import numpy as np
import scipy.sparse as sp
from scipy import linalg
from itertools import product
import pytest
from sklearn.utils._testing import assert_almost_equal
from sklearn.utils._testing import assert_allclose
from sklearn.utils._testing import assert_array_almost_equal
from sklearn.utils._testing import assert_array_equal
from sklearn.utils._testing import assert_raises
from sklearn.utils._testing import assert_raise_message
from sklearn.utils._testing import assert_raises_regex
from sklearn.utils._testing import ignore_warnings
from sklearn.utils._testing import assert_warns
from sklearn.exceptions import ConvergenceWarning
from sklearn import datasets
from sklearn.metrics import mean_squared_error
from sklearn.metrics import make_scorer
from sklearn.metrics import get_scorer
from sklearn.linear_model import LinearRegression
from sklearn.linear_model import ridge_regression
from sklearn.linear_model import Ridge
from sklearn.linear_model._ridge import _RidgeGCV
from sklearn.linear_model import RidgeCV
from sklearn.linear_model import RidgeClassifier
from sklearn.linear_model import RidgeClassifierCV
from sklearn.linear_model._ridge import _solve_cholesky
from sklearn.linear_model._ridge import _solve_cholesky_kernel
from sklearn.linear_model._ridge import _check_gcv_mode
from sklearn.linear_model._ridge import _X_CenterStackOp
from sklearn.datasets import make_regression
from sklearn.model_selection import GridSearchCV
from sklearn.model_selection import KFold, GroupKFold, cross_val_predict
from sklearn.utils import check_random_state
from sklearn.datasets import make_multilabel_classification
diabetes = datasets.load_diabetes()
X_diabetes, y_diabetes = diabetes.data, diabetes.target
ind = np.arange(X_diabetes.shape[0])
rng = np.random.RandomState(0)
rng.shuffle(ind)
ind = ind[:200]
X_diabetes, y_diabetes = X_diabetes[ind], y_diabetes[ind]
iris = datasets.load_iris()
X_iris = sp.csr_matrix(iris.data)
y_iris = iris.target
DENSE_FILTER = lambda X: X
SPARSE_FILTER = lambda X: sp.csr_matrix(X)
@pytest.mark.parametrize('solver',
("svd", "sparse_cg", "cholesky", "lsqr", "sag"))
def test_ridge(solver):
# Ridge regression convergence test using score
# TODO: for this test to be robust, we should use a dataset instead
# of np.random.
rng = np.random.RandomState(0)
alpha = 1.0
# With more samples than features
n_samples, n_features = 6, 5
y = rng.randn(n_samples)
X = rng.randn(n_samples, n_features)
ridge = Ridge(alpha=alpha, solver=solver)
ridge.fit(X, y)
assert ridge.coef_.shape == (X.shape[1], )
assert ridge.score(X, y) > 0.47
if solver in ("cholesky", "sag"):
# Currently the only solvers to support sample_weight.
ridge.fit(X, y, sample_weight=np.ones(n_samples))
assert ridge.score(X, y) > 0.47
# With more features than samples
n_samples, n_features = 5, 10
y = rng.randn(n_samples)
X = rng.randn(n_samples, n_features)
ridge = Ridge(alpha=alpha, solver=solver)
ridge.fit(X, y)
assert ridge.score(X, y) > .9
if solver in ("cholesky", "sag"):
# Currently the only solvers to support sample_weight.
ridge.fit(X, y, sample_weight=np.ones(n_samples))
assert ridge.score(X, y) > 0.9
def test_primal_dual_relationship():
y = y_diabetes.reshape(-1, 1)
coef = _solve_cholesky(X_diabetes, y, alpha=[1e-2])
K = np.dot(X_diabetes, X_diabetes.T)
dual_coef = _solve_cholesky_kernel(K, y, alpha=[1e-2])
coef2 = np.dot(X_diabetes.T, dual_coef).T
assert_array_almost_equal(coef, coef2)
def test_ridge_singular():
# test on a singular matrix
rng = np.random.RandomState(0)
n_samples, n_features = 6, 6
y = rng.randn(n_samples // 2)
y = np.concatenate((y, y))
X = rng.randn(n_samples // 2, n_features)
X = np.concatenate((X, X), axis=0)
ridge = Ridge(alpha=0)
ridge.fit(X, y)
assert ridge.score(X, y) > 0.9
def test_ridge_regression_sample_weights():
rng = np.random.RandomState(0)
for solver in ("cholesky", ):
for n_samples, n_features in ((6, 5), (5, 10)):
for alpha in (1.0, 1e-2):
y = rng.randn(n_samples)
X = rng.randn(n_samples, n_features)
sample_weight = 1.0 + rng.rand(n_samples)
coefs = ridge_regression(X, y,
alpha=alpha,
sample_weight=sample_weight,
solver=solver)
# Sample weight can be implemented via a simple rescaling
# for the square loss.
coefs2 = ridge_regression(
X * np.sqrt(sample_weight)[:, np.newaxis],
y * np.sqrt(sample_weight),
alpha=alpha, solver=solver)
assert_array_almost_equal(coefs, coefs2)
def test_ridge_regression_convergence_fail():
rng = np.random.RandomState(0)
y = rng.randn(5)
X = rng.randn(5, 10)
assert_warns(ConvergenceWarning, ridge_regression,
X, y, alpha=1.0, solver="sparse_cg",
tol=0., max_iter=None, verbose=1)
def test_ridge_sample_weights():
# TODO: loop over sparse data as well
# Note: parametrizing this test with pytest results in failed
# assertions, meaning that is is not extremely robust
rng = np.random.RandomState(0)
param_grid = product((1.0, 1e-2), (True, False),
('svd', 'cholesky', 'lsqr', 'sparse_cg'))
for n_samples, n_features in ((6, 5), (5, 10)):
y = rng.randn(n_samples)
X = rng.randn(n_samples, n_features)
sample_weight = 1.0 + rng.rand(n_samples)
for (alpha, intercept, solver) in param_grid:
# Ridge with explicit sample_weight
est = Ridge(alpha=alpha, fit_intercept=intercept,
solver=solver, tol=1e-6)
est.fit(X, y, sample_weight=sample_weight)
coefs = est.coef_
inter = est.intercept_
# Closed form of the weighted regularized least square
# theta = (X^T W X + alpha I)^(-1) * X^T W y
W = np.diag(sample_weight)
if intercept is False:
X_aug = X
I = np.eye(n_features)
else:
dummy_column = np.ones(shape=(n_samples, 1))
X_aug = np.concatenate((dummy_column, X), axis=1)
I = np.eye(n_features + 1)
I[0, 0] = 0
cf_coefs = linalg.solve(X_aug.T.dot(W).dot(X_aug) + alpha * I,
X_aug.T.dot(W).dot(y))
if intercept is False:
assert_array_almost_equal(coefs, cf_coefs)
else:
assert_array_almost_equal(coefs, cf_coefs[1:])
assert_almost_equal(inter, cf_coefs[0])
def test_ridge_shapes():
# Test shape of coef_ and intercept_
rng = np.random.RandomState(0)
n_samples, n_features = 5, 10
X = rng.randn(n_samples, n_features)
y = rng.randn(n_samples)
Y1 = y[:, np.newaxis]
Y = np.c_[y, 1 + y]
ridge = Ridge()
ridge.fit(X, y)
assert ridge.coef_.shape == (n_features,)
assert ridge.intercept_.shape == ()
ridge.fit(X, Y1)
assert ridge.coef_.shape == (1, n_features)
assert ridge.intercept_.shape == (1, )
ridge.fit(X, Y)
assert ridge.coef_.shape == (2, n_features)
assert ridge.intercept_.shape == (2, )
def test_ridge_intercept():
# Test intercept with multiple targets GH issue #708
rng = np.random.RandomState(0)
n_samples, n_features = 5, 10
X = rng.randn(n_samples, n_features)
y = rng.randn(n_samples)
Y = np.c_[y, 1. + y]
ridge = Ridge()
ridge.fit(X, y)
intercept = ridge.intercept_
ridge.fit(X, Y)
assert_almost_equal(ridge.intercept_[0], intercept)
assert_almost_equal(ridge.intercept_[1], intercept + 1.)
def test_toy_ridge_object():
# Test BayesianRegression ridge classifier
# TODO: test also n_samples > n_features
X = np.array([[1], [2]])
Y = np.array([1, 2])
reg = Ridge(alpha=0.0)
reg.fit(X, Y)
X_test = [[1], [2], [3], [4]]
assert_almost_equal(reg.predict(X_test), [1., 2, 3, 4])
assert len(reg.coef_.shape) == 1
assert type(reg.intercept_) == np.float64
Y = np.vstack((Y, Y)).T
reg.fit(X, Y)
X_test = [[1], [2], [3], [4]]
assert len(reg.coef_.shape) == 2
assert type(reg.intercept_) == np.ndarray
def test_ridge_vs_lstsq():
# On alpha=0., Ridge and OLS yield the same solution.
rng = np.random.RandomState(0)
# we need more samples than features
n_samples, n_features = 5, 4
y = rng.randn(n_samples)
X = rng.randn(n_samples, n_features)
ridge = Ridge(alpha=0., fit_intercept=False)
ols = LinearRegression(fit_intercept=False)
ridge.fit(X, y)
ols.fit(X, y)
assert_almost_equal(ridge.coef_, ols.coef_)
ridge.fit(X, y)
ols.fit(X, y)
assert_almost_equal(ridge.coef_, ols.coef_)
def test_ridge_individual_penalties():
# Tests the ridge object using individual penalties
rng = np.random.RandomState(42)
n_samples, n_features, n_targets = 20, 10, 5
X = rng.randn(n_samples, n_features)
y = rng.randn(n_samples, n_targets)
penalties = np.arange(n_targets)
coef_cholesky = np.array([
Ridge(alpha=alpha, solver="cholesky").fit(X, target).coef_
for alpha, target in zip(penalties, y.T)])
coefs_indiv_pen = [
Ridge(alpha=penalties, solver=solver, tol=1e-8).fit(X, y).coef_
for solver in ['svd', 'sparse_cg', 'lsqr', 'cholesky', 'sag', 'saga']]
for coef_indiv_pen in coefs_indiv_pen:
assert_array_almost_equal(coef_cholesky, coef_indiv_pen)
# Test error is raised when number of targets and penalties do not match.
ridge = Ridge(alpha=penalties[:-1])
assert_raises(ValueError, ridge.fit, X, y)
@pytest.mark.parametrize('n_col', [(), (1,), (3,)])
def test_X_CenterStackOp(n_col):
rng = np.random.RandomState(0)
X = rng.randn(11, 8)
X_m = rng.randn(8)
sqrt_sw = rng.randn(len(X))
Y = rng.randn(11, *n_col)
A = rng.randn(9, *n_col)
operator = _X_CenterStackOp(sp.csr_matrix(X), X_m, sqrt_sw)
reference_operator = np.hstack(
[X - sqrt_sw[:, None] * X_m, sqrt_sw[:, None]])
assert_allclose(reference_operator.dot(A), operator.dot(A))
assert_allclose(reference_operator.T.dot(Y), operator.T.dot(Y))
@pytest.mark.parametrize('shape', [(10, 1), (13, 9), (3, 7), (2, 2), (20, 20)])
@pytest.mark.parametrize('uniform_weights', [True, False])
def test_compute_gram(shape, uniform_weights):
rng = np.random.RandomState(0)
X = rng.randn(*shape)
if uniform_weights:
sw = np.ones(X.shape[0])
else:
sw = rng.chisquare(1, shape[0])
sqrt_sw = np.sqrt(sw)
X_mean = np.average(X, axis=0, weights=sw)
X_centered = (X - X_mean) * sqrt_sw[:, None]
true_gram = X_centered.dot(X_centered.T)
X_sparse = sp.csr_matrix(X * sqrt_sw[:, None])
gcv = _RidgeGCV(fit_intercept=True)
computed_gram, computed_mean = gcv._compute_gram(X_sparse, sqrt_sw)
assert_allclose(X_mean, computed_mean)
assert_allclose(true_gram, computed_gram)
@pytest.mark.parametrize('shape', [(10, 1), (13, 9), (3, 7), (2, 2), (20, 20)])
@pytest.mark.parametrize('uniform_weights', [True, False])
def test_compute_covariance(shape, uniform_weights):
rng = np.random.RandomState(0)
X = rng.randn(*shape)
if uniform_weights:
sw = np.ones(X.shape[0])
else:
sw = rng.chisquare(1, shape[0])
sqrt_sw = np.sqrt(sw)
X_mean = np.average(X, axis=0, weights=sw)
X_centered = (X - X_mean) * sqrt_sw[:, None]
true_covariance = X_centered.T.dot(X_centered)
X_sparse = sp.csr_matrix(X * sqrt_sw[:, None])
gcv = _RidgeGCV(fit_intercept=True)
computed_cov, computed_mean = gcv._compute_covariance(X_sparse, sqrt_sw)
assert_allclose(X_mean, computed_mean)
assert_allclose(true_covariance, computed_cov)
def _make_sparse_offset_regression(
n_samples=100, n_features=100, proportion_nonzero=.5,
n_informative=10, n_targets=1, bias=13., X_offset=30.,
noise=30., shuffle=True, coef=False, random_state=None):
X, y, c = make_regression(
n_samples=n_samples, n_features=n_features,
n_informative=n_informative, n_targets=n_targets, bias=bias,
noise=noise, shuffle=shuffle,
coef=True, random_state=random_state)
if n_features == 1:
c = np.asarray([c])
X += X_offset
mask = np.random.RandomState(random_state).binomial(
1, proportion_nonzero, X.shape) > 0
removed_X = X.copy()
X[~mask] = 0.
removed_X[mask] = 0.
y -= removed_X.dot(c)
if n_features == 1:
c = c[0]
if coef:
return X, y, c
return X, y
@pytest.mark.parametrize(
'solver, sparse_X',
((solver, sparse_X) for
(solver, sparse_X) in product(
['cholesky', 'sag', 'sparse_cg', 'lsqr', 'saga', 'ridgecv'],
[False, True])
if not (sparse_X and solver not in ['sparse_cg', 'ridgecv'])))
@pytest.mark.parametrize(
'n_samples,dtype,proportion_nonzero',
[(20, 'float32', .1), (40, 'float32', 1.), (20, 'float64', .2)])
@pytest.mark.parametrize('seed', np.arange(3))
def test_solver_consistency(
solver, proportion_nonzero, n_samples, dtype, sparse_X, seed):
alpha = 1.
noise = 50. if proportion_nonzero > .9 else 500.
X, y = _make_sparse_offset_regression(
bias=10, n_features=30, proportion_nonzero=proportion_nonzero,
noise=noise, random_state=seed, n_samples=n_samples)
svd_ridge = Ridge(
solver='svd', normalize=True, alpha=alpha).fit(X, y)
X = X.astype(dtype, copy=False)
y = y.astype(dtype, copy=False)
if sparse_X:
X = sp.csr_matrix(X)
if solver == 'ridgecv':
ridge = RidgeCV(alphas=[alpha], normalize=True)
else:
ridge = Ridge(solver=solver, tol=1e-10, normalize=True, alpha=alpha)
ridge.fit(X, y)
assert_allclose(
ridge.coef_, svd_ridge.coef_, atol=1e-3, rtol=1e-3)
assert_allclose(
ridge.intercept_, svd_ridge.intercept_, atol=1e-3, rtol=1e-3)
@pytest.mark.parametrize('gcv_mode', ['svd', 'eigen'])
@pytest.mark.parametrize('X_constructor', [np.asarray, sp.csr_matrix])
@pytest.mark.parametrize('X_shape', [(11, 8), (11, 20)])
@pytest.mark.parametrize('fit_intercept', [True, False])
@pytest.mark.parametrize(
'y_shape, normalize, noise',
[
((11,), True, 1.),
((11, 1), False, 30.),
((11, 3), False, 150.),
]
)
def test_ridge_gcv_vs_ridge_loo_cv(
gcv_mode, X_constructor, X_shape, y_shape,
fit_intercept, normalize, noise):
n_samples, n_features = X_shape
n_targets = y_shape[-1] if len(y_shape) == 2 else 1
X, y = _make_sparse_offset_regression(
n_samples=n_samples, n_features=n_features, n_targets=n_targets,
random_state=0, shuffle=False, noise=noise, n_informative=5
)
y = y.reshape(y_shape)
alphas = [1e-3, .1, 1., 10., 1e3]
loo_ridge = RidgeCV(cv=n_samples, fit_intercept=fit_intercept,
alphas=alphas, scoring='neg_mean_squared_error',
normalize=normalize)
gcv_ridge = RidgeCV(gcv_mode=gcv_mode, fit_intercept=fit_intercept,
alphas=alphas, normalize=normalize)
loo_ridge.fit(X, y)
X_gcv = X_constructor(X)
gcv_ridge.fit(X_gcv, y)
assert gcv_ridge.alpha_ == pytest.approx(loo_ridge.alpha_)
assert_allclose(gcv_ridge.coef_, loo_ridge.coef_, rtol=1e-3)
assert_allclose(gcv_ridge.intercept_, loo_ridge.intercept_, rtol=1e-3)
def test_ridge_loo_cv_asym_scoring():
# checking on asymmetric scoring
scoring = 'explained_variance'
n_samples, n_features = 10, 5
n_targets = 1
X, y = _make_sparse_offset_regression(
n_samples=n_samples, n_features=n_features, n_targets=n_targets,
random_state=0, shuffle=False, noise=1, n_informative=5
)
alphas = [1e-3, .1, 1., 10., 1e3]
loo_ridge = RidgeCV(cv=n_samples, fit_intercept=True,
alphas=alphas, scoring=scoring,
normalize=True)
gcv_ridge = RidgeCV(fit_intercept=True,
alphas=alphas, scoring=scoring,
normalize=True)
loo_ridge.fit(X, y)
gcv_ridge.fit(X, y)
assert gcv_ridge.alpha_ == pytest.approx(loo_ridge.alpha_)
assert_allclose(gcv_ridge.coef_, loo_ridge.coef_, rtol=1e-3)
assert_allclose(gcv_ridge.intercept_, loo_ridge.intercept_, rtol=1e-3)
@pytest.mark.parametrize('gcv_mode', ['svd', 'eigen'])
@pytest.mark.parametrize('X_constructor', [np.asarray, sp.csr_matrix])
@pytest.mark.parametrize('n_features', [8, 20])
@pytest.mark.parametrize('y_shape, fit_intercept, noise',
[((11,), True, 1.),
((11, 1), True, 20.),
((11, 3), True, 150.),
((11, 3), False, 30.)])
def test_ridge_gcv_sample_weights(
gcv_mode, X_constructor, fit_intercept, n_features, y_shape, noise):
alphas = [1e-3, .1, 1., 10., 1e3]
rng = np.random.RandomState(0)
n_targets = y_shape[-1] if len(y_shape) == 2 else 1
X, y = _make_sparse_offset_regression(
n_samples=11, n_features=n_features, n_targets=n_targets,
random_state=0, shuffle=False, noise=noise)
y = y.reshape(y_shape)
sample_weight = 3 * rng.randn(len(X))
sample_weight = (sample_weight - sample_weight.min() + 1).astype(int)
indices = np.repeat(np.arange(X.shape[0]), sample_weight)
sample_weight = sample_weight.astype(float)
X_tiled, y_tiled = X[indices], y[indices]
cv = GroupKFold(n_splits=X.shape[0])
splits = cv.split(X_tiled, y_tiled, groups=indices)
kfold = RidgeCV(
alphas=alphas, cv=splits, scoring='neg_mean_squared_error',
fit_intercept=fit_intercept)
# ignore warning from GridSearchCV: FutureWarning: The default
# of the `iid` parameter will change from True to False in version 0.22
# and will be removed in 0.24
with ignore_warnings(category=FutureWarning):
kfold.fit(X_tiled, y_tiled)
ridge_reg = Ridge(alpha=kfold.alpha_, fit_intercept=fit_intercept)
splits = cv.split(X_tiled, y_tiled, groups=indices)
predictions = cross_val_predict(ridge_reg, X_tiled, y_tiled, cv=splits)
kfold_errors = (y_tiled - predictions)**2
kfold_errors = [
np.sum(kfold_errors[indices == i], axis=0) for
i in np.arange(X.shape[0])]
kfold_errors = np.asarray(kfold_errors)
X_gcv = X_constructor(X)
gcv_ridge = RidgeCV(
alphas=alphas, store_cv_values=True,
gcv_mode=gcv_mode, fit_intercept=fit_intercept)
gcv_ridge.fit(X_gcv, y, sample_weight=sample_weight)
if len(y_shape) == 2:
gcv_errors = gcv_ridge.cv_values_[:, :, alphas.index(kfold.alpha_)]
else:
gcv_errors = gcv_ridge.cv_values_[:, alphas.index(kfold.alpha_)]
assert kfold.alpha_ == pytest.approx(gcv_ridge.alpha_)
assert_allclose(gcv_errors, kfold_errors, rtol=1e-3)
assert_allclose(gcv_ridge.coef_, kfold.coef_, rtol=1e-3)
assert_allclose(gcv_ridge.intercept_, kfold.intercept_, rtol=1e-3)
@pytest.mark.parametrize('mode', [True, 1, 5, 'bad', 'gcv'])
def test_check_gcv_mode_error(mode):
X, y = make_regression(n_samples=5, n_features=2)
gcv = RidgeCV(gcv_mode=mode)
with pytest.raises(ValueError, match="Unknown value for 'gcv_mode'"):
gcv.fit(X, y)
with pytest.raises(ValueError, match="Unknown value for 'gcv_mode'"):
_check_gcv_mode(X, mode)
@pytest.mark.parametrize("sparse", [True, False])
@pytest.mark.parametrize(
'mode, mode_n_greater_than_p, mode_p_greater_than_n',
[(None, 'svd', 'eigen'),
('auto', 'svd', 'eigen'),
('eigen', 'eigen', 'eigen'),
('svd', 'svd', 'svd')]
)
def test_check_gcv_mode_choice(sparse, mode, mode_n_greater_than_p,
mode_p_greater_than_n):
X, _ = make_regression(n_samples=5, n_features=2)
if sparse:
X = sp.csr_matrix(X)
assert _check_gcv_mode(X, mode) == mode_n_greater_than_p
assert _check_gcv_mode(X.T, mode) == mode_p_greater_than_n
def _test_ridge_loo(filter_):
# test that can work with both dense or sparse matrices
n_samples = X_diabetes.shape[0]
ret = []
fit_intercept = filter_ == DENSE_FILTER
ridge_gcv = _RidgeGCV(fit_intercept=fit_intercept)
# check best alpha
ridge_gcv.fit(filter_(X_diabetes), y_diabetes)
alpha_ = ridge_gcv.alpha_
ret.append(alpha_)
# check that we get same best alpha with custom loss_func
f = ignore_warnings
scoring = make_scorer(mean_squared_error, greater_is_better=False)
ridge_gcv2 = RidgeCV(fit_intercept=False, scoring=scoring)
f(ridge_gcv2.fit)(filter_(X_diabetes), y_diabetes)
assert ridge_gcv2.alpha_ == pytest.approx(alpha_)
# check that we get same best alpha with custom score_func
func = lambda x, y: -mean_squared_error(x, y)
scoring = make_scorer(func)
ridge_gcv3 = RidgeCV(fit_intercept=False, scoring=scoring)
f(ridge_gcv3.fit)(filter_(X_diabetes), y_diabetes)
assert ridge_gcv3.alpha_ == pytest.approx(alpha_)
# check that we get same best alpha with a scorer
scorer = get_scorer('neg_mean_squared_error')
ridge_gcv4 = RidgeCV(fit_intercept=False, scoring=scorer)
ridge_gcv4.fit(filter_(X_diabetes), y_diabetes)
assert ridge_gcv4.alpha_ == pytest.approx(alpha_)
# check that we get same best alpha with sample weights
if filter_ == DENSE_FILTER:
ridge_gcv.fit(filter_(X_diabetes), y_diabetes,
sample_weight=np.ones(n_samples))
assert ridge_gcv.alpha_ == pytest.approx(alpha_)
# simulate several responses
Y = np.vstack((y_diabetes, y_diabetes)).T
ridge_gcv.fit(filter_(X_diabetes), Y)
Y_pred = ridge_gcv.predict(filter_(X_diabetes))
ridge_gcv.fit(filter_(X_diabetes), y_diabetes)
y_pred = ridge_gcv.predict(filter_(X_diabetes))
assert_allclose(np.vstack((y_pred, y_pred)).T,
Y_pred, rtol=1e-5)
return ret
def _test_ridge_cv_normalize(filter_):
ridge_cv = RidgeCV(normalize=True, cv=3)
ridge_cv.fit(filter_(10. * X_diabetes), y_diabetes)
gs = GridSearchCV(Ridge(normalize=True, solver='sparse_cg'), cv=3,
param_grid={'alpha': ridge_cv.alphas})
gs.fit(filter_(10. * X_diabetes), y_diabetes)
assert gs.best_estimator_.alpha == ridge_cv.alpha_
def _test_ridge_cv(filter_):
ridge_cv = RidgeCV()
ridge_cv.fit(filter_(X_diabetes), y_diabetes)
ridge_cv.predict(filter_(X_diabetes))
assert len(ridge_cv.coef_.shape) == 1
assert type(ridge_cv.intercept_) == np.float64
cv = KFold(5)
ridge_cv.set_params(cv=cv)
ridge_cv.fit(filter_(X_diabetes), y_diabetes)
ridge_cv.predict(filter_(X_diabetes))
assert len(ridge_cv.coef_.shape) == 1
assert type(ridge_cv.intercept_) == np.float64
def _test_ridge_diabetes(filter_):
ridge = Ridge(fit_intercept=False)
ridge.fit(filter_(X_diabetes), y_diabetes)
return np.round(ridge.score(filter_(X_diabetes), y_diabetes), 5)
def _test_multi_ridge_diabetes(filter_):
# simulate several responses
Y = np.vstack((y_diabetes, y_diabetes)).T
n_features = X_diabetes.shape[1]
ridge = Ridge(fit_intercept=False)
ridge.fit(filter_(X_diabetes), Y)
assert ridge.coef_.shape == (2, n_features)
Y_pred = ridge.predict(filter_(X_diabetes))
ridge.fit(filter_(X_diabetes), y_diabetes)
y_pred = ridge.predict(filter_(X_diabetes))
assert_array_almost_equal(np.vstack((y_pred, y_pred)).T,
Y_pred, decimal=3)
def _test_ridge_classifiers(filter_):
n_classes = np.unique(y_iris).shape[0]
n_features = X_iris.shape[1]
for reg in (RidgeClassifier(), RidgeClassifierCV()):
reg.fit(filter_(X_iris), y_iris)
assert reg.coef_.shape == (n_classes, n_features)
y_pred = reg.predict(filter_(X_iris))
assert np.mean(y_iris == y_pred) > .79
cv = KFold(5)
reg = RidgeClassifierCV(cv=cv)
reg.fit(filter_(X_iris), y_iris)
y_pred = reg.predict(filter_(X_iris))
assert np.mean(y_iris == y_pred) >= 0.8
def _test_tolerance(filter_):
ridge = Ridge(tol=1e-5, fit_intercept=False)
ridge.fit(filter_(X_diabetes), y_diabetes)
score = ridge.score(filter_(X_diabetes), y_diabetes)
ridge2 = Ridge(tol=1e-3, fit_intercept=False)
ridge2.fit(filter_(X_diabetes), y_diabetes)
score2 = ridge2.score(filter_(X_diabetes), y_diabetes)
assert score >= score2
def check_dense_sparse(test_func):
# test dense matrix
ret_dense = test_func(DENSE_FILTER)
# test sparse matrix
ret_sparse = test_func(SPARSE_FILTER)
# test that the outputs are the same
if ret_dense is not None and ret_sparse is not None:
assert_array_almost_equal(ret_dense, ret_sparse, decimal=3)
@pytest.mark.filterwarnings('ignore: The default value of multioutput') # 0.23
@pytest.mark.parametrize(
'test_func',
(_test_ridge_loo, _test_ridge_cv, _test_ridge_cv_normalize,
_test_ridge_diabetes, _test_multi_ridge_diabetes,
_test_ridge_classifiers, _test_tolerance))
def test_dense_sparse(test_func):
check_dense_sparse(test_func)
def test_ridge_sparse_svd():
X = sp.csc_matrix(rng.rand(100, 10))
y = rng.rand(100)
ridge = Ridge(solver='svd', fit_intercept=False)
assert_raises(TypeError, ridge.fit, X, y)
def test_class_weights():
# Test class weights.
X = np.array([[-1.0, -1.0], [-1.0, 0], [-.8, -1.0],
[1.0, 1.0], [1.0, 0.0]])
y = [1, 1, 1, -1, -1]
reg = RidgeClassifier(class_weight=None)
reg.fit(X, y)
assert_array_equal(reg.predict([[0.2, -1.0]]), np.array([1]))
# we give a small weights to class 1
reg = RidgeClassifier(class_weight={1: 0.001})
reg.fit(X, y)
# now the hyperplane should rotate clock-wise and
# the prediction on this point should shift
assert_array_equal(reg.predict([[0.2, -1.0]]), np.array([-1]))
# check if class_weight = 'balanced' can handle negative labels.
reg = RidgeClassifier(class_weight='balanced')
reg.fit(X, y)
assert_array_equal(reg.predict([[0.2, -1.0]]), np.array([1]))
# class_weight = 'balanced', and class_weight = None should return
# same values when y has equal number of all labels
X = np.array([[-1.0, -1.0], [-1.0, 0], [-.8, -1.0], [1.0, 1.0]])
y = [1, 1, -1, -1]
reg = RidgeClassifier(class_weight=None)
reg.fit(X, y)
rega = RidgeClassifier(class_weight='balanced')
rega.fit(X, y)
assert len(rega.classes_) == 2
assert_array_almost_equal(reg.coef_, rega.coef_)
assert_array_almost_equal(reg.intercept_, rega.intercept_)
@pytest.mark.parametrize('reg', (RidgeClassifier, RidgeClassifierCV))
def test_class_weight_vs_sample_weight(reg):
"""Check class_weights resemble sample_weights behavior."""
# Iris is balanced, so no effect expected for using 'balanced' weights
reg1 = reg()
reg1.fit(iris.data, iris.target)
reg2 = reg(class_weight='balanced')
reg2.fit(iris.data, iris.target)
assert_almost_equal(reg1.coef_, reg2.coef_)
# Inflate importance of class 1, check against user-defined weights
sample_weight = np.ones(iris.target.shape)
sample_weight[iris.target == 1] *= 100
class_weight = {0: 1., 1: 100., 2: 1.}
reg1 = reg()
reg1.fit(iris.data, iris.target, sample_weight)
reg2 = reg(class_weight=class_weight)
reg2.fit(iris.data, iris.target)
assert_almost_equal(reg1.coef_, reg2.coef_)
# Check that sample_weight and class_weight are multiplicative
reg1 = reg()
reg1.fit(iris.data, iris.target, sample_weight ** 2)
reg2 = reg(class_weight=class_weight)
reg2.fit(iris.data, iris.target, sample_weight)
assert_almost_equal(reg1.coef_, reg2.coef_)
def test_class_weights_cv():
# Test class weights for cross validated ridge classifier.
X = np.array([[-1.0, -1.0], [-1.0, 0], [-.8, -1.0],
[1.0, 1.0], [1.0, 0.0]])
y = [1, 1, 1, -1, -1]
reg = RidgeClassifierCV(class_weight=None, alphas=[.01, .1, 1])
reg.fit(X, y)
# we give a small weights to class 1
reg = RidgeClassifierCV(class_weight={1: 0.001}, alphas=[.01, .1, 1, 10])
reg.fit(X, y)
assert_array_equal(reg.predict([[-.2, 2]]), np.array([-1]))
def test_ridgecv_store_cv_values():
rng = np.random.RandomState(42)
n_samples = 8
n_features = 5
x = rng.randn(n_samples, n_features)
alphas = [1e-1, 1e0, 1e1]
n_alphas = len(alphas)
r = RidgeCV(alphas=alphas, cv=None, store_cv_values=True)
# with len(y.shape) == 1
y = rng.randn(n_samples)
r.fit(x, y)
assert r.cv_values_.shape == (n_samples, n_alphas)
# with len(y.shape) == 2
n_targets = 3
y = rng.randn(n_samples, n_targets)
r.fit(x, y)
assert r.cv_values_.shape == (n_samples, n_targets, n_alphas)
r = RidgeCV(cv=3, store_cv_values=True)
assert_raises_regex(ValueError, 'cv!=None and store_cv_values',
r.fit, x, y)
def test_ridge_classifier_cv_store_cv_values():
x = np.array([[-1.0, -1.0], [-1.0, 0], [-.8, -1.0],
[1.0, 1.0], [1.0, 0.0]])
y = np.array([1, 1, 1, -1, -1])
n_samples = x.shape[0]
alphas = [1e-1, 1e0, 1e1]
n_alphas = len(alphas)
r = RidgeClassifierCV(alphas=alphas, cv=None, store_cv_values=True)
# with len(y.shape) == 1
n_targets = 1
r.fit(x, y)
assert r.cv_values_.shape == (n_samples, n_targets, n_alphas)
# with len(y.shape) == 2
y = np.array([[1, 1, 1, -1, -1],
[1, -1, 1, -1, 1],
[-1, -1, 1, -1, -1]]).transpose()
n_targets = y.shape[1]
r.fit(x, y)
assert r.cv_values_.shape == (n_samples, n_targets, n_alphas)
def test_ridgecv_sample_weight():
rng = np.random.RandomState(0)
alphas = (0.1, 1.0, 10.0)
# There are different algorithms for n_samples > n_features
# and the opposite, so test them both.
for n_samples, n_features in ((6, 5), (5, 10)):
y = rng.randn(n_samples)
X = rng.randn(n_samples, n_features)
sample_weight = 1.0 + rng.rand(n_samples)
cv = KFold(5)
ridgecv = RidgeCV(alphas=alphas, cv=cv)
ridgecv.fit(X, y, sample_weight=sample_weight)
# Check using GridSearchCV directly
parameters = {'alpha': alphas}
gs = GridSearchCV(Ridge(), parameters, cv=cv)
gs.fit(X, y, sample_weight=sample_weight)
assert ridgecv.alpha_ == gs.best_estimator_.alpha
assert_array_almost_equal(ridgecv.coef_, gs.best_estimator_.coef_)
def test_raises_value_error_if_sample_weights_greater_than_1d():
# Sample weights must be either scalar or 1D
n_sampless = [2, 3]
n_featuress = [3, 2]
rng = np.random.RandomState(42)
for n_samples, n_features in zip(n_sampless, n_featuress):
X = rng.randn(n_samples, n_features)
y = rng.randn(n_samples)
sample_weights_OK = rng.randn(n_samples) ** 2 + 1
sample_weights_OK_1 = 1.
sample_weights_OK_2 = 2.
sample_weights_not_OK = sample_weights_OK[:, np.newaxis]
sample_weights_not_OK_2 = sample_weights_OK[np.newaxis, :]
ridge = Ridge(alpha=1)
# make sure the "OK" sample weights actually work
ridge.fit(X, y, sample_weights_OK)
ridge.fit(X, y, sample_weights_OK_1)
ridge.fit(X, y, sample_weights_OK_2)
def fit_ridge_not_ok():
ridge.fit(X, y, sample_weights_not_OK)
def fit_ridge_not_ok_2():
ridge.fit(X, y, sample_weights_not_OK_2)
assert_raise_message(ValueError,
"Sample weights must be 1D array or scalar",
fit_ridge_not_ok)
assert_raise_message(ValueError,
"Sample weights must be 1D array or scalar",
fit_ridge_not_ok_2)
def test_sparse_design_with_sample_weights():
# Sample weights must work with sparse matrices
n_sampless = [2, 3]
n_featuress = [3, 2]
rng = np.random.RandomState(42)
sparse_matrix_converters = [sp.coo_matrix,
sp.csr_matrix,
sp.csc_matrix,
sp.lil_matrix,
sp.dok_matrix
]
sparse_ridge = Ridge(alpha=1., fit_intercept=False)
dense_ridge = Ridge(alpha=1., fit_intercept=False)
for n_samples, n_features in zip(n_sampless, n_featuress):
X = rng.randn(n_samples, n_features)
y = rng.randn(n_samples)
sample_weights = rng.randn(n_samples) ** 2 + 1
for sparse_converter in sparse_matrix_converters:
X_sparse = sparse_converter(X)
sparse_ridge.fit(X_sparse, y, sample_weight=sample_weights)
dense_ridge.fit(X, y, sample_weight=sample_weights)
assert_array_almost_equal(sparse_ridge.coef_, dense_ridge.coef_,
decimal=6)
def test_ridgecv_int_alphas():
X = np.array([[-1.0, -1.0], [-1.0, 0], [-.8, -1.0],
[1.0, 1.0], [1.0, 0.0]])
y = [1, 1, 1, -1, -1]
# Integers
ridge = RidgeCV(alphas=(1, 10, 100))
ridge.fit(X, y)
def test_ridgecv_negative_alphas():
X = np.array([[-1.0, -1.0], [-1.0, 0], [-.8, -1.0],
[1.0, 1.0], [1.0, 0.0]])
y = [1, 1, 1, -1, -1]
# Negative integers
ridge = RidgeCV(alphas=(-1, -10, -100))
assert_raises_regex(ValueError,
"alphas must be positive",
ridge.fit, X, y)
# Negative floats
ridge = RidgeCV(alphas=(-0.1, -1.0, -10.0))
assert_raises_regex(ValueError,
"alphas must be positive",
ridge.fit, X, y)
def test_raises_value_error_if_solver_not_supported():
# Tests whether a ValueError is raised if a non-identified solver
# is passed to ridge_regression
wrong_solver = "This is not a solver (MagritteSolveCV QuantumBitcoin)"
exception = ValueError
message = ("Known solvers are 'sparse_cg', 'cholesky', 'svd'"
" 'lsqr', 'sag' or 'saga'. Got %s." % wrong_solver)
def func():
X = np.eye(3)
y = np.ones(3)
ridge_regression(X, y, alpha=1., solver=wrong_solver)
assert_raise_message(exception, message, func)
def test_sparse_cg_max_iter():
reg = Ridge(solver="sparse_cg", max_iter=1)
reg.fit(X_diabetes, y_diabetes)
assert reg.coef_.shape[0] == X_diabetes.shape[1]
@ignore_warnings
def test_n_iter():
# Test that self.n_iter_ is correct.
n_targets = 2
X, y = X_diabetes, y_diabetes
y_n = np.tile(y, (n_targets, 1)).T
for max_iter in range(1, 4):
for solver in ('sag', 'saga', 'lsqr'):
reg = Ridge(solver=solver, max_iter=max_iter, tol=1e-12)
reg.fit(X, y_n)
assert_array_equal(reg.n_iter_, np.tile(max_iter, n_targets))
for solver in ('sparse_cg', 'svd', 'cholesky'):
reg = Ridge(solver=solver, max_iter=1, tol=1e-1)
reg.fit(X, y_n)
assert reg.n_iter_ is None
@pytest.mark.parametrize('solver', ['sparse_cg', 'auto'])
def test_ridge_fit_intercept_sparse(solver):
X, y = _make_sparse_offset_regression(n_features=20, random_state=0)
X_csr = sp.csr_matrix(X)
# for now only sparse_cg can correctly fit an intercept with sparse X with
# default tol and max_iter.
# sag is tested separately in test_ridge_fit_intercept_sparse_sag
# because it requires more iterations and should raise a warning if default
# max_iter is used.
# other solvers raise an exception, as checked in
# test_ridge_fit_intercept_sparse_error
#
# "auto" should switch to "sparse_cg" when X is sparse
# so the reference we use for both ("auto" and "sparse_cg") is
# Ridge(solver="sparse_cg"), fitted using the dense representation (note
# that "sparse_cg" can fit sparse or dense data)
dense_ridge = Ridge(solver='sparse_cg')
sparse_ridge = Ridge(solver=solver)
dense_ridge.fit(X, y)
with pytest.warns(None) as record:
sparse_ridge.fit(X_csr, y)
assert len(record) == 0
assert np.allclose(dense_ridge.intercept_, sparse_ridge.intercept_)
assert np.allclose(dense_ridge.coef_, sparse_ridge.coef_)
@pytest.mark.parametrize('solver', ['saga', 'lsqr', 'svd', 'cholesky'])
def test_ridge_fit_intercept_sparse_error(solver):
X, y = _make_sparse_offset_regression(n_features=20, random_state=0)
X_csr = sp.csr_matrix(X)
sparse_ridge = Ridge(solver=solver)
err_msg = "solver='{}' does not support".format(solver)
with pytest.raises(ValueError, match=err_msg):
sparse_ridge.fit(X_csr, y)
def test_ridge_fit_intercept_sparse_sag():
X, y = _make_sparse_offset_regression(
n_features=5, n_samples=20, random_state=0, X_offset=5.)
X_csr = sp.csr_matrix(X)
params = dict(alpha=1., solver='sag', fit_intercept=True,
tol=1e-10, max_iter=100000)
dense_ridge = Ridge(**params)
sparse_ridge = Ridge(**params)
dense_ridge.fit(X, y)
with pytest.warns(None) as record:
sparse_ridge.fit(X_csr, y)
assert len(record) == 0
assert np.allclose(dense_ridge.intercept_, sparse_ridge.intercept_,
rtol=1e-4)
assert np.allclose(dense_ridge.coef_, sparse_ridge.coef_, rtol=1e-4)
with pytest.warns(UserWarning, match='"sag" solver requires.*'):
Ridge(solver='sag').fit(X_csr, y)
@pytest.mark.parametrize('return_intercept', [False, True])
@pytest.mark.parametrize('sample_weight', [None, np.ones(1000)])
@pytest.mark.parametrize('arr_type', [np.array, sp.csr_matrix])
@pytest.mark.parametrize('solver', ['auto', 'sparse_cg', 'cholesky', 'lsqr',
'sag', 'saga'])
def test_ridge_regression_check_arguments_validity(return_intercept,
sample_weight, arr_type,
solver):
"""check if all combinations of arguments give valid estimations"""
# test excludes 'svd' solver because it raises exception for sparse inputs
rng = check_random_state(42)
X = rng.rand(1000, 3)
true_coefs = [1, 2, 0.1]
y = np.dot(X, true_coefs)
true_intercept = 0.
if return_intercept:
true_intercept = 10000.
y += true_intercept
X_testing = arr_type(X)
alpha, atol, tol = 1e-3, 1e-4, 1e-6
if solver not in ['sag', 'auto'] and return_intercept:
assert_raises_regex(ValueError,
"In Ridge, only 'sag' solver",
ridge_regression, X_testing, y,
alpha=alpha,
solver=solver,
sample_weight=sample_weight,
return_intercept=return_intercept,
tol=tol)
return
out = ridge_regression(X_testing, y, alpha=alpha,
solver=solver,
sample_weight=sample_weight,
return_intercept=return_intercept,
tol=tol,
)
if return_intercept:
coef, intercept = out
assert_allclose(coef, true_coefs, rtol=0, atol=atol)
assert_allclose(intercept, true_intercept, rtol=0, atol=atol)
else:
assert_allclose(out, true_coefs, rtol=0, atol=atol)
def test_ridge_classifier_no_support_multilabel():
X, y = make_multilabel_classification(n_samples=10, random_state=0)
assert_raises(ValueError, RidgeClassifier().fit, X, y)
@pytest.mark.parametrize(
"solver", ["svd", "sparse_cg", "cholesky", "lsqr", "sag", "saga"])
def test_dtype_match(solver):
rng = np.random.RandomState(0)
alpha = 1.0
n_samples, n_features = 6, 5
X_64 = rng.randn(n_samples, n_features)
y_64 = rng.randn(n_samples)
X_32 = X_64.astype(np.float32)
y_32 = y_64.astype(np.float32)
tol = 2 * np.finfo(np.float32).resolution
# Check type consistency 32bits
ridge_32 = Ridge(alpha=alpha, solver=solver, max_iter=500, tol=tol)
ridge_32.fit(X_32, y_32)
coef_32 = ridge_32.coef_
# Check type consistency 64 bits
ridge_64 = Ridge(alpha=alpha, solver=solver, max_iter=500, tol=tol)
ridge_64.fit(X_64, y_64)
coef_64 = ridge_64.coef_
# Do the actual checks at once for easier debug
assert coef_32.dtype == X_32.dtype
assert coef_64.dtype == X_64.dtype
assert ridge_32.predict(X_32).dtype == X_32.dtype
assert ridge_64.predict(X_64).dtype == X_64.dtype
assert_allclose(ridge_32.coef_, ridge_64.coef_, rtol=1e-4, atol=5e-4)
def test_dtype_match_cholesky():
# Test different alphas in cholesky solver to ensure full coverage.
# This test is separated from test_dtype_match for clarity.
rng = np.random.RandomState(0)
alpha = (1.0, 0.5)
n_samples, n_features, n_target = 6, 7, 2
X_64 = rng.randn(n_samples, n_features)
y_64 = rng.randn(n_samples, n_target)
X_32 = X_64.astype(np.float32)
y_32 = y_64.astype(np.float32)
# Check type consistency 32bits
ridge_32 = Ridge(alpha=alpha, solver='cholesky')
ridge_32.fit(X_32, y_32)
coef_32 = ridge_32.coef_
# Check type consistency 64 bits
ridge_64 = Ridge(alpha=alpha, solver='cholesky')
ridge_64.fit(X_64, y_64)
coef_64 = ridge_64.coef_
# Do all the checks at once, like this is easier to debug
assert coef_32.dtype == X_32.dtype
assert coef_64.dtype == X_64.dtype
assert ridge_32.predict(X_32).dtype == X_32.dtype
assert ridge_64.predict(X_64).dtype == X_64.dtype
assert_almost_equal(ridge_32.coef_, ridge_64.coef_, decimal=5)
@pytest.mark.parametrize(
'solver', ['svd', 'cholesky', 'lsqr', 'sparse_cg', 'sag', 'saga'])
@pytest.mark.parametrize('seed', range(1))
def test_ridge_regression_dtype_stability(solver, seed):
random_state = np.random.RandomState(seed)
n_samples, n_features = 6, 5
X = random_state.randn(n_samples, n_features)
coef = random_state.randn(n_features)
y = np.dot(X, coef) + 0.01 * random_state.randn(n_samples)
alpha = 1.0
results = dict()
# XXX: Sparse CG seems to be far less numerically stable than the
# others, maybe we should not enable float32 for this one.
atol = 1e-3 if solver == "sparse_cg" else 1e-5
for current_dtype in (np.float32, np.float64):
results[current_dtype] = ridge_regression(X.astype(current_dtype),
y.astype(current_dtype),
alpha=alpha,
solver=solver,
random_state=random_state,
sample_weight=None,
max_iter=500,
tol=1e-10,
return_n_iter=False,
return_intercept=False)
assert results[np.float32].dtype == np.float32
assert results[np.float64].dtype == np.float64
assert_allclose(results[np.float32], results[np.float64], atol=atol)
def test_ridge_sag_with_X_fortran():
# check that Fortran array are converted when using SAG solver
X, y = make_regression(random_state=42)
# for the order of X and y to not be C-ordered arrays
X = np.asfortranarray(X)
X = X[::2, :]
y = y[::2]
Ridge(solver='sag').fit(X, y)