PRISM

Phenotype-Resolved Inference in Single-cell Mixed models via latent disease states and contextualized differential expression

Not every cell from a disease donor is in a disease state. PRISM is a negative-binomial mixed model for multi-donor single-cell RNA-seq. For each cell of a disease donor it infers the posterior probability q that the cell is in the disease state (cells from control donors are fixed to the healthy state). It then estimates, per gene, a constant disease effect alpha and its modulation by cell-level context z, theta. Parameters are fit by EM.

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Citation

PRISM: Phenotype-Resolved Inference in Single-Cell Mixed Models via Latent Disease States and Contextualized Differential Expression. NeurIPS 2026. The BibTeX entry will be added here when the proceedings are online.