""" Testing for Support Vector Machine module (sklearn.svm) TODO: remove hard coded numerical results when possible """ import numpy as np import itertools import pytest from numpy.testing import assert_array_equal, assert_array_almost_equal from numpy.testing import assert_almost_equal from numpy.testing import assert_allclose from scipy import sparse from sklearn import svm, linear_model, datasets, metrics, base from sklearn.svm import LinearSVC from sklearn.svm import LinearSVR from sklearn.model_selection import train_test_split from sklearn.datasets import make_classification, make_blobs from sklearn.metrics import f1_score from sklearn.metrics.pairwise import rbf_kernel from sklearn.utils import check_random_state from sklearn.utils._testing import assert_warns from sklearn.utils._testing import assert_raise_message from sklearn.utils._testing import ignore_warnings from sklearn.utils._testing import assert_no_warnings from sklearn.utils.validation import _num_samples from sklearn.utils import shuffle from sklearn.exceptions import ConvergenceWarning from sklearn.exceptions import NotFittedError, UndefinedMetricWarning from sklearn.multiclass import OneVsRestClassifier # mypy error: Module 'sklearn.svm' has no attribute '_libsvm' from sklearn.svm import _libsvm # type: ignore # toy sample X = [[-2, -1], [-1, -1], [-1, -2], [1, 1], [1, 2], [2, 1]] Y = [1, 1, 1, 2, 2, 2] T = [[-1, -1], [2, 2], [3, 2]] true_result = [1, 2, 2] # also load the iris dataset iris = datasets.load_iris() rng = check_random_state(42) perm = rng.permutation(iris.target.size) iris.data = iris.data[perm] iris.target = iris.target[perm] def test_libsvm_parameters(): # Test parameters on classes that make use of libsvm. clf = svm.SVC(kernel='linear').fit(X, Y) assert_array_equal(clf.dual_coef_, [[-0.25, .25]]) assert_array_equal(clf.support_, [1, 3]) assert_array_equal(clf.support_vectors_, (X[1], X[3])) assert_array_equal(clf.intercept_, [0.]) assert_array_equal(clf.predict(X), Y) def test_libsvm_iris(): # Check consistency on dataset iris. # shuffle the dataset so that labels are not ordered for k in ('linear', 'rbf'): clf = svm.SVC(kernel=k).fit(iris.data, iris.target) assert np.mean(clf.predict(iris.data) == iris.target) > 0.9 assert hasattr(clf, "coef_") == (k == 'linear') assert_array_equal(clf.classes_, np.sort(clf.classes_)) # check also the low-level API model = _libsvm.fit(iris.data, iris.target.astype(np.float64)) pred = _libsvm.predict(iris.data, *model) assert np.mean(pred == iris.target) > .95 model = _libsvm.fit(iris.data, iris.target.astype(np.float64), kernel='linear') pred = _libsvm.predict(iris.data, *model, kernel='linear') assert np.mean(pred == iris.target) > .95 pred = _libsvm.cross_validation(iris.data, iris.target.astype(np.float64), 5, kernel='linear', random_seed=0) assert np.mean(pred == iris.target) > .95 # If random_seed >= 0, the libsvm rng is seeded (by calling `srand`), hence # we should get deterministic results (assuming that there is no other # thread calling this wrapper calling `srand` concurrently). pred2 = _libsvm.cross_validation(iris.data, iris.target.astype(np.float64), 5, kernel='linear', random_seed=0) assert_array_equal(pred, pred2) def test_precomputed(): # SVC with a precomputed kernel. # We test it with a toy dataset and with iris. clf = svm.SVC(kernel='precomputed') # Gram matrix for train data (square matrix) # (we use just a linear kernel) K = np.dot(X, np.array(X).T) clf.fit(K, Y) # Gram matrix for test data (rectangular matrix) KT = np.dot(T, np.array(X).T) pred = clf.predict(KT) with pytest.raises(ValueError): clf.predict(KT.T) assert_array_equal(clf.dual_coef_, [[-0.25, .25]]) assert_array_equal(clf.support_, [1, 3]) assert_array_equal(clf.intercept_, [0]) assert_array_almost_equal(clf.support_, [1, 3]) assert_array_equal(pred, true_result) # Gram matrix for test data but compute KT[i,j] # for support vectors j only. KT = np.zeros_like(KT) for i in range(len(T)): for j in clf.support_: KT[i, j] = np.dot(T[i], X[j]) pred = clf.predict(KT) assert_array_equal(pred, true_result) # same as before, but using a callable function instead of the kernel # matrix. kernel is just a linear kernel kfunc = lambda x, y: np.dot(x, y.T) clf = svm.SVC(kernel=kfunc) clf.fit(np.array(X), Y) pred = clf.predict(T) assert_array_equal(clf.dual_coef_, [[-0.25, .25]]) assert_array_equal(clf.intercept_, [0]) assert_array_almost_equal(clf.support_, [1, 3]) assert_array_equal(pred, true_result) # test a precomputed kernel with the iris dataset # and check parameters against a linear SVC clf = svm.SVC(kernel='precomputed') clf2 = svm.SVC(kernel='linear') K = np.dot(iris.data, iris.data.T) clf.fit(K, iris.target) clf2.fit(iris.data, iris.target) pred = clf.predict(K) assert_array_almost_equal(clf.support_, clf2.support_) assert_array_almost_equal(clf.dual_coef_, clf2.dual_coef_) assert_array_almost_equal(clf.intercept_, clf2.intercept_) assert_almost_equal(np.mean(pred == iris.target), .99, decimal=2) # Gram matrix for test data but compute KT[i,j] # for support vectors j only. K = np.zeros_like(K) for i in range(len(iris.data)): for j in clf.support_: K[i, j] = np.dot(iris.data[i], iris.data[j]) pred = clf.predict(K) assert_almost_equal(np.mean(pred == iris.target), .99, decimal=2) clf = svm.SVC(kernel=kfunc) clf.fit(iris.data, iris.target) assert_almost_equal(np.mean(pred == iris.target), .99, decimal=2) def test_svr(): # Test Support Vector Regression diabetes = datasets.load_diabetes() for clf in (svm.NuSVR(kernel='linear', nu=.4, C=1.0), svm.NuSVR(kernel='linear', nu=.4, C=10.), svm.SVR(kernel='linear', C=10.), svm.LinearSVR(C=10.), svm.LinearSVR(C=10.)): clf.fit(diabetes.data, diabetes.target) assert clf.score(diabetes.data, diabetes.target) > 0.02 # non-regression test; previously, BaseLibSVM would check that # len(np.unique(y)) < 2, which must only be done for SVC svm.SVR().fit(diabetes.data, np.ones(len(diabetes.data))) svm.LinearSVR().fit(diabetes.data, np.ones(len(diabetes.data))) def test_linearsvr(): # check that SVR(kernel='linear') and LinearSVC() give # comparable results diabetes = datasets.load_diabetes() lsvr = svm.LinearSVR(C=1e3).fit(diabetes.data, diabetes.target) score1 = lsvr.score(diabetes.data, diabetes.target) svr = svm.SVR(kernel='linear', C=1e3).fit(diabetes.data, diabetes.target) score2 = svr.score(diabetes.data, diabetes.target) assert_allclose(np.linalg.norm(lsvr.coef_), np.linalg.norm(svr.coef_), 1, 0.0001) assert_almost_equal(score1, score2, 2) def test_linearsvr_fit_sampleweight(): # check correct result when sample_weight is 1 # check that SVR(kernel='linear') and LinearSVC() give # comparable results diabetes = datasets.load_diabetes() n_samples = len(diabetes.target) unit_weight = np.ones(n_samples) lsvr = svm.LinearSVR(C=1e3, tol=1e-12, max_iter=10000).fit( diabetes.data, diabetes.target, sample_weight=unit_weight) score1 = lsvr.score(diabetes.data, diabetes.target) lsvr_no_weight = svm.LinearSVR(C=1e3, tol=1e-12, max_iter=10000).fit( diabetes.data, diabetes.target) score2 = lsvr_no_weight.score(diabetes.data, diabetes.target) assert_allclose(np.linalg.norm(lsvr.coef_), np.linalg.norm(lsvr_no_weight.coef_), 1, 0.0001) assert_almost_equal(score1, score2, 2) # check that fit(X) = fit([X1, X2, X3],sample_weight = [n1, n2, n3]) where # X = X1 repeated n1 times, X2 repeated n2 times and so forth random_state = check_random_state(0) random_weight = random_state.randint(0, 10, n_samples) lsvr_unflat = svm.LinearSVR(C=1e3, tol=1e-12, max_iter=10000).fit( diabetes.data, diabetes.target, sample_weight=random_weight) score3 = lsvr_unflat.score(diabetes.data, diabetes.target, sample_weight=random_weight) X_flat = np.repeat(diabetes.data, random_weight, axis=0) y_flat = np.repeat(diabetes.target, random_weight, axis=0) lsvr_flat = svm.LinearSVR(C=1e3, tol=1e-12, max_iter=10000).fit( X_flat, y_flat) score4 = lsvr_flat.score(X_flat, y_flat) assert_almost_equal(score3, score4, 2) def test_svr_errors(): X = [[0.0], [1.0]] y = [0.0, 0.5] # Bad kernel clf = svm.SVR(kernel=lambda x, y: np.array([[1.0]])) clf.fit(X, y) with pytest.raises(ValueError): clf.predict(X) def test_oneclass(): # Test OneClassSVM clf = svm.OneClassSVM() clf.fit(X) pred = clf.predict(T) assert_array_equal(pred, [1, -1, -1]) assert pred.dtype == np.dtype('intp') assert_array_almost_equal(clf.intercept_, [-1.218], decimal=3) assert_array_almost_equal(clf.dual_coef_, [[0.750, 0.750, 0.750, 0.750]], decimal=3) with pytest.raises(AttributeError): (lambda: clf.coef_)() def test_oneclass_decision_function(): # Test OneClassSVM decision function clf = svm.OneClassSVM() rnd = check_random_state(2) # Generate train data X = 0.3 * rnd.randn(100, 2) X_train = np.r_[X + 2, X - 2] # Generate some regular novel observations X = 0.3 * rnd.randn(20, 2) X_test = np.r_[X + 2, X - 2] # Generate some abnormal novel observations X_outliers = rnd.uniform(low=-4, high=4, size=(20, 2)) # fit the model clf = svm.OneClassSVM(nu=0.1, kernel="rbf", gamma=0.1) clf.fit(X_train) # predict things y_pred_test = clf.predict(X_test) assert np.mean(y_pred_test == 1) > .9 y_pred_outliers = clf.predict(X_outliers) assert np.mean(y_pred_outliers == -1) > .9 dec_func_test = clf.decision_function(X_test) assert_array_equal((dec_func_test > 0).ravel(), y_pred_test == 1) dec_func_outliers = clf.decision_function(X_outliers) assert_array_equal((dec_func_outliers > 0).ravel(), y_pred_outliers == 1) def test_oneclass_score_samples(): X_train = [[1, 1], [1, 2], [2, 1]] clf = svm.OneClassSVM(gamma=1).fit(X_train) assert_array_equal(clf.score_samples([[2., 2.]]), clf.decision_function([[2., 2.]]) + clf.offset_) def test_tweak_params(): # Make sure some tweaking of parameters works. # We change clf.dual_coef_ at run time and expect .predict() to change # accordingly. Notice that this is not trivial since it involves a lot # of C/Python copying in the libsvm bindings. # The success of this test ensures that the mapping between libsvm and # the python classifier is complete. clf = svm.SVC(kernel='linear', C=1.0) clf.fit(X, Y) assert_array_equal(clf.dual_coef_, [[-.25, .25]]) assert_array_equal(clf.predict([[-.1, -.1]]), [1]) clf._dual_coef_ = np.array([[.0, 1.]]) assert_array_equal(clf.predict([[-.1, -.1]]), [2]) def test_probability(): # Predict probabilities using SVC # This uses cross validation, so we use a slightly bigger testing set. for clf in (svm.SVC(probability=True, random_state=0, C=1.0), svm.NuSVC(probability=True, random_state=0)): clf.fit(iris.data, iris.target) prob_predict = clf.predict_proba(iris.data) assert_array_almost_equal( np.sum(prob_predict, 1), np.ones(iris.data.shape[0])) assert np.mean(np.argmax(prob_predict, 1) == clf.predict(iris.data)) > 0.9 assert_almost_equal(clf.predict_proba(iris.data), np.exp(clf.predict_log_proba(iris.data)), 8) def test_decision_function(): # Test decision_function # Sanity check, test that decision_function implemented in python # returns the same as the one in libsvm # multi class: clf = svm.SVC(kernel='linear', C=0.1, decision_function_shape='ovo').fit(iris.data, iris.target) dec = np.dot(iris.data, clf.coef_.T) + clf.intercept_ assert_array_almost_equal(dec, clf.decision_function(iris.data)) # binary: clf.fit(X, Y) dec = np.dot(X, clf.coef_.T) + clf.intercept_ prediction = clf.predict(X) assert_array_almost_equal(dec.ravel(), clf.decision_function(X)) assert_array_almost_equal( prediction, clf.classes_[(clf.decision_function(X) > 0).astype(np.int)]) expected = np.array([-1., -0.66, -1., 0.66, 1., 1.]) assert_array_almost_equal(clf.decision_function(X), expected, 2) # kernel binary: clf = svm.SVC(kernel='rbf', gamma=1, decision_function_shape='ovo') clf.fit(X, Y) rbfs = rbf_kernel(X, clf.support_vectors_, gamma=clf.gamma) dec = np.dot(rbfs, clf.dual_coef_.T) + clf.intercept_ assert_array_almost_equal(dec.ravel(), clf.decision_function(X)) @pytest.mark.parametrize('SVM', (svm.SVC, svm.NuSVC)) def test_decision_function_shape(SVM): # check that decision_function_shape='ovr' or 'ovo' gives # correct shape and is consistent with predict clf = SVM(kernel='linear', decision_function_shape='ovr').fit(iris.data, iris.target) dec = clf.decision_function(iris.data) assert dec.shape == (len(iris.data), 3) assert_array_equal(clf.predict(iris.data), np.argmax(dec, axis=1)) # with five classes: X, y = make_blobs(n_samples=80, centers=5, random_state=0) X_train, X_test, y_train, y_test = train_test_split(X, y, random_state=0) clf = SVM(kernel='linear', decision_function_shape='ovr').fit(X_train, y_train) dec = clf.decision_function(X_test) assert dec.shape == (len(X_test), 5) assert_array_equal(clf.predict(X_test), np.argmax(dec, axis=1)) # check shape of ovo_decition_function=True clf = SVM(kernel='linear', decision_function_shape='ovo').fit(X_train, y_train) dec = clf.decision_function(X_train) assert dec.shape == (len(X_train), 10) with pytest.raises(ValueError, match="must be either 'ovr' or 'ovo'"): SVM(decision_function_shape='bad').fit(X_train, y_train) def test_svr_predict(): # Test SVR's decision_function # Sanity check, test that predict implemented in python # returns the same as the one in libsvm X = iris.data y = iris.target # linear kernel reg = svm.SVR(kernel='linear', C=0.1).fit(X, y) dec = np.dot(X, reg.coef_.T) + reg.intercept_ assert_array_almost_equal(dec.ravel(), reg.predict(X).ravel()) # rbf kernel reg = svm.SVR(kernel='rbf', gamma=1).fit(X, y) rbfs = rbf_kernel(X, reg.support_vectors_, gamma=reg.gamma) dec = np.dot(rbfs, reg.dual_coef_.T) + reg.intercept_ assert_array_almost_equal(dec.ravel(), reg.predict(X).ravel()) def test_weight(): # Test class weights clf = svm.SVC(class_weight={1: 0.1}) # we give a small weights to class 1 clf.fit(X, Y) # so all predicted values belong to class 2 assert_array_almost_equal(clf.predict(X), [2] * 6) X_, y_ = make_classification(n_samples=200, n_features=10, weights=[0.833, 0.167], random_state=2) for clf in (linear_model.LogisticRegression(), svm.LinearSVC(random_state=0), svm.SVC()): clf.set_params(class_weight={0: .1, 1: 10}) clf.fit(X_[:100], y_[:100]) y_pred = clf.predict(X_[100:]) assert f1_score(y_[100:], y_pred) > .3 @pytest.mark.parametrize("estimator", [svm.SVC(C=1e-2), svm.NuSVC()]) def test_svm_classifier_sided_sample_weight(estimator): # fit a linear SVM and check that giving more weight to opposed samples # in the space will flip the decision toward these samples. X = [[-2, 0], [-1, -1], [0, -2], [0, 2], [1, 1], [2, 0]] estimator.set_params(kernel='linear') # check that with unit weights, a sample is supposed to be predicted on # the boundary sample_weight = [1] * 6 estimator.fit(X, Y, sample_weight=sample_weight) y_pred = estimator.decision_function([[-1., 1.]]) assert y_pred == pytest.approx(0) # give more weights to opposed samples sample_weight = [10., .1, .1, .1, .1, 10] estimator.fit(X, Y, sample_weight=sample_weight) y_pred = estimator.decision_function([[-1., 1.]]) assert y_pred < 0 sample_weight = [1., .1, 10., 10., .1, .1] estimator.fit(X, Y, sample_weight=sample_weight) y_pred = estimator.decision_function([[-1., 1.]]) assert y_pred > 0 @pytest.mark.parametrize( "estimator", [svm.SVR(C=1e-2), svm.NuSVR(C=1e-2)] ) def test_svm_regressor_sided_sample_weight(estimator): # similar test to test_svm_classifier_sided_sample_weight but for # SVM regressors X = [[-2, 0], [-1, -1], [0, -2], [0, 2], [1, 1], [2, 0]] estimator.set_params(kernel='linear') # check that with unit weights, a sample is supposed to be predicted on # the boundary sample_weight = [1] * 6 estimator.fit(X, Y, sample_weight=sample_weight) y_pred = estimator.predict([[-1., 1.]]) assert y_pred == pytest.approx(1.5) # give more weights to opposed samples sample_weight = [10., .1, .1, .1, .1, 10] estimator.fit(X, Y, sample_weight=sample_weight) y_pred = estimator.predict([[-1., 1.]]) assert y_pred < 1.5 sample_weight = [1., .1, 10., 10., .1, .1] estimator.fit(X, Y, sample_weight=sample_weight) y_pred = estimator.predict([[-1., 1.]]) assert y_pred > 1.5 def test_svm_equivalence_sample_weight_C(): # test that rescaling all samples is the same as changing C clf = svm.SVC() clf.fit(X, Y) dual_coef_no_weight = clf.dual_coef_ clf.set_params(C=100) clf.fit(X, Y, sample_weight=np.repeat(0.01, len(X))) assert_allclose(dual_coef_no_weight, clf.dual_coef_) @pytest.mark.parametrize( "Estimator, err_msg", [(svm.SVC, 'Invalid input - all samples have zero or negative weights.'), (svm.NuSVC, '(negative dimensions are not allowed|nu is infeasible)'), (svm.SVR, 'Invalid input - all samples have zero or negative weights.'), (svm.NuSVR, 'Invalid input - all samples have zero or negative weights.'), (svm.OneClassSVM, 'Invalid input - all samples have zero or negative weights.') ], ids=['SVC', 'NuSVC', 'SVR', 'NuSVR', 'OneClassSVM'] ) @pytest.mark.parametrize( "sample_weight", [[0] * len(Y), [-0.3] * len(Y)], ids=['weights-are-zero', 'weights-are-negative'] ) def test_negative_sample_weights_mask_all_samples(Estimator, err_msg, sample_weight): est = Estimator(kernel='linear') with pytest.raises(ValueError, match=err_msg): est.fit(X, Y, sample_weight=sample_weight) @pytest.mark.parametrize( "Classifier, err_msg", [(svm.SVC, 'Invalid input - all samples with positive weights have the same label'), (svm.NuSVC, 'specified nu is infeasible')], ids=['SVC', 'NuSVC'] ) @pytest.mark.parametrize( "sample_weight", [[0, -0.5, 0, 1, 1, 1], [1, 1, 1, 0, -0.1, -0.3]], ids=['mask-label-1', 'mask-label-2'] ) def test_negative_weights_svc_leave_just_one_label(Classifier, err_msg, sample_weight): clf = Classifier(kernel='linear') with pytest.raises(ValueError, match=err_msg): clf.fit(X, Y, sample_weight=sample_weight) @pytest.mark.parametrize( "Classifier, model", [(svm.SVC, {'when-left': [0.3998, 0.4], 'when-right': [0.4, 0.3999]}), (svm.NuSVC, {'when-left': [0.3333, 0.3333], 'when-right': [0.3333, 0.3333]})], ids=['SVC', 'NuSVC'] ) @pytest.mark.parametrize( "sample_weight, mask_side", [([1, -0.5, 1, 1, 1, 1], 'when-left'), ([1, 1, 1, 0, 1, 1], 'when-right')], ids=['partial-mask-label-1', 'partial-mask-label-2'] ) def test_negative_weights_svc_leave_two_labels(Classifier, model, sample_weight, mask_side): clf = Classifier(kernel='linear') clf.fit(X, Y, sample_weight=sample_weight) assert_allclose(clf.coef_, [model[mask_side]], rtol=1e-3) @pytest.mark.parametrize( "Estimator", [svm.SVC, svm.NuSVC, svm.NuSVR], ids=['SVC', 'NuSVC', 'NuSVR'] ) @pytest.mark.parametrize( "sample_weight", [[1, -0.5, 1, 1, 1, 1], [1, 1, 1, 0, 1, 1]], ids=['partial-mask-label-1', 'partial-mask-label-2'] ) def test_negative_weight_equal_coeffs(Estimator, sample_weight): # model generates equal coefficients est = Estimator(kernel='linear') est.fit(X, Y, sample_weight=sample_weight) coef = np.abs(est.coef_).ravel() assert coef[0] == pytest.approx(coef[1], rel=1e-3) @ignore_warnings(category=UndefinedMetricWarning) def test_auto_weight(): # Test class weights for imbalanced data from sklearn.linear_model import LogisticRegression # We take as dataset the two-dimensional projection of iris so # that it is not separable and remove half of predictors from # class 1. # We add one to the targets as a non-regression test: # class_weight="balanced" # used to work only when the labels where a range [0..K). from sklearn.utils import compute_class_weight X, y = iris.data[:, :2], iris.target + 1 unbalanced = np.delete(np.arange(y.size), np.where(y > 2)[0][::2]) classes = np.unique(y[unbalanced]) class_weights = compute_class_weight('balanced', classes=classes, y=y[unbalanced]) assert np.argmax(class_weights) == 2 for clf in (svm.SVC(kernel='linear'), svm.LinearSVC(random_state=0), LogisticRegression()): # check that score is better when class='balanced' is set. y_pred = clf.fit(X[unbalanced], y[unbalanced]).predict(X) clf.set_params(class_weight='balanced') y_pred_balanced = clf.fit(X[unbalanced], y[unbalanced],).predict(X) assert (metrics.f1_score(y, y_pred, average='macro') <= metrics.f1_score(y, y_pred_balanced, average='macro')) def test_bad_input(): # Test that it gives proper exception on deficient input # impossible value of C with pytest.raises(ValueError): svm.SVC(C=-1).fit(X, Y) # impossible value of nu clf = svm.NuSVC(nu=0.0) with pytest.raises(ValueError): clf.fit(X, Y) Y2 = Y[:-1] # wrong dimensions for labels with pytest.raises(ValueError): clf.fit(X, Y2) # Test with arrays that are non-contiguous. for clf in (svm.SVC(), svm.LinearSVC(random_state=0)): Xf = np.asfortranarray(X) assert not Xf.flags['C_CONTIGUOUS'] yf = np.ascontiguousarray(np.tile(Y, (2, 1)).T) yf = yf[:, -1] assert not yf.flags['F_CONTIGUOUS'] assert not yf.flags['C_CONTIGUOUS'] clf.fit(Xf, yf) assert_array_equal(clf.predict(T), true_result) # error for precomputed kernelsx clf = svm.SVC(kernel='precomputed') with pytest.raises(ValueError): clf.fit(X, Y) # predict with sparse input when trained with dense clf = svm.SVC().fit(X, Y) with pytest.raises(ValueError): clf.predict(sparse.lil_matrix(X)) Xt = np.array(X).T clf.fit(np.dot(X, Xt), Y) with pytest.raises(ValueError): clf.predict(X) clf = svm.SVC() clf.fit(X, Y) with pytest.raises(ValueError): clf.predict(Xt) @pytest.mark.parametrize( 'Estimator, data', [(svm.SVC, datasets.load_iris(return_X_y=True)), (svm.NuSVC, datasets.load_iris(return_X_y=True)), (svm.SVR, datasets.load_diabetes(return_X_y=True)), (svm.NuSVR, datasets.load_diabetes(return_X_y=True)), (svm.OneClassSVM, datasets.load_iris(return_X_y=True))] ) def test_svm_gamma_error(Estimator, data): X, y = data est = Estimator(gamma='auto_deprecated') err_msg = "When 'gamma' is a string, it should be either 'scale' or 'auto'" with pytest.raises(ValueError, match=err_msg): est.fit(X, y) def test_unicode_kernel(): # Test that a unicode kernel name does not cause a TypeError clf = svm.SVC(kernel='linear', probability=True) clf.fit(X, Y) clf.predict_proba(T) _libsvm.cross_validation(iris.data, iris.target.astype(np.float64), 5, kernel='linear', random_seed=0) def test_sparse_precomputed(): clf = svm.SVC(kernel='precomputed') sparse_gram = sparse.csr_matrix([[1, 0], [0, 1]]) with pytest.raises(TypeError, match="Sparse precomputed"): clf.fit(sparse_gram, [0, 1]) def test_sparse_fit_support_vectors_empty(): # Regression test for #14893 X_train = sparse.csr_matrix([[0, 1, 0, 0], [0, 0, 0, 1], [0, 0, 1, 0], [0, 0, 0, 1]]) y_train = np.array([0.04, 0.04, 0.10, 0.16]) model = svm.SVR(kernel='linear') model.fit(X_train, y_train) assert not model.support_vectors_.data.size assert not model.dual_coef_.data.size def test_linearsvc_parameters(): # Test possible parameter combinations in LinearSVC # Generate list of possible parameter combinations losses = ['hinge', 'squared_hinge', 'logistic_regression', 'foo'] penalties, duals = ['l1', 'l2', 'bar'], [True, False] X, y = make_classification(n_samples=5, n_features=5) for loss, penalty, dual in itertools.product(losses, penalties, duals): clf = svm.LinearSVC(penalty=penalty, loss=loss, dual=dual) if ((loss, penalty) == ('hinge', 'l1') or (loss, penalty, dual) == ('hinge', 'l2', False) or (penalty, dual) == ('l1', True) or loss == 'foo' or penalty == 'bar'): with pytest.raises(ValueError, match="Unsupported set of " "arguments.*penalty='%s.*loss='%s.*dual=%s" % (penalty, loss, dual)): clf.fit(X, y) else: clf.fit(X, y) # Incorrect loss value - test if explicit error message is raised with pytest.raises(ValueError, match=".*loss='l3' is not supported.*"): svm.LinearSVC(loss="l3").fit(X, y) def test_linear_svx_uppercase_loss_penality_raises_error(): # Check if Upper case notation raises error at _fit_liblinear # which is called by fit X, y = [[0.0], [1.0]], [0, 1] assert_raise_message(ValueError, "loss='SQuared_hinge' is not supported", svm.LinearSVC(loss="SQuared_hinge").fit, X, y) assert_raise_message(ValueError, ("The combination of penalty='L2'" " and loss='squared_hinge' is not supported"), svm.LinearSVC(penalty="L2").fit, X, y) def test_linearsvc(): # Test basic routines using LinearSVC clf = svm.LinearSVC(random_state=0).fit(X, Y) # by default should have intercept assert clf.fit_intercept assert_array_equal(clf.predict(T), true_result) assert_array_almost_equal(clf.intercept_, [0], decimal=3) # the same with l1 penalty clf = svm.LinearSVC(penalty='l1', loss='squared_hinge', dual=False, random_state=0).fit(X, Y) assert_array_equal(clf.predict(T), true_result) # l2 penalty with dual formulation clf = svm.LinearSVC(penalty='l2', dual=True, random_state=0).fit(X, Y) assert_array_equal(clf.predict(T), true_result) # l2 penalty, l1 loss clf = svm.LinearSVC(penalty='l2', loss='hinge', dual=True, random_state=0) clf.fit(X, Y) assert_array_equal(clf.predict(T), true_result) # test also decision function dec = clf.decision_function(T) res = (dec > 0).astype(np.int) + 1 assert_array_equal(res, true_result) def test_linearsvc_crammer_singer(): # Test LinearSVC with crammer_singer multi-class svm ovr_clf = svm.LinearSVC(random_state=0).fit(iris.data, iris.target) cs_clf = svm.LinearSVC(multi_class='crammer_singer', random_state=0) cs_clf.fit(iris.data, iris.target) # similar prediction for ovr and crammer-singer: assert (ovr_clf.predict(iris.data) == cs_clf.predict(iris.data)).mean() > .9 # classifiers shouldn't be the same assert (ovr_clf.coef_ != cs_clf.coef_).all() # test decision function assert_array_equal(cs_clf.predict(iris.data), np.argmax(cs_clf.decision_function(iris.data), axis=1)) dec_func = np.dot(iris.data, cs_clf.coef_.T) + cs_clf.intercept_ assert_array_almost_equal(dec_func, cs_clf.decision_function(iris.data)) def test_linearsvc_fit_sampleweight(): # check correct result when sample_weight is 1 n_samples = len(X) unit_weight = np.ones(n_samples) clf = svm.LinearSVC(random_state=0).fit(X, Y) clf_unitweight = svm.LinearSVC(random_state=0, tol=1e-12, max_iter=1000).\ fit(X, Y, sample_weight=unit_weight) # check if same as sample_weight=None assert_array_equal(clf_unitweight.predict(T), clf.predict(T)) assert_allclose(clf.coef_, clf_unitweight.coef_, 1, 0.0001) # check that fit(X) = fit([X1, X2, X3],sample_weight = [n1, n2, n3]) where # X = X1 repeated n1 times, X2 repeated n2 times and so forth random_state = check_random_state(0) random_weight = random_state.randint(0, 10, n_samples) lsvc_unflat = svm.LinearSVC(random_state=0, tol=1e-12, max_iter=1000).\ fit(X, Y, sample_weight=random_weight) pred1 = lsvc_unflat.predict(T) X_flat = np.repeat(X, random_weight, axis=0) y_flat = np.repeat(Y, random_weight, axis=0) lsvc_flat = svm.LinearSVC(random_state=0, tol=1e-12, max_iter=1000).fit( X_flat, y_flat) pred2 = lsvc_flat.predict(T) assert_array_equal(pred1, pred2) assert_allclose(lsvc_unflat.coef_, lsvc_flat.coef_, 1, 0.0001) def test_crammer_singer_binary(): # Test Crammer-Singer formulation in the binary case X, y = make_classification(n_classes=2, random_state=0) for fit_intercept in (True, False): acc = svm.LinearSVC(fit_intercept=fit_intercept, multi_class="crammer_singer", random_state=0).fit(X, y).score(X, y) assert acc > 0.9 def test_linearsvc_iris(): # Test that LinearSVC gives plausible predictions on the iris dataset # Also, test symbolic class names (classes_). target = iris.target_names[iris.target] clf = svm.LinearSVC(random_state=0).fit(iris.data, target) assert set(clf.classes_) == set(iris.target_names) assert np.mean(clf.predict(iris.data) == target) > 0.8 dec = clf.decision_function(iris.data) pred = iris.target_names[np.argmax(dec, 1)] assert_array_equal(pred, clf.predict(iris.data)) def test_dense_liblinear_intercept_handling(classifier=svm.LinearSVC): # Test that dense liblinear honours intercept_scaling param X = [[2, 1], [3, 1], [1, 3], [2, 3]] y = [0, 0, 1, 1] clf = classifier(fit_intercept=True, penalty='l1', loss='squared_hinge', dual=False, C=4, tol=1e-7, random_state=0) assert clf.intercept_scaling == 1, clf.intercept_scaling assert clf.fit_intercept # when intercept_scaling is low the intercept value is highly "penalized" # by regularization clf.intercept_scaling = 1 clf.fit(X, y) assert_almost_equal(clf.intercept_, 0, decimal=5) # when intercept_scaling is sufficiently high, the intercept value # is not affected by regularization clf.intercept_scaling = 100 clf.fit(X, y) intercept1 = clf.intercept_ assert intercept1 < -1 # when intercept_scaling is sufficiently high, the intercept value # doesn't depend on intercept_scaling value clf.intercept_scaling = 1000 clf.fit(X, y) intercept2 = clf.intercept_ assert_array_almost_equal(intercept1, intercept2, decimal=2) def test_liblinear_set_coef(): # multi-class case clf = svm.LinearSVC().fit(iris.data, iris.target) values = clf.decision_function(iris.data) clf.coef_ = clf.coef_.copy() clf.intercept_ = clf.intercept_.copy() values2 = clf.decision_function(iris.data) assert_array_almost_equal(values, values2) # binary-class case X = [[2, 1], [3, 1], [1, 3], [2, 3]] y = [0, 0, 1, 1] clf = svm.LinearSVC().fit(X, y) values = clf.decision_function(X) clf.coef_ = clf.coef_.copy() clf.intercept_ = clf.intercept_.copy() values2 = clf.decision_function(X) assert_array_equal(values, values2) def test_immutable_coef_property(): # Check that primal coef modification are not silently ignored svms = [ svm.SVC(kernel='linear').fit(iris.data, iris.target), svm.NuSVC(kernel='linear').fit(iris.data, iris.target), svm.SVR(kernel='linear').fit(iris.data, iris.target), svm.NuSVR(kernel='linear').fit(iris.data, iris.target), svm.OneClassSVM(kernel='linear').fit(iris.data), ] for clf in svms: with pytest.raises(AttributeError): clf.__setattr__('coef_', np.arange(3)) with pytest.raises((RuntimeError, ValueError)): clf.coef_.__setitem__((0, 0), 0) def test_linearsvc_verbose(): # stdout: redirect import os stdout = os.dup(1) # save original stdout os.dup2(os.pipe()[1], 1) # replace it # actual call clf = svm.LinearSVC(verbose=1) clf.fit(X, Y) # stdout: restore os.dup2(stdout, 1) # restore original stdout def test_svc_clone_with_callable_kernel(): # create SVM with callable linear kernel, check that results are the same # as with built-in linear kernel svm_callable = svm.SVC(kernel=lambda x, y: np.dot(x, y.T), probability=True, random_state=0, decision_function_shape='ovr') # clone for checking clonability with lambda functions.. svm_cloned = base.clone(svm_callable) svm_cloned.fit(iris.data, iris.target) svm_builtin = svm.SVC(kernel='linear', probability=True, random_state=0, decision_function_shape='ovr') svm_builtin.fit(iris.data, iris.target) assert_array_almost_equal(svm_cloned.dual_coef_, svm_builtin.dual_coef_) assert_array_almost_equal(svm_cloned.intercept_, svm_builtin.intercept_) assert_array_equal(svm_cloned.predict(iris.data), svm_builtin.predict(iris.data)) assert_array_almost_equal(svm_cloned.predict_proba(iris.data), svm_builtin.predict_proba(iris.data), decimal=4) assert_array_almost_equal(svm_cloned.decision_function(iris.data), svm_builtin.decision_function(iris.data)) def test_svc_bad_kernel(): svc = svm.SVC(kernel=lambda x, y: x) with pytest.raises(ValueError): svc.fit(X, Y) def test_timeout(): a = svm.SVC(kernel=lambda x, y: np.dot(x, y.T), probability=True, random_state=0, max_iter=1) assert_warns(ConvergenceWarning, a.fit, np.array(X), Y) def test_unfitted(): X = "foo!" # input validation not required when SVM not fitted clf = svm.SVC() with pytest.raises(Exception, match=r".*\bSVC\b.*\bnot\b.*\bfitted\b"): clf.predict(X) clf = svm.NuSVR() with pytest.raises(Exception, match=r".*\bNuSVR\b.*\bnot\b.*\bfitted\b"): clf.predict(X) # ignore convergence warnings from max_iter=1 @ignore_warnings def test_consistent_proba(): a = svm.SVC(probability=True, max_iter=1, random_state=0) proba_1 = a.fit(X, Y).predict_proba(X) a = svm.SVC(probability=True, max_iter=1, random_state=0) proba_2 = a.fit(X, Y).predict_proba(X) assert_array_almost_equal(proba_1, proba_2) def test_linear_svm_convergence_warnings(): # Test that warnings are raised if model does not converge lsvc = svm.LinearSVC(random_state=0, max_iter=2) assert_warns(ConvergenceWarning, lsvc.fit, X, Y) assert lsvc.n_iter_ == 2 lsvr = svm.LinearSVR(random_state=0, max_iter=2) assert_warns(ConvergenceWarning, lsvr.fit, iris.data, iris.target) assert lsvr.n_iter_ == 2 def test_svr_coef_sign(): # Test that SVR(kernel="linear") has coef_ with the right sign. # Non-regression test for #2933. X = np.random.RandomState(21).randn(10, 3) y = np.random.RandomState(12).randn(10) for svr in [svm.SVR(kernel='linear'), svm.NuSVR(kernel='linear'), svm.LinearSVR()]: svr.fit(X, y) assert_array_almost_equal( svr.predict(X), np.dot(X, svr.coef_.ravel()) + svr.intercept_ ) def test_linear_svc_intercept_scaling(): # Test that the right error message is thrown when intercept_scaling <= 0 for i in [-1, 0]: lsvc = svm.LinearSVC(intercept_scaling=i) msg = ('Intercept scaling is %r but needs to be greater than 0.' ' To disable fitting an intercept,' ' set fit_intercept=False.' % lsvc.intercept_scaling) assert_raise_message(ValueError, msg, lsvc.fit, X, Y) def test_lsvc_intercept_scaling_zero(): # Test that intercept_scaling is ignored when fit_intercept is False lsvc = svm.LinearSVC(fit_intercept=False) lsvc.fit(X, Y) assert lsvc.intercept_ == 0. def test_hasattr_predict_proba(): # Method must be (un)available before or after fit, switched by # `probability` param G = svm.SVC(probability=True) assert hasattr(G, 'predict_proba') G.fit(iris.data, iris.target) assert hasattr(G, 'predict_proba') G = svm.SVC(probability=False) assert not hasattr(G, 'predict_proba') G.fit(iris.data, iris.target) assert not hasattr(G, 'predict_proba') # Switching to `probability=True` after fitting should make # predict_proba available, but calling it must not work: G.probability = True assert hasattr(G, 'predict_proba') msg = "predict_proba is not available when fitted with probability=False" assert_raise_message(NotFittedError, msg, G.predict_proba, iris.data) def test_decision_function_shape_two_class(): for n_classes in [2, 3]: X, y = make_blobs(centers=n_classes, random_state=0) for estimator in [svm.SVC, svm.NuSVC]: clf = OneVsRestClassifier( estimator(decision_function_shape="ovr")).fit(X, y) assert len(clf.predict(X)) == len(y) def test_ovr_decision_function(): # One point from each quadrant represents one class X_train = np.array([[1, 1], [-1, 1], [-1, -1], [1, -1]]) y_train = [0, 1, 2, 3] # First point is closer to the decision boundaries than the second point base_points = np.array([[5, 5], [10, 10]]) # For all the quadrants (classes) X_test = np.vstack(( base_points * [1, 1], # Q1 base_points * [-1, 1], # Q2 base_points * [-1, -1], # Q3 base_points * [1, -1] # Q4 )) y_test = [0] * 2 + [1] * 2 + [2] * 2 + [3] * 2 clf = svm.SVC(kernel='linear', decision_function_shape='ovr') clf.fit(X_train, y_train) y_pred = clf.predict(X_test) # Test if the prediction is the same as y assert_array_equal(y_pred, y_test) deci_val = clf.decision_function(X_test) # Assert that the predicted class has the maximum value assert_array_equal(np.argmax(deci_val, axis=1), y_pred) # Get decision value at test points for the predicted class pred_class_deci_val = deci_val[range(8), y_pred].reshape((4, 2)) # Assert pred_class_deci_val > 0 here assert np.min(pred_class_deci_val) > 0.0 # Test if the first point has lower decision value on every quadrant # compared to the second point assert np.all(pred_class_deci_val[:, 0] < pred_class_deci_val[:, 1]) @pytest.mark.parametrize("SVCClass", [svm.SVC, svm.NuSVC]) def test_svc_invalid_break_ties_param(SVCClass): X, y = make_blobs(random_state=42) svm = SVCClass(kernel="linear", decision_function_shape='ovo', break_ties=True, random_state=42).fit(X, y) with pytest.raises(ValueError, match="break_ties must be False"): svm.predict(y) @pytest.mark.parametrize("SVCClass", [svm.SVC, svm.NuSVC]) def test_svc_ovr_tie_breaking(SVCClass): """Test if predict breaks ties in OVR mode. Related issue: https://github.com/scikit-learn/scikit-learn/issues/8277 """ X, y = make_blobs(random_state=27) xs = np.linspace(X[:, 0].min(), X[:, 0].max(), 1000) ys = np.linspace(X[:, 1].min(), X[:, 1].max(), 1000) xx, yy = np.meshgrid(xs, ys) svm = SVCClass(kernel="linear", decision_function_shape='ovr', break_ties=False, random_state=42).fit(X, y) pred = svm.predict(np.c_[xx.ravel(), yy.ravel()]) dv = svm.decision_function(np.c_[xx.ravel(), yy.ravel()]) assert not np.all(pred == np.argmax(dv, axis=1)) svm = SVCClass(kernel="linear", decision_function_shape='ovr', break_ties=True, random_state=42).fit(X, y) pred = svm.predict(np.c_[xx.ravel(), yy.ravel()]) dv = svm.decision_function(np.c_[xx.ravel(), yy.ravel()]) assert np.all(pred == np.argmax(dv, axis=1)) def test_gamma_auto(): X, y = [[0.0, 1.2], [1.0, 1.3]], [0, 1] assert_no_warnings(svm.SVC(kernel='linear').fit, X, y) assert_no_warnings(svm.SVC(kernel='precomputed').fit, X, y) def test_gamma_scale(): X, y = [[0.], [1.]], [0, 1] clf = svm.SVC() assert_no_warnings(clf.fit, X, y) assert_almost_equal(clf._gamma, 4) # X_var ~= 1 shouldn't raise warning, for when # gamma is not explicitly set. X, y = [[1, 2], [3, 2 * np.sqrt(6) / 3 + 2]], [0, 1] assert_no_warnings(clf.fit, X, y) @pytest.mark.parametrize( "SVM, params", [(LinearSVC, {'penalty': 'l1', 'loss': 'squared_hinge', 'dual': False}), (LinearSVC, {'penalty': 'l2', 'loss': 'squared_hinge', 'dual': True}), (LinearSVC, {'penalty': 'l2', 'loss': 'squared_hinge', 'dual': False}), (LinearSVC, {'penalty': 'l2', 'loss': 'hinge', 'dual': True}), (LinearSVR, {'loss': 'epsilon_insensitive', 'dual': True}), (LinearSVR, {'loss': 'squared_epsilon_insensitive', 'dual': True}), (LinearSVR, {'loss': 'squared_epsilon_insensitive', 'dual': True})] ) def test_linearsvm_liblinear_sample_weight(SVM, params): X = np.array([[1, 3], [1, 3], [1, 3], [1, 3], [2, 1], [2, 1], [2, 1], [2, 1], [3, 3], [3, 3], [3, 3], [3, 3], [4, 1], [4, 1], [4, 1], [4, 1]], dtype=np.dtype('float')) y = np.array([1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2], dtype=np.dtype('int')) X2 = np.vstack([X, X]) y2 = np.hstack([y, 3 - y]) sample_weight = np.ones(shape=len(y) * 2) sample_weight[len(y):] = 0 X2, y2, sample_weight = shuffle(X2, y2, sample_weight, random_state=0) base_estimator = SVM(random_state=42) base_estimator.set_params(**params) base_estimator.set_params(tol=1e-12, max_iter=1000) est_no_weight = base.clone(base_estimator).fit(X, y) est_with_weight = base.clone(base_estimator).fit( X2, y2, sample_weight=sample_weight ) for method in ("predict", "decision_function"): if hasattr(base_estimator, method): X_est_no_weight = getattr(est_no_weight, method)(X) X_est_with_weight = getattr(est_with_weight, method)(X) assert_allclose(X_est_no_weight, X_est_with_weight) def test_n_support_oneclass_svr(): # Make n_support is correct for oneclass and SVR (used to be # non-initialized) # this is a non regression test for issue #14774 X = np.array([[0], [0.44], [0.45], [0.46], [1]]) clf = svm.OneClassSVM() assert not hasattr(clf, 'n_support_') clf.fit(X) assert clf.n_support_ == clf.support_vectors_.shape[0] assert clf.n_support_.size == 1 assert clf.n_support_ == 3 y = np.arange(X.shape[0]) reg = svm.SVR().fit(X, y) assert reg.n_support_ == reg.support_vectors_.shape[0] assert reg.n_support_.size == 1 assert reg.n_support_ == 4 # TODO: Remove in 0.25 when probA_ and probB_ are deprecated @pytest.mark.parametrize("SVMClass, data", [ (svm.OneClassSVM, (X, )), (svm.SVR, (X, Y)) ]) @pytest.mark.parametrize("deprecated_prob", ["probA_", "probB_"]) def test_svm_probA_proB_deprecated(SVMClass, data, deprecated_prob): clf = SVMClass().fit(*data) msg = ("The {} attribute is deprecated in version 0.23 and will be " "removed in version 0.25.").format(deprecated_prob) with pytest.warns(FutureWarning, match=msg): getattr(clf, deprecated_prob) @pytest.mark.parametrize("Estimator", [svm.SVC, svm.SVR]) def test_custom_kernel_not_array_input(Estimator): """Test using a custom kernel that is not fed with array-like for floats""" data = ["A A", "A", "B", "B B", "A B"] X = np.array([[2, 0], [1, 0], [0, 1], [0, 2], [1, 1]]) # count encoding y = np.array([1, 1, 2, 2, 1]) def string_kernel(X1, X2): assert isinstance(X1[0], str) n_samples1 = _num_samples(X1) n_samples2 = _num_samples(X2) K = np.zeros((n_samples1, n_samples2)) for ii in range(n_samples1): for jj in range(ii, n_samples2): K[ii, jj] = X1[ii].count('A') * X2[jj].count('A') K[ii, jj] += X1[ii].count('B') * X2[jj].count('B') K[jj, ii] = K[ii, jj] return K K = string_kernel(data, data) assert_array_equal(np.dot(X, X.T), K) svc1 = Estimator(kernel=string_kernel).fit(data, y) svc2 = Estimator(kernel='linear').fit(X, y) svc3 = Estimator(kernel='precomputed').fit(K, y) assert svc1.score(data, y) == svc3.score(K, y) assert svc1.score(data, y) == svc2.score(X, y) if hasattr(svc1, 'decision_function'): # classifier assert_allclose(svc1.decision_function(data), svc2.decision_function(X)) assert_allclose(svc1.decision_function(data), svc3.decision_function(K)) assert_array_equal(svc1.predict(data), svc2.predict(X)) assert_array_equal(svc1.predict(data), svc3.predict(K)) else: # regressor assert_allclose(svc1.predict(data), svc2.predict(X)) assert_allclose(svc1.predict(data), svc3.predict(K))