Fig. 3: Multi-omic velocity inference and comparison with MultiVelo.
a Inferred velocity streams on a UMAP colored by cell types (Top) or latent time (Bottom), from MultiVeloVAE (Left) or MultiVelo (Right). b Generated spliced mRNA values of PAX6, ENC1, and SAT1 as functions of latent time, from either MultiVeloVAE (Left) or MultiVelo (Right). c MultiVeloVAE inferred velocity streams on the HSPC UMAP colored by cell types (Left) or latent time (Right). d MultiVelo latent time inference result for HSPCs. e Uncertainty of cell states captured by MultiVeloVAE via variational inference. f Example modality priming pattern and distribution captured by MultiVeloVAE for Wnt3 gene in a mouse skin dataset. The arrows on UMAPs indicate the expected differentiation order. From left to right, the UMAPs are colored by the original chromatin accessibility, unspliced counts, spliced counts, and cell-state difference computed as kc − ρ. g Generalized CBDir scores across four datasets over 5 steps of neighbors (higher is better). The means are shown as solid lines, and credible intervals are shown as ribbons. The metric is computed on either the entire gene space (Left) or embedded space (Right) h Runtime comparison (n = 5) with MultiVelo. The boxes represent the interquartile ranges (IQRs), the middle line represents the median, and whiskers extend to 1.5 times the IQRs. Source data are provided as a Source Data file.
