python3-sklearn 0.17.0-4 / usr / lib / python3 / dist-packages / sklearn / linear_model / tests / test_sparse_coordinate_descent.py

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import numpy as np
import scipy.sparse as sp

from sklearn.utils.testing import assert_array_almost_equal
from sklearn.utils.testing import assert_almost_equal
from sklearn.utils.testing import assert_equal
from sklearn.utils.testing import assert_less
from sklearn.utils.testing import assert_true

from sklearn.utils.testing import assert_greater
from sklearn.utils.testing import ignore_warnings

from sklearn.linear_model.coordinate_descent import (Lasso, ElasticNet,
                                                     LassoCV, ElasticNetCV)


def test_sparse_coef():
    # Check that the sparse_coef propery works
    clf = ElasticNet()
    clf.coef_ = [1, 2, 3]

    assert_true(sp.isspmatrix(clf.sparse_coef_))
    assert_equal(clf.sparse_coef_.toarray().tolist()[0], clf.coef_)


def test_normalize_option():
    # Check that the normalize option in enet works
    X = sp.csc_matrix([[-1], [0], [1]])
    y = [-1, 0, 1]
    clf_dense = ElasticNet(fit_intercept=True, normalize=True)
    clf_sparse = ElasticNet(fit_intercept=True, normalize=True)
    clf_dense.fit(X, y)
    X = sp.csc_matrix(X)
    clf_sparse.fit(X, y)
    assert_almost_equal(clf_dense.dual_gap_, 0)
    assert_array_almost_equal(clf_dense.coef_, clf_sparse.coef_)


def test_lasso_zero():
    # Check that the sparse lasso can handle zero data without crashing
    X = sp.csc_matrix((3, 1))
    y = [0, 0, 0]
    T = np.array([[1], [2], [3]])
    clf = Lasso().fit(X, y)
    pred = clf.predict(T)
    assert_array_almost_equal(clf.coef_, [0])
    assert_array_almost_equal(pred, [0, 0, 0])
    assert_almost_equal(clf.dual_gap_,  0)


def test_enet_toy_list_input():
    # Test ElasticNet for various values of alpha and l1_ratio with list X

    X = np.array([[-1], [0], [1]])
    X = sp.csc_matrix(X)
    Y = [-1, 0, 1]       # just a straight line
    T = np.array([[2], [3], [4]])  # test sample

    # this should be the same as unregularized least squares
    clf = ElasticNet(alpha=0, l1_ratio=1.0)
    # catch warning about alpha=0.
    # this is discouraged but should work.
    ignore_warnings(clf.fit)(X, Y)
    pred = clf.predict(T)
    assert_array_almost_equal(clf.coef_, [1])
    assert_array_almost_equal(pred, [2, 3, 4])
    assert_almost_equal(clf.dual_gap_, 0)

    clf = ElasticNet(alpha=0.5, l1_ratio=0.3, max_iter=1000)
    clf.fit(X, Y)
    pred = clf.predict(T)
    assert_array_almost_equal(clf.coef_, [0.50819], decimal=3)
    assert_array_almost_equal(pred, [1.0163,  1.5245,  2.0327], decimal=3)
    assert_almost_equal(clf.dual_gap_, 0)

    clf = ElasticNet(alpha=0.5, l1_ratio=0.5)
    clf.fit(X, Y)
    pred = clf.predict(T)
    assert_array_almost_equal(clf.coef_, [0.45454], 3)
    assert_array_almost_equal(pred, [0.9090,  1.3636,  1.8181], 3)
    assert_almost_equal(clf.dual_gap_, 0)


def test_enet_toy_explicit_sparse_input():
    # Test ElasticNet for various values of alpha and l1_ratio with sparse X
    f = ignore_warnings
    # training samples
    X = sp.lil_matrix((3, 1))
    X[0, 0] = -1
    # X[1, 0] = 0
    X[2, 0] = 1
    Y = [-1, 0, 1]       # just a straight line (the identity function)

    # test samples
    T = sp.lil_matrix((3, 1))
    T[0, 0] = 2
    T[1, 0] = 3
    T[2, 0] = 4

    # this should be the same as lasso
    clf = ElasticNet(alpha=0, l1_ratio=1.0)
    f(clf.fit)(X, Y)
    pred = clf.predict(T)
    assert_array_almost_equal(clf.coef_, [1])
    assert_array_almost_equal(pred, [2, 3, 4])
    assert_almost_equal(clf.dual_gap_, 0)

    clf = ElasticNet(alpha=0.5, l1_ratio=0.3, max_iter=1000)
    clf.fit(X, Y)
    pred = clf.predict(T)
    assert_array_almost_equal(clf.coef_, [0.50819], decimal=3)
    assert_array_almost_equal(pred, [1.0163,  1.5245,  2.0327], decimal=3)
    assert_almost_equal(clf.dual_gap_, 0)

    clf = ElasticNet(alpha=0.5, l1_ratio=0.5)
    clf.fit(X, Y)
    pred = clf.predict(T)
    assert_array_almost_equal(clf.coef_, [0.45454], 3)
    assert_array_almost_equal(pred, [0.9090,  1.3636,  1.8181], 3)
    assert_almost_equal(clf.dual_gap_, 0)


def make_sparse_data(n_samples=100, n_features=100, n_informative=10, seed=42,
                     positive=False, n_targets=1):
    random_state = np.random.RandomState(seed)

    # build an ill-posed linear regression problem with many noisy features and
    # comparatively few samples

    # generate a ground truth model
    w = random_state.randn(n_features, n_targets)
    w[n_informative:] = 0.0  # only the top features are impacting the model
    if positive:
        w = np.abs(w)

    X = random_state.randn(n_samples, n_features)
    rnd = random_state.uniform(size=(n_samples, n_features))
    X[rnd > 0.5] = 0.0  # 50% of zeros in input signal

    # generate training ground truth labels
    y = np.dot(X, w)
    X = sp.csc_matrix(X)
    if n_targets == 1:
        y = np.ravel(y)
    return X, y


def _test_sparse_enet_not_as_toy_dataset(alpha, fit_intercept, positive):
    n_samples, n_features, max_iter = 100, 100, 1000
    n_informative = 10

    X, y = make_sparse_data(n_samples, n_features, n_informative,
                            positive=positive)

    X_train, X_test = X[n_samples // 2:], X[:n_samples // 2]
    y_train, y_test = y[n_samples // 2:], y[:n_samples // 2]

    s_clf = ElasticNet(alpha=alpha, l1_ratio=0.8, fit_intercept=fit_intercept,
                       max_iter=max_iter, tol=1e-7, positive=positive,
                       warm_start=True)
    s_clf.fit(X_train, y_train)

    assert_almost_equal(s_clf.dual_gap_, 0, 4)
    assert_greater(s_clf.score(X_test, y_test), 0.85)

    # check the convergence is the same as the dense version
    d_clf = ElasticNet(alpha=alpha, l1_ratio=0.8, fit_intercept=fit_intercept,
                       max_iter=max_iter, tol=1e-7, positive=positive,
                       warm_start=True)
    d_clf.fit(X_train.toarray(), y_train)

    assert_almost_equal(d_clf.dual_gap_, 0, 4)
    assert_greater(d_clf.score(X_test, y_test), 0.85)

    assert_almost_equal(s_clf.coef_, d_clf.coef_, 5)
    assert_almost_equal(s_clf.intercept_, d_clf.intercept_, 5)

    # check that the coefs are sparse
    assert_less(np.sum(s_clf.coef_ != 0.0), 2 * n_informative)


def test_sparse_enet_not_as_toy_dataset():
    _test_sparse_enet_not_as_toy_dataset(alpha=0.1, fit_intercept=False,
                                         positive=False)
    _test_sparse_enet_not_as_toy_dataset(alpha=0.1, fit_intercept=True,
                                         positive=False)
    _test_sparse_enet_not_as_toy_dataset(alpha=1e-3, fit_intercept=False,
                                         positive=True)
    _test_sparse_enet_not_as_toy_dataset(alpha=1e-3, fit_intercept=True,
                                         positive=True)


def test_sparse_lasso_not_as_toy_dataset():
    n_samples = 100
    max_iter = 1000
    n_informative = 10
    X, y = make_sparse_data(n_samples=n_samples, n_informative=n_informative)

    X_train, X_test = X[n_samples // 2:], X[:n_samples // 2]
    y_train, y_test = y[n_samples // 2:], y[:n_samples // 2]

    s_clf = Lasso(alpha=0.1, fit_intercept=False, max_iter=max_iter, tol=1e-7)
    s_clf.fit(X_train, y_train)
    assert_almost_equal(s_clf.dual_gap_, 0, 4)
    assert_greater(s_clf.score(X_test, y_test), 0.85)

    # check the convergence is the same as the dense version
    d_clf = Lasso(alpha=0.1, fit_intercept=False, max_iter=max_iter, tol=1e-7)
    d_clf.fit(X_train.toarray(), y_train)
    assert_almost_equal(d_clf.dual_gap_, 0, 4)
    assert_greater(d_clf.score(X_test, y_test), 0.85)

    # check that the coefs are sparse
    assert_equal(np.sum(s_clf.coef_ != 0.0), n_informative)


def test_enet_multitarget():
    n_targets = 3
    X, y = make_sparse_data(n_targets=n_targets)

    estimator = ElasticNet(alpha=0.01, fit_intercept=True, precompute=None)
    # XXX: There is a bug when precompute is not None!
    estimator.fit(X, y)
    coef, intercept, dual_gap = (estimator.coef_,
                                 estimator.intercept_,
                                 estimator.dual_gap_)

    for k in range(n_targets):
        estimator.fit(X, y[:, k])
        assert_array_almost_equal(coef[k, :], estimator.coef_)
        assert_array_almost_equal(intercept[k], estimator.intercept_)
        assert_array_almost_equal(dual_gap[k], estimator.dual_gap_)


def test_path_parameters():
    X, y = make_sparse_data()
    max_iter = 50
    n_alphas = 10
    clf = ElasticNetCV(n_alphas=n_alphas, eps=1e-3, max_iter=max_iter,
                       l1_ratio=0.5, fit_intercept=False)
    ignore_warnings(clf.fit)(X, y)  # new params
    assert_almost_equal(0.5, clf.l1_ratio)
    assert_equal(n_alphas, clf.n_alphas)
    assert_equal(n_alphas, len(clf.alphas_))
    sparse_mse_path = clf.mse_path_
    ignore_warnings(clf.fit)(X.toarray(), y)  # compare with dense data
    assert_almost_equal(clf.mse_path_, sparse_mse_path)


def test_same_output_sparse_dense_lasso_and_enet_cv():
    X, y = make_sparse_data(n_samples=40, n_features=10)
    for normalize in [True, False]:
        clfs = ElasticNetCV(max_iter=100, cv=5, normalize=normalize)
        ignore_warnings(clfs.fit)(X, y)
        clfd = ElasticNetCV(max_iter=100, cv=5, normalize=normalize)
        ignore_warnings(clfd.fit)(X.toarray(), y)
        assert_almost_equal(clfs.alpha_, clfd.alpha_, 7)
        assert_almost_equal(clfs.intercept_, clfd.intercept_, 7)
        assert_array_almost_equal(clfs.mse_path_, clfd.mse_path_)
        assert_array_almost_equal(clfs.alphas_, clfd.alphas_)

        clfs = LassoCV(max_iter=100, cv=4, normalize=normalize)
        ignore_warnings(clfs.fit)(X, y)
        clfd = LassoCV(max_iter=100, cv=4, normalize=normalize)
        ignore_warnings(clfd.fit)(X.toarray(), y)
        assert_almost_equal(clfs.alpha_, clfd.alpha_, 7)
        assert_almost_equal(clfs.intercept_, clfd.intercept_, 7)
        assert_array_almost_equal(clfs.mse_path_, clfd.mse_path_)
        assert_array_almost_equal(clfs.alphas_, clfd.alphas_)

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