scikit-learn/sklearn/linear_model/ridge.py

767 lines
25 KiB
Python

"""
Ridge regression
"""
# Author: Mathieu Blondel <mathieu@mblondel.org>
# Reuben Fletcher-Costin <reuben.fletchercostin@gmail.com>
# License: Simplified BSD
import warnings
import numpy as np
from .base import LinearModel
from ..utils.extmath import safe_sparse_dot
from ..utils import safe_asarray
from ..preprocessing import LabelBinarizer
from ..grid_search import GridSearchCV
def _solve(A, b, solver, tol):
# helper method for ridge_regression, A is symmetric positive
if solver == 'auto':
if hasattr(A, 'todense'):
solver = 'sparse_cg'
else:
solver = 'dense_cholesky'
if solver == 'sparse_cg':
if b.ndim < 2:
from scipy.sparse import linalg as sp_linalg
sol, error = sp_linalg.cg(A, b, tol=tol)
if error:
raise ValueError("Failed with error code %d" % error)
return sol
else:
# sparse_cg cannot handle a 2-d b.
sol = []
for j in range(b.shape[1]):
sol.append(_solve(A, b[:, j], solver="sparse_cg", tol=tol))
return np.array(sol).T
elif solver == 'dense_cholesky':
from scipy import linalg
if hasattr(A, 'todense'):
A = A.todense()
return linalg.solve(A, b, sym_pos=True, overwrite_a=True)
else:
raise NotImplementedError('Solver %s not implemented' % solver)
def ridge_regression(X, y, alpha, sample_weight=1.0, solver='auto', tol=1e-3):
"""Solve the ridge equation by the method of normal equations.
Parameters
----------
X : {array-like, sparse matrix}, shape = [n_samples, n_features]
Training data
y : array-like, shape = [n_samples] or [n_samples, n_responses]
Target values
sample_weight : float or numpy array of shape [n_samples]
Individual weights for each sample
solver : {'auto', 'dense_cholesky', 'sparse_cg'}, optional
Solver to use in the computational routines. 'delse_cholesky'
will use the standard scipy.linalg.solve function, 'sparse_cg'
will use the conjugate gradient solver as found in
scipy.sparse.linalg.cg while 'auto' will chose the most
appropriate depending on the matrix X.
tol: float
Precision of the solution.
Returns
-------
coef: array, shape = [n_features] or [n_responses, n_features]
Weight vector(s).
Notes
-----
This function won't compute the intercept.
"""
n_samples, n_features = X.shape
is_sparse = False
if hasattr(X, 'todense'): # lazy import of scipy.sparse
from scipy import sparse
is_sparse = sparse.issparse(X)
if is_sparse:
if n_features > n_samples or \
isinstance(sample_weight, np.ndarray) or \
sample_weight != 1.0:
I = sparse.lil_matrix((n_samples, n_samples))
I.setdiag(np.ones(n_samples) * alpha * sample_weight)
c = _solve(X * X.T + I, y, solver, tol)
coef = X.T * c
else:
I = sparse.lil_matrix((n_features, n_features))
I.setdiag(np.ones(n_features) * alpha)
coef = _solve(X.T * X + I, X.T * y, solver, tol)
else:
if n_features > n_samples or \
isinstance(sample_weight, np.ndarray) or \
sample_weight != 1.0:
# kernel ridge
# w = X.T * inv(X X^t + alpha*Id) y
A = np.dot(X, X.T)
A.flat[::n_samples + 1] += alpha * sample_weight
coef = np.dot(X.T, _solve(A, y, solver, tol))
else:
# ridge
# w = inv(X^t X + alpha*Id) * X.T y
A = np.dot(X.T, X)
A.flat[::n_features + 1] += alpha
coef = _solve(A, np.dot(X.T, y), solver, tol)
return coef.T
class Ridge(LinearModel):
"""Linear least squares with l2 regularization.
This model solves a regression model where the loss function is
the linear least squares function and regularization is given by
the l2-norm. Also known as Ridge Regression or Tikhonov regularization.
This estimator has built-in support for multi-variate regression
(i.e., when y is a 2d-array of shape [n_samples, n_responses]).
Parameters
----------
alpha : float
Small positive values of alpha improve the conditioning of the
problem and reduce the variance of the estimates.
Alpha corresponds to (2*C)^-1 in other linear models such as
LogisticRegression or LinearSVC.
fit_intercept : boolean
Whether to calculate the intercept for this model. If set
to false, no intercept will be used in calculations
(e.g. data is expected to be already centered).
normalize : boolean, optional
If True, the regressors X are normalized
copy_X : boolean, optional, default True
If True, X will be copied; else, it may be overwritten.
tol: float
Precision of the solution.
Attributes
----------
`coef_` : array, shape = [n_features] or [n_responses, n_features]
Weight vector(s).
See also
--------
RidgeClassifier, RidgeCV
Examples
--------
>>> from sklearn.linear_model import Ridge
>>> import numpy as np
>>> n_samples, n_features = 10, 5
>>> np.random.seed(0)
>>> y = np.random.randn(n_samples)
>>> X = np.random.randn(n_samples, n_features)
>>> clf = Ridge(alpha=1.0)
>>> clf.fit(X, y) # doctest: +NORMALIZE_WHITESPACE
Ridge(alpha=1.0, copy_X=True, fit_intercept=True, normalize=False,
tol=0.001)
"""
def __init__(self, alpha=1.0, fit_intercept=True, normalize=False,
copy_X=True, tol=1e-3):
self.alpha = alpha
self.fit_intercept = fit_intercept
self.normalize = normalize
self.copy_X = copy_X
self.tol = tol
def fit(self, X, y, sample_weight=1.0, solver='auto'):
"""Fit Ridge regression model
Parameters
----------
X : {array-like, sparse matrix}, shape = [n_samples, n_features]
Training data
y : array-like, shape = [n_samples] or [n_samples, n_responses]
Target values
sample_weight : float or numpy array of shape [n_samples]
Individual weights for each sample
solver : {'auto', 'dense_cholesky', 'sparse_cg'}
Solver to use in the computational
routines. 'delse_cholesky' will use the standard
scipy.linalg.solve function, 'sparse_cg' will use the
conjugate gradient solver as found in
scipy.sparse.linalg.cg while 'auto' will chose the most
appropriate depending on the matrix X.
Returns
-------
self : returns an instance of self.
"""
X = safe_asarray(X, dtype=np.float)
y = np.asarray(y, dtype=np.float)
X, y, X_mean, y_mean, X_std = \
self._center_data(X, y, self.fit_intercept,
self.normalize, self.copy_X)
self.coef_ = ridge_regression(X, y, self.alpha, sample_weight,
solver, self.tol)
self._set_intercept(X_mean, y_mean, X_std)
return self
class RidgeClassifier(Ridge):
"""Classifier using Ridge regression.
Parameters
----------
alpha : float
Small positive values of alpha improve the conditioning of the
problem and reduce the variance of the estimates.
Alpha corresponds to (2*C)^-1 in other linear models such as
LogisticRegression or LinearSVC.
fit_intercept : boolean
Whether to calculate the intercept for this model. If set
to false, no intercept will be used in calculations
(e.g. data is expected to be already centered).
normalize : boolean, optional
If True, the regressors X are normalized
copy_X : boolean, optional, default True
If True, X will be copied; else, it may be overwritten.
tol: float
Precision of the solution.
class_weight : dict, optional
Weights associated with classes in the form
{class_label : weight}. If not given, all classes are
supposed to have weight one.
Attributes
----------
`coef_` : array, shape = [n_features] or [n_classes, n_features]
Weight vector(s).
See also
--------
Ridge, RidgeClassifierCV
Notes
-----
For multi-class classification, n_class classifiers are trained in
a one-versus-all approach. Concretely, this is implemented by taking
advantage of the multi-variate response support in Ridge.
"""
def __init__(self, alpha=1.0, fit_intercept=True, normalize=False,
copy_X=True, tol=1e-3, class_weight=None):
super(RidgeClassifier, self).__init__(alpha=alpha,
fit_intercept=fit_intercept, normalize=normalize,
copy_X=copy_X, tol=tol)
self.class_weight = class_weight
def fit(self, X, y, solver='auto'):
"""Fit Ridge regression model.
Parameters
----------
X : {array-like, sparse matrix}, shape = [n_samples,n_features]
Training data
y : array-like, shape = [n_samples]
Target values
solver : {'auto', 'dense_cholesky', 'sparse_cg'}
Solver to use in the computational
routines. 'delse_cholesky' will use the standard
scipy.linalg.solve function, 'sparse_cg' will use the
conjugate gradient solver as found in
scipy.sparse.linalg.cg while 'auto' will chose the most
appropriate depending on the matrix X.
Returns
-------
self : returns an instance of self.
"""
if self.class_weight is None:
class_weight = {}
else:
class_weight = self.class_weight
sample_weight_classes = np.array([class_weight.get(k, 1.0) for k in y])
self.label_binarizer = LabelBinarizer()
Y = self.label_binarizer.fit_transform(y)
Ridge.fit(self, X, Y, solver=solver, sample_weight=sample_weight_classes)
return self
def decision_function(self, X):
return Ridge.decision_function(self, X)
def predict(self, X):
"""Predict target values according to the fitted model.
Parameters
----------
X : array-like, shape = [n_samples, n_features]
Returns
-------
y : array, shape = [n_samples]
"""
Y = self.decision_function(X)
return self.label_binarizer.inverse_transform(Y)
class _RidgeGCV(LinearModel):
"""Ridge regression with built-in Generalized Cross-Validation
It allows efficient Leave-One-Out cross-validation.
This class is not intended to be used directly. Use RidgeCV instead.
Notes
-----
We want to solve (K + alpha*Id)c = y,
where K = X X^T is the kernel matrix.
Let G = (K + alpha*Id)^-1.
Dual solution: c = Gy
Primal solution: w = X^T c
Compute eigendecomposition K = Q V Q^T.
Then G = Q (V + alpha*Id)^-1 Q^T,
where (V + alpha*Id) is diagonal.
It is thus inexpensive to inverse for many alphas.
Let loov be the vector of prediction values for each example
when the model was fitted with all examples but this example.
loov = (KGY - diag(KG)Y) / diag(I-KG)
Let looe be the vector of prediction errors for each example
when the model was fitted with all examples but this example.
looe = y - loov = c / diag(G)
References
----------
http://cbcl.mit.edu/projects/cbcl/publications/ps/MIT-CSAIL-TR-2007-025.pdf
http://www.mit.edu/~9.520/spring07/Classes/rlsslides.pdf
"""
def __init__(self, alphas=[0.1, 1.0, 10.0], fit_intercept=True,
normalize=False, score_func=None, loss_func=None, copy_X=True,
gcv_mode=None):
self.alphas = np.asarray(alphas)
self.fit_intercept = fit_intercept
self.normalize = normalize
self.score_func = score_func
self.loss_func = loss_func
self.copy_X = copy_X
self.gcv_mode = gcv_mode
def _pre_compute(self, X, y):
# even if X is very sparse, K is usually very dense
K = safe_sparse_dot(X, X.T, dense_output=True)
from scipy import linalg
v, Q = linalg.eigh(K)
QT_y = np.dot(Q.T, y)
return v, Q, QT_y
def _decomp_diag(self, v_prime, Q):
# compute diagonal of the matrix: dot(Q, dot(diag(v_prime), Q^T))
return (v_prime * Q ** 2).sum(axis=-1)
def _diag_dot(self, D, B):
# compute dot(diag(D), B)
if len(B.shape) > 1:
# handle case where B is > 1-d
D = D[(slice(None), ) + (np.newaxis, ) * (len(B.shape) - 1)]
return D * B
def _errors(self, alpha, y, v, Q, QT_y):
# don't construct matrix G, instead compute action on y & diagonal
w = 1.0 / (v + alpha)
c = np.dot(Q, self._diag_dot(w, QT_y))
G_diag = self._decomp_diag(w, Q)
# handle case where y is 2-d
if len(y.shape) != 1:
G_diag = G_diag[:, np.newaxis]
return (c / G_diag) ** 2, c
def _values(self, alpha, y, v, Q, QT_y):
# don't construct matrix G, instead compute action on y & diagonal
w = 1.0 / (v + alpha)
c = np.dot(Q, self._diag_dot(w, QT_y))
G_diag = self._decomp_diag(w, Q)
# handle case where y is 2-d
if len(y.shape) != 1:
G_diag = G_diag[:, np.newaxis]
return y - (c / G_diag), c
def _pre_compute_svd(self, X, y):
from scipy import sparse
if sparse.issparse(X) and hasattr(X, 'toarray'):
X = X.toarray()
U, s, _ = np.linalg.svd(X, full_matrices=0)
v = s ** 2
UT_y = np.dot(U.T, y)
return v, U, UT_y
def _errors_svd(self, alpha, y, v, U, UT_y):
w = ((v + alpha) ** -1) - (alpha ** -1)
c = np.dot(U, self._diag_dot(w, UT_y)) + (alpha ** -1) * y
G_diag = self._decomp_diag(w, U) + (alpha ** -1)
if len(y.shape) != 1:
# handle case where y is 2-d
G_diag = G_diag[:, np.newaxis]
return (c / G_diag) ** 2, c
def _values_svd(self, alpha, y, v, U, UT_y):
w = ((v + alpha) ** -1) - (alpha ** -1)
c = np.dot(U, self._diag_dot(w, UT_y)) + (alpha ** -1) * y
G_diag = self._decomp_diag(w, U) + (alpha ** -1)
if len(y.shape) != 1:
# handle case when y is 2-d
G_diag = G_diag[:, np.newaxis]
return y - (c / G_diag), c
def fit(self, X, y, sample_weight=1.0):
"""Fit Ridge regression model
Parameters
----------
X : {array-like, sparse matrix}, shape = [n_samples, n_features]
Training data
y : array-like, shape = [n_samples] or [n_samples, n_responses]
Target values
sample_weight : float or array-like of shape [n_samples]
Sample weight
Returns
-------
self : Returns self.
"""
X = safe_asarray(X, dtype=np.float)
y = np.asarray(y, dtype=np.float)
n_samples, n_features = X.shape
X, y, X_mean, y_mean, X_std = LinearModel._center_data(X, y,
self.fit_intercept, self.normalize, self.copy_X)
gcv_mode = self.gcv_mode
with_sw = len(np.shape(sample_weight))
if gcv_mode is None or gcv_mode == 'auto':
if n_features > n_samples or with_sw:
gcv_mode = 'eigen'
else:
gcv_mode = 'svd'
elif gcv_mode == "svd" and with_sw:
# FIXME non-uniform sample weights not yet supported
warnings.warn("non-uniform sample weights unsupported for svd, "
"forcing usage of eigen")
gcv_mode = 'eigen'
if gcv_mode == 'eigen':
_pre_compute = self._pre_compute
_errors = self._errors
_values = self._values
elif gcv_mode == 'svd':
# assert n_samples >= n_features
_pre_compute = self._pre_compute_svd
_errors = self._errors_svd
_values = self._values_svd
else:
raise ValueError('bad gcv_mode "%s"' % gcv_mode)
v, Q, QT_y = _pre_compute(X, y)
n_y = 1 if len(y.shape) == 1 else y.shape[1]
M = np.zeros((n_samples * n_y, len(self.alphas)))
C = []
error = self.score_func is None and self.loss_func is None
for i, alpha in enumerate(self.alphas):
if error:
out, c = _errors(sample_weight * alpha, y, v, Q, QT_y)
else:
out, c = _values(sample_weight * alpha, y, v, Q, QT_y)
M[:, i] = out.ravel()
C.append(c)
if error:
best = M.mean(axis=0).argmin()
else:
func = self.score_func if self.score_func else self.loss_func
out = [func(y.ravel(), M[:, i]) for i in range(len(self.alphas))]
best = np.argmax(out) if self.score_func else np.argmin(out)
self.best_alpha = self.alphas[best]
self.dual_coef_ = C[best]
self.coef_ = safe_sparse_dot(self.dual_coef_.T, X)
self._set_intercept(X_mean, y_mean, X_std)
return self
class RidgeCV(LinearModel):
"""Ridge regression with built-in cross-validation.
By default, it performs Generalized Cross-Validation, which is a form of
efficient Leave-One-Out cross-validation.
Parameters
----------
alphas: numpy array of shape [n_alpha]
Array of alpha values to try.
Small positive values of alpha improve the conditioning of the
problem and reduce the variance of the estimates.
Alpha corresponds to ``(2*C)^-1`` in other linear models such as
LogisticRegression or LinearSVC.
fit_intercept : boolean
Whether to calculate the intercept for this model. If set
to false, no intercept will be used in calculations
(e.g. data is expected to be already centered).
normalize : boolean, optional
If True, the regressors X are normalized
score_func: callable, optional
function that takes 2 arguments and compares them in
order to evaluate the performance of prediction (big is good)
if None is passed, the score of the estimator is maximized
loss_func: callable, optional
function that takes 2 arguments and compares them in
order to evaluate the performance of prediction (small is good)
if None is passed, the score of the estimator is maximized
cv : cross-validation generator, optional
If None, Generalized Cross-Validation (efficient Leave-One-Out)
will be used.
Attributes
----------
`coef_` : array, shape = [n_features] or [n_classes, n_features]
Weight vector(s).
gcv_mode: {None, 'auto', 'svd', eigen'}, optional
Flag indicating which strategy to use when performing Generalized
Cross-Validation. Options are::
'auto' : use svd if n_samples > n_features, otherwise use eigen
'svd' : force computation via svd of X
'eigen' : force computation via eigendecomposition of X^T X
The 'auto' mode is the default and is intended to pick the cheaper
option of the two depending upon the shape of the training data.
See also
--------
Ridge: Ridge regression
RidgeClassifier: Ridge classifier
RidgeCV: Ridge regression with built-in cross validation
"""
def __init__(self, alphas=np.array([0.1, 1.0, 10.0]), fit_intercept=True,
normalize=False, score_func=None, loss_func=None, cv=None,
gcv_mode=None):
self.alphas = alphas
self.fit_intercept = fit_intercept
self.normalize = normalize
self.score_func = score_func
self.loss_func = loss_func
self.cv = cv
self.gcv_mode = gcv_mode
def fit(self, X, y, sample_weight=1.0):
"""Fit Ridge regression model
Parameters
----------
X : array-like, shape = [n_samples, n_features]
Training data
y : array-like, shape = [n_samples] or [n_samples, n_responses]
Target values
sample_weight : float or array-like of shape [n_samples]
Sample weight
Returns
-------
self : Returns self.
"""
if self.cv is None:
estimator = _RidgeGCV(self.alphas, self.fit_intercept,
self.score_func, self.loss_func, gcv_mode=self.gcv_mode)
estimator.fit(X, y, sample_weight=sample_weight)
self.best_alpha = estimator.best_alpha
else:
parameters = {'alpha': self.alphas}
# FIXME: sample_weight must be split into training/validation data
# too!
#fit_params = {'sample_weight' : sample_weight}
fit_params = {}
gs = GridSearchCV(Ridge(fit_intercept=self.fit_intercept),
parameters, fit_params=fit_params, cv=self.cv)
gs.fit(X, y)
estimator = gs.best_estimator_
self.best_alpha = gs.best_estimator_.alpha
self.coef_ = estimator.coef_
self.intercept_ = estimator.intercept_
return self
class RidgeClassifierCV(RidgeCV):
"""Ridge classifier with built-in cross-validation.
By default, it performs Generalized Cross-Validation, which is a form of
efficient Leave-One-Out cross-validation. Currently, only the n_features >
n_samples case is handled efficiently.
Parameters
----------
alphas: numpy array of shape [n_alpha]
Array of alpha values to try.
Small positive values of alpha improve the conditioning of the
problem and reduce the variance of the estimates.
Alpha corresponds to (2*C)^-1 in other linear models such as
LogisticRegression or LinearSVC.
fit_intercept : boolean
Whether to calculate the intercept for this model. If set
to false, no intercept will be used in calculations
(e.g. data is expected to be already centered).
normalize : boolean, optional
If True, the regressors X are normalized
score_func: callable, optional
function that takes 2 arguments and compares them in
order to evaluate the performance of prediction (big is good)
if None is passed, the score of the estimator is maximized
loss_func: callable, optional
function that takes 2 arguments and compares them in
order to evaluate the performance of prediction (small is good)
if None is passed, the score of the estimator is maximized
cv : cross-validation generator, optional
If None, Generalized Cross-Validation (efficient Leave-One-Out)
will be used.
class_weight : dict, optional
Weights associated with classes in the form
{class_label : weight}. If not given, all classes are
supposed to have weight one.
See also
--------
Ridge: Ridge regression
RidgeClassifier: Ridge classifier
RidgeCV: Ridge regression with built-in cross validation
Notes
-----
For multi-class classification, n_class classifiers are trained in
a one-versus-all approach. Concretely, this is implemented by taking
advantage of the multi-variate response support in Ridge.
"""
def __init__(self, alphas=np.array([0.1, 1.0, 10.0]), fit_intercept=True,
normalize=False, score_func=None, loss_func=None, cv=None,
class_weight=None):
super(RidgeClassifierCV, self).__init__(alphas=alphas,
fit_intercept=fit_intercept, normalize=normalize,
score_func=score_func, loss_func=loss_func, cv=cv)
self.class_weight = class_weight
def fit(self, X, y, sample_weight=1.0, class_weight=None):
"""Fit the ridge classifier.
Parameters
----------
X : array-like, shape = [n_samples, n_features]
Training vectors, where n_samples is the number of samples
and n_features is the number of features.
y : array-like, shape = [n_samples]
Target values.
sample_weight : float or numpy array of shape [n_samples]
Sample weight
class_weight : dict, optional
Weights associated with classes in the form
{class_label : weight}. If not given, all classes are
supposed to have weight one.
Returns
-------
self : object
Returns self.
"""
if class_weight != None:
warnings.warn("'class_weight' is now an initialization parameter."
"Using it in the 'fit' method is deprecated.",
DeprecationWarning)
self.class_weight_ = class_weight
else:
self.class_weight_ = self.class_weight
if self.class_weight_ is None:
self.class_weight_ = {}
sample_weight2 = np.array([self.class_weight_.get(k, 1.0) for k in y])
self.label_binarizer = LabelBinarizer()
Y = self.label_binarizer.fit_transform(y)
RidgeCV.fit(self, X, Y, sample_weight=sample_weight * sample_weight2)
return self
def decision_function(self, X):
return RidgeCV.decision_function(self, X)
def predict(self, X):
"""Predict target values according to the fitted model.
Parameters
----------
X : array-like, shape = [n_samples, n_features]
Returns
-------
y : array, shape = [n_samples]
"""
Y = self.decision_function(X)
return self.label_binarizer.inverse_transform(Y)