Sandeep Chowdary Vejandla

Single-cell multi-omics integration must place cells into one representation when only some cells have both RNA and chromatin accessibility measured, a mosaic design. Mosaic Cell Relation Factorization (MCRF) skips rebuilding molecular measurements and instead computes similarities between cells, then factorizes those relations into cell factors plus a separate weight matrix per modality, with paired cells sharing one set of factors across RNA and ATAC. On scMultiSim simulations, MCRF had higher median NMI than UINMF in 22 of 36 original configurations and than MIDAS in 28, often with smaller variation across simulation replicates; on 102 newly generated larger datasets, UINMF and MIDAS had higher median ARI in all 24 configurations with four replicates.

Single-cell multi-omics integration must place cells into one representation when only some cells have both RNA and chromatin accessibility measured, a mosaic design. Mosaic Cell Relation Factorization (MCRF) skips rebuilding molecular measurements and instead computes similarities between cells, then factorizes those relations into cell factors plus a separate weight matrix per modality, with paired cells sharing one set of factors across RNA and ATAC. On scMultiSim simulations, MCRF had higher median NMI than UINMF in 22 of 36 original configurations and than MIDAS in 28, often with smaller variation across simulation replicates; on 102 newly generated larger datasets, UINMF and MIDAS had higher median ARI in all 24 configurations with four replicates.