def test_weights():
sparse_X = 1
X, y = build_dataset(n_samples=30, n_features=50, sparse_X=sparse_X)
np.random.seed(0)
weights = np.abs(np.random.randn(X.shape[1]))
tol = 1e-12
params = {'n_alphas': 10, 'tol': tol}
alphas1, coefs1, gaps1 = celer_path(X,
y,
"lasso",
weights=weights,
verbose=1,
**params)
alphas2, coefs2, gaps2 = celer_path(X / weights[None, :], y, "lasso",
**params)
np.testing.assert_allclose(alphas1, alphas2)
np.testing.assert_allclose(coefs1,
coefs2 / weights[:, None],
atol=1e-5,
rtol=1e-3)
np.testing.assert_array_less(gaps1, tol)
np.testing.assert_array_less(gaps2, tol)
def test_weights():
sparse_X = 1
X, y = build_dataset(n_samples=30, n_features=50, sparse_X=sparse_X)
np.random.seed(0)
weights = np.abs(np.random.randn(X.shape[1]))
tol = 1e-14
params = {'n_alphas': 10, 'tol': tol}
alphas1, coefs1, gaps1 = celer_path(X,
y,
"lasso",
weights=weights,
verbose=1,
**params)
alphas2, coefs2, gaps2 = celer_path(X / weights[None, :], y, "lasso",
**params)
assert_allclose(alphas1, alphas2)
assert_allclose(coefs1, coefs2 / weights[:, None], atol=1e-4, rtol=1e-3)
assert_array_less(gaps1, tol * norm(y)**2 / len(y))
assert_array_less(gaps2, tol * norm(y)**2 / len(y))
alpha = 0.001
clf1 = Lasso(alpha=alpha, weights=weights, fit_intercept=False).fit(X, y)
clf2 = Lasso(alpha=alpha, fit_intercept=False).fit(X / weights, y)
assert_allclose(clf1.coef_, clf2.coef_ / weights)
# weights must be > 0
clf1.weights[0] = 0.
np.testing.assert_raises(ValueError, clf1.fit, X=X, y=y)
def test_group_lasso_lasso(sparse_X, fit_intercept, normalize):
# check that group Lasso with groups of size 1 gives Lasso
n_features = 1000
X, y = build_dataset(n_samples=100,
n_features=n_features,
sparse_X=sparse_X)[:2]
alpha_max = norm(X.T @ y, ord=np.inf) / len(y)
alpha = alpha_max / 10
clf = Lasso(alpha,
tol=1e-12,
fit_intercept=fit_intercept,
normalize=normalize,
verbose=0)
clf.fit(X, y)
# take groups of size 1:
clf1 = GroupLasso(alpha=alpha,
groups=1,
tol=1e-12,
fit_intercept=fit_intercept,
normalize=normalize,
verbose=0)
clf1.fit(X, y)
np.testing.assert_allclose(clf1.coef_, clf.coef_, atol=1e-6)
np.testing.assert_allclose(clf1.intercept_, clf.intercept_, rtol=1e-4)
def test_weights_group_lasso():
n_samples, n_features = 30, 50
X, y = build_dataset(n_samples, n_features, sparse_X=True)
groups = 5
n_groups = n_features // groups
np.random.seed(0)
weights = np.abs(np.random.randn(n_groups))
tol = 1e-14
params = {'n_alphas': 10, 'tol': tol, 'verbose': 1}
augmented_weights = np.repeat(weights, groups)
alphas1, coefs1, gaps1 = celer_path(
X, y, "grouplasso", groups=groups, weights=weights,
eps=1e-2, **params)
alphas2, coefs2, gaps2 = celer_path(
X.multiply(1 / augmented_weights[None, :]), y, "grouplasso",
groups=groups, eps=1e-2, **params)
assert_allclose(alphas1, alphas2)
assert_allclose(
coefs1, coefs2 / augmented_weights[:, None], rtol=1e-3)
assert_array_less(gaps1, tol * norm(y) ** 2 / len(y))
assert_array_less(gaps2, tol * norm(y) ** 2 / len(y))
def test_LogisticRegression(sparse_X):
np.random.seed(1409)
X, y = build_dataset(
n_samples=30, n_features=60, sparse_X=sparse_X)
y = np.sign(y)
alpha_max = norm(X.T.dot(y), ord=np.inf) / 2
C = 30. / alpha_max
tol = 1e-8
clf1 = LogisticRegression(C=C, tol=tol, verbose=2)
clf1.fit(X, y)
clf2 = sklearn_Logreg(
C=C, penalty='l1', solver='liblinear', fit_intercept=False, tol=tol)
clf2.fit(X, y)
np.testing.assert_allclose(clf1.coef_, clf2.coef_, rtol=1e-3, atol=1e-5)
# this uses float32 so we increase the tol else there are precision issues
clf1.tol = 1e-4
check_estimator(clf1)
# multinomial test, need to have a slightly lower tol
# for results to be comparable
y = np.random.choice(4, len(y))
clf3 = LogisticRegression(C=C, tol=tol, verbose=2)
clf3.fit(X, y)
clf4 = sklearn_Logreg(
C=C, penalty='l1', solver='liblinear', fit_intercept=False, tol=tol)
clf4.fit(X, y)
np.testing.assert_allclose(clf3.coef_, clf4.coef_, rtol=1e-3, atol=1e-3)
clf3.tol = 1e-3
check_estimator(clf3)
def test_celer_path(sparse_X, alphas, pb):
"""Test Lasso path convergence."""
X, y = build_dataset(n_samples=30, n_features=50, sparse_X=sparse_X)
tol = 1e-6
if pb == "logreg":
y = np.sign(y)
tol_scaled = tol * len(y) * np.log(2)
else:
tol_scaled = tol * norm(y)**2 / len(y)
n_samples = X.shape[0]
if alphas is not None:
alpha_max = np.max(np.abs(X.T.dot(y))) / n_samples
n_alphas = 10
alphas = alpha_max * np.logspace(0, -2, n_alphas)
alphas, _, gaps, _, n_iters = celer_path(X,
y,
pb,
alphas=alphas,
tol=tol,
return_thetas=True,
verbose=1,
return_n_iter=True)
assert_array_less(gaps, tol_scaled)
# hack because array_less wants strict inequality
assert_array_less(0.99, n_iters)
def test_celer_path_logreg(solver):
X, y = build_dataset(n_samples=60, n_features=100, sparse_X=True)
y = np.sign(y)
alpha_max = norm(X.T.dot(y), ord=np.inf) / 2
alphas = alpha_max * np.geomspace(1, 1e-2, 10)
tol = 1e-8
coefs, Cs, n_iters = _logistic_regression_path(X,
y,
Cs=1. / alphas,
fit_intercept=False,
penalty='l1',
solver='liblinear',
tol=tol)
_, coefs_c, gaps = celer_path(X,
y,
"logreg",
alphas=alphas,
tol=tol,
verbose=1,
use_PN=(solver == "celer-pn"))
np.testing.assert_array_less(gaps, tol)
np.testing.assert_allclose(coefs != 0, coefs_c.T != 0)
np.testing.assert_allclose(coefs, coefs_c.T, atol=1e-5, rtol=1e-3)
def test_MultiTaskLassoCV():
"""Test that our MultitaskLassoCV behaves like sklearn's."""
X, y = build_dataset(n_samples=30, n_features=50, n_targets=3)
params = dict(eps=1e-2, n_alphas=10, tol=1e-10, cv=2, n_jobs=1,
fit_intercept=False, verbose=2)
clf = MultiTaskLassoCV(**params)
clf.fit(X, y)
clf2 = sklearn_MultiTaskLassoCV(**params)
clf2.max_iter = 10000 # increase max_iter bc of low tol
clf2.fit(X, y)
np.testing.assert_allclose(clf.mse_path_, clf2.mse_path_,
atol=1e-4, rtol=1e-04)
np.testing.assert_allclose(clf.alpha_, clf2.alpha_,
atol=1e-4, rtol=1e-04)
np.testing.assert_allclose(clf.coef_, clf2.coef_,
atol=1e-4, rtol=1e-04)
# check_estimator tests float32 so using tol < 1e-7 causes precision
# issues
clf.tol = 1e-5
check_estimator(clf)
def test_infinite_weights(pb):
n_samples, n_features = 50, 100
X, y = build_dataset(n_samples, n_features)
if pb == "logreg":
y = np.sign(y)
np.random.seed(1)
weights = np.abs(np.random.randn(n_features))
n_inf = n_features // 10
inf_indices = np.random.choice(n_features, size=n_inf, replace=False)
weights[inf_indices] = np.inf
alpha = norm(X.T @ y / weights, ord=np.inf) / n_samples / 100
tol = 1e-8
_, coefs, dual_gaps = celer_path(X,
y,
pb=pb,
alphas=[alpha],
weights=weights,
tol=tol)
if pb == "logreg":
assert_array_less(dual_gaps[0], tol * n_samples * np.log(2))
else:
assert_array_less(dual_gaps[0], tol * norm(y)**2 / 2.)
assert_array_equal(coefs[inf_indices], 0)
def test_dropin_logreg():
np.random.seed(1409)
check_estimator(LogisticRegression)
X, y, _, _ = build_dataset(n_samples=100, n_features=100, sparse_X=True)
y = np.sign(y)
alpha_max = norm(X.T.dot(y), ord=np.inf) / 2
C = 30. / alpha_max
tol = 1e-8
clf1 = LogisticRegression(C=C, tol=tol)
clf1.fit(X, y)
clf2 = sklearn_Logreg(C=C,
penalty='l1',
solver='liblinear',
fit_intercept=False,
tol=tol)
clf2.fit(X, y)
np.testing.assert_allclose(clf1.coef_, clf2.coef_, rtol=1e-3, atol=1e-5)
# multinomial test:
y = np.random.choice(4, len(y))
clf3 = LogisticRegression(C=C, tol=tol)
clf3.fit(X, y)
clf4 = sklearn_Logreg(C=C,
penalty='l1',
solver='liblinear',
fit_intercept=False,
tol=tol)
clf4.fit(X, y)
np.testing.assert_allclose(clf3.coef_, clf4.coef_, rtol=1e-3, atol=1e-4)
def test_group_lasso_path(sparse_X):
n_features = 50
X, y = build_dataset(
n_samples=11, n_features=n_features, sparse_X=sparse_X)
alphas, coefs, gaps = celer_path(
X, y, "grouplasso", groups=5, eps=1e-2, n_alphas=10, tol=1e-8)
tol = 1e-8
np.testing.assert_array_less(gaps, tol)
def test_celer_single_alpha(sparse_X, pb):
X, y = build_dataset(n_samples=20, n_features=100, sparse_X=sparse_X)
if pb == "logreg":
y = np.sign(y)
alpha_max = norm(X.T.dot(y), ord=np.inf) / X.shape[0]
tol = 1e-6
_, coefs, gaps = celer_path(X, y, pb, alphas=[alpha_max / 10.], tol=tol)
np.testing.assert_array_less(gaps, tol)
def test_check_weights():
X, y = build_dataset(30, 42)
weights = np.ones(X.shape[1] // 7)
weights[0] = 0
clf = GroupLasso(weights=weights, groups=7) # groups of size 7
# weights must be > 0
np.testing.assert_raises(ValueError, clf.fit, X=X, y=y)
# len(weights) must be equal to number of groups (6 here)
clf.weights = np.ones(8)
np.testing.assert_raises(ValueError, clf.fit, X=X, y=y)
def test_GroupLasso(sparse_X):
n_features = 50
X, y = build_dataset(n_samples=11,
n_features=n_features,
sparse_X=sparse_X,
n_informative_features=n_features)[:2]
tol = 1e-4
clf = GroupLasso(alpha=0.01, groups=10, tol=tol)
clf.fit(X, y)
np.testing.assert_array_less(clf.dual_gap_, tol)
def test_mtl_path():
X, Y = build_dataset(n_targets=3)
tol = 1e-10
params = dict(eps=0.01, tol=tol, n_alphas=10)
alphas, coefs, gaps = mtl_path(X, Y, **params)
np.testing.assert_array_less(gaps, tol)
sk_alphas, sk_coefs, sk_gaps = lasso_path(X, Y, **params, max_iter=10000)
np.testing.assert_array_less(sk_gaps, tol * np.linalg.norm(Y, 'fro')**2)
np.testing.assert_array_almost_equal(coefs, sk_coefs, decimal=5)
np.testing.assert_allclose(alphas, sk_alphas)
def test_zero_iter():
X, y = build_dataset(n_samples=30, n_features=50)
# convergence warning is raised bc we return -1 as gap
with warnings.catch_warnings(record=True):
assert_allclose(Lasso(max_iter=0).fit(X, y).coef_, 0)
y = 2 * (y > 0) - 1
assert_allclose(
LogisticRegression(max_iter=0, solver="celer-pn").fit(X, y).coef_,
0)
assert_allclose(
LogisticRegression(max_iter=0, solver="celer").fit(X, y).coef_, 0)
def test_mtl():
# n_samples, n_features = 30, 70
# X, Y, _, _ = build_dataset(n_samples, n_features, n_targets=10)
X, Y, _, _ = build_dataset(n_targets=10)
tol = 1e-9
alphas, coefs, gaps = mtl_path(X, Y, eps=1e-2, tol=tol)
np.testing.assert_array_less(gaps, tol)
sk_alphas, sk_coefs, sk_gaps = lasso_path(X, Y, eps=1e-2, tol=tol)
np.testing.assert_array_less(sk_gaps, tol * np.linalg.norm(Y, 'fro')**2)
np.testing.assert_array_almost_equal(coefs, sk_coefs, decimal=5)
np.testing.assert_allclose(alphas, sk_alphas)
def test_convergence_warning():
X, y = build_dataset(n_samples=10, n_features=10)
tol = -1 # gap canot be negative, a covnergence warning should be raised
alpha_max = np.max(np.abs(X.T.dot(y))) / X.shape[0]
clf = Lasso(alpha_max / 10, max_iter=1, max_epochs=100, tol=tol)
with warnings.catch_warnings(record=True) as w:
# Cause all warnings to always be triggered.
warnings.simplefilter("always")
clf.fit(X, y)
assert len(w) == 1
assert issubclass(w[-1].category, ConvergenceWarning)
def test_GroupLassoCV(sparse_X):
n_features = 50
X, y = build_dataset(
n_samples=11, n_features=n_features, sparse_X=sparse_X)
tol = 1e-8
clf = GroupLassoCV(groups=10, tol=tol)
clf.fit(X, y)
np.testing.assert_array_less(clf.dual_gap_, tol)
clf.tol = 1e-6
clf.groups = 1 # unsatisfying but sklearn will fit with 5 features
check_estimator(clf)
def test_GroupLasso(sparse_X):
n_features = 50
X, y = build_dataset(
n_samples=11, n_features=n_features, sparse_X=sparse_X)
tol = 1e-8
clf = GroupLasso(alpha=0.8, groups=10, tol=tol)
clf.fit(X, y)
np.testing.assert_array_less(clf.dual_gap_, tol * norm(y) ** 2 / len(y))
clf.tol = 1e-6
clf.groups = 1 # unsatisfying but sklearn will fit out of 5 features
check_estimator(clf)
def test_celer_single_alpha(sparse_X, pb):
X, y = build_dataset(n_samples=20, n_features=100, sparse_X=sparse_X)
tol = 1e-6
if pb == "logreg":
y = np.sign(y)
tol_scaled = tol * np.log(2) * len(y)
else:
tol_scaled = tol * norm(y)**2 / len(y)
alpha_max = norm(X.T.dot(y), ord=np.inf) / X.shape[0]
_, _, gaps = celer_path(X, y, pb, alphas=[alpha_max / 10.], tol=tol)
assert_array_less(gaps, tol_scaled)
def test_zero_column(sparse_X):
X, y = build_dataset(n_samples=60, n_features=50, sparse_X=sparse_X)
n_zero_columns = 20
if sparse_X:
X.data[:X.indptr[n_zero_columns]].fill(0.)
else:
X[:, :n_zero_columns].fill(0.)
alpha_max = norm(X.T.dot(y), ord=np.inf) / X.shape[0]
tol = 1e-6
_, coefs, gaps = celer_path(
X, y, "lasso", alphas=[alpha_max / 10.], tol=tol, p0=50, prune=0)
w = coefs.T[0]
np.testing.assert_array_less(gaps, tol)
np.testing.assert_equal(w.shape[0], X.shape[1])
def test_multinomial(sparse_X):
np.random.seed(1409)
X, y = build_dataset(n_samples=30, n_features=60, sparse_X=sparse_X)
y = np.random.choice(4, len(y))
tol = 1e-8
clf = LogisticRegression(C=1, tol=tol, verbose=0)
clf.fit(X, y)
clf_sk = sklearn_Logreg(C=1,
penalty='l1',
solver='liblinear',
fit_intercept=False,
tol=tol)
clf_sk.fit(X, y)
assert_allclose(clf.coef_, clf_sk.coef_, rtol=1e-3, atol=1e-3)
def test_celer_path_vs_lasso_path(sparse_X, prune):
"""Test that celer_path matches sklearn lasso_path."""
X, y = build_dataset(n_samples=30, n_features=50, sparse_X=sparse_X)
tol = 1e-12
params = dict(eps=1e-3, n_alphas=10, tol=tol)
alphas1, coefs1, gaps1 = celer_path(
X, y, "lasso", return_thetas=False, verbose=1, prune=prune,
max_iter=30, **params)
alphas2, coefs2, _ = lasso_path(X, y, verbose=False, **params,
max_iter=10000)
np.testing.assert_allclose(alphas1, alphas2)
np.testing.assert_array_less(gaps1, tol)
np.testing.assert_allclose(coefs1, coefs2, rtol=1e-03, atol=1e-5)
def test_MultiTaskLasso(fit_intercept):
"""Test that our MultiTaskLasso behaves as sklearn's."""
X, Y = build_dataset(n_samples=20, n_features=30, n_targets=10)
alpha_max = np.max(norm(X.T.dot(Y), axis=1)) / X.shape[0]
alpha = alpha_max / 2.
params = dict(alpha=alpha, fit_intercept=fit_intercept, tol=1e-10)
clf = MultiTaskLasso(**params)
clf.verbose = 2
clf.fit(X, Y)
clf2 = sklearn_MultiTaskLasso(**params)
clf2.fit(X, Y)
np.testing.assert_allclose(clf.coef_, clf2.coef_, rtol=1e-5)
if fit_intercept:
np.testing.assert_allclose(clf.intercept_, clf2.intercept_)
def test_celer_path_vs_lasso_path(sparse_X, prune):
"""Test that celer_path matches sklearn lasso_path."""
X, y, _, _ = build_dataset(n_samples=30, n_features=50, sparse_X=sparse_X)
params = dict(eps=1e-2, n_alphas=10, tol=1e-12)
alphas1, coefs1, gaps1 = celer_path(X,
y,
"lasso",
return_thetas=False,
verbose=1,
prune=prune,
**params)
alphas2, coefs2, gaps2 = lasso_path(X, y, verbose=False, **params)
np.testing.assert_allclose(alphas1, alphas2)
np.testing.assert_allclose(coefs1, coefs2, rtol=2e-03, atol=1e-4)
def test_LassoCV(sparse_X, fit_intercept, positive):
"""Test that our LassoCV behaves like sklearn's LassoCV."""
X, y = build_dataset(n_samples=20, n_features=30, sparse_X=sparse_X)
params = dict(eps=0.05, n_alphas=10, tol=1e-10, cv=2,
fit_intercept=fit_intercept, positive=positive, verbose=2,
n_jobs=-1)
clf = LassoCV(**params)
clf.fit(X, y)
clf2 = sklearn_LassoCV(**params, max_iter=10000)
clf2.fit(X, y)
np.testing.assert_allclose(clf.mse_path_, clf2.mse_path_, atol=1e-4)
np.testing.assert_allclose(clf.alpha_, clf2.alpha_)
np.testing.assert_allclose(clf.coef_, clf2.coef_, atol=1e-5)
def test_dropin_MultiTaskLasso():
"""Test that our MultiTaskLasso class behaves as sklearn's."""
X, Y, _, _ = build_dataset(n_samples=20, n_features=30, n_targets=10)
alpha_max = np.max(norm(X.T.dot(Y), axis=1)) / X.shape[0]
alpha = alpha_max / 2.
params = dict(alpha=alpha, fit_intercept=False, tol=1e-10, normalize=True)
clf = MultiTaskLasso(**params)
clf.fit(X, Y)
clf2 = sklearn_MultiTaskLasso(**params)
clf2.fit(X, Y)
np.testing.assert_allclose(clf.coef_, clf2.coef_, rtol=1e-5)
# if fit_intercept:
# np.testing.assert_allclose(clf.intercept_, clf2.intercept_)
check_estimator(MultiTaskLasso)
def test_group_lasso_path(sparse_X):
n_features = 50
X, y = build_dataset(n_samples=11,
n_features=n_features,
sparse_X=sparse_X,
n_informative_features=n_features)[:2]
alphas, coefs, gaps = celer_path(X,
y,
"grouplasso",
groups=5,
eps=1e-2,
n_alphas=10,
tol=1e-8)
tol = 1e-8
np.testing.assert_array_less(gaps, tol)
check_estimator(GroupLasso)
def test_warm_start():
"""Test Lasso path convergence."""
X, y = build_dataset(n_samples=100, n_features=100, sparse_X=True)
n_samples, n_features = X.shape
alpha_max = np.max(np.abs(X.T.dot(y))) / n_samples
n_alphas = 10
alphas = alpha_max * np.logspace(0, -2, n_alphas)
reg1 = Lasso(tol=1e-6, warm_start=True, p0=10)
reg1.coef_ = np.zeros(n_features)
for alpha in alphas:
reg1.set_params(alpha=alpha)
reg1.fit(X, y)
# refitting with warm start should take less than 2 iters:
reg1.fit(X, y)
# hack because assert_array_less does strict comparison...
np.testing.assert_array_less(reg1.n_iter_, 2.01)