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# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# License: BSD 3 clause
from tempfile import mkdtemp
import shutil
import numpy as np
from scipy import sparse
from sklearn.utils.testing import assert_equal
from sklearn.utils.testing import assert_array_equal
from sklearn.utils.testing import assert_raises
from sklearn.utils.testing import assert_raises_regex
from sklearn.utils.testing import assert_allclose
from sklearn.utils.testing import ignore_warnings
from sklearn.utils.testing import assert_warns_message
from sklearn.linear_model.randomized_l1 import(lasso_stability_path,
RandomizedLasso,
RandomizedLogisticRegression)
from sklearn.datasets import load_diabetes, load_iris
from sklearn.feature_selection import f_regression, f_classif
from sklearn.preprocessing import StandardScaler
from sklearn.linear_model.base import _preprocess_data
diabetes = load_diabetes()
X = diabetes.data
y = diabetes.target
X = StandardScaler().fit_transform(X)
X = X[:, [2, 3, 6, 7, 8]]
# test that the feature score of the best features
F, _ = f_regression(X, y)
@ignore_warnings(category=DeprecationWarning)
def test_lasso_stability_path():
# Check lasso stability path
# Load diabetes data and add noisy features
scaling = 0.3
coef_grid, scores_path = lasso_stability_path(X, y, scaling=scaling,
random_state=42,
n_resampling=30)
assert_array_equal(np.argsort(F)[-3:],
np.argsort(np.sum(scores_path, axis=1))[-3:])
@ignore_warnings(category=DeprecationWarning)
def test_randomized_lasso_error_memory():
scaling = 0.3
selection_threshold = 0.5
tempdir = 5
clf = RandomizedLasso(verbose=False, alpha=[1, 0.8], random_state=42,
scaling=scaling,
selection_threshold=selection_threshold,
memory=tempdir)
assert_raises_regex(ValueError, "'memory' should either be a string or"
" a sklearn.utils.Memory instance",
clf.fit, X, y)
@ignore_warnings(category=DeprecationWarning)
def test_randomized_lasso():
# Check randomized lasso
scaling = 0.3
selection_threshold = 0.5
n_resampling = 20
# or with 1 alpha
clf = RandomizedLasso(verbose=False, alpha=1, random_state=42,
scaling=scaling, n_resampling=n_resampling,
selection_threshold=selection_threshold)
feature_scores = clf.fit(X, y).scores_
assert_array_equal(np.argsort(F)[-3:], np.argsort(feature_scores)[-3:])
# or with many alphas
clf = RandomizedLasso(verbose=False, alpha=[1, 0.8], random_state=42,
scaling=scaling, n_resampling=n_resampling,
selection_threshold=selection_threshold)
feature_scores = clf.fit(X, y).scores_
assert_equal(clf.all_scores_.shape, (X.shape[1], 2))
assert_array_equal(np.argsort(F)[-3:], np.argsort(feature_scores)[-3:])
# test caching
try:
tempdir = mkdtemp()
clf = RandomizedLasso(verbose=False, alpha=[1, 0.8], random_state=42,
scaling=scaling,
selection_threshold=selection_threshold,
memory=tempdir)
feature_scores = clf.fit(X, y).scores_
assert_equal(clf.all_scores_.shape, (X.shape[1], 2))
assert_array_equal(np.argsort(F)[-3:], np.argsort(feature_scores)[-3:])
finally:
shutil.rmtree(tempdir)
X_r = clf.transform(X)
X_full = clf.inverse_transform(X_r)
assert_equal(X_r.shape[1], np.sum(feature_scores > selection_threshold))
assert_equal(X_full.shape, X.shape)
clf = RandomizedLasso(verbose=False, alpha='aic', random_state=42,
scaling=scaling, n_resampling=100)
feature_scores = clf.fit(X, y).scores_
assert_allclose(feature_scores, [1., 1., 1., 0.225, 1.], rtol=0.2)
clf = RandomizedLasso(verbose=False, scaling=-0.1)
assert_raises(ValueError, clf.fit, X, y)
clf = RandomizedLasso(verbose=False, scaling=1.1)
assert_raises(ValueError, clf.fit, X, y)
@ignore_warnings(category=DeprecationWarning)
def test_randomized_lasso_precompute():
# Check randomized lasso for different values of precompute
n_resampling = 20
alpha = 1
random_state = 42
G = np.dot(X.T, X)
clf = RandomizedLasso(alpha=alpha, random_state=random_state,
precompute=G, n_resampling=n_resampling)
feature_scores_1 = clf.fit(X, y).scores_
for precompute in [True, False, None, 'auto']:
clf = RandomizedLasso(alpha=alpha, random_state=random_state,
precompute=precompute, n_resampling=n_resampling)
feature_scores_2 = clf.fit(X, y).scores_
assert_array_equal(feature_scores_1, feature_scores_2)
@ignore_warnings(category=DeprecationWarning)
def test_randomized_logistic():
# Check randomized sparse logistic regression
iris = load_iris()
X = iris.data[:, [0, 2]]
y = iris.target
X = X[y != 2]
y = y[y != 2]
F, _ = f_classif(X, y)
scaling = 0.3
clf = RandomizedLogisticRegression(verbose=False, C=1., random_state=42,
scaling=scaling, n_resampling=50,
tol=1e-3)
X_orig = X.copy()
feature_scores = clf.fit(X, y).scores_
assert_array_equal(X, X_orig) # fit does not modify X
assert_array_equal(np.argsort(F), np.argsort(feature_scores))
clf = RandomizedLogisticRegression(verbose=False, C=[1., 0.5],
random_state=42, scaling=scaling,
n_resampling=50, tol=1e-3)
feature_scores = clf.fit(X, y).scores_
assert_array_equal(np.argsort(F), np.argsort(feature_scores))
clf = RandomizedLogisticRegression(verbose=False, C=[[1., 0.5]])
assert_raises(ValueError, clf.fit, X, y)
@ignore_warnings(category=DeprecationWarning)
def test_randomized_logistic_sparse():
# Check randomized sparse logistic regression on sparse data
iris = load_iris()
X = iris.data[:, [0, 2]]
y = iris.target
X = X[y != 2]
y = y[y != 2]
# center here because sparse matrices are usually not centered
# labels should not be centered
X, _, _, _, _ = _preprocess_data(X, y, True, True)
X_sp = sparse.csr_matrix(X)
F, _ = f_classif(X, y)
scaling = 0.3
clf = RandomizedLogisticRegression(verbose=False, C=1., random_state=42,
scaling=scaling, n_resampling=50,
tol=1e-3)
feature_scores = clf.fit(X, y).scores_
clf = RandomizedLogisticRegression(verbose=False, C=1., random_state=42,
scaling=scaling, n_resampling=50,
tol=1e-3)
feature_scores_sp = clf.fit(X_sp, y).scores_
assert_array_equal(feature_scores, feature_scores_sp)
def test_warning_raised():
scaling = 0.3
selection_threshold = 0.5
tempdir = 5
assert_warns_message(DeprecationWarning, "The function"
" lasso_stability_path is "
"deprecated in 0.19 and will be removed in 0.21.",
lasso_stability_path, X, y, scaling=scaling,
random_state=42, n_resampling=30)
assert_warns_message(DeprecationWarning, "Class RandomizedLasso is"
" deprecated; The class RandomizedLasso is "
"deprecated in 0.19 and will be removed in 0.21.",
RandomizedLasso, verbose=False, alpha=[1, 0.8],
random_state=42, scaling=scaling,
selection_threshold=selection_threshold,
memory=tempdir)
assert_warns_message(DeprecationWarning, "The class"
" RandomizedLogisticRegression is "
"deprecated in 0.19 and will be removed in 0.21.",
RandomizedLogisticRegression,
verbose=False, C=1., random_state=42,
scaling=scaling, n_resampling=50,
tol=1e-3)
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