import numpy as np import pytest from scipy import linalg from sklearn.cluster import KMeans from sklearn.covariance import LedoitWolf, ShrunkCovariance, ledoit_wolf from sklearn.datasets import make_blobs from sklearn.discriminant_analysis import ( LinearDiscriminantAnalysis, QuadraticDiscriminantAnalysis, _cov, ) from sklearn.preprocessing import StandardScaler from sklearn.utils import check_random_state from sklearn.utils._testing import ( _convert_container, assert_allclose, assert_almost_equal, assert_array_almost_equal, assert_array_equal, ) from sklearn.utils.fixes import _IS_WASM # Data is just 6 separable points in the plane X = np.array([[-2, -1], [-1, -1], [-1, -2], [1, 1], [1, 2], [2, 1]], dtype="f") y = np.array([1, 1, 1, 2, 2, 2]) y3 = np.array([1, 1, 2, 2, 3, 3]) # Degenerate data with only one feature (still should be separable) X1 = np.array( [[-2], [-1], [-1], [1], [1], [2]], dtype="f", ) # Data is just 9 separable points in the plane X6 = np.array( [[0, 0], [-2, -2], [-2, -1], [-1, -1], [-1, -2], [1, 3], [1, 2], [2, 1], [2, 2]] ) y6 = np.array([1, 1, 1, 1, 1, 2, 2, 2, 2]) y7 = np.array([1, 2, 3, 2, 3, 1, 2, 3, 1]) # Degenerate data with 1 feature (still should be separable) X7 = np.array([[-3], [-2], [-1], [-1], [0], [1], [1], [2], [3]]) # Data that has zero variance in one dimension and needs regularization X2 = np.array( [[-3, 0], [-2, 0], [-1, 0], [-1, 0], [0, 0], [1, 0], [1, 0], [2, 0], [3, 0]] ) # One element class y4 = np.array([1, 1, 1, 1, 1, 1, 1, 1, 2]) # Data with less samples in a class than n_features X5 = np.c_[np.arange(8), np.zeros((8, 3))] y5 = np.array([0, 0, 0, 0, 0, 1, 1, 1]) solver_shrinkage = [ ("svd", None), ("lsqr", None), ("eigen", None), ("lsqr", "auto"), ("lsqr", 0), ("lsqr", 0.43), ("eigen", "auto"), ("eigen", 0), ("eigen", 0.43), ] def test_lda_predict(): # Test LDA classification. # This checks that LDA implements fit and predict and returns correct # values for simple toy data. for test_case in solver_shrinkage: solver, shrinkage = test_case clf = LinearDiscriminantAnalysis(solver=solver, shrinkage=shrinkage) y_pred = clf.fit(X, y).predict(X) assert_array_equal(y_pred, y, "solver %s" % solver) # Assert that it works with 1D data y_pred1 = clf.fit(X1, y).predict(X1) assert_array_equal(y_pred1, y, "solver %s" % solver) # Test probability estimates y_proba_pred1 = clf.predict_proba(X1) assert_array_equal((y_proba_pred1[:, 1] > 0.5) + 1, y, "solver %s" % solver) y_log_proba_pred1 = clf.predict_log_proba(X1) assert_allclose( np.exp(y_log_proba_pred1), y_proba_pred1, rtol=1e-6, atol=1e-6, err_msg="solver %s" % solver, ) # Primarily test for commit 2f34950 -- "reuse" of priors y_pred3 = clf.fit(X, y3).predict(X) # LDA shouldn't be able to separate those assert np.any(y_pred3 != y3), "solver %s" % solver clf = LinearDiscriminantAnalysis(solver="svd", shrinkage="auto") with pytest.raises(NotImplementedError): clf.fit(X, y) clf = LinearDiscriminantAnalysis( solver="lsqr", shrinkage=0.1, covariance_estimator=ShrunkCovariance() ) with pytest.raises( ValueError, match=( "covariance_estimator and shrinkage " "parameters are not None. " "Only one of the two can be set." ), ): clf.fit(X, y) # test bad solver with covariance_estimator clf = LinearDiscriminantAnalysis(solver="svd", covariance_estimator=LedoitWolf()) with pytest.raises( ValueError, match="covariance estimator is not supported with svd" ): clf.fit(X, y) # test bad covariance estimator clf = LinearDiscriminantAnalysis( solver="lsqr", covariance_estimator=KMeans(n_clusters=2, n_init="auto") ) with pytest.raises(ValueError): clf.fit(X, y) @pytest.mark.parametrize("n_classes", [2, 3]) @pytest.mark.parametrize("solver", ["svd", "lsqr", "eigen"]) def test_lda_predict_proba(solver, n_classes): def generate_dataset(n_samples, centers, covariances, random_state=None): """Generate a multivariate normal data given some centers and covariances""" rng = check_random_state(random_state) X = np.vstack( [ rng.multivariate_normal(mean, cov, size=n_samples // len(centers)) for mean, cov in zip(centers, covariances) ] ) y = np.hstack( [[clazz] * (n_samples // len(centers)) for clazz in range(len(centers))] ) return X, y blob_centers = np.array([[0, 0], [-10, 40], [-30, 30]])[:n_classes] blob_stds = np.array([[[10, 10], [10, 100]]] * len(blob_centers)) X, y = generate_dataset( n_samples=90000, centers=blob_centers, covariances=blob_stds, random_state=42 ) lda = LinearDiscriminantAnalysis( solver=solver, store_covariance=True, shrinkage=None ).fit(X, y) # check that the empirical means and covariances are close enough to the # one used to generate the data assert_allclose(lda.means_, blob_centers, atol=1e-1) assert_allclose(lda.covariance_, blob_stds[0], atol=1) # implement the method to compute the probability given in The Elements # of Statistical Learning (cf. p.127, Sect. 4.4.5 "Logistic Regression # or LDA?") precision = linalg.inv(blob_stds[0]) alpha_k = [] alpha_k_0 = [] for clazz in range(len(blob_centers) - 1): alpha_k.append( np.dot(precision, (blob_centers[clazz] - blob_centers[-1])[:, np.newaxis]) ) alpha_k_0.append( np.dot( -0.5 * (blob_centers[clazz] + blob_centers[-1])[np.newaxis, :], alpha_k[-1], ) ) sample = np.array([[-22, 22]]) def discriminant_func(sample, coef, intercept, clazz): return np.exp(intercept[clazz] + np.dot(sample, coef[clazz])).item() prob = np.array( [ float( discriminant_func(sample, alpha_k, alpha_k_0, clazz) / ( 1 + sum( [ discriminant_func(sample, alpha_k, alpha_k_0, clazz) for clazz in range(n_classes - 1) ] ) ) ) for clazz in range(n_classes - 1) ] ) prob_ref = 1 - np.sum(prob) # check the consistency of the computed probability # all probabilities should sum to one prob_ref_2 = float( 1 / ( 1 + sum( [ discriminant_func(sample, alpha_k, alpha_k_0, clazz) for clazz in range(n_classes - 1) ] ) ) ) assert prob_ref == pytest.approx(prob_ref_2) # check that the probability of LDA are close to the theoretical # probabilities assert_allclose( lda.predict_proba(sample), np.hstack([prob, prob_ref])[np.newaxis], atol=1e-2 ) def test_lda_priors(): # Test priors (negative priors) priors = np.array([0.5, -0.5]) clf = LinearDiscriminantAnalysis(priors=priors) msg = "priors must be non-negative" with pytest.raises(ValueError, match=msg): clf.fit(X, y) # Test that priors passed as a list are correctly handled (run to see if # failure) clf = LinearDiscriminantAnalysis(priors=[0.5, 0.5]) clf.fit(X, y) # Test that priors always sum to 1 priors = np.array([0.5, 0.6]) prior_norm = np.array([0.45, 0.55]) clf = LinearDiscriminantAnalysis(priors=priors) with pytest.warns(UserWarning): clf.fit(X, y) assert_array_almost_equal(clf.priors_, prior_norm, 2) def test_lda_coefs(): # Test if the coefficients of the solvers are approximately the same. n_features = 2 n_classes = 2 n_samples = 1000 X, y = make_blobs( n_samples=n_samples, n_features=n_features, centers=n_classes, random_state=11 ) clf_lda_svd = LinearDiscriminantAnalysis(solver="svd") clf_lda_lsqr = LinearDiscriminantAnalysis(solver="lsqr") clf_lda_eigen = LinearDiscriminantAnalysis(solver="eigen") clf_lda_svd.fit(X, y) clf_lda_lsqr.fit(X, y) clf_lda_eigen.fit(X, y) assert_array_almost_equal(clf_lda_svd.coef_, clf_lda_lsqr.coef_, 1) assert_array_almost_equal(clf_lda_svd.coef_, clf_lda_eigen.coef_, 1) assert_array_almost_equal(clf_lda_eigen.coef_, clf_lda_lsqr.coef_, 1) def test_lda_transform(): # Test LDA transform. clf = LinearDiscriminantAnalysis(solver="svd", n_components=1) X_transformed = clf.fit(X, y).transform(X) assert X_transformed.shape[1] == 1 clf = LinearDiscriminantAnalysis(solver="eigen", n_components=1) X_transformed = clf.fit(X, y).transform(X) assert X_transformed.shape[1] == 1 clf = LinearDiscriminantAnalysis(solver="lsqr", n_components=1) clf.fit(X, y) msg = "transform not implemented for 'lsqr'" with pytest.raises(NotImplementedError, match=msg): clf.transform(X) def test_lda_explained_variance_ratio(): # Test if the sum of the normalized eigen vectors values equals 1, # Also tests whether the explained_variance_ratio_ formed by the # eigen solver is the same as the explained_variance_ratio_ formed # by the svd solver state = np.random.RandomState(0) X = state.normal(loc=0, scale=100, size=(40, 20)) y = state.randint(0, 3, size=(40,)) clf_lda_eigen = LinearDiscriminantAnalysis(solver="eigen") clf_lda_eigen.fit(X, y) assert_almost_equal(clf_lda_eigen.explained_variance_ratio_.sum(), 1.0, 3) assert clf_lda_eigen.explained_variance_ratio_.shape == ( 2, ), "Unexpected length for explained_variance_ratio_" clf_lda_svd = LinearDiscriminantAnalysis(solver="svd") clf_lda_svd.fit(X, y) assert_almost_equal(clf_lda_svd.explained_variance_ratio_.sum(), 1.0, 3) assert clf_lda_svd.explained_variance_ratio_.shape == ( 2, ), "Unexpected length for explained_variance_ratio_" assert_array_almost_equal( clf_lda_svd.explained_variance_ratio_, clf_lda_eigen.explained_variance_ratio_ ) def test_lda_orthogonality(): # arrange four classes with their means in a kite-shaped pattern # the longer distance should be transformed to the first component, and # the shorter distance to the second component. means = np.array([[0, 0, -1], [0, 2, 0], [0, -2, 0], [0, 0, 5]]) # We construct perfectly symmetric distributions, so the LDA can estimate # precise means. scatter = np.array( [ [0.1, 0, 0], [-0.1, 0, 0], [0, 0.1, 0], [0, -0.1, 0], [0, 0, 0.1], [0, 0, -0.1], ] ) X = (means[:, np.newaxis, :] + scatter[np.newaxis, :, :]).reshape((-1, 3)) y = np.repeat(np.arange(means.shape[0]), scatter.shape[0]) # Fit LDA and transform the means clf = LinearDiscriminantAnalysis(solver="svd").fit(X, y) means_transformed = clf.transform(means) d1 = means_transformed[3] - means_transformed[0] d2 = means_transformed[2] - means_transformed[1] d1 /= np.sqrt(np.sum(d1**2)) d2 /= np.sqrt(np.sum(d2**2)) # the transformed within-class covariance should be the identity matrix assert_almost_equal(np.cov(clf.transform(scatter).T), np.eye(2)) # the means of classes 0 and 3 should lie on the first component assert_almost_equal(np.abs(np.dot(d1[:2], [1, 0])), 1.0) # the means of classes 1 and 2 should lie on the second component assert_almost_equal(np.abs(np.dot(d2[:2], [0, 1])), 1.0) def test_lda_scaling(): # Test if classification works correctly with differently scaled features. n = 100 rng = np.random.RandomState(1234) # use uniform distribution of features to make sure there is absolutely no # overlap between classes. x1 = rng.uniform(-1, 1, (n, 3)) + [-10, 0, 0] x2 = rng.uniform(-1, 1, (n, 3)) + [10, 0, 0] x = np.vstack((x1, x2)) * [1, 100, 10000] y = [-1] * n + [1] * n for solver in ("svd", "lsqr", "eigen"): clf = LinearDiscriminantAnalysis(solver=solver) # should be able to separate the data perfectly assert clf.fit(x, y).score(x, y) == 1.0, "using covariance: %s" % solver def test_lda_store_covariance(): # Test for solver 'lsqr' and 'eigen' # 'store_covariance' has no effect on 'lsqr' and 'eigen' solvers for solver in ("lsqr", "eigen"): clf = LinearDiscriminantAnalysis(solver=solver).fit(X6, y6) assert hasattr(clf, "covariance_") # Test the actual attribute: clf = LinearDiscriminantAnalysis(solver=solver, store_covariance=True).fit( X6, y6 ) assert hasattr(clf, "covariance_") assert_array_almost_equal( clf.covariance_, np.array([[0.422222, 0.088889], [0.088889, 0.533333]]) ) # Test for SVD solver, the default is to not set the covariances_ attribute clf = LinearDiscriminantAnalysis(solver="svd").fit(X6, y6) assert not hasattr(clf, "covariance_") # Test the actual attribute: clf = LinearDiscriminantAnalysis(solver=solver, store_covariance=True).fit(X6, y6) assert hasattr(clf, "covariance_") assert_array_almost_equal( clf.covariance_, np.array([[0.422222, 0.088889], [0.088889, 0.533333]]) ) @pytest.mark.parametrize("seed", range(10)) def test_lda_shrinkage(seed): # Test that shrunk covariance estimator and shrinkage parameter behave the # same rng = np.random.RandomState(seed) X = rng.rand(100, 10) y = rng.randint(3, size=(100)) c1 = LinearDiscriminantAnalysis(store_covariance=True, shrinkage=0.5, solver="lsqr") c2 = LinearDiscriminantAnalysis( store_covariance=True, covariance_estimator=ShrunkCovariance(shrinkage=0.5), solver="lsqr", ) c1.fit(X, y) c2.fit(X, y) assert_allclose(c1.means_, c2.means_) assert_allclose(c1.covariance_, c2.covariance_) def test_lda_ledoitwolf(): # When shrinkage="auto" current implementation uses ledoitwolf estimation # of covariance after standardizing the data. This checks that it is indeed # the case class StandardizedLedoitWolf: def fit(self, X): sc = StandardScaler() # standardize features X_sc = sc.fit_transform(X) s = ledoit_wolf(X_sc)[0] # rescale s = sc.scale_[:, np.newaxis] * s * sc.scale_[np.newaxis, :] self.covariance_ = s rng = np.random.RandomState(0) X = rng.rand(100, 10) y = rng.randint(3, size=(100,)) c1 = LinearDiscriminantAnalysis( store_covariance=True, shrinkage="auto", solver="lsqr" ) c2 = LinearDiscriminantAnalysis( store_covariance=True, covariance_estimator=StandardizedLedoitWolf(), solver="lsqr", ) c1.fit(X, y) c2.fit(X, y) assert_allclose(c1.means_, c2.means_) assert_allclose(c1.covariance_, c2.covariance_) @pytest.mark.parametrize("n_features", [3, 5]) @pytest.mark.parametrize("n_classes", [5, 3]) def test_lda_dimension_warning(n_classes, n_features): rng = check_random_state(0) n_samples = 10 X = rng.randn(n_samples, n_features) # we create n_classes labels by repeating and truncating a # range(n_classes) until n_samples y = np.tile(range(n_classes), n_samples // n_classes + 1)[:n_samples] max_components = min(n_features, n_classes - 1) for n_components in [max_components - 1, None, max_components]: # if n_components <= min(n_classes - 1, n_features), no warning lda = LinearDiscriminantAnalysis(n_components=n_components) lda.fit(X, y) for n_components in [max_components + 1, max(n_features, n_classes - 1) + 1]: # if n_components > min(n_classes - 1, n_features), raise error. # We test one unit higher than max_components, and then something # larger than both n_features and n_classes - 1 to ensure the test # works for any value of n_component lda = LinearDiscriminantAnalysis(n_components=n_components) msg = "n_components cannot be larger than " with pytest.raises(ValueError, match=msg): lda.fit(X, y) @pytest.mark.parametrize( "data_type, expected_type", [ (np.float32, np.float32), (np.float64, np.float64), (np.int32, np.float64), (np.int64, np.float64), ], ) def test_lda_dtype_match(data_type, expected_type): for solver, shrinkage in solver_shrinkage: clf = LinearDiscriminantAnalysis(solver=solver, shrinkage=shrinkage) clf.fit(X.astype(data_type), y.astype(data_type)) assert clf.coef_.dtype == expected_type def test_lda_numeric_consistency_float32_float64(): for solver, shrinkage in solver_shrinkage: clf_32 = LinearDiscriminantAnalysis(solver=solver, shrinkage=shrinkage) clf_32.fit(X.astype(np.float32), y.astype(np.float32)) clf_64 = LinearDiscriminantAnalysis(solver=solver, shrinkage=shrinkage) clf_64.fit(X.astype(np.float64), y.astype(np.float64)) # Check value consistency between types rtol = 1e-6 assert_allclose(clf_32.coef_, clf_64.coef_, rtol=rtol) def test_qda(): # QDA classification. # This checks that QDA implements fit and predict and returns # correct values for a simple toy dataset. clf = QuadraticDiscriminantAnalysis() y_pred = clf.fit(X6, y6).predict(X6) assert_array_equal(y_pred, y6) # Assure that it works with 1D data y_pred1 = clf.fit(X7, y6).predict(X7) assert_array_equal(y_pred1, y6) # Test probas estimates y_proba_pred1 = clf.predict_proba(X7) assert_array_equal((y_proba_pred1[:, 1] > 0.5) + 1, y6) y_log_proba_pred1 = clf.predict_log_proba(X7) assert_array_almost_equal(np.exp(y_log_proba_pred1), y_proba_pred1, 8) y_pred3 = clf.fit(X6, y7).predict(X6) # QDA shouldn't be able to separate those assert np.any(y_pred3 != y7) # Classes should have at least 2 elements with pytest.raises(ValueError): clf.fit(X6, y4) def test_qda_priors(): clf = QuadraticDiscriminantAnalysis() y_pred = clf.fit(X6, y6).predict(X6) n_pos = np.sum(y_pred == 2) neg = 1e-10 clf = QuadraticDiscriminantAnalysis(priors=np.array([neg, 1 - neg])) y_pred = clf.fit(X6, y6).predict(X6) n_pos2 = np.sum(y_pred == 2) assert n_pos2 > n_pos @pytest.mark.parametrize("priors_type", ["list", "tuple", "array"]) def test_qda_prior_type(priors_type): """Check that priors accept array-like.""" priors = [0.5, 0.5] clf = QuadraticDiscriminantAnalysis( priors=_convert_container([0.5, 0.5], priors_type) ).fit(X6, y6) assert isinstance(clf.priors_, np.ndarray) assert_array_equal(clf.priors_, priors) def test_qda_prior_copy(): """Check that altering `priors` without `fit` doesn't change `priors_`""" priors = np.array([0.5, 0.5]) qda = QuadraticDiscriminantAnalysis(priors=priors).fit(X, y) # we expect the following assert_array_equal(qda.priors_, qda.priors) # altering `priors` without `fit` should not change `priors_` priors[0] = 0.2 assert qda.priors_[0] != qda.priors[0] def test_qda_store_covariance(): # The default is to not set the covariances_ attribute clf = QuadraticDiscriminantAnalysis().fit(X6, y6) assert not hasattr(clf, "covariance_") # Test the actual attribute: clf = QuadraticDiscriminantAnalysis(store_covariance=True).fit(X6, y6) assert hasattr(clf, "covariance_") assert_array_almost_equal(clf.covariance_[0], np.array([[0.7, 0.45], [0.45, 0.7]])) assert_array_almost_equal( clf.covariance_[1], np.array([[0.33333333, -0.33333333], [-0.33333333, 0.66666667]]), ) @pytest.mark.xfail( _IS_WASM, reason=( "no floating point exceptions, see" " https://github.com/numpy/numpy/pull/21895#issuecomment-1311525881" ), ) def test_qda_regularization(): # The default is reg_param=0. and will cause issues when there is a # constant variable. # Fitting on data with constant variable triggers an UserWarning. collinear_msg = "Variables are collinear" clf = QuadraticDiscriminantAnalysis() with pytest.warns(UserWarning, match=collinear_msg): y_pred = clf.fit(X2, y6) # XXX: RuntimeWarning is also raised at predict time because of divisions # by zero when the model is fit with a constant feature and without # regularization: should this be considered a bug? Either by the fit-time # message more informative, raising and exception instead of a warning in # this case or somehow changing predict to avoid division by zero. with pytest.warns(RuntimeWarning, match="divide by zero"): y_pred = clf.predict(X2) assert np.any(y_pred != y6) # Adding a little regularization fixes the division by zero at predict # time. But UserWarning will persist at fit time. clf = QuadraticDiscriminantAnalysis(reg_param=0.01) with pytest.warns(UserWarning, match=collinear_msg): clf.fit(X2, y6) y_pred = clf.predict(X2) assert_array_equal(y_pred, y6) # UserWarning should also be there for the n_samples_in_a_class < # n_features case. clf = QuadraticDiscriminantAnalysis(reg_param=0.1) with pytest.warns(UserWarning, match=collinear_msg): clf.fit(X5, y5) y_pred5 = clf.predict(X5) assert_array_equal(y_pred5, y5) def test_covariance(): x, y = make_blobs(n_samples=100, n_features=5, centers=1, random_state=42) # make features correlated x = np.dot(x, np.arange(x.shape[1] ** 2).reshape(x.shape[1], x.shape[1])) c_e = _cov(x, "empirical") assert_almost_equal(c_e, c_e.T) c_s = _cov(x, "auto") assert_almost_equal(c_s, c_s.T) @pytest.mark.parametrize("solver", ["svd", "lsqr", "eigen"]) def test_raises_value_error_on_same_number_of_classes_and_samples(solver): """ Tests that if the number of samples equals the number of classes, a ValueError is raised. """ X = np.array([[0.5, 0.6], [0.6, 0.5]]) y = np.array(["a", "b"]) clf = LinearDiscriminantAnalysis(solver=solver) with pytest.raises(ValueError, match="The number of samples must be more"): clf.fit(X, y) def test_get_feature_names_out(): """Check get_feature_names_out uses class name as prefix.""" est = LinearDiscriminantAnalysis().fit(X, y) names_out = est.get_feature_names_out() class_name_lower = "LinearDiscriminantAnalysis".lower() expected_names_out = np.array( [ f"{class_name_lower}{i}" for i in range(est.explained_variance_ratio_.shape[0]) ], dtype=object, ) assert_array_equal(names_out, expected_names_out)