Fig. 2: Silhouette-based metrics are unreliable for assessing bio-conservation and batch effect removal.
From: Shortcomings of silhouette in single-cell integration benchmarking
a, Uniform manifold approximation and projections (UMAPs) of NeurIPS minimal example embeddings integrated with increasing success, colored by cell type and sample. b,d, Batch removal metrics: batch ASW, BRAS and an alternative cell-type-adjusted diversity score, CiLISI. Bio-conservation metrics: cell type ASW and ARI. c, UMAPs of healthy HLCA embeddings integrated with increasing success colored by cell type and dataset, shown for a consistent random 10% data subset. Suboptimal embeddings were obtained through batch-aware HVG selection for specified batch variables.
