import numpy as np import scipy.sparse as sp from scipy import linalg, optimize, sparse from sklearn.datasets import load_iris, make_classification from sklearn.metrics import log_loss from sklearn.model_selection import StratifiedKFold from sklearn.preprocessing import LabelEncoder from sklearn.utils import compute_class_weight from sklearn.utils.testing import assert_almost_equal from sklearn.utils.testing import assert_array_almost_equal from sklearn.utils.testing import assert_array_equal from sklearn.utils.testing import assert_equal from sklearn.utils.testing import assert_greater from sklearn.utils.testing import assert_raise_message from sklearn.utils.testing import assert_raises from sklearn.utils.testing import assert_true from sklearn.utils.testing import assert_warns from sklearn.utils.testing import ignore_warnings from sklearn.utils.testing import assert_warns_message from sklearn.utils.testing import raises from sklearn.utils.testing import SkipTest from sklearn.exceptions import ConvergenceWarning from sklearn.linear_model.logistic import ( LogisticRegression, logistic_regression_path, LogisticRegressionCV, _logistic_loss_and_grad, _logistic_grad_hess, _multinomial_grad_hess, _logistic_loss, ) X = [[-1, 0], [0, 1], [1, 1]] X_sp = sp.csr_matrix(X) Y1 = [0, 1, 1] Y2 = [2, 1, 0] iris = load_iris() def check_predictions(clf, X, y): """Check that the model is able to fit the classification data""" n_samples = len(y) classes = np.unique(y) n_classes = classes.shape[0] predicted = clf.fit(X, y).predict(X) assert_array_equal(clf.classes_, classes) assert_equal(predicted.shape, (n_samples,)) assert_array_equal(predicted, y) probabilities = clf.predict_proba(X) assert_equal(probabilities.shape, (n_samples, n_classes)) assert_array_almost_equal(probabilities.sum(axis=1), np.ones(n_samples)) assert_array_equal(probabilities.argmax(axis=1), y) def test_predict_2_classes(): # Simple sanity check on a 2 classes dataset # Make sure it predicts the correct result on simple datasets. check_predictions(LogisticRegression(random_state=0), X, Y1) check_predictions(LogisticRegression(random_state=0), X_sp, Y1) check_predictions(LogisticRegression(C=100, random_state=0), X, Y1) check_predictions(LogisticRegression(C=100, random_state=0), X_sp, Y1) check_predictions(LogisticRegression(fit_intercept=False, random_state=0), X, Y1) check_predictions(LogisticRegression(fit_intercept=False, random_state=0), X_sp, Y1) def test_error(): # Test for appropriate exception on errors msg = "Penalty term must be positive" assert_raise_message(ValueError, msg, LogisticRegression(C=-1).fit, X, Y1) assert_raise_message(ValueError, msg, LogisticRegression(C="test").fit, X, Y1) for LR in [LogisticRegression, LogisticRegressionCV]: msg = "Tolerance for stopping criteria must be positive" assert_raise_message(ValueError, msg, LR(tol=-1).fit, X, Y1) assert_raise_message(ValueError, msg, LR(tol="test").fit, X, Y1) msg = "Maximum number of iteration must be positive" assert_raise_message(ValueError, msg, LR(max_iter=-1).fit, X, Y1) assert_raise_message(ValueError, msg, LR(max_iter="test").fit, X, Y1) def test_lr_liblinear_warning(): n_samples, n_features = iris.data.shape target = iris.target_names[iris.target] lr = LogisticRegression(solver='liblinear', n_jobs=2) assert_warns_message(UserWarning, "'n_jobs' > 1 does not have any effect when" " 'solver' is set to 'liblinear'. Got 'n_jobs'" " = 2.", lr.fit, iris.data, target) def test_predict_3_classes(): check_predictions(LogisticRegression(C=10), X, Y2) check_predictions(LogisticRegression(C=10), X_sp, Y2) def test_predict_iris(): # Test logistic regression with the iris dataset n_samples, n_features = iris.data.shape target = iris.target_names[iris.target] # Test that both multinomial and OvR solvers handle # multiclass data correctly and give good accuracy # score (>0.95) for the training data. for clf in [LogisticRegression(C=len(iris.data)), LogisticRegression(C=len(iris.data), solver='lbfgs', multi_class='multinomial'), LogisticRegression(C=len(iris.data), solver='newton-cg', multi_class='multinomial'), LogisticRegression(C=len(iris.data), solver='sag', tol=1e-2, multi_class='ovr', random_state=42), LogisticRegression(C=len(iris.data), solver='saga', tol=1e-2, multi_class='ovr', random_state=42) ]: clf.fit(iris.data, target) assert_array_equal(np.unique(target), clf.classes_) pred = clf.predict(iris.data) assert_greater(np.mean(pred == target), .95) probabilities = clf.predict_proba(iris.data) assert_array_almost_equal(probabilities.sum(axis=1), np.ones(n_samples)) pred = iris.target_names[probabilities.argmax(axis=1)] assert_greater(np.mean(pred == target), .95) def test_multinomial_validation(): for solver in ['lbfgs', 'newton-cg', 'sag', 'saga']: lr = LogisticRegression(C=-1, solver=solver, multi_class='multinomial') assert_raises(ValueError, lr.fit, [[0, 1], [1, 0]], [0, 1]) def test_check_solver_option(): X, y = iris.data, iris.target for LR in [LogisticRegression, LogisticRegressionCV]: msg = ('Logistic Regression supports only liblinear, newton-cg, ' 'lbfgs, sag and saga solvers, got wrong_name') lr = LR(solver="wrong_name") assert_raise_message(ValueError, msg, lr.fit, X, y) msg = "multi_class should be either multinomial or ovr, got wrong_name" lr = LR(solver='newton-cg', multi_class="wrong_name") assert_raise_message(ValueError, msg, lr.fit, X, y) # only 'liblinear' solver msg = "Solver liblinear does not support a multinomial backend." lr = LR(solver='liblinear', multi_class='multinomial') assert_raise_message(ValueError, msg, lr.fit, X, y) # all solvers except 'liblinear' for solver in ['newton-cg', 'lbfgs', 'sag']: msg = ("Solver %s supports only l2 penalties, got l1 penalty." % solver) lr = LR(solver=solver, penalty='l1') assert_raise_message(ValueError, msg, lr.fit, X, y) for solver in ['newton-cg', 'lbfgs', 'sag', 'saga']: msg = ("Solver %s supports only dual=False, got dual=True" % solver) lr = LR(solver=solver, dual=True) assert_raise_message(ValueError, msg, lr.fit, X, y) def test_multinomial_binary(): # Test multinomial LR on a binary problem. target = (iris.target > 0).astype(np.intp) target = np.array(["setosa", "not-setosa"])[target] for solver in ['lbfgs', 'newton-cg', 'sag', 'saga']: clf = LogisticRegression(solver=solver, multi_class='multinomial', random_state=42, max_iter=2000) clf.fit(iris.data, target) assert_equal(clf.coef_.shape, (1, iris.data.shape[1])) assert_equal(clf.intercept_.shape, (1,)) assert_array_equal(clf.predict(iris.data), target) mlr = LogisticRegression(solver=solver, multi_class='multinomial', random_state=42, fit_intercept=False) mlr.fit(iris.data, target) pred = clf.classes_[np.argmax(clf.predict_log_proba(iris.data), axis=1)] assert_greater(np.mean(pred == target), .9) def test_sparsify(): # Test sparsify and densify members. n_samples, n_features = iris.data.shape target = iris.target_names[iris.target] clf = LogisticRegression(random_state=0).fit(iris.data, target) pred_d_d = clf.decision_function(iris.data) clf.sparsify() assert_true(sp.issparse(clf.coef_)) pred_s_d = clf.decision_function(iris.data) sp_data = sp.coo_matrix(iris.data) pred_s_s = clf.decision_function(sp_data) clf.densify() pred_d_s = clf.decision_function(sp_data) assert_array_almost_equal(pred_d_d, pred_s_d) assert_array_almost_equal(pred_d_d, pred_s_s) assert_array_almost_equal(pred_d_d, pred_d_s) def test_inconsistent_input(): # Test that an exception is raised on inconsistent input rng = np.random.RandomState(0) X_ = rng.random_sample((5, 10)) y_ = np.ones(X_.shape[0]) y_[0] = 0 clf = LogisticRegression(random_state=0) # Wrong dimensions for training data y_wrong = y_[:-1] assert_raises(ValueError, clf.fit, X, y_wrong) # Wrong dimensions for test data assert_raises(ValueError, clf.fit(X_, y_).predict, rng.random_sample((3, 12))) def test_write_parameters(): # Test that we can write to coef_ and intercept_ clf = LogisticRegression(random_state=0) clf.fit(X, Y1) clf.coef_[:] = 0 clf.intercept_[:] = 0 assert_array_almost_equal(clf.decision_function(X), 0) @raises(ValueError) def test_nan(): # Test proper NaN handling. # Regression test for Issue #252: fit used to go into an infinite loop. Xnan = np.array(X, dtype=np.float64) Xnan[0, 1] = np.nan LogisticRegression(random_state=0).fit(Xnan, Y1) def test_consistency_path(): # Test that the path algorithm is consistent rng = np.random.RandomState(0) X = np.concatenate((rng.randn(100, 2) + [1, 1], rng.randn(100, 2))) y = [1] * 100 + [-1] * 100 Cs = np.logspace(0, 4, 10) f = ignore_warnings # can't test with fit_intercept=True since LIBLINEAR # penalizes the intercept for solver in ['sag', 'saga']: coefs, Cs, _ = f(logistic_regression_path)( X, y, Cs=Cs, fit_intercept=False, tol=1e-5, solver=solver, max_iter=1000, random_state=0) for i, C in enumerate(Cs): lr = LogisticRegression(C=C, fit_intercept=False, tol=1e-5, solver=solver, random_state=0) lr.fit(X, y) lr_coef = lr.coef_.ravel() assert_array_almost_equal(lr_coef, coefs[i], decimal=4, err_msg="with solver = %s" % solver) # test for fit_intercept=True for solver in ('lbfgs', 'newton-cg', 'liblinear', 'sag', 'saga'): Cs = [1e3] coefs, Cs, _ = f(logistic_regression_path)( X, y, Cs=Cs, fit_intercept=True, tol=1e-6, solver=solver, intercept_scaling=10000., random_state=0) lr = LogisticRegression(C=Cs[0], fit_intercept=True, tol=1e-4, intercept_scaling=10000., random_state=0) lr.fit(X, y) lr_coef = np.concatenate([lr.coef_.ravel(), lr.intercept_]) assert_array_almost_equal(lr_coef, coefs[0], decimal=4, err_msg="with solver = %s" % solver) def test_liblinear_dual_random_state(): # random_state is relevant for liblinear solver only if dual=True X, y = make_classification(n_samples=20, random_state=0) lr1 = LogisticRegression(random_state=0, dual=True, max_iter=1, tol=1e-15) lr1.fit(X, y) lr2 = LogisticRegression(random_state=0, dual=True, max_iter=1, tol=1e-15) lr2.fit(X, y) lr3 = LogisticRegression(random_state=8, dual=True, max_iter=1, tol=1e-15) lr3.fit(X, y) # same result for same random state assert_array_almost_equal(lr1.coef_, lr2.coef_) # different results for different random states msg = "Arrays are not almost equal to 6 decimals" assert_raise_message(AssertionError, msg, assert_array_almost_equal, lr1.coef_, lr3.coef_) def test_logistic_loss_and_grad(): X_ref, y = make_classification(n_samples=20, random_state=0) n_features = X_ref.shape[1] X_sp = X_ref.copy() X_sp[X_sp < .1] = 0 X_sp = sp.csr_matrix(X_sp) for X in (X_ref, X_sp): w = np.zeros(n_features) # First check that our derivation of the grad is correct loss, grad = _logistic_loss_and_grad(w, X, y, alpha=1.) approx_grad = optimize.approx_fprime( w, lambda w: _logistic_loss_and_grad(w, X, y, alpha=1.)[0], 1e-3 ) assert_array_almost_equal(grad, approx_grad, decimal=2) # Second check that our intercept implementation is good w = np.zeros(n_features + 1) loss_interp, grad_interp = _logistic_loss_and_grad( w, X, y, alpha=1. ) assert_array_almost_equal(loss, loss_interp) approx_grad = optimize.approx_fprime( w, lambda w: _logistic_loss_and_grad(w, X, y, alpha=1.)[0], 1e-3 ) assert_array_almost_equal(grad_interp, approx_grad, decimal=2) def test_logistic_grad_hess(): rng = np.random.RandomState(0) n_samples, n_features = 50, 5 X_ref = rng.randn(n_samples, n_features) y = np.sign(X_ref.dot(5 * rng.randn(n_features))) X_ref -= X_ref.mean() X_ref /= X_ref.std() X_sp = X_ref.copy() X_sp[X_sp < .1] = 0 X_sp = sp.csr_matrix(X_sp) for X in (X_ref, X_sp): w = .1 * np.ones(n_features) # First check that _logistic_grad_hess is consistent # with _logistic_loss_and_grad loss, grad = _logistic_loss_and_grad(w, X, y, alpha=1.) grad_2, hess = _logistic_grad_hess(w, X, y, alpha=1.) assert_array_almost_equal(grad, grad_2) # Now check our hessian along the second direction of the grad vector = np.zeros_like(grad) vector[1] = 1 hess_col = hess(vector) # Computation of the Hessian is particularly fragile to numerical # errors when doing simple finite differences. Here we compute the # grad along a path in the direction of the vector and then use a # least-square regression to estimate the slope e = 1e-3 d_x = np.linspace(-e, e, 30) d_grad = np.array([ _logistic_loss_and_grad(w + t * vector, X, y, alpha=1.)[1] for t in d_x ]) d_grad -= d_grad.mean(axis=0) approx_hess_col = linalg.lstsq(d_x[:, np.newaxis], d_grad)[0].ravel() assert_array_almost_equal(approx_hess_col, hess_col, decimal=3) # Second check that our intercept implementation is good w = np.zeros(n_features + 1) loss_interp, grad_interp = _logistic_loss_and_grad(w, X, y, alpha=1.) loss_interp_2 = _logistic_loss(w, X, y, alpha=1.) grad_interp_2, hess = _logistic_grad_hess(w, X, y, alpha=1.) assert_array_almost_equal(loss_interp, loss_interp_2) assert_array_almost_equal(grad_interp, grad_interp_2) def test_logistic_cv(): # test for LogisticRegressionCV object n_samples, n_features = 50, 5 rng = np.random.RandomState(0) X_ref = rng.randn(n_samples, n_features) y = np.sign(X_ref.dot(5 * rng.randn(n_features))) X_ref -= X_ref.mean() X_ref /= X_ref.std() lr_cv = LogisticRegressionCV(Cs=[1.], fit_intercept=False, solver='liblinear') lr_cv.fit(X_ref, y) lr = LogisticRegression(C=1., fit_intercept=False) lr.fit(X_ref, y) assert_array_almost_equal(lr.coef_, lr_cv.coef_) assert_array_equal(lr_cv.coef_.shape, (1, n_features)) assert_array_equal(lr_cv.classes_, [-1, 1]) assert_equal(len(lr_cv.classes_), 2) coefs_paths = np.asarray(list(lr_cv.coefs_paths_.values())) assert_array_equal(coefs_paths.shape, (1, 3, 1, n_features)) assert_array_equal(lr_cv.Cs_.shape, (1,)) scores = np.asarray(list(lr_cv.scores_.values())) assert_array_equal(scores.shape, (1, 3, 1)) def test_multinomial_logistic_regression_string_inputs(): # Test with string labels for LogisticRegression(CV) n_samples, n_features, n_classes = 50, 5, 3 X_ref, y = make_classification(n_samples=n_samples, n_features=n_features, n_classes=n_classes, n_informative=3, random_state=0) y_str = LabelEncoder().fit(['bar', 'baz', 'foo']).inverse_transform(y) # For numerical labels, let y values be taken from set (-1, 0, 1) y = np.array(y) - 1 # Test for string labels lr = LogisticRegression(solver='lbfgs', multi_class='multinomial') lr_cv = LogisticRegressionCV(solver='lbfgs', multi_class='multinomial') lr_str = LogisticRegression(solver='lbfgs', multi_class='multinomial') lr_cv_str = LogisticRegressionCV(solver='lbfgs', multi_class='multinomial') lr.fit(X_ref, y) lr_cv.fit(X_ref, y) lr_str.fit(X_ref, y_str) lr_cv_str.fit(X_ref, y_str) assert_array_almost_equal(lr.coef_, lr_str.coef_) assert_equal(sorted(lr_str.classes_), ['bar', 'baz', 'foo']) assert_array_almost_equal(lr_cv.coef_, lr_cv_str.coef_) assert_equal(sorted(lr_str.classes_), ['bar', 'baz', 'foo']) assert_equal(sorted(lr_cv_str.classes_), ['bar', 'baz', 'foo']) # The predictions should be in original labels assert_equal(sorted(np.unique(lr_str.predict(X_ref))), ['bar', 'baz', 'foo']) assert_equal(sorted(np.unique(lr_cv_str.predict(X_ref))), ['bar', 'baz', 'foo']) # Make sure class weights can be given with string labels lr_cv_str = LogisticRegression( solver='lbfgs', class_weight={'bar': 1, 'baz': 2, 'foo': 0}, multi_class='multinomial').fit(X_ref, y_str) assert_equal(sorted(np.unique(lr_cv_str.predict(X_ref))), ['bar', 'baz']) def test_logistic_cv_sparse(): X, y = make_classification(n_samples=50, n_features=5, random_state=0) X[X < 1.0] = 0.0 csr = sp.csr_matrix(X) clf = LogisticRegressionCV(fit_intercept=True) clf.fit(X, y) clfs = LogisticRegressionCV(fit_intercept=True) clfs.fit(csr, y) assert_array_almost_equal(clfs.coef_, clf.coef_) assert_array_almost_equal(clfs.intercept_, clf.intercept_) assert_equal(clfs.C_, clf.C_) def test_intercept_logistic_helper(): n_samples, n_features = 10, 5 X, y = make_classification(n_samples=n_samples, n_features=n_features, random_state=0) # Fit intercept case. alpha = 1. w = np.ones(n_features + 1) grad_interp, hess_interp = _logistic_grad_hess(w, X, y, alpha) loss_interp = _logistic_loss(w, X, y, alpha) # Do not fit intercept. This can be considered equivalent to adding # a feature vector of ones, i.e column of one vectors. X_ = np.hstack((X, np.ones(10)[:, np.newaxis])) grad, hess = _logistic_grad_hess(w, X_, y, alpha) loss = _logistic_loss(w, X_, y, alpha) # In the fit_intercept=False case, the feature vector of ones is # penalized. This should be taken care of. assert_almost_equal(loss_interp + 0.5 * (w[-1] ** 2), loss) # Check gradient. assert_array_almost_equal(grad_interp[:n_features], grad[:n_features]) assert_almost_equal(grad_interp[-1] + alpha * w[-1], grad[-1]) rng = np.random.RandomState(0) grad = rng.rand(n_features + 1) hess_interp = hess_interp(grad) hess = hess(grad) assert_array_almost_equal(hess_interp[:n_features], hess[:n_features]) assert_almost_equal(hess_interp[-1] + alpha * grad[-1], hess[-1]) def test_ovr_multinomial_iris(): # Test that OvR and multinomial are correct using the iris dataset. train, target = iris.data, iris.target n_samples, n_features = train.shape # The cv indices from stratified kfold (where stratification is done based # on the fine-grained iris classes, i.e, before the classes 0 and 1 are # conflated) is used for both clf and clf1 n_cv = 2 cv = StratifiedKFold(n_cv) precomputed_folds = list(cv.split(train, target)) # Train clf on the original dataset where classes 0 and 1 are separated clf = LogisticRegressionCV(cv=precomputed_folds) clf.fit(train, target) # Conflate classes 0 and 1 and train clf1 on this modified dataset clf1 = LogisticRegressionCV(cv=precomputed_folds) target_copy = target.copy() target_copy[target_copy == 0] = 1 clf1.fit(train, target_copy) # Ensure that what OvR learns for class2 is same regardless of whether # classes 0 and 1 are separated or not assert_array_almost_equal(clf.scores_[2], clf1.scores_[2]) assert_array_almost_equal(clf.intercept_[2:], clf1.intercept_) assert_array_almost_equal(clf.coef_[2][np.newaxis, :], clf1.coef_) # Test the shape of various attributes. assert_equal(clf.coef_.shape, (3, n_features)) assert_array_equal(clf.classes_, [0, 1, 2]) coefs_paths = np.asarray(list(clf.coefs_paths_.values())) assert_array_almost_equal(coefs_paths.shape, (3, n_cv, 10, n_features + 1)) assert_equal(clf.Cs_.shape, (10,)) scores = np.asarray(list(clf.scores_.values())) assert_equal(scores.shape, (3, n_cv, 10)) # Test that for the iris data multinomial gives a better accuracy than OvR for solver in ['lbfgs', 'newton-cg', 'sag', 'saga']: max_iter = 2000 if solver in ['sag', 'saga'] else 15 clf_multi = LogisticRegressionCV( solver=solver, multi_class='multinomial', max_iter=max_iter, random_state=42, tol=1e-5 if solver in ['sag', 'saga'] else 1e-2, cv=2) clf_multi.fit(train, target) multi_score = clf_multi.score(train, target) ovr_score = clf.score(train, target) assert_greater(multi_score, ovr_score) # Test attributes of LogisticRegressionCV assert_equal(clf.coef_.shape, clf_multi.coef_.shape) assert_array_equal(clf_multi.classes_, [0, 1, 2]) coefs_paths = np.asarray(list(clf_multi.coefs_paths_.values())) assert_array_almost_equal(coefs_paths.shape, (3, n_cv, 10, n_features + 1)) assert_equal(clf_multi.Cs_.shape, (10,)) scores = np.asarray(list(clf_multi.scores_.values())) assert_equal(scores.shape, (3, n_cv, 10)) def test_logistic_regression_solvers(): X, y = make_classification(n_features=10, n_informative=5, random_state=0) ncg = LogisticRegression(solver='newton-cg', fit_intercept=False) lbf = LogisticRegression(solver='lbfgs', fit_intercept=False) lib = LogisticRegression(fit_intercept=False) sag = LogisticRegression(solver='sag', fit_intercept=False, random_state=42) saga = LogisticRegression(solver='saga', fit_intercept=False, random_state=42) ncg.fit(X, y) lbf.fit(X, y) sag.fit(X, y) saga.fit(X, y) lib.fit(X, y) assert_array_almost_equal(ncg.coef_, lib.coef_, decimal=3) assert_array_almost_equal(lib.coef_, lbf.coef_, decimal=3) assert_array_almost_equal(ncg.coef_, lbf.coef_, decimal=3) assert_array_almost_equal(sag.coef_, lib.coef_, decimal=3) assert_array_almost_equal(sag.coef_, ncg.coef_, decimal=3) assert_array_almost_equal(sag.coef_, lbf.coef_, decimal=3) assert_array_almost_equal(saga.coef_, sag.coef_, decimal=3) assert_array_almost_equal(saga.coef_, lbf.coef_, decimal=3) assert_array_almost_equal(saga.coef_, ncg.coef_, decimal=3) assert_array_almost_equal(saga.coef_, lib.coef_, decimal=3) def test_logistic_regression_solvers_multiclass(): X, y = make_classification(n_samples=20, n_features=20, n_informative=10, n_classes=3, random_state=0) tol = 1e-7 ncg = LogisticRegression(solver='newton-cg', fit_intercept=False, tol=tol) lbf = LogisticRegression(solver='lbfgs', fit_intercept=False, tol=tol) lib = LogisticRegression(fit_intercept=False, tol=tol) sag = LogisticRegression(solver='sag', fit_intercept=False, tol=tol, max_iter=1000, random_state=42) saga = LogisticRegression(solver='saga', fit_intercept=False, tol=tol, max_iter=10000, random_state=42) ncg.fit(X, y) lbf.fit(X, y) sag.fit(X, y) saga.fit(X, y) lib.fit(X, y) assert_array_almost_equal(ncg.coef_, lib.coef_, decimal=4) assert_array_almost_equal(lib.coef_, lbf.coef_, decimal=4) assert_array_almost_equal(ncg.coef_, lbf.coef_, decimal=4) assert_array_almost_equal(sag.coef_, lib.coef_, decimal=4) assert_array_almost_equal(sag.coef_, ncg.coef_, decimal=4) assert_array_almost_equal(sag.coef_, lbf.coef_, decimal=4) assert_array_almost_equal(saga.coef_, sag.coef_, decimal=4) assert_array_almost_equal(saga.coef_, lbf.coef_, decimal=4) assert_array_almost_equal(saga.coef_, ncg.coef_, decimal=4) assert_array_almost_equal(saga.coef_, lib.coef_, decimal=4) def test_logistic_regressioncv_class_weights(): for weight in [{0: 0.1, 1: 0.2}, {0: 0.1, 1: 0.2, 2: 0.5}]: n_classes = len(weight) for class_weight in (weight, 'balanced'): X, y = make_classification(n_samples=30, n_features=3, n_repeated=0, n_informative=3, n_redundant=0, n_classes=n_classes, random_state=0) clf_lbf = LogisticRegressionCV(solver='lbfgs', Cs=1, fit_intercept=False, class_weight=class_weight) clf_ncg = LogisticRegressionCV(solver='newton-cg', Cs=1, fit_intercept=False, class_weight=class_weight) clf_lib = LogisticRegressionCV(solver='liblinear', Cs=1, fit_intercept=False, class_weight=class_weight) clf_sag = LogisticRegressionCV(solver='sag', Cs=1, fit_intercept=False, class_weight=class_weight, tol=1e-5, max_iter=10000, random_state=0) clf_saga = LogisticRegressionCV(solver='saga', Cs=1, fit_intercept=False, class_weight=class_weight, tol=1e-5, max_iter=10000, random_state=0) clf_lbf.fit(X, y) clf_ncg.fit(X, y) clf_lib.fit(X, y) clf_sag.fit(X, y) clf_saga.fit(X, y) assert_array_almost_equal(clf_lib.coef_, clf_lbf.coef_, decimal=4) assert_array_almost_equal(clf_ncg.coef_, clf_lbf.coef_, decimal=4) assert_array_almost_equal(clf_sag.coef_, clf_lbf.coef_, decimal=4) assert_array_almost_equal(clf_saga.coef_, clf_lbf.coef_, decimal=4) def test_logistic_regression_sample_weights(): X, y = make_classification(n_samples=20, n_features=5, n_informative=3, n_classes=2, random_state=0) sample_weight = y + 1 for LR in [LogisticRegression, LogisticRegressionCV]: # Test that passing sample_weight as ones is the same as # not passing them at all (default None) for solver in ['lbfgs', 'liblinear']: clf_sw_none = LR(solver=solver, fit_intercept=False, random_state=42) clf_sw_none.fit(X, y) clf_sw_ones = LR(solver=solver, fit_intercept=False, random_state=42) clf_sw_ones.fit(X, y, sample_weight=np.ones(y.shape[0])) assert_array_almost_equal( clf_sw_none.coef_, clf_sw_ones.coef_, decimal=4) # Test that sample weights work the same with the lbfgs, # newton-cg, and 'sag' solvers clf_sw_lbfgs = LR(solver='lbfgs', fit_intercept=False, random_state=42) clf_sw_lbfgs.fit(X, y, sample_weight=sample_weight) clf_sw_n = LR(solver='newton-cg', fit_intercept=False, random_state=42) clf_sw_n.fit(X, y, sample_weight=sample_weight) clf_sw_sag = LR(solver='sag', fit_intercept=False, tol=1e-10, random_state=42) # ignore convergence warning due to small dataset with ignore_warnings(): clf_sw_sag.fit(X, y, sample_weight=sample_weight) clf_sw_liblinear = LR(solver='liblinear', fit_intercept=False, random_state=42) clf_sw_liblinear.fit(X, y, sample_weight=sample_weight) assert_array_almost_equal( clf_sw_lbfgs.coef_, clf_sw_n.coef_, decimal=4) assert_array_almost_equal( clf_sw_lbfgs.coef_, clf_sw_sag.coef_, decimal=4) assert_array_almost_equal( clf_sw_lbfgs.coef_, clf_sw_liblinear.coef_, decimal=4) # Test that passing class_weight as [1,2] is the same as # passing class weight = [1,1] but adjusting sample weights # to be 2 for all instances of class 2 for solver in ['lbfgs', 'liblinear']: clf_cw_12 = LR(solver=solver, fit_intercept=False, class_weight={0: 1, 1: 2}, random_state=42) clf_cw_12.fit(X, y) clf_sw_12 = LR(solver=solver, fit_intercept=False, random_state=42) clf_sw_12.fit(X, y, sample_weight=sample_weight) assert_array_almost_equal( clf_cw_12.coef_, clf_sw_12.coef_, decimal=4) # Test the above for l1 penalty and l2 penalty with dual=True. # since the patched liblinear code is different. clf_cw = LogisticRegression( solver="liblinear", fit_intercept=False, class_weight={0: 1, 1: 2}, penalty="l1", tol=1e-5, random_state=42) clf_cw.fit(X, y) clf_sw = LogisticRegression( solver="liblinear", fit_intercept=False, penalty="l1", tol=1e-5, random_state=42) clf_sw.fit(X, y, sample_weight) assert_array_almost_equal(clf_cw.coef_, clf_sw.coef_, decimal=4) clf_cw = LogisticRegression( solver="liblinear", fit_intercept=False, class_weight={0: 1, 1: 2}, penalty="l2", dual=True, random_state=42) clf_cw.fit(X, y) clf_sw = LogisticRegression( solver="liblinear", fit_intercept=False, penalty="l2", dual=True, random_state=42) clf_sw.fit(X, y, sample_weight) assert_array_almost_equal(clf_cw.coef_, clf_sw.coef_, decimal=4) def _compute_class_weight_dictionary(y): # helper for returning a dictionary instead of an array classes = np.unique(y) class_weight = compute_class_weight("balanced", classes, y) class_weight_dict = dict(zip(classes, class_weight)) return class_weight_dict def test_logistic_regression_class_weights(): # Multinomial case: remove 90% of class 0 X = iris.data[45:, :] y = iris.target[45:] solvers = ("lbfgs", "newton-cg") class_weight_dict = _compute_class_weight_dictionary(y) for solver in solvers: clf1 = LogisticRegression(solver=solver, multi_class="multinomial", class_weight="balanced") clf2 = LogisticRegression(solver=solver, multi_class="multinomial", class_weight=class_weight_dict) clf1.fit(X, y) clf2.fit(X, y) assert_array_almost_equal(clf1.coef_, clf2.coef_, decimal=4) # Binary case: remove 90% of class 0 and 100% of class 2 X = iris.data[45:100, :] y = iris.target[45:100] solvers = ("lbfgs", "newton-cg", "liblinear") class_weight_dict = _compute_class_weight_dictionary(y) for solver in solvers: clf1 = LogisticRegression(solver=solver, multi_class="ovr", class_weight="balanced") clf2 = LogisticRegression(solver=solver, multi_class="ovr", class_weight=class_weight_dict) clf1.fit(X, y) clf2.fit(X, y) assert_array_almost_equal(clf1.coef_, clf2.coef_, decimal=6) def test_logistic_regression_convergence_warnings(): # Test that warnings are raised if model does not converge X, y = make_classification(n_samples=20, n_features=20, random_state=0) clf_lib = LogisticRegression(solver='liblinear', max_iter=2, verbose=1) assert_warns(ConvergenceWarning, clf_lib.fit, X, y) assert_equal(clf_lib.n_iter_, 2) def test_logistic_regression_multinomial(): # Tests for the multinomial option in logistic regression # Some basic attributes of Logistic Regression n_samples, n_features, n_classes = 50, 20, 3 X, y = make_classification(n_samples=n_samples, n_features=n_features, n_informative=10, n_classes=n_classes, random_state=0) # 'lbfgs' is used as a referenced solver = 'lbfgs' ref_i = LogisticRegression(solver=solver, multi_class='multinomial') ref_w = LogisticRegression(solver=solver, multi_class='multinomial', fit_intercept=False) ref_i.fit(X, y) ref_w.fit(X, y) assert_array_equal(ref_i.coef_.shape, (n_classes, n_features)) assert_array_equal(ref_w.coef_.shape, (n_classes, n_features)) for solver in ['sag', 'saga', 'newton-cg']: clf_i = LogisticRegression(solver=solver, multi_class='multinomial', random_state=42, max_iter=2000, tol=1e-7, ) clf_w = LogisticRegression(solver=solver, multi_class='multinomial', random_state=42, max_iter=2000, tol=1e-7, fit_intercept=False) clf_i.fit(X, y) clf_w.fit(X, y) assert_array_equal(clf_i.coef_.shape, (n_classes, n_features)) assert_array_equal(clf_w.coef_.shape, (n_classes, n_features)) # Compare solutions between lbfgs and the other solvers assert_almost_equal(ref_i.coef_, clf_i.coef_, decimal=3) assert_almost_equal(ref_w.coef_, clf_w.coef_, decimal=3) assert_almost_equal(ref_i.intercept_, clf_i.intercept_, decimal=3) # Test that the path give almost the same results. However since in this # case we take the average of the coefs after fitting across all the # folds, it need not be exactly the same. for solver in ['lbfgs', 'newton-cg', 'sag', 'saga']: clf_path = LogisticRegressionCV(solver=solver, max_iter=2000, tol=1e-6, multi_class='multinomial', Cs=[1.]) clf_path.fit(X, y) assert_array_almost_equal(clf_path.coef_, ref_i.coef_, decimal=3) assert_almost_equal(clf_path.intercept_, ref_i.intercept_, decimal=3) def test_multinomial_grad_hess(): rng = np.random.RandomState(0) n_samples, n_features, n_classes = 100, 5, 3 X = rng.randn(n_samples, n_features) w = rng.rand(n_classes, n_features) Y = np.zeros((n_samples, n_classes)) ind = np.argmax(np.dot(X, w.T), axis=1) Y[range(0, n_samples), ind] = 1 w = w.ravel() sample_weights = np.ones(X.shape[0]) grad, hessp = _multinomial_grad_hess(w, X, Y, alpha=1., sample_weight=sample_weights) # extract first column of hessian matrix vec = np.zeros(n_features * n_classes) vec[0] = 1 hess_col = hessp(vec) # Estimate hessian using least squares as done in # test_logistic_grad_hess e = 1e-3 d_x = np.linspace(-e, e, 30) d_grad = np.array([ _multinomial_grad_hess(w + t * vec, X, Y, alpha=1., sample_weight=sample_weights)[0] for t in d_x ]) d_grad -= d_grad.mean(axis=0) approx_hess_col = linalg.lstsq(d_x[:, np.newaxis], d_grad)[0].ravel() assert_array_almost_equal(hess_col, approx_hess_col) def test_liblinear_decision_function_zero(): # Test negative prediction when decision_function values are zero. # Liblinear predicts the positive class when decision_function values # are zero. This is a test to verify that we do not do the same. # See Issue: https://github.com/scikit-learn/scikit-learn/issues/3600 # and the PR https://github.com/scikit-learn/scikit-learn/pull/3623 X, y = make_classification(n_samples=5, n_features=5, random_state=0) clf = LogisticRegression(fit_intercept=False) clf.fit(X, y) # Dummy data such that the decision function becomes zero. X = np.zeros((5, 5)) assert_array_equal(clf.predict(X), np.zeros(5)) def test_liblinear_logregcv_sparse(): # Test LogRegCV with solver='liblinear' works for sparse matrices X, y = make_classification(n_samples=10, n_features=5, random_state=0) clf = LogisticRegressionCV(solver='liblinear') clf.fit(sparse.csr_matrix(X), y) def test_saga_sparse(): # Test LogRegCV with solver='liblinear' works for sparse matrices X, y = make_classification(n_samples=10, n_features=5, random_state=0) clf = LogisticRegressionCV(solver='saga') clf.fit(sparse.csr_matrix(X), y) def test_logreg_intercept_scaling(): # Test that the right error message is thrown when intercept_scaling <= 0 for i in [-1, 0]: clf = LogisticRegression(intercept_scaling=i) msg = ('Intercept scaling is %r but needs to be greater than 0.' ' To disable fitting an intercept,' ' set fit_intercept=False.' % clf.intercept_scaling) assert_raise_message(ValueError, msg, clf.fit, X, Y1) def test_logreg_intercept_scaling_zero(): # Test that intercept_scaling is ignored when fit_intercept is False clf = LogisticRegression(fit_intercept=False) clf.fit(X, Y1) assert_equal(clf.intercept_, 0.) def test_logreg_l1(): # Because liblinear penalizes the intercept and saga does not, we do not # fit the intercept to make it possible to compare the coefficients of # the two models at convergence. rng = np.random.RandomState(42) n_samples = 50 X, y = make_classification(n_samples=n_samples, n_features=20, random_state=0) X_noise = rng.normal(size=(n_samples, 3)) X_constant = np.ones(shape=(n_samples, 2)) X = np.concatenate((X, X_noise, X_constant), axis=1) lr_liblinear = LogisticRegression(penalty="l1", C=1.0, solver='liblinear', fit_intercept=False, tol=1e-10) lr_liblinear.fit(X, y) lr_saga = LogisticRegression(penalty="l1", C=1.0, solver='saga', fit_intercept=False, max_iter=1000, tol=1e-10) lr_saga.fit(X, y) assert_array_almost_equal(lr_saga.coef_, lr_liblinear.coef_) # Noise and constant features should be regularized to zero by the l1 # penalty assert_array_almost_equal(lr_liblinear.coef_[0, -5:], np.zeros(5)) assert_array_almost_equal(lr_saga.coef_[0, -5:], np.zeros(5)) def test_logreg_l1_sparse_data(): # Because liblinear penalizes the intercept and saga does not, we do not # fit the intercept to make it possible to compare the coefficients of # the two models at convergence. rng = np.random.RandomState(42) n_samples = 50 X, y = make_classification(n_samples=n_samples, n_features=20, random_state=0) X_noise = rng.normal(scale=0.1, size=(n_samples, 3)) X_constant = np.zeros(shape=(n_samples, 2)) X = np.concatenate((X, X_noise, X_constant), axis=1) X[X < 1] = 0 X = sparse.csr_matrix(X) lr_liblinear = LogisticRegression(penalty="l1", C=1.0, solver='liblinear', fit_intercept=False, tol=1e-10) lr_liblinear.fit(X, y) lr_saga = LogisticRegression(penalty="l1", C=1.0, solver='saga', fit_intercept=False, max_iter=1000, tol=1e-10) lr_saga.fit(X, y) assert_array_almost_equal(lr_saga.coef_, lr_liblinear.coef_) # Noise and constant features should be regularized to zero by the l1 # penalty assert_array_almost_equal(lr_liblinear.coef_[0, -5:], np.zeros(5)) assert_array_almost_equal(lr_saga.coef_[0, -5:], np.zeros(5)) # Check that solving on the sparse and dense data yield the same results lr_saga_dense = LogisticRegression(penalty="l1", C=1.0, solver='saga', fit_intercept=False, max_iter=1000, tol=1e-10) lr_saga_dense.fit(X.toarray(), y) assert_array_almost_equal(lr_saga.coef_, lr_saga_dense.coef_) def test_logreg_cv_penalty(): # Test that the correct penalty is passed to the final fit. X, y = make_classification(n_samples=50, n_features=20, random_state=0) lr_cv = LogisticRegressionCV(penalty="l1", Cs=[1.0], solver='liblinear') lr_cv.fit(X, y) lr = LogisticRegression(penalty="l1", C=1.0, solver='liblinear') lr.fit(X, y) assert_equal(np.count_nonzero(lr_cv.coef_), np.count_nonzero(lr.coef_)) def test_logreg_predict_proba_multinomial(): X, y = make_classification(n_samples=10, n_features=20, random_state=0, n_classes=3, n_informative=10) # Predicted probabilities using the true-entropy loss should give a # smaller loss than those using the ovr method. clf_multi = LogisticRegression(multi_class="multinomial", solver="lbfgs") clf_multi.fit(X, y) clf_multi_loss = log_loss(y, clf_multi.predict_proba(X)) clf_ovr = LogisticRegression(multi_class="ovr", solver="lbfgs") clf_ovr.fit(X, y) clf_ovr_loss = log_loss(y, clf_ovr.predict_proba(X)) assert_greater(clf_ovr_loss, clf_multi_loss) # Predicted probabilities using the soft-max function should give a # smaller loss than those using the logistic function. clf_multi_loss = log_loss(y, clf_multi.predict_proba(X)) clf_wrong_loss = log_loss(y, clf_multi._predict_proba_lr(X)) assert_greater(clf_wrong_loss, clf_multi_loss) @ignore_warnings def test_max_iter(): # Test that the maximum number of iteration is reached X, y_bin = iris.data, iris.target.copy() y_bin[y_bin == 2] = 0 solvers = ['newton-cg', 'liblinear', 'sag', 'saga', 'lbfgs'] for max_iter in range(1, 5): for solver in solvers: for multi_class in ['ovr', 'multinomial']: if solver == 'liblinear' and multi_class == 'multinomial': continue lr = LogisticRegression(max_iter=max_iter, tol=1e-15, multi_class=multi_class, random_state=0, solver=solver) lr.fit(X, y_bin) assert_equal(lr.n_iter_[0], max_iter) def test_n_iter(): # Test that self.n_iter_ has the correct format. X, y = iris.data, iris.target y_bin = y.copy() y_bin[y_bin == 2] = 0 n_Cs = 4 n_cv_fold = 2 for solver in ['newton-cg', 'liblinear', 'sag', 'saga', 'lbfgs']: # OvR case n_classes = 1 if solver == 'liblinear' else np.unique(y).shape[0] clf = LogisticRegression(tol=1e-2, multi_class='ovr', solver=solver, C=1., random_state=42, max_iter=100) clf.fit(X, y) assert_equal(clf.n_iter_.shape, (n_classes,)) n_classes = np.unique(y).shape[0] clf = LogisticRegressionCV(tol=1e-2, multi_class='ovr', solver=solver, Cs=n_Cs, cv=n_cv_fold, random_state=42, max_iter=100) clf.fit(X, y) assert_equal(clf.n_iter_.shape, (n_classes, n_cv_fold, n_Cs)) clf.fit(X, y_bin) assert_equal(clf.n_iter_.shape, (1, n_cv_fold, n_Cs)) # multinomial case n_classes = 1 if solver in ('liblinear', 'sag', 'saga'): break clf = LogisticRegression(tol=1e-2, multi_class='multinomial', solver=solver, C=1., random_state=42, max_iter=100) clf.fit(X, y) assert_equal(clf.n_iter_.shape, (n_classes,)) clf = LogisticRegressionCV(tol=1e-2, multi_class='multinomial', solver=solver, Cs=n_Cs, cv=n_cv_fold, random_state=42, max_iter=100) clf.fit(X, y) assert_equal(clf.n_iter_.shape, (n_classes, n_cv_fold, n_Cs)) clf.fit(X, y_bin) assert_equal(clf.n_iter_.shape, (1, n_cv_fold, n_Cs)) def test_warm_start(): # A 1-iteration second fit on same data should give almost same result # with warm starting, and quite different result without warm starting. # Warm starting does not work with liblinear solver. X, y = iris.data, iris.target solvers = ['newton-cg', 'sag', 'saga', 'lbfgs'] for warm_start in [True, False]: for fit_intercept in [True, False]: for solver in solvers: for multi_class in ['ovr', 'multinomial']: clf = LogisticRegression(tol=1e-4, multi_class=multi_class, warm_start=warm_start, solver=solver, random_state=42, max_iter=100, fit_intercept=fit_intercept) with ignore_warnings(category=ConvergenceWarning): clf.fit(X, y) coef_1 = clf.coef_ clf.max_iter = 1 clf.fit(X, y) cum_diff = np.sum(np.abs(coef_1 - clf.coef_)) msg = ("Warm starting issue with %s solver in %s mode " "with fit_intercept=%s and warm_start=%s" % (solver, multi_class, str(fit_intercept), str(warm_start))) if warm_start: assert_greater(2.0, cum_diff, msg) else: assert_greater(cum_diff, 2.0, msg) def test_saga_vs_liblinear(): iris = load_iris() X, y = iris.data, iris.target X = np.concatenate([X] * 10) y = np.concatenate([y] * 10) X_bin = X[y <= 1] y_bin = y[y <= 1] * 2 - 1 X_sparse, y_sparse = make_classification(n_samples=50, n_features=20, random_state=0) X_sparse = sparse.csr_matrix(X_sparse) for (X, y) in ((X_bin, y_bin), (X_sparse, y_sparse)): for penalty in ['l1', 'l2']: n_samples = X.shape[0] # alpha=1e-3 is time consuming for alpha in np.logspace(-1, 1, 3): saga = LogisticRegression( C=1. / (n_samples * alpha), solver='saga', multi_class='ovr', max_iter=200, fit_intercept=False, penalty=penalty, random_state=0, tol=1e-24) liblinear = LogisticRegression( C=1. / (n_samples * alpha), solver='liblinear', multi_class='ovr', max_iter=200, fit_intercept=False, penalty=penalty, random_state=0, tol=1e-24) saga.fit(X, y) liblinear.fit(X, y) # Convergence for alpha=1e-3 is very slow assert_array_almost_equal(saga.coef_, liblinear.coef_, 3) def test_dtype_match(): # Disabled to unblock the 0.19.2 release. See: # https://github.com/scikit-learn/scikit-learn/issues/11438 # Test that np.float32 input data is not cast to np.float64 when possible raise SkipTest() X_32 = np.array(X).astype(np.float32) y_32 = np.array(Y1).astype(np.float32) X_64 = np.array(X).astype(np.float64) y_64 = np.array(Y1).astype(np.float64) X_sparse_32 = sp.csr_matrix(X, dtype=np.float32) for solver in ['newton-cg']: for multi_class in ['ovr', 'multinomial']: # Check type consistency lr_32 = LogisticRegression(solver=solver, multi_class=multi_class) lr_32.fit(X_32, y_32) assert_equal(lr_32.coef_.dtype, X_32.dtype) # check consistency with sparsity lr_32_sparse = LogisticRegression(solver=solver, multi_class=multi_class) lr_32_sparse.fit(X_sparse_32, y_32) assert_equal(lr_32_sparse.coef_.dtype, X_sparse_32.dtype) # Check accuracy consistency lr_64 = LogisticRegression(solver=solver, multi_class=multi_class) lr_64.fit(X_64, y_64) assert_equal(lr_64.coef_.dtype, X_64.dtype) assert_almost_equal(lr_32.coef_, lr_64.coef_.astype(np.float32))