By visualizing the output activations for individual cells, SCEMILA revealed AML subtype-specific cell clusters (Fig 3D): While PML::RARA cells (orange) formed two isolated promyeloid clusters, two types of NPM1 blasts appeared (red) that partly overlapped with RUNX1::RUNX1T1 blasts (blue). The gene discussed is RUNX1; the disease is acute myeloid leukemia.