Skip the cell-type labels: NetMap reads regulatory networks and cell identity together from mixed single-cell data
Regulatory network inference no longer needs cell types called first. Earlier pipelines clustered cells, annotated types with marker genes, then inferred one network per cluster, so clustering and annotation errors propagated into the network. NetMap infers a gene regulatory network per cell before any clustering, uses GradientShap to attribute network edges to input genes, and reaches clustering scores of 1.0, 0.99 and 0.99 across three PBMC multiome evaluation cases.