Fig. 3. Cell embedding and clustering benchmark in complex and heterogeneous datasets.

A Schematic representation of the benchmarking process; B The first three columns of this panel are devoted to silhouette scores, Adjusted Rand Indices (ARIs), and purity scores for the different methods on five complex paired single-cell multi-omics data already largely used to benchmark integrative methods. The following six columns provide UMAP visualizations for the six benchmarked methods (Mowgli, MOFA+, NMF, Seurat v4, Multigrate, Cobolt) on the same data. Different colors in these UMAP plots correspond to the different ground truth cell type annotations provided with the data.