pyriemann.classification.FgMDM

class pyriemann.classification.FgMDM(metric='riemann', tsupdate=False, n_jobs=1)

Classification by Minimum Distance to Mean with geodesic filtering.

Apply geodesic filtering described in [1], and classify using MDM. The geodesic filtering is achieved in tangent space with a Linear Discriminant Analysis, then data are projected back to the manifold and classifier with a regular MDM. This is basically a pipeline of FGDA and MDM.

Parameters:
metricstring | dict, default=”riemann”

Metric used for reference matrix estimation (for the list of supported metrics, see pyriemann.utils.mean.mean_covariance()), for distance estimation (see pyriemann.utils.distance.distance()) and for tangent space map (see pyriemann.utils.tangent_space.tangent_space()). The metric can be a dict with three keys, “mean”, “dist” and “map” in order to pass different metrics.

tsupdatebool, default=False

Activate tangent space update for covariante shift correction between training and test, as described in [2]. This is not compatible with online implementation. Performance are better when the number of matrices for prediction is higher.

n_jobsint, default=1

Number of jobs to use for the computation. This works by computing each of the class centroid in parallel. If -1 all CPUs are used. If 1 is given, no parallel computing code is used at all, which is useful for debugging. For n_jobs below -1, (n_cpus + 1 + n_jobs) are used. Thus for n_jobs = -2, all CPUs but one are used.

Attributes:
classes_ndarray, shape (n_classes,)

Labels for each class.

See also

MDM
FGDA
TangentSpace

References

[1]

Riemannian geometry applied to BCI classification A. Barachant, S. Bonnet, M. Congedo and C. Jutten. 9th International Conference Latent Variable Analysis and Signal Separation (LVA/ICA 2010), LNCS vol. 6365, 2010, p. 629-636.

[2]

Classification of covariance matrices using a Riemannian-based kernel for BCI applications A. Barachant, S. Bonnet, M. Congedo and C. Jutten. Neurocomputing, Elsevier, 2013, 112, pp.172-178.

__init__(metric='riemann', tsupdate=False, n_jobs=1)

Init.

fit(X, y, sample_weight=None)

Fit FgMDM.

Parameters:
Xndarray, shape (n_matrices, n_channels, n_channels)

Set of SPD matrices.

yndarray, shape (n_matrices,)

Labels for each matrix.

sample_weightNone | ndarray, shape (n_matrices,), default=None

Weights for each matrix. If None, it uses equal weights.

Returns:
selfFgMDM instance

The FgMDM instance.

fit_transform(X, y, sample_weight=None)

Fit and transform in a single function.

Parameters:
Xndarray, shape (n_matrices, n_channels, n_channels)

Set of SPD matrices.

yndarray, shape (n_matrices,)

Labels for each matrix.

sample_weightNone | ndarray, shape (n_matrices,), default=None

Weights for each matrix. If None, it uses equal weights.

Returns:
distndarray, shape (n_matrices, n_cluster)

Distance to each centroid according to the metric.

get_metadata_routing()

Get metadata routing of this object.

Please check User Guide on how the routing mechanism works.

Returns:
routingMetadataRequest

A MetadataRequest encapsulating routing information.

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.

predict(X)

Get the predictions after FGDA filtering.

Parameters:
Xndarray, shape (n_matrices, n_channels, n_channels)

Set of SPD matrices.

Returns:
predndarray of int, shape (n_matrices,)

Predictions for each matrix according to the nearest centroid.

predict_proba(X)

Predict proba using softmax after FGDA filtering.

Parameters:
Xndarray, shape (n_matrices, n_channels, n_channels)

Set of SPD matrices.

Returns:
probndarray, shape (n_matrices, n_classes)

The softmax probabilities for each class.

score(X, y, sample_weight=None)

Return the mean accuracy on the given test data and labels.

Parameters:
Xndarray, shape (n_matrices, n_channels, n_channels)

Test set of SPD matrices.

yndarray, shape (n_matrices,)

True labels for each matrix.

sample_weightNone | ndarray, shape (n_matrices,), default=None

Weights for each matrix.

Returns:
scorefloat

Mean accuracy of clf.predict(X) wrt. y.

set_fit_request(*, sample_weight: bool | None | str = '$UNCHANGED$') → FgMDM

Request metadata passed to the fit method.

Note that this method is only relevant if enable_metadata_routing=True (see sklearn.set_config()). Please see User Guide on how the routing mechanism works.

The options for each parameter are:

  • True: metadata is requested, and passed to fit if provided. The request is ignored if metadata is not provided.

  • False: metadata is not requested and the meta-estimator will not pass it to fit.

  • None: metadata is not requested, and the meta-estimator will raise an error if the user provides it.

  • str: metadata should be passed to the meta-estimator with this given alias instead of the original name.

The default (sklearn.utils.metadata_routing.UNCHANGED) retains the existing request. This allows you to change the request for some parameters and not others.

Added in version 1.3.

Note

This method is only relevant if this estimator is used as a sub-estimator of a meta-estimator, e.g. used inside a Pipeline. Otherwise it has no effect.

Parameters:
sample_weightstr, True, False, or None, default=sklearn.utils.metadata_routing.UNCHANGED

Metadata routing for sample_weight parameter in fit.

Returns:
selfobject

The updated object.

set_output(*, transform=None)

Set output container.

See Introducing the set_output API for an example on how to use the API.

Parameters:
transform{“default”, “pandas”, “polars”}, default=None

Configure output of transform and fit_transform.

  • “default”: Default output format of a transformer

  • “pandas”: DataFrame output

  • “polars”: Polars output

  • None: Transform configuration is unchanged

Added in version 1.4: “polars” option was added.

Returns:
selfestimator instance

Estimator instance.

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.

set_score_request(*, sample_weight: bool | None | str = '$UNCHANGED$') → FgMDM

Request metadata passed to the score method.

Note that this method is only relevant if enable_metadata_routing=True (see sklearn.set_config()). Please see User Guide on how the routing mechanism works.

The options for each parameter are:

  • True: metadata is requested, and passed to score if provided. The request is ignored if metadata is not provided.

  • False: metadata is not requested and the meta-estimator will not pass it to score.

  • None: metadata is not requested, and the meta-estimator will raise an error if the user provides it.

  • str: metadata should be passed to the meta-estimator with this given alias instead of the original name.

The default (sklearn.utils.metadata_routing.UNCHANGED) retains the existing request. This allows you to change the request for some parameters and not others.

Added in version 1.3.

Note

This method is only relevant if this estimator is used as a sub-estimator of a meta-estimator, e.g. used inside a Pipeline. Otherwise it has no effect.

Parameters:
sample_weightstr, True, False, or None, default=sklearn.utils.metadata_routing.UNCHANGED

Metadata routing for sample_weight parameter in score.

Returns:
selfobject

The updated object.

transform(X)

Get the distance to each centroid after FGDA filtering.

Parameters:
Xndarray, shape (n_matrices, n_channels, n_channels)

Set of SPD matrices.

Returns:
distndarray, shape (n_matrices, n_cluster)

Distance to each centroid according to the metric.

Examples using pyriemann.classification.FgMDM

Ensemble learning on functional connectivity

Ensemble learning on functional connectivity