Metrics

Metrics computed for the scRNA pipelines benchmark.

Agreement metrics

Reported agreement of Leiden and Louvain predicted clusters with true labels:

• Adjusted Rand Index
• Normalized Mutual Information
• Fowlkes-Mallows
• Homogeneity
• Completeness
• V-measure

Structure metrics

Computed on PCA coordinates for predicted clusters of Leiden and Louvain:

• Silhouette score
• Davies-Bouldin score
• Calinski-Harabasz score

Other outputs

• n_clusters: number of clusters for Leiden and Louvain
• dropped_cells: number of cells removed from agreement metrics computations due to missing truth labels
• timings: runtime breakdown from the pipeline, with louvain and leiden stored as average seconds per clustering invocation during resolution search
• clustering_info: clustering search metadata with resolutions and num_runs