assert len(reg.estimators_) > 1
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# Check for distinct random states (see issue #7408)
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assert len(set(est.random_state for est in reg.estimators_)) == len(reg.estimators_)
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@pytest.mark.parametrize("algorithm", ["SAMME", "SAMME.R"])
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def test_staged_predict(algorithm):
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# Check staged predictions.
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rng = np.random.RandomState(0)
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iris_weights = rng.randint(10, size=iris.target.shape)
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diabetes_weights = rng.randint(10, size=diabetes.target.shape)
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clf = AdaBoostClassifier(algorithm=algorithm, n_estimators=10)
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clf.fit(iris.data, iris.target, sample_weight=iris_weights)
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predictions = clf.predict(iris.data)
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staged_predictions = [p for p in clf.staged_predict(iris.data)]
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proba = clf.predict_proba(iris.data)
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staged_probas = [p for p in clf.staged_predict_proba(iris.data)]
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score = clf.score(iris.data, iris.target, sample_weight=iris_weights)
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staged_scores = [
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s for s in clf.staged_score(iris.data, iris.target, sample_weight=iris_weights)
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]
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assert len(staged_predictions) == 10
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assert_array_almost_equal(predictions, staged_predictions[-1])
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assert len(staged_probas) == 10
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assert_array_almost_equal(proba, staged_probas[-1])
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assert len(staged_scores) == 10
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assert_array_almost_equal(score, staged_scores[-1])
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# AdaBoost regression
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clf = AdaBoostRegressor(n_estimators=10, random_state=0)
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clf.fit(diabetes.data, diabetes.target, sample_weight=diabetes_weights)
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predictions = clf.predict(diabetes.data)
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staged_predictions = [p for p in clf.staged_predict(diabetes.data)]
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score = clf.score(diabetes.data, diabetes.target, sample_weight=diabetes_weights)
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staged_scores = [
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s
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for s in clf.staged_score(
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diabetes.data, diabetes.target, sample_weight=diabetes_weights
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)
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]
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assert len(staged_predictions) == 10
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assert_array_almost_equal(predictions, staged_predictions[-1])
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assert len(staged_scores) == 10
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assert_array_almost_equal(score, staged_scores[-1])
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def test_gridsearch():
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# Check that base trees can be grid-searched.
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# AdaBoost classification
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boost = AdaBoostClassifier(estimator=DecisionTreeClassifier())
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parameters = {
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"n_estimators": (1, 2),
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"estimator__max_depth": (1, 2),
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"algorithm": ("SAMME", "SAMME.R"),
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}
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clf = GridSearchCV(boost, parameters)
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clf.fit(iris.data, iris.target)
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# AdaBoost regression
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boost = AdaBoostRegressor(estimator=DecisionTreeRegressor(), random_state=0)
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parameters = {"n_estimators": (1, 2), "estimator__max_depth": (1, 2)}
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clf = GridSearchCV(boost, parameters)
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clf.fit(diabetes.data, diabetes.target)
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def test_pickle():
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# Check pickability.
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import pickle
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# Adaboost classifier
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for alg in ["SAMME", "SAMME.R"]:
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obj = AdaBoostClassifier(algorithm=alg)
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obj.fit(iris.data, iris.target)
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score = obj.score(iris.data, iris.target)
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s = pickle.dumps(obj)
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obj2 = pickle.loads(s)
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assert type(obj2) == obj.__class__
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score2 = obj2.score(iris.data, iris.target)
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assert score == score2
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# Adaboost regressor
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obj = AdaBoostRegressor(random_state=0)
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obj.fit(diabetes.data, diabetes.target)
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score = obj.score(diabetes.data, diabetes.target)
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s = pickle.dumps(obj)
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obj2 = pickle.loads(s)
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assert type(obj2) == obj.__class__
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score2 = obj2.score(diabetes.data, diabetes.target)
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assert score == score2
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def test_importances():
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# Check variable importances.
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X, y = datasets.make_classification(
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n_samples=2000,
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n_features=10,
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n_informative=3,
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n_redundant=0,
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n_repeated=0,
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shuffle=False,
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random_state=1,
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)
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for alg in ["SAMME", "SAMME.R"]:
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clf = AdaBoostClassifier(algorithm=alg)
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clf.fit(X, y)
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importances = clf.feature_importances_
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assert importances.shape[0] == 10
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assert (importances[:3, np.newaxis] >= importances[3:]).all()
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def test_adaboost_classifier_sample_weight_error():
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# Test that it gives proper exception on incorrect sample weight.
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clf = AdaBoostClassifier()
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msg = re.escape("sample_weight.shape == (1,), expected (6,)")
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with pytest.raises(ValueError, match=msg):
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clf.fit(X, y_class, sample_weight=np.asarray([-1]))
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def test_estimator():
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# Test different estimators.
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from sklearn.ensemble import RandomForestClassifier
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# XXX doesn't work with y_class because RF doesn't support classes_
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# Shouldn't AdaBoost run a LabelBinarizer?
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clf = AdaBoostClassifier(RandomForestClassifier())
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clf.fit(X, y_regr)
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clf = AdaBoostClassifier(SVC(), algorithm="SAMME")
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clf.fit(X, y_class)
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from sklearn.ensemble import RandomForestRegressor
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clf = AdaBoostRegressor(RandomForestRegressor(), random_state=0)
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clf.fit(X, y_regr)
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clf = AdaBoostRegressor(SVR(), random_state=0)
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clf.fit(X, y_regr)
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# Check that an empty discrete ensemble fails in fit, not predict.
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X_fail = [[1, 1], [1, 1], [1, 1], [1, 1]]
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y_fail = ["foo", "bar", 1, 2]
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clf = AdaBoostClassifier(SVC(), algorithm="SAMME")
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with pytest.raises(ValueError, match="worse than random"):
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clf.fit(X_fail, y_fail)
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def test_sample_weights_infinite():
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msg = "Sample weights have reached infinite values"
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clf = AdaBoostClassifier(n_estimators=30, learning_rate=23.0, algorithm="SAMME")
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with pytest.warns(UserWarning, match=msg):
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clf.fit(iris.data, iris.target)
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def test_sparse_classification():
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# Check classification with sparse input.
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class CustomSVC(SVC):
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"""SVC variant that records the nature of the training set."""
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def fit(self, X, y, sample_weight=None):
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"""Modification on fit caries data type for later verification."""
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super().fit(X, y, sample_weight=sample_weight)
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self.data_type_ = type(X)
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return self
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X, y = datasets.make_multilabel_classification(
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n_classes=1, n_samples=15, n_features=5, random_state=42
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)
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# Flatten y to a 1d array
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y = np.ravel(y)
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X_train, X_test, y_train, y_test = train_test_split(X, y, random_state=0)
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for sparse_format in [csc_matrix, csr_matrix, lil_matrix, coo_matrix, dok_matrix]:
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X_train_sparse = sparse_format(X_train)
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X_test_sparse = sparse_format(X_test)
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# Trained on sparse format
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sparse_classifier = AdaBoostClassifier(
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estimator=CustomSVC(probability=True),
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random_state=1,
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algorithm="SAMME",
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).fit(X_train_sparse, y_train)
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# Trained on dense format
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dense_classifier = AdaBoostClassifier(
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estimator=CustomSVC(probability=True),
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random_state=1,
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algorithm="SAMME",
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).fit(X_train, y_train)
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# predict
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sparse_results = sparse_classifier.predict(X_test_sparse)
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dense_results = dense_classifier.predict(X_test)
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assert_array_equal(sparse_results, dense_results)
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# decision_function
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sparse_results = sparse_classifier.decision_function(X_test_sparse)
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dense_results = dense_classifier.decision_function(X_test)
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assert_array_almost_equal(sparse_results, dense_results)
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# predict_log_proba
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sparse_results = sparse_classifier.predict_log_proba(X_test_sparse)
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dense_results = dense_classifier.predict_log_proba(X_test)
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assert_array_almost_equal(sparse_results, dense_results)
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# predict_proba
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sparse_results = sparse_classifier.predict_proba(X_test_sparse)
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dense_results = dense_classifier.predict_proba(X_test)
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assert_array_almost_equal(sparse_results, dense_results)
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# score
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sparse_results = sparse_classifier.score(X_test_sparse, y_test)
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dense_results = dense_classifier.score(X_test, y_test)
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assert_array_almost_equal(sparse_results, dense_results)
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# staged_decision_function
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sparse_results = sparse_classifier.staged_decision_function(X_test_sparse)
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dense_results = dense_classifier.staged_decision_function(X_test)
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for sprase_res, dense_res in zip(sparse_results, dense_results):
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assert_array_almost_equal(sprase_res, dense_res)
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# staged_predict
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sparse_results = sparse_classifier.staged_predict(X_test_sparse)
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dense_results = dense_classifier.staged_predict(X_test)
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for sprase_res, dense_res in zip(sparse_results, dense_results):
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assert_array_equal(sprase_res, dense_res)
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# staged_predict_proba
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sparse_results = sparse_classifier.staged_predict_proba(X_test_sparse)
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dense_results = dense_classifier.staged_predict_proba(X_test)
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for sprase_res, dense_res in zip(sparse_results, dense_results):
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assert_array_almost_equal(sprase_res, dense_res)
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# staged_score
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sparse_results = sparse_classifier.staged_score(X_test_sparse, y_test)
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dense_results = dense_classifier.staged_score(X_test, y_test)
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for sprase_res, dense_res in zip(sparse_results, dense_results):
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assert_array_equal(sprase_res, dense_res)
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# Verify sparsity of data is maintained during training
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types = [i.data_type_ for i in sparse_classifier.estimators_]
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assert all([(t == csc_matrix or t == csr_matrix) for t in types])
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def test_sparse_regression():
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# Check regression with sparse input.
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class CustomSVR(SVR):
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"""SVR variant that records the nature of the training set."""
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def fit(self, X, y, sample_weight=None):
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"""Modification on fit caries data type for later verification."""
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super().fit(X, y, sample_weight=sample_weight)
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self.data_type_ = type(X)
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return self
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X, y = datasets.make_regression(
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n_samples=15, n_features=50, n_targets=1, random_state=42
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)
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X_train, X_test, y_train, y_test = train_test_split(X, y, random_state=0)
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for sparse_format in [csc_matrix, csr_matrix, lil_matrix, coo_matrix, dok_matrix]:
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X_train_sparse = sparse_format(X_train)
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X_test_sparse = sparse_format(X_test)
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# Trained on sparse format
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sparse_classifier = AdaBoostRegressor(
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estimator=CustomSVR(), random_state=1
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).fit(X_train_sparse, y_train)
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# Trained on dense format
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dense_classifier = dense_results = AdaBoostRegressor(
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estimator=CustomSVR(), random_state=1
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).fit(X_train, y_train)
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# predict
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sparse_results = sparse_classifier.predict(X_test_sparse)
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dense_results = dense_classifier.predict(X_test)
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assert_array_almost_equal(sparse_results, dense_results)
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# staged_predict
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sparse_results = sparse_classifier.staged_predict(X_test_sparse)
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dense_results = dense_classifier.staged_predict(X_test)
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|
for sprase_res, dense_res in zip(sparse_results, dense_results):
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|
assert_array_almost_equal(sprase_res, dense_res)
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|
|
|
types = [i.data_type_ for i in sparse_classifier.estimators_]
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|
|
|
assert all([(t == csc_matrix or t == csr_matrix) for t in types])
|
|
|
|
|
|
def test_sample_weight_adaboost_regressor():
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|
"""
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|
AdaBoostRegressor should work without sample_weights in the base estimator
|
|
The random weighted sampling is done internally in the _boost method in
|
|
AdaBoostRegressor.
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|
"""
|
|
|
|
class DummyEstimator(BaseEstimator):
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|
def fit(self, X, y):
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|
pass
|
|
|
|
def predict(self, X):
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|
return np.zeros(X.shape[0])
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|
|
|
boost = AdaBoostRegressor(DummyEstimator(), n_estimators=3)
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|
boost.fit(X, y_regr)
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|
assert len(boost.estimator_weights_) == len(boost.estimator_errors_)
|
|
|
|
|
|
def test_multidimensional_X():
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|
"""
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|
Check that the AdaBoost estimators can work with n-dimensional
|
|
data matrix
|
|
"""
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|
rng = np.random.RandomState(0)
|
|
|
|
X = rng.randn(50, 3, 3)
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|
yc = rng.choice([0, 1], 50)
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|
yr = rng.randn(50)
|
|
|
|
boost = AdaBoostClassifier(DummyClassifier(strategy="most_frequent"))
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|
boost.fit(X, yc)
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|
boost.predict(X)
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|
boost.predict_proba(X)
|
|
|
|
boost = AdaBoostRegressor(DummyRegressor())
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|
boost.fit(X, yr)
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|
boost.predict(X)
|
|
|
|
|
|
@pytest.mark.parametrize("algorithm", ["SAMME", "SAMME.R"])
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|
def test_adaboostclassifier_without_sample_weight(algorithm):
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|
X, y = iris.data, iris.target
|
|
estimator = NoSampleWeightWrapper(DummyClassifier())
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|
clf = AdaBoostClassifier(estimator=estimator, algorithm=algorithm)
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|
err_msg = "{} doesn't support sample_weight".format(estimator.__class__.__name__)
|
|
with pytest.raises(ValueError, match=err_msg):
|
|
clf.fit(X, y)
|
|
|
|
|
|
def test_adaboostregressor_sample_weight():
|
|
# check that giving weight will have an influence on the error computed
|
|
# for a weak learner
|
|
rng = np.random.RandomState(42)
|
|
X = np.linspace(0, 100, num=1000)
|
|
y = (0.8 * X + 0.2) + (rng.rand(X.shape[0]) * 0.0001)
|
|
X = X.reshape(-1, 1)
|
|
|
|
# add an arbitrary outlier
|
|
X[-1] *= 10
|
|
y[-1] = 10000
|
|
|
|
# random_state=0 ensure that the underlying bootstrap will use the outlier
|
|
regr_no_outlier = AdaBoostRegressor(
|
|
estimator=LinearRegression(), n_estimators=1, random_state=0
|
|
)
|
|
regr_with_weight = clone(regr_no_outlier)
|
|
regr_with_outlier = clone(regr_no_outlier)
|
|
|
|
# fit 3 models:
|
|
# - a model containing the outlier
|
|
# - a model without the outlier
|
|
# - a model containing the outlier but with a null sample-weight
|
|
regr_with_outlier.fit(X, y)
|
|
regr_no_outlier.fit(X[:-1], y[:-1])
|
|
sample_weight = np.ones_like(y)
|
|
sample_weight[-1] = 0
|
|
regr_with_weight.fit(X, y, sample_weight=sample_weight)
|
|
|
|
score_with_outlier = regr_with_outlier.score(X[:-1], y[:-1])
|
|
score_no_outlier = regr_no_outlier.score(X[:-1], y[:-1])
|
|
score_with_weight = regr_with_weight.score(X[:-1], y[:-1])
|
|
|
|
assert score_with_outlier < score_no_outlier
|
|
assert score_with_outlier < score_with_weight
|
|
assert score_no_outlier == pytest.approx(score_with_weight)
|
|
|
|
|
|
@pytest.mark.parametrize("algorithm", ["SAMME", "SAMME.R"])
|
|
def test_adaboost_consistent_predict(algorithm):
|
|
# check that predict_proba and predict give consistent results
|
|
# regression test for:
|
|
# https://github.com/scikit-learn/scikit-learn/issues/14084
|
|
X_train, X_test, y_train, y_test = train_test_split(
|
|
*datasets.load_digits(return_X_y=True), random_state=42
|
|
)
|
|
model = AdaBoostClassifier(algorithm=algorithm, random_state=42)
|
|
model.fit(X_train, y_train)
|
|
|
|
assert_array_equal(
|
|
np.argmax(model.predict_proba(X_test), axis=1), model.predict(X_test)
|
|
)
|
|
|
|
|
|
@pytest.mark.parametrize(
|
|
"model, X, y",
|
|
[
|
|
(AdaBoostClassifier(), iris.data, iris.target),
|
|
(AdaBoostRegressor(), diabetes.data, diabetes.target),
|
|
],
|
|
)
|
|
def test_adaboost_negative_weight_error(model, X, y):
|
|
sample_weight = np.ones_like(y)
|
|
sample_weight[-1] = -10
|
|
|
|
err_msg = "Negative values in data passed to `sample_weight`"
|
|
with pytest.raises(ValueError, match=err_msg):
|
|
model.fit(X, y, sample_weight=sample_weight)
|
|
|
|
|
|
def test_adaboost_numerically_stable_feature_importance_with_small_weights():
|
|
"""Check that we don't create NaN feature importance with numerically
|
|
instable inputs.
|
|
|
|
Non-regression test for:
|
|
https://github.com/scikit-learn/scikit-learn/issues/20320
|
|
"""
|
|
rng = np.random.RandomState(42)
|
|
X = rng.normal(size=(1000, 10))
|
|
y = rng.choice([0, 1], size=1000)
|
|
sample_weight = np.ones_like(y) * 1e-263
|
|
tree = DecisionTreeClassifier(max_depth=10, random_state=12)
|
|
ada_model = AdaBoostClassifier(estimator=tree, n_estimators=20, random_state=12)
|
|
ada_model.fit(X, y, sample_weight=sample_weight)
|
|
assert np.isnan(ada_model.feature_importances_).sum() == 0
|
|
|
|
|
|
# TODO(1.4): remove in 1.4
|
|
@pytest.mark.parametrize(
|
|
"AdaBoost, Estimator",
|
|
[
|
|
(AdaBoostClassifier, DecisionTreeClassifier),
|
|
(AdaBoostRegressor, DecisionTreeRegressor),
|
|
],
|
|
)
|
|
def test_base_estimator_argument_deprecated(AdaBoost, Estimator):
|
|
X = np.array([[1, 2], [3, 4]])
|
|
y = np.array([1, 0])
|
|
model = AdaBoost(base_estimator=Estimator())
|
|
|
|
warn_msg = (
|
|
"`base_estimator` was renamed to `estimator` in version 1.2 and "
|
|
"will be removed in 1.4."
|
|
)
|
|
with pytest.warns(FutureWarning, match=warn_msg):
|
|
model.fit(X, y)
|
|
|
|
|
|
# TODO(1.4): remove in 1.4
|
|
@pytest.mark.parametrize(
|
|
"AdaBoost",
|
|
[AdaBoostClassifier, AdaBoostRegressor],
|
|
)
|
|
def test_base_estimator_property_deprecated(AdaBoost):
|
|
X = np.array([[1, 2], [3, 4]])
|
|
y = np.array([1, 0])
|
|
model = AdaBoost()
|
|
model.fit(X, y)
|
|
|
|
warn_msg = (
|
|
"Attribute `base_estimator_` was deprecated in version 1.2 and "
|
|
"will be removed in 1.4. Use `estimator_` instead."
|
|
)
|
|
with pytest.warns(FutureWarning, match=warn_msg):
|
|
model.base_estimator_
|
|
|
|
|
|
# TODO(1.4): remove in 1.4
|
|
def test_deprecated_base_estimator_parameters_can_be_set():
|
|
"""Check that setting base_estimator parameters works.
|
|
|
|
During the deprecation cycle setting "base_estimator__*" params should
|
|
work.
|
|
|
|
Non-regression test for https://github.com/scikit-learn/scikit-learn/issues/25470
|
|
"""
|
|
# This implicitly sets "estimator", it is how old code (pre v1.2) would
|
|
# have instantiated AdaBoostClassifier and back then it would set
|
|
# "base_estimator".
|
|
clf = AdaBoostClassifier(DecisionTreeClassifier())
|
|
|
|
with pytest.warns(FutureWarning, match="Parameter 'base_estimator' of"):
|
|
clf.set_params(base_estimator__max_depth=2)
|