2458 lines
90 KiB
Python
2458 lines
90 KiB
Python
# Author: Alexandre Gramfort <alexandre.gramfort@inria.fr>
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# Fabian Pedregosa <fabian.pedregosa@inria.fr>
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# Olivier Grisel <olivier.grisel@ensta.org>
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# Gael Varoquaux <gael.varoquaux@inria.fr>
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#
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# License: BSD 3 clause
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import sys
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import warnings
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import numbers
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from abc import ABCMeta, abstractmethod
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import numpy as np
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from scipy import sparse
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from joblib import Parallel, effective_n_jobs
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from ._base import LinearModel, _pre_fit
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from ..base import RegressorMixin, MultiOutputMixin
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from ._base import _preprocess_data
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from ..utils import check_array
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from ..utils.validation import check_random_state
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from ..model_selection import check_cv
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from ..utils.extmath import safe_sparse_dot
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from ..utils.fixes import _astype_copy_false, _joblib_parallel_args
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from ..utils.validation import check_is_fitted, _check_sample_weight
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from ..utils.validation import column_or_1d
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from ..utils.validation import _deprecate_positional_args
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from ..utils.fixes import delayed
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# mypy error: Module 'sklearn.linear_model' has no attribute '_cd_fast'
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from . import _cd_fast as cd_fast # type: ignore
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def _set_order(X, y, order='C'):
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"""Change the order of X and y if necessary.
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Parameters
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----------
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X : {array-like, sparse matrix} of shape (n_samples, n_features)
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Training data.
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y : ndarray of shape (n_samples,)
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Target values.
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order : {None, 'C', 'F'}
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If 'C', dense arrays are returned as C-ordered, sparse matrices in csr
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format. If 'F', dense arrays are return as F-ordered, sparse matrices
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in csc format.
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Returns
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-------
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X : {array-like, sparse matrix} of shape (n_samples, n_features)
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Training data with guaranteed order.
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y : ndarray of shape (n_samples,)
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Target values with guaranteed order.
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"""
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if order not in [None, 'C', 'F']:
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raise ValueError("Unknown value for order. Got {} instead of "
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"None, 'C' or 'F'.".format(order))
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sparse_X = sparse.issparse(X)
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sparse_y = sparse.issparse(y)
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if order is not None:
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sparse_format = "csc" if order == "F" else "csr"
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if sparse_X:
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# As of scipy 1.1.0, new argument copy=False by default.
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# This is what we want.
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X = X.asformat(sparse_format, **_astype_copy_false(X))
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else:
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X = np.asarray(X, order=order)
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if sparse_y:
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y = y.asformat(sparse_format)
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else:
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y = np.asarray(y, order=order)
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return X, y
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###############################################################################
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# Paths functions
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def _alpha_grid(X, y, Xy=None, l1_ratio=1.0, fit_intercept=True,
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eps=1e-3, n_alphas=100, normalize=False, copy_X=True):
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""" Compute the grid of alpha values for elastic net parameter search
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Parameters
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----------
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X : {array-like, sparse matrix} of shape (n_samples, n_features)
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Training data. Pass directly as Fortran-contiguous data to avoid
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unnecessary memory duplication
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y : ndarray of shape (n_samples,)
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Target values
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Xy : array-like of shape (n_features,), default=None
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Xy = np.dot(X.T, y) that can be precomputed.
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l1_ratio : float, default=1.0
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The elastic net mixing parameter, with ``0 < l1_ratio <= 1``.
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For ``l1_ratio = 0`` the penalty is an L2 penalty. (currently not
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supported) ``For l1_ratio = 1`` it is an L1 penalty. For
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``0 < l1_ratio <1``, the penalty is a combination of L1 and L2.
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eps : float, default=1e-3
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Length of the path. ``eps=1e-3`` means that
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``alpha_min / alpha_max = 1e-3``
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n_alphas : int, default=100
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Number of alphas along the regularization path
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fit_intercept : bool, default=True
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Whether to fit an intercept or not
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normalize : bool, default=False
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This parameter is ignored when ``fit_intercept`` is set to False.
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If True, the regressors X will be normalized before regression by
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subtracting the mean and dividing by the l2-norm.
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If you wish to standardize, please use
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:class:`~sklearn.preprocessing.StandardScaler` before calling ``fit``
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on an estimator with ``normalize=False``.
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copy_X : bool, default=True
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If ``True``, X will be copied; else, it may be overwritten.
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"""
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if l1_ratio == 0:
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raise ValueError("Automatic alpha grid generation is not supported for"
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" l1_ratio=0. Please supply a grid by providing "
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"your estimator with the appropriate `alphas=` "
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"argument.")
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n_samples = len(y)
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sparse_center = False
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if Xy is None:
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X_sparse = sparse.isspmatrix(X)
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sparse_center = X_sparse and (fit_intercept or normalize)
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X = check_array(X, accept_sparse='csc',
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copy=(copy_X and fit_intercept and not X_sparse))
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if not X_sparse:
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# X can be touched inplace thanks to the above line
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X, y, _, _, _ = _preprocess_data(X, y, fit_intercept,
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normalize, copy=False)
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Xy = safe_sparse_dot(X.T, y, dense_output=True)
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if sparse_center:
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# Workaround to find alpha_max for sparse matrices.
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# since we should not destroy the sparsity of such matrices.
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_, _, X_offset, _, X_scale = _preprocess_data(X, y, fit_intercept,
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normalize,
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return_mean=True)
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mean_dot = X_offset * np.sum(y)
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if Xy.ndim == 1:
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Xy = Xy[:, np.newaxis]
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if sparse_center:
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if fit_intercept:
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Xy -= mean_dot[:, np.newaxis]
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if normalize:
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Xy /= X_scale[:, np.newaxis]
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alpha_max = (np.sqrt(np.sum(Xy ** 2, axis=1)).max() /
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(n_samples * l1_ratio))
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if alpha_max <= np.finfo(float).resolution:
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alphas = np.empty(n_alphas)
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alphas.fill(np.finfo(float).resolution)
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return alphas
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return np.logspace(np.log10(alpha_max * eps), np.log10(alpha_max),
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num=n_alphas)[::-1]
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@_deprecate_positional_args
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def lasso_path(X, y, *, eps=1e-3, n_alphas=100, alphas=None,
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precompute='auto', Xy=None, copy_X=True, coef_init=None,
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verbose=False, return_n_iter=False, positive=False, **params):
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"""Compute Lasso path with coordinate descent
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The Lasso optimization function varies for mono and multi-outputs.
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For mono-output tasks it is::
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(1 / (2 * n_samples)) * ||y - Xw||^2_2 + alpha * ||w||_1
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For multi-output tasks it is::
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(1 / (2 * n_samples)) * ||Y - XW||^2_Fro + alpha * ||W||_21
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Where::
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||W||_21 = \\sum_i \\sqrt{\\sum_j w_{ij}^2}
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i.e. the sum of norm of each row.
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Read more in the :ref:`User Guide <lasso>`.
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Parameters
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----------
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X : {array-like, sparse matrix} of shape (n_samples, n_features)
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Training data. Pass directly as Fortran-contiguous data to avoid
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unnecessary memory duplication. If ``y`` is mono-output then ``X``
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can be sparse.
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y : {array-like, sparse matrix} of shape (n_samples,) or \
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(n_samples, n_outputs)
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Target values
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eps : float, default=1e-3
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Length of the path. ``eps=1e-3`` means that
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``alpha_min / alpha_max = 1e-3``
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n_alphas : int, default=100
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Number of alphas along the regularization path
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alphas : ndarray, default=None
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List of alphas where to compute the models.
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If ``None`` alphas are set automatically
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precompute : 'auto', bool or array-like of shape (n_features, n_features),\
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default='auto'
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Whether to use a precomputed Gram matrix to speed up
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calculations. If set to ``'auto'`` let us decide. The Gram
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matrix can also be passed as argument.
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Xy : array-like of shape (n_features,) or (n_features, n_outputs),\
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default=None
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Xy = np.dot(X.T, y) that can be precomputed. It is useful
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only when the Gram matrix is precomputed.
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copy_X : bool, default=True
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If ``True``, X will be copied; else, it may be overwritten.
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coef_init : ndarray of shape (n_features, ), default=None
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The initial values of the coefficients.
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verbose : bool or int, default=False
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Amount of verbosity.
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return_n_iter : bool, default=False
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whether to return the number of iterations or not.
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positive : bool, default=False
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If set to True, forces coefficients to be positive.
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(Only allowed when ``y.ndim == 1``).
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**params : kwargs
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keyword arguments passed to the coordinate descent solver.
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Returns
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-------
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alphas : ndarray of shape (n_alphas,)
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The alphas along the path where models are computed.
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coefs : ndarray of shape (n_features, n_alphas) or \
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(n_outputs, n_features, n_alphas)
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Coefficients along the path.
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dual_gaps : ndarray of shape (n_alphas,)
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The dual gaps at the end of the optimization for each alpha.
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n_iters : list of int
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The number of iterations taken by the coordinate descent optimizer to
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reach the specified tolerance for each alpha.
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Notes
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-----
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For an example, see
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:ref:`examples/linear_model/plot_lasso_coordinate_descent_path.py
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<sphx_glr_auto_examples_linear_model_plot_lasso_coordinate_descent_path.py>`.
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To avoid unnecessary memory duplication the X argument of the fit method
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should be directly passed as a Fortran-contiguous numpy array.
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Note that in certain cases, the Lars solver may be significantly
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faster to implement this functionality. In particular, linear
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interpolation can be used to retrieve model coefficients between the
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values output by lars_path
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Examples
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--------
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Comparing lasso_path and lars_path with interpolation:
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>>> X = np.array([[1, 2, 3.1], [2.3, 5.4, 4.3]]).T
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>>> y = np.array([1, 2, 3.1])
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>>> # Use lasso_path to compute a coefficient path
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>>> _, coef_path, _ = lasso_path(X, y, alphas=[5., 1., .5])
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>>> print(coef_path)
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[[0. 0. 0.46874778]
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[0.2159048 0.4425765 0.23689075]]
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>>> # Now use lars_path and 1D linear interpolation to compute the
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>>> # same path
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>>> from sklearn.linear_model import lars_path
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>>> alphas, active, coef_path_lars = lars_path(X, y, method='lasso')
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>>> from scipy import interpolate
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>>> coef_path_continuous = interpolate.interp1d(alphas[::-1],
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... coef_path_lars[:, ::-1])
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>>> print(coef_path_continuous([5., 1., .5]))
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[[0. 0. 0.46915237]
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[0.2159048 0.4425765 0.23668876]]
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See Also
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--------
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lars_path
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Lasso
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LassoLars
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LassoCV
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LassoLarsCV
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sklearn.decomposition.sparse_encode
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"""
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return enet_path(X, y, l1_ratio=1., eps=eps, n_alphas=n_alphas,
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alphas=alphas, precompute=precompute, Xy=Xy,
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copy_X=copy_X, coef_init=coef_init, verbose=verbose,
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positive=positive, return_n_iter=return_n_iter, **params)
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@_deprecate_positional_args
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def enet_path(X, y, *, l1_ratio=0.5, eps=1e-3, n_alphas=100, alphas=None,
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precompute='auto', Xy=None, copy_X=True, coef_init=None,
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verbose=False, return_n_iter=False, positive=False,
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check_input=True, **params):
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"""
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Compute elastic net path with coordinate descent.
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The elastic net optimization function varies for mono and multi-outputs.
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For mono-output tasks it is::
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1 / (2 * n_samples) * ||y - Xw||^2_2
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+ alpha * l1_ratio * ||w||_1
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+ 0.5 * alpha * (1 - l1_ratio) * ||w||^2_2
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For multi-output tasks it is::
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(1 / (2 * n_samples)) * ||Y - XW||_Fro^2
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+ alpha * l1_ratio * ||W||_21
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+ 0.5 * alpha * (1 - l1_ratio) * ||W||_Fro^2
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Where::
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||W||_21 = \\sum_i \\sqrt{\\sum_j w_{ij}^2}
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i.e. the sum of norm of each row.
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Read more in the :ref:`User Guide <elastic_net>`.
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Parameters
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----------
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X : {array-like, sparse matrix} of shape (n_samples, n_features)
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Training data. Pass directly as Fortran-contiguous data to avoid
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unnecessary memory duplication. If ``y`` is mono-output then ``X``
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can be sparse.
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y : {array-like, sparse matrix} of shape (n_samples,) or \
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(n_samples, n_outputs)
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Target values.
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l1_ratio : float, default=0.5
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Number between 0 and 1 passed to elastic net (scaling between
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l1 and l2 penalties). ``l1_ratio=1`` corresponds to the Lasso.
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eps : float, default=1e-3
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Length of the path. ``eps=1e-3`` means that
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``alpha_min / alpha_max = 1e-3``.
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n_alphas : int, default=100
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Number of alphas along the regularization path.
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alphas : ndarray, default=None
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List of alphas where to compute the models.
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If None alphas are set automatically.
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precompute : 'auto', bool or array-like of shape (n_features, n_features),\
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default='auto'
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Whether to use a precomputed Gram matrix to speed up
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calculations. If set to ``'auto'`` let us decide. The Gram
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matrix can also be passed as argument.
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Xy : array-like of shape (n_features,) or (n_features, n_outputs),\
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default=None
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Xy = np.dot(X.T, y) that can be precomputed. It is useful
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only when the Gram matrix is precomputed.
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copy_X : bool, default=True
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If ``True``, X will be copied; else, it may be overwritten.
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coef_init : ndarray of shape (n_features, ), default=None
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The initial values of the coefficients.
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verbose : bool or int, default=False
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Amount of verbosity.
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return_n_iter : bool, default=False
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Whether to return the number of iterations or not.
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positive : bool, default=False
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If set to True, forces coefficients to be positive.
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(Only allowed when ``y.ndim == 1``).
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check_input : bool, default=True
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If set to False, the input validation checks are skipped (including the
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Gram matrix when provided). It is assumed that they are handled
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by the caller.
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**params : kwargs
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Keyword arguments passed to the coordinate descent solver.
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Returns
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-------
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alphas : ndarray of shape (n_alphas,)
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The alphas along the path where models are computed.
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coefs : ndarray of shape (n_features, n_alphas) or \
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(n_outputs, n_features, n_alphas)
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Coefficients along the path.
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dual_gaps : ndarray of shape (n_alphas,)
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The dual gaps at the end of the optimization for each alpha.
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n_iters : list of int
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The number of iterations taken by the coordinate descent optimizer to
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reach the specified tolerance for each alpha.
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(Is returned when ``return_n_iter`` is set to True).
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See Also
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--------
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MultiTaskElasticNet
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MultiTaskElasticNetCV
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ElasticNet
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ElasticNetCV
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Notes
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-----
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For an example, see
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:ref:`examples/linear_model/plot_lasso_coordinate_descent_path.py
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<sphx_glr_auto_examples_linear_model_plot_lasso_coordinate_descent_path.py>`.
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"""
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# We expect X and y to be already Fortran ordered when bypassing
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# checks
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if check_input:
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X = check_array(X, accept_sparse='csc', dtype=[np.float64, np.float32],
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order='F', copy=copy_X)
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y = check_array(y, accept_sparse='csc', dtype=X.dtype.type,
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order='F', copy=False, ensure_2d=False)
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if Xy is not None:
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# Xy should be a 1d contiguous array or a 2D C ordered array
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Xy = check_array(Xy, dtype=X.dtype.type, order='C', copy=False,
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ensure_2d=False)
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n_samples, n_features = X.shape
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multi_output = False
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if y.ndim != 1:
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multi_output = True
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_, n_outputs = y.shape
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if multi_output and positive:
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raise ValueError('positive=True is not allowed for multi-output'
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' (y.ndim != 1)')
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# MultiTaskElasticNet does not support sparse matrices
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if not multi_output and sparse.isspmatrix(X):
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if 'X_offset' in params:
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# As sparse matrices are not actually centered we need this
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# to be passed to the CD solver.
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X_sparse_scaling = params['X_offset'] / params['X_scale']
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X_sparse_scaling = np.asarray(X_sparse_scaling, dtype=X.dtype)
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else:
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X_sparse_scaling = np.zeros(n_features, dtype=X.dtype)
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# X should be normalized and fit already if function is called
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# from ElasticNet.fit
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if check_input:
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X, y, X_offset, y_offset, X_scale, precompute, Xy = \
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_pre_fit(X, y, Xy, precompute, normalize=False,
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fit_intercept=False, copy=False, check_input=check_input)
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if alphas is None:
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# No need to normalize of fit_intercept: it has been done
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# above
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alphas = _alpha_grid(X, y, Xy=Xy, l1_ratio=l1_ratio,
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fit_intercept=False, eps=eps, n_alphas=n_alphas,
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normalize=False, copy_X=False)
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else:
|
|
alphas = np.sort(alphas)[::-1] # make sure alphas are properly ordered
|
|
|
|
n_alphas = len(alphas)
|
|
tol = params.get('tol', 1e-4)
|
|
max_iter = params.get('max_iter', 1000)
|
|
dual_gaps = np.empty(n_alphas)
|
|
n_iters = []
|
|
|
|
rng = check_random_state(params.get('random_state', None))
|
|
selection = params.get('selection', 'cyclic')
|
|
if selection not in ['random', 'cyclic']:
|
|
raise ValueError("selection should be either random or cyclic.")
|
|
random = (selection == 'random')
|
|
|
|
if not multi_output:
|
|
coefs = np.empty((n_features, n_alphas), dtype=X.dtype)
|
|
else:
|
|
coefs = np.empty((n_outputs, n_features, n_alphas),
|
|
dtype=X.dtype)
|
|
|
|
if coef_init is None:
|
|
coef_ = np.zeros(coefs.shape[:-1], dtype=X.dtype, order='F')
|
|
else:
|
|
coef_ = np.asfortranarray(coef_init, dtype=X.dtype)
|
|
|
|
for i, alpha in enumerate(alphas):
|
|
l1_reg = alpha * l1_ratio * n_samples
|
|
l2_reg = alpha * (1.0 - l1_ratio) * n_samples
|
|
if not multi_output and sparse.isspmatrix(X):
|
|
model = cd_fast.sparse_enet_coordinate_descent(
|
|
coef_, l1_reg, l2_reg, X.data, X.indices,
|
|
X.indptr, y, X_sparse_scaling,
|
|
max_iter, tol, rng, random, positive)
|
|
elif multi_output:
|
|
model = cd_fast.enet_coordinate_descent_multi_task(
|
|
coef_, l1_reg, l2_reg, X, y, max_iter, tol, rng, random)
|
|
elif isinstance(precompute, np.ndarray):
|
|
# We expect precompute to be already Fortran ordered when bypassing
|
|
# checks
|
|
if check_input:
|
|
precompute = check_array(precompute, dtype=X.dtype.type,
|
|
order='C')
|
|
model = cd_fast.enet_coordinate_descent_gram(
|
|
coef_, l1_reg, l2_reg, precompute, Xy, y, max_iter,
|
|
tol, rng, random, positive)
|
|
elif precompute is False:
|
|
model = cd_fast.enet_coordinate_descent(
|
|
coef_, l1_reg, l2_reg, X, y, max_iter, tol, rng, random,
|
|
positive)
|
|
else:
|
|
raise ValueError("Precompute should be one of True, False, "
|
|
"'auto' or array-like. Got %r" % precompute)
|
|
coef_, dual_gap_, eps_, n_iter_ = model
|
|
coefs[..., i] = coef_
|
|
dual_gaps[i] = dual_gap_
|
|
n_iters.append(n_iter_)
|
|
|
|
if verbose:
|
|
if verbose > 2:
|
|
print(model)
|
|
elif verbose > 1:
|
|
print('Path: %03i out of %03i' % (i, n_alphas))
|
|
else:
|
|
sys.stderr.write('.')
|
|
|
|
if return_n_iter:
|
|
return alphas, coefs, dual_gaps, n_iters
|
|
return alphas, coefs, dual_gaps
|
|
|
|
|
|
###############################################################################
|
|
# ElasticNet model
|
|
|
|
|
|
class ElasticNet(MultiOutputMixin, RegressorMixin, LinearModel):
|
|
"""Linear regression with combined L1 and L2 priors as regularizer.
|
|
|
|
Minimizes the objective function::
|
|
|
|
1 / (2 * n_samples) * ||y - Xw||^2_2
|
|
+ alpha * l1_ratio * ||w||_1
|
|
+ 0.5 * alpha * (1 - l1_ratio) * ||w||^2_2
|
|
|
|
If you are interested in controlling the L1 and L2 penalty
|
|
separately, keep in mind that this is equivalent to::
|
|
|
|
a * ||w||_1 + 0.5 * b * ||w||_2^2
|
|
|
|
where::
|
|
|
|
alpha = a + b and l1_ratio = a / (a + b)
|
|
|
|
The parameter l1_ratio corresponds to alpha in the glmnet R package while
|
|
alpha corresponds to the lambda parameter in glmnet. Specifically, l1_ratio
|
|
= 1 is the lasso penalty. Currently, l1_ratio <= 0.01 is not reliable,
|
|
unless you supply your own sequence of alpha.
|
|
|
|
Read more in the :ref:`User Guide <elastic_net>`.
|
|
|
|
Parameters
|
|
----------
|
|
alpha : float, default=1.0
|
|
Constant that multiplies the penalty terms. Defaults to 1.0.
|
|
See the notes for the exact mathematical meaning of this
|
|
parameter. ``alpha = 0`` is equivalent to an ordinary least square,
|
|
solved by the :class:`LinearRegression` object. For numerical
|
|
reasons, using ``alpha = 0`` with the ``Lasso`` object is not advised.
|
|
Given this, you should use the :class:`LinearRegression` object.
|
|
|
|
l1_ratio : float, default=0.5
|
|
The ElasticNet mixing parameter, with ``0 <= l1_ratio <= 1``. For
|
|
``l1_ratio = 0`` the penalty is an L2 penalty. ``For l1_ratio = 1`` it
|
|
is an L1 penalty. For ``0 < l1_ratio < 1``, the penalty is a
|
|
combination of L1 and L2.
|
|
|
|
fit_intercept : bool, default=True
|
|
Whether the intercept should be estimated or not. If ``False``, the
|
|
data is assumed to be already centered.
|
|
|
|
normalize : bool, default=False
|
|
This parameter is ignored when ``fit_intercept`` is set to False.
|
|
If True, the regressors X will be normalized before regression by
|
|
subtracting the mean and dividing by the l2-norm.
|
|
If you wish to standardize, please use
|
|
:class:`~sklearn.preprocessing.StandardScaler` before calling ``fit``
|
|
on an estimator with ``normalize=False``.
|
|
|
|
precompute : bool or array-like of shape (n_features, n_features),\
|
|
default=False
|
|
Whether to use a precomputed Gram matrix to speed up
|
|
calculations. The Gram matrix can also be passed as argument.
|
|
For sparse input this option is always ``False`` to preserve sparsity.
|
|
|
|
max_iter : int, default=1000
|
|
The maximum number of iterations.
|
|
|
|
copy_X : bool, default=True
|
|
If ``True``, X will be copied; else, it may be overwritten.
|
|
|
|
tol : float, default=1e-4
|
|
The tolerance for the optimization: if the updates are
|
|
smaller than ``tol``, the optimization code checks the
|
|
dual gap for optimality and continues until it is smaller
|
|
than ``tol``.
|
|
|
|
warm_start : bool, default=False
|
|
When set to ``True``, reuse the solution of the previous call to fit as
|
|
initialization, otherwise, just erase the previous solution.
|
|
See :term:`the Glossary <warm_start>`.
|
|
|
|
positive : bool, default=False
|
|
When set to ``True``, forces the coefficients to be positive.
|
|
|
|
random_state : int, RandomState instance, default=None
|
|
The seed of the pseudo random number generator that selects a random
|
|
feature to update. Used when ``selection`` == 'random'.
|
|
Pass an int for reproducible output across multiple function calls.
|
|
See :term:`Glossary <random_state>`.
|
|
|
|
selection : {'cyclic', 'random'}, default='cyclic'
|
|
If set to 'random', a random coefficient is updated every iteration
|
|
rather than looping over features sequentially by default. This
|
|
(setting to 'random') often leads to significantly faster convergence
|
|
especially when tol is higher than 1e-4.
|
|
|
|
Attributes
|
|
----------
|
|
coef_ : ndarray of shape (n_features,) or (n_targets, n_features)
|
|
Parameter vector (w in the cost function formula).
|
|
|
|
sparse_coef_ : sparse matrix of shape (n_features,) or \
|
|
(n_tasks, n_features)
|
|
Sparse representation of the `coef_`.
|
|
|
|
intercept_ : float or ndarray of shape (n_targets,)
|
|
Independent term in decision function.
|
|
|
|
n_iter_ : list of int
|
|
Number of iterations run by the coordinate descent solver to reach
|
|
the specified tolerance.
|
|
|
|
dual_gap_ : float or ndarray of shape (n_targets,)
|
|
Given param alpha, the dual gaps at the end of the optimization,
|
|
same shape as each observation of y.
|
|
|
|
Examples
|
|
--------
|
|
>>> from sklearn.linear_model import ElasticNet
|
|
>>> from sklearn.datasets import make_regression
|
|
|
|
>>> X, y = make_regression(n_features=2, random_state=0)
|
|
>>> regr = ElasticNet(random_state=0)
|
|
>>> regr.fit(X, y)
|
|
ElasticNet(random_state=0)
|
|
>>> print(regr.coef_)
|
|
[18.83816048 64.55968825]
|
|
>>> print(regr.intercept_)
|
|
1.451...
|
|
>>> print(regr.predict([[0, 0]]))
|
|
[1.451...]
|
|
|
|
|
|
Notes
|
|
-----
|
|
To avoid unnecessary memory duplication the X argument of the fit method
|
|
should be directly passed as a Fortran-contiguous numpy array.
|
|
|
|
See Also
|
|
--------
|
|
ElasticNetCV : Elastic net model with best model selection by
|
|
cross-validation.
|
|
SGDRegressor : Implements elastic net regression with incremental training.
|
|
SGDClassifier : Implements logistic regression with elastic net penalty
|
|
(``SGDClassifier(loss="log", penalty="elasticnet")``).
|
|
"""
|
|
path = staticmethod(enet_path)
|
|
|
|
@_deprecate_positional_args
|
|
def __init__(self, alpha=1.0, *, l1_ratio=0.5, fit_intercept=True,
|
|
normalize=False, precompute=False, max_iter=1000,
|
|
copy_X=True, tol=1e-4, warm_start=False, positive=False,
|
|
random_state=None, selection='cyclic'):
|
|
self.alpha = alpha
|
|
self.l1_ratio = l1_ratio
|
|
self.fit_intercept = fit_intercept
|
|
self.normalize = normalize
|
|
self.precompute = precompute
|
|
self.max_iter = max_iter
|
|
self.copy_X = copy_X
|
|
self.tol = tol
|
|
self.warm_start = warm_start
|
|
self.positive = positive
|
|
self.random_state = random_state
|
|
self.selection = selection
|
|
|
|
def fit(self, X, y, sample_weight=None, check_input=True):
|
|
"""Fit model with coordinate descent.
|
|
|
|
Parameters
|
|
----------
|
|
X : {ndarray, sparse matrix} of (n_samples, n_features)
|
|
Data.
|
|
|
|
y : {ndarray, sparse matrix} of shape (n_samples,) or \
|
|
(n_samples, n_targets)
|
|
Target. Will be cast to X's dtype if necessary.
|
|
|
|
sample_weight : float or array-like of shape (n_samples,), default=None
|
|
Sample weight.
|
|
|
|
.. versionadded:: 0.23
|
|
|
|
check_input : bool, default=True
|
|
Allow to bypass several input checking.
|
|
Don't use this parameter unless you know what you do.
|
|
|
|
Notes
|
|
-----
|
|
|
|
Coordinate descent is an algorithm that considers each column of
|
|
data at a time hence it will automatically convert the X input
|
|
as a Fortran-contiguous numpy array if necessary.
|
|
|
|
To avoid memory re-allocation it is advised to allocate the
|
|
initial data in memory directly using that format.
|
|
"""
|
|
|
|
if self.alpha == 0:
|
|
warnings.warn("With alpha=0, this algorithm does not converge "
|
|
"well. You are advised to use the LinearRegression "
|
|
"estimator", stacklevel=2)
|
|
|
|
if isinstance(self.precompute, str):
|
|
raise ValueError('precompute should be one of True, False or'
|
|
' array-like. Got %r' % self.precompute)
|
|
|
|
if (not isinstance(self.l1_ratio, numbers.Number) or
|
|
self.l1_ratio < 0 or self.l1_ratio > 1):
|
|
raise ValueError("l1_ratio must be between 0 and 1; "
|
|
f"got l1_ratio={self.l1_ratio}")
|
|
|
|
# Remember if X is copied
|
|
X_copied = False
|
|
# We expect X and y to be float64 or float32 Fortran ordered arrays
|
|
# when bypassing checks
|
|
if check_input:
|
|
X_copied = self.copy_X and self.fit_intercept
|
|
X, y = self._validate_data(X, y, accept_sparse='csc',
|
|
order='F',
|
|
dtype=[np.float64, np.float32],
|
|
copy=X_copied, multi_output=True,
|
|
y_numeric=True)
|
|
y = check_array(y, order='F', copy=False, dtype=X.dtype.type,
|
|
ensure_2d=False)
|
|
|
|
n_samples, n_features = X.shape
|
|
alpha = self.alpha
|
|
|
|
if isinstance(sample_weight, numbers.Number):
|
|
sample_weight = None
|
|
if sample_weight is not None:
|
|
if check_input:
|
|
if sparse.issparse(X):
|
|
raise ValueError("Sample weights do not (yet) support "
|
|
"sparse matrices.")
|
|
sample_weight = _check_sample_weight(sample_weight, X,
|
|
dtype=X.dtype)
|
|
# simplify things by rescaling sw to sum up to n_samples
|
|
# => np.average(x, weights=sw) = np.mean(sw * x)
|
|
sample_weight *= (n_samples / np.sum(sample_weight))
|
|
# Objective function is:
|
|
# 1/2 * np.average(squared error, weights=sw) + alpha * penalty
|
|
# but coordinate descent minimizes:
|
|
# 1/2 * sum(squared error) + alpha * penalty
|
|
# enet_path therefore sets alpha = n_samples * alpha
|
|
# With sw, enet_path should set alpha = sum(sw) * alpha
|
|
# Therefore, we rescale alpha = sum(sw) / n_samples * alpha
|
|
# Note: As we rescaled sample_weights to sum up to n_samples,
|
|
# we don't need this
|
|
# alpha *= np.sum(sample_weight) / n_samples
|
|
|
|
# Ensure copying happens only once, don't do it again if done above.
|
|
# X and y will be rescaled if sample_weight is not None, order='F'
|
|
# ensures that the returned X and y are still F-contiguous.
|
|
should_copy = self.copy_X and not X_copied
|
|
X, y, X_offset, y_offset, X_scale, precompute, Xy = \
|
|
_pre_fit(X, y, None, self.precompute, self.normalize,
|
|
self.fit_intercept, copy=should_copy,
|
|
check_input=check_input, sample_weight=sample_weight)
|
|
# coordinate descent needs F-ordered arrays and _pre_fit might have
|
|
# called _rescale_data
|
|
if check_input or sample_weight is not None:
|
|
X, y = _set_order(X, y, order='F')
|
|
if y.ndim == 1:
|
|
y = y[:, np.newaxis]
|
|
if Xy is not None and Xy.ndim == 1:
|
|
Xy = Xy[:, np.newaxis]
|
|
|
|
n_targets = y.shape[1]
|
|
|
|
if self.selection not in ['cyclic', 'random']:
|
|
raise ValueError("selection should be either random or cyclic.")
|
|
|
|
if not self.warm_start or not hasattr(self, "coef_"):
|
|
coef_ = np.zeros((n_targets, n_features), dtype=X.dtype,
|
|
order='F')
|
|
else:
|
|
coef_ = self.coef_
|
|
if coef_.ndim == 1:
|
|
coef_ = coef_[np.newaxis, :]
|
|
|
|
dual_gaps_ = np.zeros(n_targets, dtype=X.dtype)
|
|
self.n_iter_ = []
|
|
|
|
for k in range(n_targets):
|
|
if Xy is not None:
|
|
this_Xy = Xy[:, k]
|
|
else:
|
|
this_Xy = None
|
|
_, this_coef, this_dual_gap, this_iter = \
|
|
self.path(X, y[:, k],
|
|
l1_ratio=self.l1_ratio, eps=None,
|
|
n_alphas=None, alphas=[alpha],
|
|
precompute=precompute, Xy=this_Xy,
|
|
fit_intercept=False, normalize=False, copy_X=True,
|
|
verbose=False, tol=self.tol, positive=self.positive,
|
|
X_offset=X_offset, X_scale=X_scale,
|
|
return_n_iter=True, coef_init=coef_[k],
|
|
max_iter=self.max_iter,
|
|
random_state=self.random_state,
|
|
selection=self.selection,
|
|
check_input=False)
|
|
coef_[k] = this_coef[:, 0]
|
|
dual_gaps_[k] = this_dual_gap[0]
|
|
self.n_iter_.append(this_iter[0])
|
|
|
|
if n_targets == 1:
|
|
self.n_iter_ = self.n_iter_[0]
|
|
self.coef_ = coef_[0]
|
|
self.dual_gap_ = dual_gaps_[0]
|
|
else:
|
|
self.coef_ = coef_
|
|
self.dual_gap_ = dual_gaps_
|
|
|
|
self._set_intercept(X_offset, y_offset, X_scale)
|
|
|
|
# workaround since _set_intercept will cast self.coef_ into X.dtype
|
|
self.coef_ = np.asarray(self.coef_, dtype=X.dtype)
|
|
|
|
# return self for chaining fit and predict calls
|
|
return self
|
|
|
|
@property
|
|
def sparse_coef_(self):
|
|
"""Sparse representation of the fitted `coef_`."""
|
|
return sparse.csr_matrix(self.coef_)
|
|
|
|
def _decision_function(self, X):
|
|
"""Decision function of the linear model.
|
|
|
|
Parameters
|
|
----------
|
|
X : numpy array or scipy.sparse matrix of shape (n_samples, n_features)
|
|
|
|
Returns
|
|
-------
|
|
T : ndarray of shape (n_samples,)
|
|
The predicted decision function.
|
|
"""
|
|
check_is_fitted(self)
|
|
if sparse.isspmatrix(X):
|
|
return safe_sparse_dot(X, self.coef_.T,
|
|
dense_output=True) + self.intercept_
|
|
else:
|
|
return super()._decision_function(X)
|
|
|
|
|
|
###############################################################################
|
|
# Lasso model
|
|
|
|
class Lasso(ElasticNet):
|
|
"""Linear Model trained with L1 prior as regularizer (aka the Lasso)
|
|
|
|
The optimization objective for Lasso is::
|
|
|
|
(1 / (2 * n_samples)) * ||y - Xw||^2_2 + alpha * ||w||_1
|
|
|
|
Technically the Lasso model is optimizing the same objective function as
|
|
the Elastic Net with ``l1_ratio=1.0`` (no L2 penalty).
|
|
|
|
Read more in the :ref:`User Guide <lasso>`.
|
|
|
|
Parameters
|
|
----------
|
|
alpha : float, default=1.0
|
|
Constant that multiplies the L1 term. Defaults to 1.0.
|
|
``alpha = 0`` is equivalent to an ordinary least square, solved
|
|
by the :class:`LinearRegression` object. For numerical
|
|
reasons, using ``alpha = 0`` with the ``Lasso`` object is not advised.
|
|
Given this, you should use the :class:`LinearRegression` object.
|
|
|
|
fit_intercept : bool, default=True
|
|
Whether to calculate the intercept for this model. If set
|
|
to False, no intercept will be used in calculations
|
|
(i.e. data is expected to be centered).
|
|
|
|
normalize : bool, default=False
|
|
This parameter is ignored when ``fit_intercept`` is set to False.
|
|
If True, the regressors X will be normalized before regression by
|
|
subtracting the mean and dividing by the l2-norm.
|
|
If you wish to standardize, please use
|
|
:class:`~sklearn.preprocessing.StandardScaler` before calling ``fit``
|
|
on an estimator with ``normalize=False``.
|
|
|
|
precompute : bool or array-like of shape (n_features, n_features),\
|
|
default=False
|
|
Whether to use a precomputed Gram matrix to speed up
|
|
calculations. The Gram matrix can also be passed as argument.
|
|
For sparse input this option is always ``False`` to preserve sparsity.
|
|
|
|
copy_X : bool, default=True
|
|
If ``True``, X will be copied; else, it may be overwritten.
|
|
|
|
max_iter : int, default=1000
|
|
The maximum number of iterations.
|
|
|
|
tol : float, default=1e-4
|
|
The tolerance for the optimization: if the updates are
|
|
smaller than ``tol``, the optimization code checks the
|
|
dual gap for optimality and continues until it is smaller
|
|
than ``tol``.
|
|
|
|
warm_start : bool, default=False
|
|
When set to True, reuse the solution of the previous call to fit as
|
|
initialization, otherwise, just erase the previous solution.
|
|
See :term:`the Glossary <warm_start>`.
|
|
|
|
positive : bool, default=False
|
|
When set to ``True``, forces the coefficients to be positive.
|
|
|
|
random_state : int, RandomState instance, default=None
|
|
The seed of the pseudo random number generator that selects a random
|
|
feature to update. Used when ``selection`` == 'random'.
|
|
Pass an int for reproducible output across multiple function calls.
|
|
See :term:`Glossary <random_state>`.
|
|
|
|
selection : {'cyclic', 'random'}, default='cyclic'
|
|
If set to 'random', a random coefficient is updated every iteration
|
|
rather than looping over features sequentially by default. This
|
|
(setting to 'random') often leads to significantly faster convergence
|
|
especially when tol is higher than 1e-4.
|
|
|
|
Attributes
|
|
----------
|
|
coef_ : ndarray of shape (n_features,) or (n_targets, n_features)
|
|
Parameter vector (w in the cost function formula).
|
|
|
|
dual_gap_ : float or ndarray of shape (n_targets,)
|
|
Given param alpha, the dual gaps at the end of the optimization,
|
|
same shape as each observation of y.
|
|
|
|
sparse_coef_ : sparse matrix of shape (n_features, 1) or \
|
|
(n_targets, n_features)
|
|
Readonly property derived from ``coef_``.
|
|
|
|
intercept_ : float or ndarray of shape (n_targets,)
|
|
Independent term in decision function.
|
|
|
|
n_iter_ : int or list of int
|
|
Number of iterations run by the coordinate descent solver to reach
|
|
the specified tolerance.
|
|
|
|
Examples
|
|
--------
|
|
>>> from sklearn import linear_model
|
|
>>> clf = linear_model.Lasso(alpha=0.1)
|
|
>>> clf.fit([[0,0], [1, 1], [2, 2]], [0, 1, 2])
|
|
Lasso(alpha=0.1)
|
|
>>> print(clf.coef_)
|
|
[0.85 0. ]
|
|
>>> print(clf.intercept_)
|
|
0.15...
|
|
|
|
See Also
|
|
--------
|
|
lars_path
|
|
lasso_path
|
|
LassoLars
|
|
LassoCV
|
|
LassoLarsCV
|
|
sklearn.decomposition.sparse_encode
|
|
|
|
Notes
|
|
-----
|
|
The algorithm used to fit the model is coordinate descent.
|
|
|
|
To avoid unnecessary memory duplication the X argument of the fit method
|
|
should be directly passed as a Fortran-contiguous numpy array.
|
|
"""
|
|
path = staticmethod(enet_path)
|
|
|
|
@_deprecate_positional_args
|
|
def __init__(self, alpha=1.0, *, fit_intercept=True, normalize=False,
|
|
precompute=False, copy_X=True, max_iter=1000,
|
|
tol=1e-4, warm_start=False, positive=False,
|
|
random_state=None, selection='cyclic'):
|
|
super().__init__(
|
|
alpha=alpha, l1_ratio=1.0, fit_intercept=fit_intercept,
|
|
normalize=normalize, precompute=precompute, copy_X=copy_X,
|
|
max_iter=max_iter, tol=tol, warm_start=warm_start,
|
|
positive=positive, random_state=random_state,
|
|
selection=selection)
|
|
|
|
|
|
###############################################################################
|
|
# Functions for CV with paths functions
|
|
|
|
def _path_residuals(X, y, train, test, path, path_params, alphas=None,
|
|
l1_ratio=1, X_order=None, dtype=None):
|
|
"""Returns the MSE for the models computed by 'path'.
|
|
|
|
Parameters
|
|
----------
|
|
X : {array-like, sparse matrix} of shape (n_samples, n_features)
|
|
Training data.
|
|
|
|
y : array-like of shape (n_samples,) or (n_samples, n_targets)
|
|
Target values.
|
|
|
|
train : list of indices
|
|
The indices of the train set.
|
|
|
|
test : list of indices
|
|
The indices of the test set.
|
|
|
|
path : callable
|
|
Function returning a list of models on the path. See
|
|
enet_path for an example of signature.
|
|
|
|
path_params : dictionary
|
|
Parameters passed to the path function.
|
|
|
|
alphas : array-like, default=None
|
|
Array of float that is used for cross-validation. If not
|
|
provided, computed using 'path'.
|
|
|
|
l1_ratio : float, default=1
|
|
float between 0 and 1 passed to ElasticNet (scaling between
|
|
l1 and l2 penalties). For ``l1_ratio = 0`` the penalty is an
|
|
L2 penalty. For ``l1_ratio = 1`` it is an L1 penalty. For ``0
|
|
< l1_ratio < 1``, the penalty is a combination of L1 and L2.
|
|
|
|
X_order : {'F', 'C'}, default=None
|
|
The order of the arrays expected by the path function to
|
|
avoid memory copies.
|
|
|
|
dtype : a numpy dtype, default=None
|
|
The dtype of the arrays expected by the path function to
|
|
avoid memory copies.
|
|
"""
|
|
X_train = X[train]
|
|
y_train = y[train]
|
|
X_test = X[test]
|
|
y_test = y[test]
|
|
|
|
if not sparse.issparse(X):
|
|
for array, array_input in ((X_train, X), (y_train, y),
|
|
(X_test, X), (y_test, y)):
|
|
if array.base is not array_input and not array.flags['WRITEABLE']:
|
|
# fancy indexing should create a writable copy but it doesn't
|
|
# for read-only memmaps (cf. numpy#14132).
|
|
array.setflags(write=True)
|
|
|
|
fit_intercept = path_params['fit_intercept']
|
|
normalize = path_params['normalize']
|
|
|
|
if y.ndim == 1:
|
|
precompute = path_params['precompute']
|
|
else:
|
|
# No Gram variant of multi-task exists right now.
|
|
# Fall back to default enet_multitask
|
|
precompute = False
|
|
|
|
X_train, y_train, X_offset, y_offset, X_scale, precompute, Xy = \
|
|
_pre_fit(X_train, y_train, None, precompute, normalize, fit_intercept,
|
|
copy=False)
|
|
|
|
path_params = path_params.copy()
|
|
path_params['Xy'] = Xy
|
|
path_params['X_offset'] = X_offset
|
|
path_params['X_scale'] = X_scale
|
|
path_params['precompute'] = precompute
|
|
path_params['copy_X'] = False
|
|
path_params['alphas'] = alphas
|
|
|
|
if 'l1_ratio' in path_params:
|
|
path_params['l1_ratio'] = l1_ratio
|
|
|
|
# Do the ordering and type casting here, as if it is done in the path,
|
|
# X is copied and a reference is kept here
|
|
X_train = check_array(X_train, accept_sparse='csc', dtype=dtype,
|
|
order=X_order)
|
|
alphas, coefs, _ = path(X_train, y_train, **path_params)
|
|
del X_train, y_train
|
|
|
|
if y.ndim == 1:
|
|
# Doing this so that it becomes coherent with multioutput.
|
|
coefs = coefs[np.newaxis, :, :]
|
|
y_offset = np.atleast_1d(y_offset)
|
|
y_test = y_test[:, np.newaxis]
|
|
|
|
if normalize:
|
|
nonzeros = np.flatnonzero(X_scale)
|
|
coefs[:, nonzeros] /= X_scale[nonzeros][:, np.newaxis]
|
|
|
|
intercepts = y_offset[:, np.newaxis] - np.dot(X_offset, coefs)
|
|
X_test_coefs = safe_sparse_dot(X_test, coefs)
|
|
residues = X_test_coefs - y_test[:, :, np.newaxis]
|
|
residues += intercepts
|
|
this_mses = ((residues ** 2).mean(axis=0)).mean(axis=0)
|
|
|
|
return this_mses
|
|
|
|
|
|
class LinearModelCV(MultiOutputMixin, LinearModel, metaclass=ABCMeta):
|
|
"""Base class for iterative model fitting along a regularization path."""
|
|
|
|
@abstractmethod
|
|
def __init__(self, eps=1e-3, n_alphas=100, alphas=None, fit_intercept=True,
|
|
normalize=False, precompute='auto', max_iter=1000, tol=1e-4,
|
|
copy_X=True, cv=None, verbose=False, n_jobs=None,
|
|
positive=False, random_state=None, selection='cyclic'):
|
|
self.eps = eps
|
|
self.n_alphas = n_alphas
|
|
self.alphas = alphas
|
|
self.fit_intercept = fit_intercept
|
|
self.normalize = normalize
|
|
self.precompute = precompute
|
|
self.max_iter = max_iter
|
|
self.tol = tol
|
|
self.copy_X = copy_X
|
|
self.cv = cv
|
|
self.verbose = verbose
|
|
self.n_jobs = n_jobs
|
|
self.positive = positive
|
|
self.random_state = random_state
|
|
self.selection = selection
|
|
|
|
@abstractmethod
|
|
def _get_estimator(self):
|
|
"""Model to be fitted after the best alpha has been determined."""
|
|
|
|
@abstractmethod
|
|
def _is_multitask(self):
|
|
"""Bool indicating if class is meant for multidimensional target."""
|
|
|
|
def fit(self, X, y):
|
|
"""Fit linear model with coordinate descent.
|
|
|
|
Fit is on grid of alphas and best alpha estimated by cross-validation.
|
|
|
|
Parameters
|
|
----------
|
|
X : {array-like, sparse matrix} of shape (n_samples, n_features)
|
|
Training data. Pass directly as Fortran-contiguous data
|
|
to avoid unnecessary memory duplication. If y is mono-output,
|
|
X can be sparse.
|
|
|
|
y : array-like of shape (n_samples,) or (n_samples, n_targets)
|
|
Target values.
|
|
"""
|
|
# This makes sure that there is no duplication in memory.
|
|
# Dealing right with copy_X is important in the following:
|
|
# Multiple functions touch X and subsamples of X and can induce a
|
|
# lot of duplication of memory
|
|
copy_X = self.copy_X and self.fit_intercept
|
|
|
|
check_y_params = dict(copy=False, dtype=[np.float64, np.float32],
|
|
ensure_2d=False)
|
|
if isinstance(X, np.ndarray) or sparse.isspmatrix(X):
|
|
# Keep a reference to X
|
|
reference_to_old_X = X
|
|
# Let us not impose fortran ordering so far: it is
|
|
# not useful for the cross-validation loop and will be done
|
|
# by the model fitting itself
|
|
|
|
# Need to validate separately here.
|
|
# We can't pass multi_ouput=True because that would allow y to be
|
|
# csr. We also want to allow y to be 64 or 32 but check_X_y only
|
|
# allows to convert for 64.
|
|
check_X_params = dict(accept_sparse='csc',
|
|
dtype=[np.float64, np.float32], copy=False)
|
|
X, y = self._validate_data(X, y,
|
|
validate_separately=(check_X_params,
|
|
check_y_params))
|
|
if sparse.isspmatrix(X):
|
|
if (hasattr(reference_to_old_X, "data") and
|
|
not np.may_share_memory(reference_to_old_X.data, X.data)):
|
|
# X is a sparse matrix and has been copied
|
|
copy_X = False
|
|
elif not np.may_share_memory(reference_to_old_X, X):
|
|
# X has been copied
|
|
copy_X = False
|
|
del reference_to_old_X
|
|
else:
|
|
# Need to validate separately here.
|
|
# We can't pass multi_ouput=True because that would allow y to be
|
|
# csr. We also want to allow y to be 64 or 32 but check_X_y only
|
|
# allows to convert for 64.
|
|
check_X_params = dict(accept_sparse='csc',
|
|
dtype=[np.float64, np.float32], order='F',
|
|
copy=copy_X)
|
|
X, y = self._validate_data(X, y,
|
|
validate_separately=(check_X_params,
|
|
check_y_params))
|
|
copy_X = False
|
|
|
|
if y.shape[0] == 0:
|
|
raise ValueError("y has 0 samples: %r" % y)
|
|
|
|
if not self._is_multitask():
|
|
if y.ndim > 1 and y.shape[1] > 1:
|
|
raise ValueError("For multi-task outputs, use "
|
|
"MultiTask%s" % self.__class__.__name__)
|
|
y = column_or_1d(y, warn=True)
|
|
else:
|
|
if sparse.isspmatrix(X):
|
|
raise TypeError("X should be dense but a sparse matrix was"
|
|
"passed")
|
|
elif y.ndim == 1:
|
|
raise ValueError("For mono-task outputs, use "
|
|
"%sCV" % self.__class__.__name__[9:])
|
|
|
|
model = self._get_estimator()
|
|
|
|
if self.selection not in ["random", "cyclic"]:
|
|
raise ValueError("selection should be either random or cyclic.")
|
|
|
|
if X.shape[0] != y.shape[0]:
|
|
raise ValueError("X and y have inconsistent dimensions (%d != %d)"
|
|
% (X.shape[0], y.shape[0]))
|
|
|
|
# All LinearModelCV parameters except 'cv' are acceptable
|
|
path_params = self.get_params()
|
|
if 'l1_ratio' in path_params:
|
|
l1_ratios = np.atleast_1d(path_params['l1_ratio'])
|
|
# For the first path, we need to set l1_ratio
|
|
path_params['l1_ratio'] = l1_ratios[0]
|
|
else:
|
|
l1_ratios = [1, ]
|
|
path_params.pop('cv', None)
|
|
path_params.pop('n_jobs', None)
|
|
|
|
alphas = self.alphas
|
|
n_l1_ratio = len(l1_ratios)
|
|
if alphas is None:
|
|
alphas = [_alpha_grid(X, y, l1_ratio=l1_ratio,
|
|
fit_intercept=self.fit_intercept,
|
|
eps=self.eps, n_alphas=self.n_alphas,
|
|
normalize=self.normalize, copy_X=self.copy_X)
|
|
for l1_ratio in l1_ratios]
|
|
else:
|
|
# Making sure alphas is properly ordered.
|
|
alphas = np.tile(np.sort(alphas)[::-1], (n_l1_ratio, 1))
|
|
# We want n_alphas to be the number of alphas used for each l1_ratio.
|
|
n_alphas = len(alphas[0])
|
|
path_params.update({'n_alphas': n_alphas})
|
|
|
|
path_params['copy_X'] = copy_X
|
|
# We are not computing in parallel, we can modify X
|
|
# inplace in the folds
|
|
if effective_n_jobs(self.n_jobs) > 1:
|
|
path_params['copy_X'] = False
|
|
|
|
# init cross-validation generator
|
|
cv = check_cv(self.cv)
|
|
|
|
# Compute path for all folds and compute MSE to get the best alpha
|
|
folds = list(cv.split(X, y))
|
|
best_mse = np.inf
|
|
|
|
# We do a double for loop folded in one, in order to be able to
|
|
# iterate in parallel on l1_ratio and folds
|
|
jobs = (delayed(_path_residuals)(X, y, train, test, self.path,
|
|
path_params, alphas=this_alphas,
|
|
l1_ratio=this_l1_ratio, X_order='F',
|
|
dtype=X.dtype.type)
|
|
for this_l1_ratio, this_alphas in zip(l1_ratios, alphas)
|
|
for train, test in folds)
|
|
mse_paths = Parallel(n_jobs=self.n_jobs, verbose=self.verbose,
|
|
**_joblib_parallel_args(prefer="threads"))(jobs)
|
|
mse_paths = np.reshape(mse_paths, (n_l1_ratio, len(folds), -1))
|
|
mean_mse = np.mean(mse_paths, axis=1)
|
|
self.mse_path_ = np.squeeze(np.rollaxis(mse_paths, 2, 1))
|
|
for l1_ratio, l1_alphas, mse_alphas in zip(l1_ratios, alphas,
|
|
mean_mse):
|
|
i_best_alpha = np.argmin(mse_alphas)
|
|
this_best_mse = mse_alphas[i_best_alpha]
|
|
if this_best_mse < best_mse:
|
|
best_alpha = l1_alphas[i_best_alpha]
|
|
best_l1_ratio = l1_ratio
|
|
best_mse = this_best_mse
|
|
|
|
self.l1_ratio_ = best_l1_ratio
|
|
self.alpha_ = best_alpha
|
|
if self.alphas is None:
|
|
self.alphas_ = np.asarray(alphas)
|
|
if n_l1_ratio == 1:
|
|
self.alphas_ = self.alphas_[0]
|
|
# Remove duplicate alphas in case alphas is provided.
|
|
else:
|
|
self.alphas_ = np.asarray(alphas[0])
|
|
|
|
# Refit the model with the parameters selected
|
|
common_params = {name: value
|
|
for name, value in self.get_params().items()
|
|
if name in model.get_params()}
|
|
model.set_params(**common_params)
|
|
model.alpha = best_alpha
|
|
model.l1_ratio = best_l1_ratio
|
|
model.copy_X = copy_X
|
|
precompute = getattr(self, "precompute", None)
|
|
if isinstance(precompute, str) and precompute == "auto":
|
|
model.precompute = False
|
|
model.fit(X, y)
|
|
if not hasattr(self, 'l1_ratio'):
|
|
del self.l1_ratio_
|
|
self.coef_ = model.coef_
|
|
self.intercept_ = model.intercept_
|
|
self.dual_gap_ = model.dual_gap_
|
|
self.n_iter_ = model.n_iter_
|
|
return self
|
|
|
|
|
|
class LassoCV(RegressorMixin, LinearModelCV):
|
|
"""Lasso linear model with iterative fitting along a regularization path.
|
|
|
|
See glossary entry for :term:`cross-validation estimator`.
|
|
|
|
The best model is selected by cross-validation.
|
|
|
|
The optimization objective for Lasso is::
|
|
|
|
(1 / (2 * n_samples)) * ||y - Xw||^2_2 + alpha * ||w||_1
|
|
|
|
Read more in the :ref:`User Guide <lasso>`.
|
|
|
|
Parameters
|
|
----------
|
|
eps : float, default=1e-3
|
|
Length of the path. ``eps=1e-3`` means that
|
|
``alpha_min / alpha_max = 1e-3``.
|
|
|
|
n_alphas : int, default=100
|
|
Number of alphas along the regularization path.
|
|
|
|
alphas : ndarray, default=None
|
|
List of alphas where to compute the models.
|
|
If ``None`` alphas are set automatically.
|
|
|
|
fit_intercept : bool, default=True
|
|
Whether to calculate the intercept for this model. If set
|
|
to false, no intercept will be used in calculations
|
|
(i.e. data is expected to be centered).
|
|
|
|
normalize : bool, default=False
|
|
This parameter is ignored when ``fit_intercept`` is set to False.
|
|
If True, the regressors X will be normalized before regression by
|
|
subtracting the mean and dividing by the l2-norm.
|
|
If you wish to standardize, please use
|
|
:class:`~sklearn.preprocessing.StandardScaler` before calling ``fit``
|
|
on an estimator with ``normalize=False``.
|
|
|
|
precompute : 'auto', bool or array-like of shape (n_features, n_features),\
|
|
default='auto'
|
|
Whether to use a precomputed Gram matrix to speed up
|
|
calculations. If set to ``'auto'`` let us decide. The Gram
|
|
matrix can also be passed as argument.
|
|
|
|
max_iter : int, default=1000
|
|
The maximum number of iterations.
|
|
|
|
tol : float, default=1e-4
|
|
The tolerance for the optimization: if the updates are
|
|
smaller than ``tol``, the optimization code checks the
|
|
dual gap for optimality and continues until it is smaller
|
|
than ``tol``.
|
|
|
|
copy_X : bool, default=True
|
|
If ``True``, X will be copied; else, it may be overwritten.
|
|
|
|
cv : int, cross-validation generator or iterable, default=None
|
|
Determines the cross-validation splitting strategy.
|
|
Possible inputs for cv are:
|
|
|
|
- None, to use the default 5-fold cross-validation,
|
|
- int, to specify the number of folds.
|
|
- :term:`CV splitter`,
|
|
- An iterable yielding (train, test) splits as arrays of indices.
|
|
|
|
For int/None inputs, :class:`KFold` is used.
|
|
|
|
Refer :ref:`User Guide <cross_validation>` for the various
|
|
cross-validation strategies that can be used here.
|
|
|
|
.. versionchanged:: 0.22
|
|
``cv`` default value if None changed from 3-fold to 5-fold.
|
|
|
|
verbose : bool or int, default=False
|
|
Amount of verbosity.
|
|
|
|
n_jobs : int, default=None
|
|
Number of CPUs to use during the cross validation.
|
|
``None`` means 1 unless in a :obj:`joblib.parallel_backend` context.
|
|
``-1`` means using all processors. See :term:`Glossary <n_jobs>`
|
|
for more details.
|
|
|
|
positive : bool, default=False
|
|
If positive, restrict regression coefficients to be positive.
|
|
|
|
random_state : int, RandomState instance, default=None
|
|
The seed of the pseudo random number generator that selects a random
|
|
feature to update. Used when ``selection`` == 'random'.
|
|
Pass an int for reproducible output across multiple function calls.
|
|
See :term:`Glossary <random_state>`.
|
|
|
|
selection : {'cyclic', 'random'}, default='cyclic'
|
|
If set to 'random', a random coefficient is updated every iteration
|
|
rather than looping over features sequentially by default. This
|
|
(setting to 'random') often leads to significantly faster convergence
|
|
especially when tol is higher than 1e-4.
|
|
|
|
Attributes
|
|
----------
|
|
alpha_ : float
|
|
The amount of penalization chosen by cross validation.
|
|
|
|
coef_ : ndarray of shape (n_features,) or (n_targets, n_features)
|
|
Parameter vector (w in the cost function formula).
|
|
|
|
intercept_ : float or ndarray of shape (n_targets,)
|
|
Independent term in decision function.
|
|
|
|
mse_path_ : ndarray of shape (n_alphas, n_folds)
|
|
Mean square error for the test set on each fold, varying alpha.
|
|
|
|
alphas_ : ndarray of shape (n_alphas,)
|
|
The grid of alphas used for fitting.
|
|
|
|
dual_gap_ : float or ndarray of shape (n_targets,)
|
|
The dual gap at the end of the optimization for the optimal alpha
|
|
(``alpha_``).
|
|
|
|
n_iter_ : int
|
|
Number of iterations run by the coordinate descent solver to reach
|
|
the specified tolerance for the optimal alpha.
|
|
|
|
Examples
|
|
--------
|
|
>>> from sklearn.linear_model import LassoCV
|
|
>>> from sklearn.datasets import make_regression
|
|
>>> X, y = make_regression(noise=4, random_state=0)
|
|
>>> reg = LassoCV(cv=5, random_state=0).fit(X, y)
|
|
>>> reg.score(X, y)
|
|
0.9993...
|
|
>>> reg.predict(X[:1,])
|
|
array([-78.4951...])
|
|
|
|
Notes
|
|
-----
|
|
For an example, see
|
|
:ref:`examples/linear_model/plot_lasso_model_selection.py
|
|
<sphx_glr_auto_examples_linear_model_plot_lasso_model_selection.py>`.
|
|
|
|
To avoid unnecessary memory duplication the X argument of the fit method
|
|
should be directly passed as a Fortran-contiguous numpy array.
|
|
|
|
See Also
|
|
--------
|
|
lars_path
|
|
lasso_path
|
|
LassoLars
|
|
Lasso
|
|
LassoLarsCV
|
|
"""
|
|
path = staticmethod(lasso_path)
|
|
|
|
@_deprecate_positional_args
|
|
def __init__(self, *, eps=1e-3, n_alphas=100, alphas=None,
|
|
fit_intercept=True,
|
|
normalize=False, precompute='auto', max_iter=1000, tol=1e-4,
|
|
copy_X=True, cv=None, verbose=False, n_jobs=None,
|
|
positive=False, random_state=None, selection='cyclic'):
|
|
super().__init__(
|
|
eps=eps, n_alphas=n_alphas, alphas=alphas,
|
|
fit_intercept=fit_intercept, normalize=normalize,
|
|
precompute=precompute, max_iter=max_iter, tol=tol, copy_X=copy_X,
|
|
cv=cv, verbose=verbose, n_jobs=n_jobs, positive=positive,
|
|
random_state=random_state, selection=selection)
|
|
|
|
def _get_estimator(self):
|
|
return Lasso()
|
|
|
|
def _is_multitask(self):
|
|
return False
|
|
|
|
def _more_tags(self):
|
|
return {'multioutput': False}
|
|
|
|
|
|
class ElasticNetCV(RegressorMixin, LinearModelCV):
|
|
"""Elastic Net model with iterative fitting along a regularization path.
|
|
|
|
See glossary entry for :term:`cross-validation estimator`.
|
|
|
|
Read more in the :ref:`User Guide <elastic_net>`.
|
|
|
|
Parameters
|
|
----------
|
|
l1_ratio : float or list of float, default=0.5
|
|
float between 0 and 1 passed to ElasticNet (scaling between
|
|
l1 and l2 penalties). For ``l1_ratio = 0``
|
|
the penalty is an L2 penalty. For ``l1_ratio = 1`` it is an L1 penalty.
|
|
For ``0 < l1_ratio < 1``, the penalty is a combination of L1 and L2
|
|
This parameter can be a list, in which case the different
|
|
values are tested by cross-validation and the one giving the best
|
|
prediction score is used. Note that a good choice of list of
|
|
values for l1_ratio is often to put more values close to 1
|
|
(i.e. Lasso) and less close to 0 (i.e. Ridge), as in ``[.1, .5, .7,
|
|
.9, .95, .99, 1]``.
|
|
|
|
eps : float, default=1e-3
|
|
Length of the path. ``eps=1e-3`` means that
|
|
``alpha_min / alpha_max = 1e-3``.
|
|
|
|
n_alphas : int, default=100
|
|
Number of alphas along the regularization path, used for each l1_ratio.
|
|
|
|
alphas : ndarray, default=None
|
|
List of alphas where to compute the models.
|
|
If None alphas are set automatically.
|
|
|
|
fit_intercept : bool, default=True
|
|
Whether to calculate the intercept for this model. If set
|
|
to false, no intercept will be used in calculations
|
|
(i.e. data is expected to be centered).
|
|
|
|
normalize : bool, default=False
|
|
This parameter is ignored when ``fit_intercept`` is set to False.
|
|
If True, the regressors X will be normalized before regression by
|
|
subtracting the mean and dividing by the l2-norm.
|
|
If you wish to standardize, please use
|
|
:class:`~sklearn.preprocessing.StandardScaler` before calling ``fit``
|
|
on an estimator with ``normalize=False``.
|
|
|
|
precompute : 'auto', bool or array-like of shape (n_features, n_features),\
|
|
default='auto'
|
|
Whether to use a precomputed Gram matrix to speed up
|
|
calculations. If set to ``'auto'`` let us decide. The Gram
|
|
matrix can also be passed as argument.
|
|
|
|
max_iter : int, default=1000
|
|
The maximum number of iterations.
|
|
|
|
tol : float, default=1e-4
|
|
The tolerance for the optimization: if the updates are
|
|
smaller than ``tol``, the optimization code checks the
|
|
dual gap for optimality and continues until it is smaller
|
|
than ``tol``.
|
|
|
|
cv : int, cross-validation generator or iterable, default=None
|
|
Determines the cross-validation splitting strategy.
|
|
Possible inputs for cv are:
|
|
|
|
- None, to use the default 5-fold cross-validation,
|
|
- int, to specify the number of folds.
|
|
- :term:`CV splitter`,
|
|
- An iterable yielding (train, test) splits as arrays of indices.
|
|
|
|
For int/None inputs, :class:`KFold` is used.
|
|
|
|
Refer :ref:`User Guide <cross_validation>` for the various
|
|
cross-validation strategies that can be used here.
|
|
|
|
.. versionchanged:: 0.22
|
|
``cv`` default value if None changed from 3-fold to 5-fold.
|
|
|
|
copy_X : bool, default=True
|
|
If ``True``, X will be copied; else, it may be overwritten.
|
|
|
|
verbose : bool or int, default=0
|
|
Amount of verbosity.
|
|
|
|
n_jobs : int, default=None
|
|
Number of CPUs to use during the cross validation.
|
|
``None`` means 1 unless in a :obj:`joblib.parallel_backend` context.
|
|
``-1`` means using all processors. See :term:`Glossary <n_jobs>`
|
|
for more details.
|
|
|
|
positive : bool, default=False
|
|
When set to ``True``, forces the coefficients to be positive.
|
|
|
|
random_state : int, RandomState instance, default=None
|
|
The seed of the pseudo random number generator that selects a random
|
|
feature to update. Used when ``selection`` == 'random'.
|
|
Pass an int for reproducible output across multiple function calls.
|
|
See :term:`Glossary <random_state>`.
|
|
|
|
selection : {'cyclic', 'random'}, default='cyclic'
|
|
If set to 'random', a random coefficient is updated every iteration
|
|
rather than looping over features sequentially by default. This
|
|
(setting to 'random') often leads to significantly faster convergence
|
|
especially when tol is higher than 1e-4.
|
|
|
|
Attributes
|
|
----------
|
|
alpha_ : float
|
|
The amount of penalization chosen by cross validation.
|
|
|
|
l1_ratio_ : float
|
|
The compromise between l1 and l2 penalization chosen by
|
|
cross validation.
|
|
|
|
coef_ : ndarray of shape (n_features,) or (n_targets, n_features)
|
|
Parameter vector (w in the cost function formula).
|
|
|
|
intercept_ : float or ndarray of shape (n_targets, n_features)
|
|
Independent term in the decision function.
|
|
|
|
mse_path_ : ndarray of shape (n_l1_ratio, n_alpha, n_folds)
|
|
Mean square error for the test set on each fold, varying l1_ratio and
|
|
alpha.
|
|
|
|
alphas_ : ndarray of shape (n_alphas,) or (n_l1_ratio, n_alphas)
|
|
The grid of alphas used for fitting, for each l1_ratio.
|
|
|
|
dual_gap_ : float
|
|
The dual gaps at the end of the optimization for the optimal alpha.
|
|
|
|
n_iter_ : int
|
|
Number of iterations run by the coordinate descent solver to reach
|
|
the specified tolerance for the optimal alpha.
|
|
|
|
Examples
|
|
--------
|
|
>>> from sklearn.linear_model import ElasticNetCV
|
|
>>> from sklearn.datasets import make_regression
|
|
|
|
>>> X, y = make_regression(n_features=2, random_state=0)
|
|
>>> regr = ElasticNetCV(cv=5, random_state=0)
|
|
>>> regr.fit(X, y)
|
|
ElasticNetCV(cv=5, random_state=0)
|
|
>>> print(regr.alpha_)
|
|
0.199...
|
|
>>> print(regr.intercept_)
|
|
0.398...
|
|
>>> print(regr.predict([[0, 0]]))
|
|
[0.398...]
|
|
|
|
|
|
Notes
|
|
-----
|
|
For an example, see
|
|
:ref:`examples/linear_model/plot_lasso_model_selection.py
|
|
<sphx_glr_auto_examples_linear_model_plot_lasso_model_selection.py>`.
|
|
|
|
To avoid unnecessary memory duplication the X argument of the fit method
|
|
should be directly passed as a Fortran-contiguous numpy array.
|
|
|
|
The parameter l1_ratio corresponds to alpha in the glmnet R package
|
|
while alpha corresponds to the lambda parameter in glmnet.
|
|
More specifically, the optimization objective is::
|
|
|
|
1 / (2 * n_samples) * ||y - Xw||^2_2
|
|
+ alpha * l1_ratio * ||w||_1
|
|
+ 0.5 * alpha * (1 - l1_ratio) * ||w||^2_2
|
|
|
|
If you are interested in controlling the L1 and L2 penalty
|
|
separately, keep in mind that this is equivalent to::
|
|
|
|
a * L1 + b * L2
|
|
|
|
for::
|
|
|
|
alpha = a + b and l1_ratio = a / (a + b).
|
|
|
|
See Also
|
|
--------
|
|
enet_path
|
|
ElasticNet
|
|
|
|
"""
|
|
path = staticmethod(enet_path)
|
|
|
|
@_deprecate_positional_args
|
|
def __init__(self, *, l1_ratio=0.5, eps=1e-3, n_alphas=100, alphas=None,
|
|
fit_intercept=True, normalize=False, precompute='auto',
|
|
max_iter=1000, tol=1e-4, cv=None, copy_X=True,
|
|
verbose=0, n_jobs=None, positive=False, random_state=None,
|
|
selection='cyclic'):
|
|
self.l1_ratio = l1_ratio
|
|
self.eps = eps
|
|
self.n_alphas = n_alphas
|
|
self.alphas = alphas
|
|
self.fit_intercept = fit_intercept
|
|
self.normalize = normalize
|
|
self.precompute = precompute
|
|
self.max_iter = max_iter
|
|
self.tol = tol
|
|
self.cv = cv
|
|
self.copy_X = copy_X
|
|
self.verbose = verbose
|
|
self.n_jobs = n_jobs
|
|
self.positive = positive
|
|
self.random_state = random_state
|
|
self.selection = selection
|
|
|
|
def _get_estimator(self):
|
|
return ElasticNet()
|
|
|
|
def _is_multitask(self):
|
|
return False
|
|
|
|
def _more_tags(self):
|
|
return {'multioutput': False}
|
|
|
|
###############################################################################
|
|
# Multi Task ElasticNet and Lasso models (with joint feature selection)
|
|
|
|
|
|
class MultiTaskElasticNet(Lasso):
|
|
"""Multi-task ElasticNet model trained with L1/L2 mixed-norm as
|
|
regularizer.
|
|
|
|
The optimization objective for MultiTaskElasticNet is::
|
|
|
|
(1 / (2 * n_samples)) * ||Y - XW||_Fro^2
|
|
+ alpha * l1_ratio * ||W||_21
|
|
+ 0.5 * alpha * (1 - l1_ratio) * ||W||_Fro^2
|
|
|
|
Where::
|
|
|
|
||W||_21 = sum_i sqrt(sum_j W_ij ^ 2)
|
|
|
|
i.e. the sum of norms of each row.
|
|
|
|
Read more in the :ref:`User Guide <multi_task_elastic_net>`.
|
|
|
|
Parameters
|
|
----------
|
|
alpha : float, default=1.0
|
|
Constant that multiplies the L1/L2 term. Defaults to 1.0.
|
|
|
|
l1_ratio : float, default=0.5
|
|
The ElasticNet mixing parameter, with 0 < l1_ratio <= 1.
|
|
For l1_ratio = 1 the penalty is an L1/L2 penalty. For l1_ratio = 0 it
|
|
is an L2 penalty.
|
|
For ``0 < l1_ratio < 1``, the penalty is a combination of L1/L2 and L2.
|
|
|
|
fit_intercept : bool, default=True
|
|
Whether to calculate the intercept for this model. If set
|
|
to false, no intercept will be used in calculations
|
|
(i.e. data is expected to be centered).
|
|
|
|
normalize : bool, default=False
|
|
This parameter is ignored when ``fit_intercept`` is set to False.
|
|
If True, the regressors X will be normalized before regression by
|
|
subtracting the mean and dividing by the l2-norm.
|
|
If you wish to standardize, please use
|
|
:class:`~sklearn.preprocessing.StandardScaler` before calling ``fit``
|
|
on an estimator with ``normalize=False``.
|
|
|
|
copy_X : bool, default=True
|
|
If ``True``, X will be copied; else, it may be overwritten.
|
|
|
|
max_iter : int, default=1000
|
|
The maximum number of iterations.
|
|
|
|
tol : float, default=1e-4
|
|
The tolerance for the optimization: if the updates are
|
|
smaller than ``tol``, the optimization code checks the
|
|
dual gap for optimality and continues until it is smaller
|
|
than ``tol``.
|
|
|
|
warm_start : bool, default=False
|
|
When set to ``True``, reuse the solution of the previous call to fit as
|
|
initialization, otherwise, just erase the previous solution.
|
|
See :term:`the Glossary <warm_start>`.
|
|
|
|
random_state : int, RandomState instance, default=None
|
|
The seed of the pseudo random number generator that selects a random
|
|
feature to update. Used when ``selection`` == 'random'.
|
|
Pass an int for reproducible output across multiple function calls.
|
|
See :term:`Glossary <random_state>`.
|
|
|
|
selection : {'cyclic', 'random'}, default='cyclic'
|
|
If set to 'random', a random coefficient is updated every iteration
|
|
rather than looping over features sequentially by default. This
|
|
(setting to 'random') often leads to significantly faster convergence
|
|
especially when tol is higher than 1e-4.
|
|
|
|
Attributes
|
|
----------
|
|
intercept_ : ndarray of shape (n_tasks,)
|
|
Independent term in decision function.
|
|
|
|
coef_ : ndarray of shape (n_tasks, n_features)
|
|
Parameter vector (W in the cost function formula). If a 1D y is
|
|
passed in at fit (non multi-task usage), ``coef_`` is then a 1D array.
|
|
Note that ``coef_`` stores the transpose of ``W``, ``W.T``.
|
|
|
|
n_iter_ : int
|
|
Number of iterations run by the coordinate descent solver to reach
|
|
the specified tolerance.
|
|
|
|
dual_gap_ : float
|
|
The dual gaps at the end of the optimization.
|
|
|
|
eps_ : float
|
|
The tolerance scaled scaled by the variance of the target `y`.
|
|
|
|
sparse_coef_ : sparse matrix of shape (n_features,) or \
|
|
(n_tasks, n_features)
|
|
Sparse representation of the `coef_`.
|
|
|
|
Examples
|
|
--------
|
|
>>> from sklearn import linear_model
|
|
>>> clf = linear_model.MultiTaskElasticNet(alpha=0.1)
|
|
>>> clf.fit([[0,0], [1, 1], [2, 2]], [[0, 0], [1, 1], [2, 2]])
|
|
MultiTaskElasticNet(alpha=0.1)
|
|
>>> print(clf.coef_)
|
|
[[0.45663524 0.45612256]
|
|
[0.45663524 0.45612256]]
|
|
>>> print(clf.intercept_)
|
|
[0.0872422 0.0872422]
|
|
|
|
See Also
|
|
--------
|
|
MultiTaskElasticNetCV : Multi-task L1/L2 ElasticNet with built-in
|
|
cross-validation.
|
|
ElasticNet
|
|
MultiTaskLasso
|
|
|
|
Notes
|
|
-----
|
|
The algorithm used to fit the model is coordinate descent.
|
|
|
|
To avoid unnecessary memory duplication the X and y arguments of the fit
|
|
method should be directly passed as Fortran-contiguous numpy arrays.
|
|
"""
|
|
@_deprecate_positional_args
|
|
def __init__(self, alpha=1.0, *, l1_ratio=0.5, fit_intercept=True,
|
|
normalize=False, copy_X=True, max_iter=1000, tol=1e-4,
|
|
warm_start=False, random_state=None, selection='cyclic'):
|
|
self.l1_ratio = l1_ratio
|
|
self.alpha = alpha
|
|
self.fit_intercept = fit_intercept
|
|
self.normalize = normalize
|
|
self.max_iter = max_iter
|
|
self.copy_X = copy_X
|
|
self.tol = tol
|
|
self.warm_start = warm_start
|
|
self.random_state = random_state
|
|
self.selection = selection
|
|
|
|
def fit(self, X, y):
|
|
"""Fit MultiTaskElasticNet model with coordinate descent
|
|
|
|
Parameters
|
|
----------
|
|
X : ndarray of shape (n_samples, n_features)
|
|
Data.
|
|
y : ndarray of shape (n_samples, n_tasks)
|
|
Target. Will be cast to X's dtype if necessary.
|
|
|
|
Notes
|
|
-----
|
|
|
|
Coordinate descent is an algorithm that considers each column of
|
|
data at a time hence it will automatically convert the X input
|
|
as a Fortran-contiguous numpy array if necessary.
|
|
|
|
To avoid memory re-allocation it is advised to allocate the
|
|
initial data in memory directly using that format.
|
|
"""
|
|
# Need to validate separately here.
|
|
# We can't pass multi_ouput=True because that would allow y to be csr.
|
|
check_X_params = dict(dtype=[np.float64, np.float32], order='F',
|
|
copy=self.copy_X and self.fit_intercept)
|
|
check_y_params = dict(ensure_2d=False, order='F')
|
|
X, y = self._validate_data(X, y, validate_separately=(check_X_params,
|
|
check_y_params))
|
|
y = y.astype(X.dtype)
|
|
|
|
if hasattr(self, 'l1_ratio'):
|
|
model_str = 'ElasticNet'
|
|
else:
|
|
model_str = 'Lasso'
|
|
if y.ndim == 1:
|
|
raise ValueError("For mono-task outputs, use %s" % model_str)
|
|
|
|
n_samples, n_features = X.shape
|
|
_, n_tasks = y.shape
|
|
|
|
if n_samples != y.shape[0]:
|
|
raise ValueError("X and y have inconsistent dimensions (%d != %d)"
|
|
% (n_samples, y.shape[0]))
|
|
|
|
X, y, X_offset, y_offset, X_scale = _preprocess_data(
|
|
X, y, self.fit_intercept, self.normalize, copy=False)
|
|
|
|
if not self.warm_start or not hasattr(self, "coef_"):
|
|
self.coef_ = np.zeros((n_tasks, n_features), dtype=X.dtype.type,
|
|
order='F')
|
|
|
|
l1_reg = self.alpha * self.l1_ratio * n_samples
|
|
l2_reg = self.alpha * (1.0 - self.l1_ratio) * n_samples
|
|
|
|
self.coef_ = np.asfortranarray(self.coef_) # coef contiguous in memory
|
|
|
|
if self.selection not in ['random', 'cyclic']:
|
|
raise ValueError("selection should be either random or cyclic.")
|
|
random = (self.selection == 'random')
|
|
|
|
self.coef_, self.dual_gap_, self.eps_, self.n_iter_ = \
|
|
cd_fast.enet_coordinate_descent_multi_task(
|
|
self.coef_, l1_reg, l2_reg, X, y, self.max_iter, self.tol,
|
|
check_random_state(self.random_state), random)
|
|
|
|
self._set_intercept(X_offset, y_offset, X_scale)
|
|
|
|
# return self for chaining fit and predict calls
|
|
return self
|
|
|
|
def _more_tags(self):
|
|
return {'multioutput_only': True}
|
|
|
|
|
|
class MultiTaskLasso(MultiTaskElasticNet):
|
|
"""Multi-task Lasso model trained with L1/L2 mixed-norm as regularizer.
|
|
|
|
The optimization objective for Lasso is::
|
|
|
|
(1 / (2 * n_samples)) * ||Y - XW||^2_Fro + alpha * ||W||_21
|
|
|
|
Where::
|
|
|
|
||W||_21 = \\sum_i \\sqrt{\\sum_j w_{ij}^2}
|
|
|
|
i.e. the sum of norm of each row.
|
|
|
|
Read more in the :ref:`User Guide <multi_task_lasso>`.
|
|
|
|
Parameters
|
|
----------
|
|
alpha : float, default=1.0
|
|
Constant that multiplies the L1/L2 term. Defaults to 1.0.
|
|
|
|
fit_intercept : bool, default=True
|
|
Whether to calculate the intercept for this model. If set
|
|
to false, no intercept will be used in calculations
|
|
(i.e. data is expected to be centered).
|
|
|
|
normalize : bool, default=False
|
|
This parameter is ignored when ``fit_intercept`` is set to False.
|
|
If True, the regressors X will be normalized before regression by
|
|
subtracting the mean and dividing by the l2-norm.
|
|
If you wish to standardize, please use
|
|
:class:`~sklearn.preprocessing.StandardScaler` before calling ``fit``
|
|
on an estimator with ``normalize=False``.
|
|
|
|
copy_X : bool, default=True
|
|
If ``True``, X will be copied; else, it may be overwritten.
|
|
|
|
max_iter : int, default=1000
|
|
The maximum number of iterations.
|
|
|
|
tol : float, default=1e-4
|
|
The tolerance for the optimization: if the updates are
|
|
smaller than ``tol``, the optimization code checks the
|
|
dual gap for optimality and continues until it is smaller
|
|
than ``tol``.
|
|
|
|
warm_start : bool, default=False
|
|
When set to ``True``, reuse the solution of the previous call to fit as
|
|
initialization, otherwise, just erase the previous solution.
|
|
See :term:`the Glossary <warm_start>`.
|
|
|
|
random_state : int, RandomState instance, default=None
|
|
The seed of the pseudo random number generator that selects a random
|
|
feature to update. Used when ``selection`` == 'random'.
|
|
Pass an int for reproducible output across multiple function calls.
|
|
See :term:`Glossary <random_state>`.
|
|
|
|
selection : {'cyclic', 'random'}, default='cyclic'
|
|
If set to 'random', a random coefficient is updated every iteration
|
|
rather than looping over features sequentially by default. This
|
|
(setting to 'random') often leads to significantly faster convergence
|
|
especially when tol is higher than 1e-4
|
|
|
|
Attributes
|
|
----------
|
|
coef_ : ndarray of shape (n_tasks, n_features)
|
|
Parameter vector (W in the cost function formula).
|
|
Note that ``coef_`` stores the transpose of ``W``, ``W.T``.
|
|
|
|
intercept_ : ndarray of shape (n_tasks,)
|
|
Independent term in decision function.
|
|
|
|
n_iter_ : int
|
|
Number of iterations run by the coordinate descent solver to reach
|
|
the specified tolerance.
|
|
|
|
dual_gap_ : ndarray of shape (n_alphas,)
|
|
The dual gaps at the end of the optimization for each alpha.
|
|
|
|
eps_ : float
|
|
The tolerance scaled scaled by the variance of the target `y`.
|
|
|
|
sparse_coef_ : sparse matrix of shape (n_features,) or \
|
|
(n_tasks, n_features)
|
|
Sparse representation of the `coef_`.
|
|
|
|
Examples
|
|
--------
|
|
>>> from sklearn import linear_model
|
|
>>> clf = linear_model.MultiTaskLasso(alpha=0.1)
|
|
>>> clf.fit([[0, 1], [1, 2], [2, 4]], [[0, 0], [1, 1], [2, 3]])
|
|
MultiTaskLasso(alpha=0.1)
|
|
>>> print(clf.coef_)
|
|
[[0. 0.60809415]
|
|
[0. 0.94592424]]
|
|
>>> print(clf.intercept_)
|
|
[-0.41888636 -0.87382323]
|
|
|
|
See Also
|
|
--------
|
|
MultiTaskLasso : Multi-task L1/L2 Lasso with built-in cross-validation.
|
|
Lasso
|
|
MultiTaskElasticNet
|
|
|
|
Notes
|
|
-----
|
|
The algorithm used to fit the model is coordinate descent.
|
|
|
|
To avoid unnecessary memory duplication the X and y arguments of the fit
|
|
method should be directly passed as Fortran-contiguous numpy arrays.
|
|
"""
|
|
@_deprecate_positional_args
|
|
def __init__(self, alpha=1.0, *, fit_intercept=True, normalize=False,
|
|
copy_X=True, max_iter=1000, tol=1e-4, warm_start=False,
|
|
random_state=None, selection='cyclic'):
|
|
self.alpha = alpha
|
|
self.fit_intercept = fit_intercept
|
|
self.normalize = normalize
|
|
self.max_iter = max_iter
|
|
self.copy_X = copy_X
|
|
self.tol = tol
|
|
self.warm_start = warm_start
|
|
self.l1_ratio = 1.0
|
|
self.random_state = random_state
|
|
self.selection = selection
|
|
|
|
|
|
class MultiTaskElasticNetCV(RegressorMixin, LinearModelCV):
|
|
"""Multi-task L1/L2 ElasticNet with built-in cross-validation.
|
|
|
|
See glossary entry for :term:`cross-validation estimator`.
|
|
|
|
The optimization objective for MultiTaskElasticNet is::
|
|
|
|
(1 / (2 * n_samples)) * ||Y - XW||^Fro_2
|
|
+ alpha * l1_ratio * ||W||_21
|
|
+ 0.5 * alpha * (1 - l1_ratio) * ||W||_Fro^2
|
|
|
|
Where::
|
|
|
|
||W||_21 = \\sum_i \\sqrt{\\sum_j w_{ij}^2}
|
|
|
|
i.e. the sum of norm of each row.
|
|
|
|
Read more in the :ref:`User Guide <multi_task_elastic_net>`.
|
|
|
|
.. versionadded:: 0.15
|
|
|
|
Parameters
|
|
----------
|
|
l1_ratio : float or list of float, default=0.5
|
|
The ElasticNet mixing parameter, with 0 < l1_ratio <= 1.
|
|
For l1_ratio = 1 the penalty is an L1/L2 penalty. For l1_ratio = 0 it
|
|
is an L2 penalty.
|
|
For ``0 < l1_ratio < 1``, the penalty is a combination of L1/L2 and L2.
|
|
This parameter can be a list, in which case the different
|
|
values are tested by cross-validation and the one giving the best
|
|
prediction score is used. Note that a good choice of list of
|
|
values for l1_ratio is often to put more values close to 1
|
|
(i.e. Lasso) and less close to 0 (i.e. Ridge), as in ``[.1, .5, .7,
|
|
.9, .95, .99, 1]``
|
|
|
|
eps : float, default=1e-3
|
|
Length of the path. ``eps=1e-3`` means that
|
|
``alpha_min / alpha_max = 1e-3``.
|
|
|
|
n_alphas : int, default=100
|
|
Number of alphas along the regularization path.
|
|
|
|
alphas : array-like, default=None
|
|
List of alphas where to compute the models.
|
|
If not provided, set automatically.
|
|
|
|
fit_intercept : bool, default=True
|
|
Whether to calculate the intercept for this model. If set
|
|
to false, no intercept will be used in calculations
|
|
(i.e. data is expected to be centered).
|
|
|
|
normalize : bool, default=False
|
|
This parameter is ignored when ``fit_intercept`` is set to False.
|
|
If True, the regressors X will be normalized before regression by
|
|
subtracting the mean and dividing by the l2-norm.
|
|
If you wish to standardize, please use
|
|
:class:`~sklearn.preprocessing.StandardScaler` before calling ``fit``
|
|
on an estimator with ``normalize=False``.
|
|
|
|
max_iter : int, default=1000
|
|
The maximum number of iterations.
|
|
|
|
tol : float, default=1e-4
|
|
The tolerance for the optimization: if the updates are
|
|
smaller than ``tol``, the optimization code checks the
|
|
dual gap for optimality and continues until it is smaller
|
|
than ``tol``.
|
|
|
|
cv : int, cross-validation generator or iterable, default=None
|
|
Determines the cross-validation splitting strategy.
|
|
Possible inputs for cv are:
|
|
|
|
- None, to use the default 5-fold cross-validation,
|
|
- int, to specify the number of folds.
|
|
- :term:`CV splitter`,
|
|
- An iterable yielding (train, test) splits as arrays of indices.
|
|
|
|
For int/None inputs, :class:`KFold` is used.
|
|
|
|
Refer :ref:`User Guide <cross_validation>` for the various
|
|
cross-validation strategies that can be used here.
|
|
|
|
.. versionchanged:: 0.22
|
|
``cv`` default value if None changed from 3-fold to 5-fold.
|
|
|
|
copy_X : bool, default=True
|
|
If ``True``, X will be copied; else, it may be overwritten.
|
|
|
|
verbose : bool or int, default=0
|
|
Amount of verbosity.
|
|
|
|
n_jobs : int, default=None
|
|
Number of CPUs to use during the cross validation. Note that this is
|
|
used only if multiple values for l1_ratio are given.
|
|
``None`` means 1 unless in a :obj:`joblib.parallel_backend` context.
|
|
``-1`` means using all processors. See :term:`Glossary <n_jobs>`
|
|
for more details.
|
|
|
|
random_state : int, RandomState instance, default=None
|
|
The seed of the pseudo random number generator that selects a random
|
|
feature to update. Used when ``selection`` == 'random'.
|
|
Pass an int for reproducible output across multiple function calls.
|
|
See :term:`Glossary <random_state>`.
|
|
|
|
selection : {'cyclic', 'random'}, default='cyclic'
|
|
If set to 'random', a random coefficient is updated every iteration
|
|
rather than looping over features sequentially by default. This
|
|
(setting to 'random') often leads to significantly faster convergence
|
|
especially when tol is higher than 1e-4.
|
|
|
|
Attributes
|
|
----------
|
|
intercept_ : ndarray of shape (n_tasks,)
|
|
Independent term in decision function.
|
|
|
|
coef_ : ndarray of shape (n_tasks, n_features)
|
|
Parameter vector (W in the cost function formula).
|
|
Note that ``coef_`` stores the transpose of ``W``, ``W.T``.
|
|
|
|
alpha_ : float
|
|
The amount of penalization chosen by cross validation.
|
|
|
|
mse_path_ : ndarray of shape (n_alphas, n_folds) or \
|
|
(n_l1_ratio, n_alphas, n_folds)
|
|
Mean square error for the test set on each fold, varying alpha.
|
|
|
|
alphas_ : ndarray of shape (n_alphas,) or (n_l1_ratio, n_alphas)
|
|
The grid of alphas used for fitting, for each l1_ratio.
|
|
|
|
l1_ratio_ : float
|
|
Best l1_ratio obtained by cross-validation.
|
|
|
|
n_iter_ : int
|
|
Number of iterations run by the coordinate descent solver to reach
|
|
the specified tolerance for the optimal alpha.
|
|
|
|
dual_gap_ : float
|
|
The dual gap at the end of the optimization for the optimal alpha.
|
|
|
|
Examples
|
|
--------
|
|
>>> from sklearn import linear_model
|
|
>>> clf = linear_model.MultiTaskElasticNetCV(cv=3)
|
|
>>> clf.fit([[0,0], [1, 1], [2, 2]],
|
|
... [[0, 0], [1, 1], [2, 2]])
|
|
MultiTaskElasticNetCV(cv=3)
|
|
>>> print(clf.coef_)
|
|
[[0.52875032 0.46958558]
|
|
[0.52875032 0.46958558]]
|
|
>>> print(clf.intercept_)
|
|
[0.00166409 0.00166409]
|
|
|
|
See Also
|
|
--------
|
|
MultiTaskElasticNet
|
|
ElasticNetCV
|
|
MultiTaskLassoCV
|
|
|
|
Notes
|
|
-----
|
|
The algorithm used to fit the model is coordinate descent.
|
|
|
|
To avoid unnecessary memory duplication the X and y arguments of the fit
|
|
method should be directly passed as Fortran-contiguous numpy arrays.
|
|
"""
|
|
path = staticmethod(enet_path)
|
|
|
|
@_deprecate_positional_args
|
|
def __init__(self, *, l1_ratio=0.5, eps=1e-3, n_alphas=100, alphas=None,
|
|
fit_intercept=True, normalize=False,
|
|
max_iter=1000, tol=1e-4, cv=None, copy_X=True,
|
|
verbose=0, n_jobs=None, random_state=None,
|
|
selection='cyclic'):
|
|
self.l1_ratio = l1_ratio
|
|
self.eps = eps
|
|
self.n_alphas = n_alphas
|
|
self.alphas = alphas
|
|
self.fit_intercept = fit_intercept
|
|
self.normalize = normalize
|
|
self.max_iter = max_iter
|
|
self.tol = tol
|
|
self.cv = cv
|
|
self.copy_X = copy_X
|
|
self.verbose = verbose
|
|
self.n_jobs = n_jobs
|
|
self.random_state = random_state
|
|
self.selection = selection
|
|
|
|
def _get_estimator(self):
|
|
return MultiTaskElasticNet()
|
|
|
|
def _is_multitask(self):
|
|
return True
|
|
|
|
def _more_tags(self):
|
|
return {'multioutput_only': True}
|
|
|
|
|
|
class MultiTaskLassoCV(RegressorMixin, LinearModelCV):
|
|
"""Multi-task Lasso model trained with L1/L2 mixed-norm as regularizer.
|
|
|
|
See glossary entry for :term:`cross-validation estimator`.
|
|
|
|
The optimization objective for MultiTaskLasso is::
|
|
|
|
(1 / (2 * n_samples)) * ||Y - XW||^Fro_2 + alpha * ||W||_21
|
|
|
|
Where::
|
|
|
|
||W||_21 = \\sum_i \\sqrt{\\sum_j w_{ij}^2}
|
|
|
|
i.e. the sum of norm of each row.
|
|
|
|
Read more in the :ref:`User Guide <multi_task_lasso>`.
|
|
|
|
.. versionadded:: 0.15
|
|
|
|
Parameters
|
|
----------
|
|
eps : float, default=1e-3
|
|
Length of the path. ``eps=1e-3`` means that
|
|
``alpha_min / alpha_max = 1e-3``.
|
|
|
|
n_alphas : int, default=100
|
|
Number of alphas along the regularization path.
|
|
|
|
alphas : array-like, default=None
|
|
List of alphas where to compute the models.
|
|
If not provided, set automatically.
|
|
|
|
fit_intercept : bool, default=True
|
|
Whether to calculate the intercept for this model. If set
|
|
to false, no intercept will be used in calculations
|
|
(i.e. data is expected to be centered).
|
|
|
|
normalize : bool, default=False
|
|
This parameter is ignored when ``fit_intercept`` is set to False.
|
|
If True, the regressors X will be normalized before regression by
|
|
subtracting the mean and dividing by the l2-norm.
|
|
If you wish to standardize, please use
|
|
:class:`~sklearn.preprocessing.StandardScaler` before calling ``fit``
|
|
on an estimator with ``normalize=False``.
|
|
|
|
max_iter : int, default=1000
|
|
The maximum number of iterations.
|
|
|
|
tol : float, default=1e-4
|
|
The tolerance for the optimization: if the updates are
|
|
smaller than ``tol``, the optimization code checks the
|
|
dual gap for optimality and continues until it is smaller
|
|
than ``tol``.
|
|
|
|
copy_X : bool, default=True
|
|
If ``True``, X will be copied; else, it may be overwritten.
|
|
|
|
cv : int, cross-validation generator or iterable, default=None
|
|
Determines the cross-validation splitting strategy.
|
|
Possible inputs for cv are:
|
|
|
|
- None, to use the default 5-fold cross-validation,
|
|
- int, to specify the number of folds.
|
|
- :term:`CV splitter`,
|
|
- An iterable yielding (train, test) splits as arrays of indices.
|
|
|
|
For int/None inputs, :class:`KFold` is used.
|
|
|
|
Refer :ref:`User Guide <cross_validation>` for the various
|
|
cross-validation strategies that can be used here.
|
|
|
|
.. versionchanged:: 0.22
|
|
``cv`` default value if None changed from 3-fold to 5-fold.
|
|
|
|
verbose : bool or int, default=False
|
|
Amount of verbosity.
|
|
|
|
n_jobs : int, default=None
|
|
Number of CPUs to use during the cross validation. Note that this is
|
|
used only if multiple values for l1_ratio are given.
|
|
``None`` means 1 unless in a :obj:`joblib.parallel_backend` context.
|
|
``-1`` means using all processors. See :term:`Glossary <n_jobs>`
|
|
for more details.
|
|
|
|
random_state : int, RandomState instance, default=None
|
|
The seed of the pseudo random number generator that selects a random
|
|
feature to update. Used when ``selection`` == 'random'.
|
|
Pass an int for reproducible output across multiple function calls.
|
|
See :term:`Glossary <random_state>`.
|
|
|
|
selection : {'cyclic', 'random'}, default='cyclic'
|
|
If set to 'random', a random coefficient is updated every iteration
|
|
rather than looping over features sequentially by default. This
|
|
(setting to 'random') often leads to significantly faster convergence
|
|
especially when tol is higher than 1e-4.
|
|
|
|
Attributes
|
|
----------
|
|
intercept_ : ndarray of shape (n_tasks,)
|
|
Independent term in decision function.
|
|
|
|
coef_ : ndarray of shape (n_tasks, n_features)
|
|
Parameter vector (W in the cost function formula).
|
|
Note that ``coef_`` stores the transpose of ``W``, ``W.T``.
|
|
|
|
alpha_ : float
|
|
The amount of penalization chosen by cross validation.
|
|
|
|
mse_path_ : ndarray of shape (n_alphas, n_folds)
|
|
Mean square error for the test set on each fold, varying alpha.
|
|
|
|
alphas_ : ndarray of shape (n_alphas,)
|
|
The grid of alphas used for fitting.
|
|
|
|
n_iter_ : int
|
|
Number of iterations run by the coordinate descent solver to reach
|
|
the specified tolerance for the optimal alpha.
|
|
|
|
dual_gap_ : float
|
|
The dual gap at the end of the optimization for the optimal alpha.
|
|
|
|
Examples
|
|
--------
|
|
>>> from sklearn.linear_model import MultiTaskLassoCV
|
|
>>> from sklearn.datasets import make_regression
|
|
>>> from sklearn.metrics import r2_score
|
|
>>> X, y = make_regression(n_targets=2, noise=4, random_state=0)
|
|
>>> reg = MultiTaskLassoCV(cv=5, random_state=0).fit(X, y)
|
|
>>> r2_score(y, reg.predict(X))
|
|
0.9994...
|
|
>>> reg.alpha_
|
|
0.5713...
|
|
>>> reg.predict(X[:1,])
|
|
array([[153.7971..., 94.9015...]])
|
|
|
|
See Also
|
|
--------
|
|
MultiTaskElasticNet
|
|
ElasticNetCV
|
|
MultiTaskElasticNetCV
|
|
|
|
Notes
|
|
-----
|
|
The algorithm used to fit the model is coordinate descent.
|
|
|
|
To avoid unnecessary memory duplication the X and y arguments of the fit
|
|
method should be directly passed as Fortran-contiguous numpy arrays.
|
|
"""
|
|
path = staticmethod(lasso_path)
|
|
|
|
@_deprecate_positional_args
|
|
def __init__(self, *, eps=1e-3, n_alphas=100, alphas=None,
|
|
fit_intercept=True,
|
|
normalize=False, max_iter=1000, tol=1e-4, copy_X=True,
|
|
cv=None, verbose=False, n_jobs=None, random_state=None,
|
|
selection='cyclic'):
|
|
super().__init__(
|
|
eps=eps, n_alphas=n_alphas, alphas=alphas,
|
|
fit_intercept=fit_intercept, normalize=normalize,
|
|
max_iter=max_iter, tol=tol, copy_X=copy_X,
|
|
cv=cv, verbose=verbose, n_jobs=n_jobs, random_state=random_state,
|
|
selection=selection)
|
|
|
|
def _get_estimator(self):
|
|
return MultiTaskLasso()
|
|
|
|
def _is_multitask(self):
|
|
return True
|
|
|
|
def _more_tags(self):
|
|
return {'multioutput_only': True}
|