Note
This page is a reference documentation. It only explains the class signature, and not how to use it. Please refer to the user guide for the big picture.
nilearn.connectome.GroupSparseCovarianceCV#
- class nilearn.connectome.GroupSparseCovarianceCV(alphas=4, n_refinements=4, cv=None, tol_cv=0.01, max_iter_cv=50, tol=0.001, max_iter=100, verbose=0, n_jobs=1, debug=False, early_stopping=True)[source]#
Sparse inverse covariance w/ cross-validated choice of the parameter.
A cross-validated value for the regularization parameter is first determined using several calls to group_sparse_covariance. Then a final optimization is run to get a value for the precision matrices, using the selected value of the parameter. Different values of tolerance and of maximum iteration number can be used in these two phases (see the tol and tol_cv keyword below for example).
- Parameters
- alphasinteger, optional
initial number of points in the grid of regularization parameter values. Each step of grid refinement adds that many points as well. Default=4.
- n_refinementsinteger, optional
number of times the initial grid should be refined. Default=4.
- cvinteger, optional
number of folds in a K-fold cross-validation scheme. If None is passed, defaults to 3.
- tol_cvfloat, optional
tolerance used to get the optimal alpha value. It has the same meaning as the tol parameter in
group_sparse_covariance. Default=1e-2.- max_iter_cvinteger, optional
maximum number of iterations for each optimization, during the alpha- selection phase. Default=50.
- tolfloat, optional
tolerance used during the final optimization for determining precision matrices value. Default=1e-3.
- max_iterinteger, optional
maximum number of iterations in the final optimization. Default=100.
- verboseinteger, optional
verbosity level. 0 means nothing is printed to the user. Default=0.
- n_jobsinteger, optional
maximum number of cpu cores to use. The number of cores actually used at the same time cannot exceed the number of folds in folding strategy (that is, the value of cv). Default=1.
- debugbool, optional
if True, activates some internal checks for consistency. Only useful for nilearn developers, not users. Default=False.
- early_stoppingbool, optional
if True, reduce computation time by using a heuristic to reduce the number of iterations required to get the optimal value for alpha. Be aware that this can lead to slightly different values for the optimal alpha compared to early_stopping=False. Default=True.
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.
- Attributes
- `covariances_`numpy.ndarray, shape (n_features, n_features, n_subjects)
covariance matrices, one per subject.
- `precisions_`numpy.ndarray, shape (n_features, n_features, n_subjects)
precision matrices, one per subject. All matrices have the same sparsity pattern (if a coefficient is zero for a given matrix, it is also zero for every other.)
- `alpha_`float
penalization parameter value selected.
- `cv_alphas_`list of floats
all values of the penalization parameter explored.
- `cv_scores_`numpy.ndarray, shape (n_alphas, n_folds)
scores obtained on test set for each value of the penalization parameter explored.
- __init__(alphas=4, n_refinements=4, cv=None, tol_cv=0.01, max_iter_cv=50, tol=0.001, max_iter=100, verbose=0, n_jobs=1, debug=False, early_stopping=True)[source]#
- fit(subjects, y=None)[source]#
Compute cross-validated group-sparse precisions.
- Parameters
- subjectslist of numpy.ndarray with shapes (n_samples, n_features)
input subjects. Each subject is a 2D array, whose columns contain signals. Sample number can vary from subject to subject, but all subjects must have the same number of features (i.e. of columns.)
- Returns
- selfGroupSparseCovarianceCV
the object instance itself.
- get_params(deep=True)#
Get parameters for this estimator.
- Parameters
- deepbool, default=True
If True, will return the parameters for this estimator and contained subobjects that are estimators.
- Returns
- paramsdict
Parameter names mapped to their values.
- set_params(**params)#
Set the parameters of this estimator.
The method works on simple estimators as well as on nested objects (such as
Pipeline). The latter have parameters of the form<component>__<parameter>so that it’s possible to update each component of a nested object.- Parameters
- **paramsdict
Estimator parameters.
- Returns
- selfestimator instance
Estimator instance.
Examples using nilearn.connectome.GroupSparseCovarianceCV#
Connectivity structure estimation on simulated data
Group Sparse inverse covariance for multi-subject connectome