A Multiome reference bridges independent unimodal RNA-only and ATAC-only PBMC cohorts. (A–C) Joint latent UMAP of Multiome reference (RNA+ATAC) with projected Ding (RNA-only) and Satpathy (ATAC-only) cells, colored by (A) data set/modality, (B) harmonized coarse PBMC label, and (C) technology/platform. (D–F) Same views after optional supervised refinement (classification head; decoders frozen), showing increased within-lineage cross-cohort co-localization. (G) Cross-cohort k-NN label transfer (k = 15) before (top) and after (bottom) refinement in both directions (Ding↔Satpathy). (H) Multiome bridge cells only, colored by modality. (I) Multiome bridge cells colored by predicted coarse label from the refinement head. (J) Marker-based validation in Multiome RNA (dot plot: fraction expressing and mean expression per predicted group).