graph_lasso_.py

"""GraphLasso: sparse inverse covariance estimation with an l1-penalized
estimator.
"""

# Author: Gael Varoquaux <gael.varoquaux@normalesup.org>
# License: BSD 3 clause
# Copyright: INRIA
import warnings
import operator
import sys
import time

import numpy as np
from scipy import linalg

from .empirical_covariance_ import (empirical_covariance, EmpiricalCovariance,
                                    log_likelihood)

from ..exceptions import ConvergenceWarning
from ..utils.validation import check_random_state, check_array
from ..utils import deprecated
from ..linear_model import lars_path
from ..linear_model import cd_fast
from ..model_selection import check_cv, cross_val_score
from ..externals.joblib import Parallel, delayed
import collections


# Helper functions to compute the objective and dual objective functions
# of the l1-penalized estimator
def _objective(mle, precision_, alpha):
    """Evaluation of the graph-lasso objective function

    the objective function is made of a shifted scaled version of the
    normalized log-likelihood (i.e. its empirical mean over the samples) and a
    penalisation term to promote sparsity
    """
    p = precision_.shape[0]
    cost = - 2. * log_likelihood(mle, precision_) + p * np.log(2 * np.pi)
    cost += alpha * (np.abs(precision_).sum()
                     - np.abs(np.diag(precision_)).sum())
    return cost


def _dual_gap(emp_cov, precision_, alpha):
    """Expression of the dual gap convergence criterion

    The specific definition is given in Duchi "Projected Subgradient Methods
    for Learning Sparse Gaussians".
    """
    gap = np.sum(emp_cov * precision_)
    gap -= precision_.shape[0]
    gap += alpha * (np.abs(precision_).sum()
                    - np.abs(np.diag(precision_)).sum())
    return gap


def alpha_max(emp_cov):
    """Find the maximum alpha for which there are some non-zeros off-diagonal.

    Parameters
    ----------
    emp_cov : 2D array, (n_features, n_features)
        The sample covariance matrix

    Notes
    -----

    This results from the bound for the all the Lasso that are solved
    in GraphLasso: each time, the row of cov corresponds to Xy. As the
    bound for alpha is given by `max(abs(Xy))`, the result follows.

    """
    A = np.copy(emp_cov)
    A.flat[::A.shape[0] + 1] = 0
    return np.max(np.abs(A))


# The g-lasso algorithm

def graph_lasso(emp_cov, alpha, cov_init=None, mode='cd', tol=1e-4,
                enet_tol=1e-4, max_iter=100, verbose=False,
                return_costs=False, eps=np.finfo(np.float64).eps,
                return_n_iter=False):
    """l1-penalized covariance estimator

    Read more in the :ref:`User Guide <sparse_inverse_covariance>`.

    Parameters
    ----------
    emp_cov : 2D ndarray, shape (n_features, n_features)
        Empirical covariance from which to compute the covariance estimate.

    alpha : positive float
        The regularization parameter: the higher alpha, the more
        regularization, the sparser the inverse covariance.

    cov_init : 2D array (n_features, n_features), optional
        The initial guess for the covariance.

    mode : {'cd', 'lars'}
        The Lasso solver to use: coordinate descent or LARS. Use LARS for
        very sparse underlying graphs, where p > n. Elsewhere prefer cd
        which is more numerically stable.

    tol : positive float, optional
        The tolerance to declare convergence: if the dual gap goes below
        this value, iterations are stopped.

    enet_tol : positive float, optional
        The tolerance for the elastic net solver used to calculate the descent
        direction. This parameter controls the accuracy of the search direction
        for a given column update, not of the overall parameter estimate. Only
        used for mode='cd'.

    max_iter : integer, optional
        The maximum number of iterations.

    verbose : boolean, optional
        If verbose is True, the objective function and dual gap are
        printed at each iteration.

    return_costs : boolean, optional
        If return_costs is True, the objective function and dual gap
        at each iteration are returned.

    eps : float, optional
        The machine-precision regularization in the computation of the
        Cholesky diagonal factors. Increase this for very ill-conditioned
        systems.

    return_n_iter : bool, optional
        Whether or not to return the number of iterations.

    Returns
    -------
    covariance : 2D ndarray, shape (n_features, n_features)
        The estimated covariance matrix.

    precision : 2D ndarray, shape (n_features, n_features)
        The estimated (sparse) precision matrix.

    costs : list of (objective, dual_gap) pairs
        The list of values of the objective function and the dual gap at
        each iteration. Returned only if return_costs is True.

    n_iter : int
        Number of iterations. Returned only if `return_n_iter` is set to True.

    See Also
    --------
    GraphLasso, GraphLassoCV

    Notes
    -----
    The algorithm employed to solve this problem is the GLasso algorithm,
    from the Friedman 2008 Biostatistics paper. It is the same algorithm
    as in the R `glasso` package.

    One possible difference with the `glasso` R package is that the
    diagonal coefficients are not penalized.

    """
    _, n_features = emp_cov.shape
    if alpha == 0:
        if return_costs:
            precision_ = linalg.inv(emp_cov)
            cost = - 2. * log_likelihood(emp_cov, precision_)
            cost += n_features * np.log(2 * np.pi)
            d_gap = np.sum(emp_cov * precision_) - n_features
            if return_n_iter:
                return emp_cov, precision_, (cost, d_gap), 0
            else:
                return emp_cov, precision_, (cost, d_gap)
        else:
            if return_n_iter:
                return emp_cov, linalg.inv(emp_cov), 0
            else:
                return emp_cov, linalg.inv(emp_cov)
    if cov_init is None:
        covariance_ = emp_cov.copy()
    else:
        covariance_ = cov_init.copy()
    # As a trivial regularization (Tikhonov like), we scale down the
    # off-diagonal coefficients of our starting point: This is needed, as
    # in the cross-validation the cov_init can easily be
    # ill-conditioned, and the CV loop blows. Beside, this takes
    # conservative stand-point on the initial conditions, and it tends to
    # make the convergence go faster.
    covariance_ *= 0.95
    diagonal = emp_cov.flat[::n_features + 1]
    covariance_.flat[::n_features + 1] = diagonal
    precision_ = linalg.pinvh(covariance_)

    indices = np.arange(n_features)
    costs = list()
    # The different l1 regression solver have different numerical errors
    if mode == 'cd':
        errors = dict(over='raise', invalid='ignore')
    else:
        errors = dict(invalid='raise')
    try:
        # be robust to the max_iter=0 edge case, see:
        # https://github.com/scikit-learn/scikit-learn/issues/4134
        d_gap = np.inf
        for i in range(max_iter):
            for idx in range(n_features):
                sub_covariance = np.ascontiguousarray(
                    covariance_[indices != idx].T[indices != idx])
                row = emp_cov[idx, indices != idx]
                with np.errstate(**errors):
                    if mode == 'cd':
                        # Use coordinate descent
                        coefs = -(precision_[indices != idx, idx]
                                  / (precision_[idx, idx] + 1000 * eps))
                        coefs, _, _, _ = cd_fast.enet_coordinate_descent_gram(
                            coefs, alpha, 0, sub_covariance, row, row,
                            max_iter, enet_tol, check_random_state(None), False)
                    else:
                        # Use LARS
                        _, _, coefs = lars_path(
                            sub_covariance, row, Xy=row, Gram=sub_covariance,
                            alpha_min=alpha / (n_features - 1), copy_Gram=True,
                            eps=eps, method='lars', return_path=False)
                # Update the precision matrix
                precision_[idx, idx] = (
                    1. / (covariance_[idx, idx]
                          - np.dot(covariance_[indices != idx, idx], coefs)))
                precision_[indices != idx, idx] = (- precision_[idx, idx]
                                                   * coefs)
                precision_[idx, indices != idx] = (- precision_[idx, idx]
                                                   * coefs)
                coefs = np.dot(sub_covariance, coefs)
                covariance_[idx, indices != idx] = coefs
                covariance_[indices != idx, idx] = coefs
            d_gap = _dual_gap(emp_cov, precision_, alpha)
            cost = _objective(emp_cov, precision_, alpha)
            if verbose:
                print(
                    '[graph_lasso] Iteration % 3i, cost % 3.2e, dual gap %.3e'
                    % (i, cost, d_gap))
            if return_costs:
                costs.append((cost, d_gap))
            if np.abs(d_gap) < tol:
                break
            if not np.isfinite(cost) and i > 0:
                raise FloatingPointError('Non SPD result: the system is '
                                         'too ill-conditioned for this solver')
        else:
            warnings.warn('graph_lasso: did not converge after %i iteration:'
                          ' dual gap: %.3e' % (max_iter, d_gap),
                          ConvergenceWarning)
    except FloatingPointError as e:
        e.args = (e.args[0]
                  + '. The system is too ill-conditioned for this solver',)
        raise e

    if return_costs:
        if return_n_iter:
            return covariance_, precision_, costs, i + 1
        else:
            return covariance_, precision_, costs
    else:
        if return_n_iter:
            return covariance_, precision_, i + 1
        else:
            return covariance_, precision_


class GraphLasso(EmpiricalCovariance):
    """Sparse inverse covariance estimation with an l1-penalized estimator.

    Read more in the :ref:`User Guide <sparse_inverse_covariance>`.

    Parameters
    ----------
    alpha : positive float, default 0.01
        The regularization parameter: the higher alpha, the more
        regularization, the sparser the inverse covariance.

    mode : {'cd', 'lars'}, default 'cd'
        The Lasso solver to use: coordinate descent or LARS. Use LARS for
        very sparse underlying graphs, where p > n. Elsewhere prefer cd
        which is more numerically stable.

    tol : positive float, default 1e-4
        The tolerance to declare convergence: if the dual gap goes below
        this value, iterations are stopped.

    enet_tol : positive float, optional
        The tolerance for the elastic net solver used to calculate the descent
        direction. This parameter controls the accuracy of the search direction
        for a given column update, not of the overall parameter estimate. Only
        used for mode='cd'.

    max_iter : integer, default 100
        The maximum number of iterations.

    verbose : boolean, default False
        If verbose is True, the objective function and dual gap are
        plotted at each iteration.

    assume_centered : boolean, default False
        If True, data are not centered before computation.
        Useful when working with data whose mean is almost, but not exactly
        zero.
        If False, data are centered before computation.

    Attributes
    ----------
    covariance_ : array-like, shape (n_features, n_features)
        Estimated covariance matrix

    precision_ : array-like, shape (n_features, n_features)
        Estimated pseudo inverse matrix.

    n_iter_ : int
        Number of iterations run.

    See Also
    --------
    graph_lasso, GraphLassoCV
    """

    def __init__(self, alpha=.01, mode='cd', tol=1e-4, enet_tol=1e-4,
                 max_iter=100, verbose=False, assume_centered=False):
        super(GraphLasso, self).__init__(assume_centered=assume_centered)
        self.alpha = alpha
        self.mode = mode
        self.tol = tol
        self.enet_tol = enet_tol
        self.max_iter = max_iter
        self.verbose = verbose

    def fit(self, X, y=None):
        """Fits the GraphLasso model to X.

        Parameters
        ----------
        X : ndarray, shape (n_samples, n_features)
            Data from which to compute the covariance estimate
        y : (ignored)
        """
        # Covariance does not make sense for a single feature
        X = check_array(X, ensure_min_features=2, ensure_min_samples=2,
                        estimator=self)

        if self.assume_centered:
            self.location_ = np.zeros(X.shape[1])
        else:
            self.location_ = X.mean(0)
        emp_cov = empirical_covariance(
            X, assume_centered=self.assume_centered)
        self.covariance_, self.precision_, self.n_iter_ = graph_lasso(
            emp_cov, alpha=self.alpha, mode=self.mode, tol=self.tol,
            enet_tol=self.enet_tol, max_iter=self.max_iter,
            verbose=self.verbose, return_n_iter=True)
        return self


# Cross-validation with GraphLasso
def graph_lasso_path(X, alphas, cov_init=None, X_test=None, mode='cd',
                     tol=1e-4, enet_tol=1e-4, max_iter=100, verbose=False):
    """l1-penalized covariance estimator along a path of decreasing alphas

    Read more in the :ref:`User Guide <sparse_inverse_covariance>`.

    Parameters
    ----------
    X : 2D ndarray, shape (n_samples, n_features)
        Data from which to compute the covariance estimate.

    alphas : list of positive floats
        The list of regularization parameters, decreasing order.

    X_test : 2D array, shape (n_test_samples, n_features), optional
        Optional test matrix to measure generalisation error.

    mode : {'cd', 'lars'}
        The Lasso solver to use: coordinate descent or LARS. Use LARS for
        very sparse underlying graphs, where p > n. Elsewhere prefer cd
        which is more numerically stable.

    tol : positive float, optional
        The tolerance to declare convergence: if the dual gap goes below
        this value, iterations are stopped.

    enet_tol : positive float, optional
        The tolerance for the elastic net solver used to calculate the descent
        direction. This parameter controls the accuracy of the search direction
        for a given column update, not of the overall parameter estimate. Only
        used for mode='cd'.

    max_iter : integer, optional
        The maximum number of iterations.

    verbose : integer, optional
        The higher the verbosity flag, the more information is printed
        during the fitting.

    Returns
    -------
    covariances_ : List of 2D ndarray, shape (n_features, n_features)
        The estimated covariance matrices.

    precisions_ : List of 2D ndarray, shape (n_features, n_features)
        The estimated (sparse) precision matrices.

    scores_ : List of float
        The generalisation error (log-likelihood) on the test data.
        Returned only if test data is passed.
    """
    inner_verbose = max(0, verbose - 1)
    emp_cov = empirical_covariance(X)
    if cov_init is None:
        covariance_ = emp_cov.copy()
    else:
        covariance_ = cov_init
    covariances_ = list()
    precisions_ = list()
    scores_ = list()
    if X_test is not None:
        test_emp_cov = empirical_covariance(X_test)

    for alpha in alphas:
        try:
            # Capture the errors, and move on
            covariance_, precision_ = graph_lasso(
                emp_cov, alpha=alpha, cov_init=covariance_, mode=mode, tol=tol,
                enet_tol=enet_tol, max_iter=max_iter, verbose=inner_verbose)
            covariances_.append(covariance_)
            precisions_.append(precision_)
            if X_test is not None:
                this_score = log_likelihood(test_emp_cov, precision_)
        except FloatingPointError:
            this_score = -np.inf
            covariances_.append(np.nan)
            precisions_.append(np.nan)
        if X_test is not None:
            if not np.isfinite(this_score):
                this_score = -np.inf
            scores_.append(this_score)
        if verbose == 1:
            sys.stderr.write('.')
        elif verbose > 1:
            if X_test is not None:
                print('[graph_lasso_path] alpha: %.2e, score: %.2e'
                      % (alpha, this_score))
            else:
                print('[graph_lasso_path] alpha: %.2e' % alpha)
    if X_test is not None:
        return covariances_, precisions_, scores_
    return covariances_, precisions_


class GraphLassoCV(GraphLasso):
    """Sparse inverse covariance w/ cross-validated choice of the l1 penalty

    Read more in the :ref:`User Guide <sparse_inverse_covariance>`.

    Parameters
    ----------
    alphas : integer, or list positive float, optional
        If an integer is given, it fixes the number of points on the
        grids of alpha to be used. If a list is given, it gives the
        grid to be used. See the notes in the class docstring for
        more details.

    n_refinements : strictly positive integer
        The number of times the grid is refined. Not used if explicit
        values of alphas are passed.

    cv : int, cross-validation generator or an iterable, optional
        Determines the cross-validation splitting strategy.
        Possible inputs for cv are:

        - None, to use the default 3-fold cross-validation,
        - integer, to specify the number of folds.
        - An object to be used as a cross-validation generator.
        - An iterable yielding train/test splits.

        For integer/None inputs :class:`KFold` is used.

        Refer :ref:`User Guide <cross_validation>` for the various
        cross-validation strategies that can be used here.

    tol : positive float, optional
        The tolerance to declare convergence: if the dual gap goes below
        this value, iterations are stopped.

    enet_tol : positive float, optional
        The tolerance for the elastic net solver used to calculate the descent
        direction. This parameter controls the accuracy of the search direction
        for a given column update, not of the overall parameter estimate. Only
        used for mode='cd'.

    max_iter : integer, optional
        Maximum number of iterations.

    mode : {'cd', 'lars'}
        The Lasso solver to use: coordinate descent or LARS. Use LARS for
        very sparse underlying graphs, where number of features is greater
        than number of samples. Elsewhere prefer cd which is more numerically
        stable.

    n_jobs : int, optional
        number of jobs to run in parallel (default 1).

    verbose : boolean, optional
        If verbose is True, the objective function and duality gap are
        printed at each iteration.

    assume_centered : Boolean
        If True, data are not centered before computation.
        Useful when working with data whose mean is almost, but not exactly
        zero.
        If False, data are centered before computation.

    Attributes
    ----------
    covariance_ : numpy.ndarray, shape (n_features, n_features)
        Estimated covariance matrix.

    precision_ : numpy.ndarray, shape (n_features, n_features)
        Estimated precision matrix (inverse covariance).

    alpha_ : float
        Penalization parameter selected.

    cv_alphas_ : list of float
        All penalization parameters explored.

    grid_scores_ : 2D numpy.ndarray (n_alphas, n_folds)
        Log-likelihood score on left-out data across folds.

    n_iter_ : int
        Number of iterations run for the optimal alpha.

    See Also
    --------
    graph_lasso, GraphLasso

    Notes
    -----
    The search for the optimal penalization parameter (alpha) is done on an
    iteratively refined grid: first the cross-validated scores on a grid are
    computed, then a new refined grid is centered around the maximum, and so
    on.

    One of the challenges which is faced here is that the solvers can
    fail to converge to a well-conditioned estimate. The corresponding
    values of alpha then come out as missing values, but the optimum may
    be close to these missing values.
    """

    def __init__(self, alphas=4, n_refinements=4, cv=None, tol=1e-4,
                 enet_tol=1e-4, max_iter=100, mode='cd', n_jobs=1,
                 verbose=False, assume_centered=False):
        super(GraphLassoCV, self).__init__(
            mode=mode, tol=tol, verbose=verbose, enet_tol=enet_tol,
            max_iter=max_iter, assume_centered=assume_centered)
        self.alphas = alphas
        self.n_refinements = n_refinements
        self.cv = cv
        self.n_jobs = n_jobs

    @property
    @deprecated("Attribute grid_scores was deprecated in version 0.19 and "
                "will be removed in 0.21. Use ``grid_scores_`` instead")
    def grid_scores(self):
        return self.grid_scores_

    def fit(self, X, y=None):
        """Fits the GraphLasso covariance model to X.

        Parameters
        ----------
        X : ndarray, shape (n_samples, n_features)
            Data from which to compute the covariance estimate
        y : (ignored)
        """
        # Covariance does not make sense for a single feature
        X = check_array(X, ensure_min_features=2, estimator=self)
        if self.assume_centered:
            self.location_ = np.zeros(X.shape[1])
        else:
            self.location_ = X.mean(0)
        emp_cov = empirical_covariance(
            X, assume_centered=self.assume_centered)

        cv = check_cv(self.cv, y, classifier=False)

        # List of (alpha, scores, covs)
        path = list()
        n_alphas = self.alphas
        inner_verbose = max(0, self.verbose - 1)

        if isinstance(n_alphas, collections.Sequence):
            alphas = self.alphas
            n_refinements = 1
        else:
            n_refinements = self.n_refinements
            alpha_1 = alpha_max(emp_cov)
            alpha_0 = 1e-2 * alpha_1
            alphas = np.logspace(np.log10(alpha_0), np.log10(alpha_1),
                                 n_alphas)[::-1]

        t0 = time.time()
        for i in range(n_refinements):
            with warnings.catch_warnings():
                # No need to see the convergence warnings on this grid:
                # they will always be points that will not converge
                # during the cross-validation
                warnings.simplefilter('ignore', ConvergenceWarning)
                # Compute the cross-validated loss on the current grid

                # NOTE: Warm-restarting graph_lasso_path has been tried, and
                # this did not allow to gain anything (same execution time with
                # or without).
                this_path = Parallel(
                    n_jobs=self.n_jobs,
                    verbose=self.verbose
                )(delayed(graph_lasso_path)(X[train], alphas=alphas,
                                            X_test=X[test], mode=self.mode,
                                            tol=self.tol,
                                            enet_tol=self.enet_tol,
                                            max_iter=int(.1 * self.max_iter),
                                            verbose=inner_verbose)
                  for train, test in cv.split(X, y))

            # Little danse to transform the list in what we need
            covs, _, scores = zip(*this_path)
            covs = zip(*covs)
            scores = zip(*scores)
            path.extend(zip(alphas, scores, covs))
            path = sorted(path, key=operator.itemgetter(0), reverse=True)

            # Find the maximum (avoid using built in 'max' function to
            # have a fully-reproducible selection of the smallest alpha
            # in case of equality)
            best_score = -np.inf
            last_finite_idx = 0
            for index, (alpha, scores, _) in enumerate(path):
                this_score = np.mean(scores)
                if this_score >= .1 / np.finfo(np.float64).eps:
                    this_score = np.nan
                if np.isfinite(this_score):
                    last_finite_idx = index
                if this_score >= best_score:
                    best_score = this_score
                    best_index = index

            # Refine the grid
            if best_index == 0:
                # We do not need to go back: we have chosen
                # the highest value of alpha for which there are
                # non-zero coefficients
                alpha_1 = path[0][0]
                alpha_0 = path[1][0]
            elif (best_index == last_finite_idx
                    and not best_index == len(path) - 1):
                # We have non-converged models on the upper bound of the
                # grid, we need to refine the grid there
                alpha_1 = path[best_index][0]
                alpha_0 = path[best_index + 1][0]
            elif best_index == len(path) - 1:
                alpha_1 = path[best_index][0]
                alpha_0 = 0.01 * path[best_index][0]
            else:
                alpha_1 = path[best_index - 1][0]
                alpha_0 = path[best_index + 1][0]

            if not isinstance(n_alphas, collections.Sequence):
                alphas = np.logspace(np.log10(alpha_1), np.log10(alpha_0),
                                     n_alphas + 2)
                alphas = alphas[1:-1]

            if self.verbose and n_refinements > 1:
                print('[GraphLassoCV] Done refinement % 2i out of %i: % 3is'
                      % (i + 1, n_refinements, time.time() - t0))

        path = list(zip(*path))
        grid_scores = list(path[1])
        alphas = list(path[0])
        # Finally, compute the score with alpha = 0
        alphas.append(0)
        grid_scores.append(cross_val_score(EmpiricalCovariance(), X,
                                           cv=cv, n_jobs=self.n_jobs,
                                           verbose=inner_verbose))
        self.grid_scores_ = np.array(grid_scores)
        best_alpha = alphas[best_index]
        self.alpha_ = best_alpha
        self.cv_alphas_ = alphas

        # Finally fit the model with the selected alpha
        self.covariance_, self.precision_, self.n_iter_ = graph_lasso(
            emp_cov, alpha=best_alpha, mode=self.mode, tol=self.tol,
            enet_tol=self.enet_tol, max_iter=self.max_iter,
            verbose=inner_verbose, return_n_iter=True)
        return self