scib_metrics.benchmark.BioConservation

class scib_metrics.benchmark.BioConservation(isolated_labels=True, nmi_ari_cluster_labels_leiden=False, nmi_ari_cluster_labels_kmeans=True, silhouette_label=True, clisi_knn=True)

Specification of bio conservation metrics to run in the pipeline.

Metrics can be included using a boolean flag. Custom keyword args can be used by passing a dictionary here. Keyword args should not set data-related parameters, such as X or labels.

Attributes table

clisi_knn
isolated_labels
nmi_ari_cluster_labels_kmeans
nmi_ari_cluster_labels_leiden
silhouette_label

Methods table

Attributes

BioConservation.clisi_knn: Union[bool, dict[str, Any]] = True

BioConservation.isolated_labels: Union[bool, dict[str, Any]] = True

BioConservation.nmi_ari_cluster_labels_kmeans: Union[bool, dict[str, Any]] = True

BioConservation.nmi_ari_cluster_labels_leiden: Union[bool, dict[str, Any]] = False

BioConservation.silhouette_label: Union[bool, dict[str, Any]] = True

Methods