Reduced paired overlap reveals an anchor threshold. Paired 10x Genomics Multiome PBMCs were evaluated under an overlap sweep that reduced the fraction of paired RNA–ATAC anchors (Supplemental Methods), either by dropping ATAC (Drop ATAC, blue) or dropping RNA (Drop RNA, orange). Lines show means across cross-validation replicates with uncertainty bands. (A) Paired correspondence (FOSCTTM; lower is better). (B,C) Paired retrieval (Recall@1, Recall@10; higher is better). (D) Cross-modality semantic consistency (bidirectional k-NN label transfer macro-F1; higher is better). (E,F) Fused-space biological structure (k-means NMI, ARI; higher is better). (G) Schematic summary of low-anchor collapse, modest-overlap stabilization, and high-overlap saturation.