ExPert paper inverts perturbation models to trace cell states back to causal causes
anshulkundaje · x · 2026-11-06
A Northwestern University team (Yogesh Goyal lab) released ExPert on bioRxiv. While most perturbation models answer the forward question "if I knock out gene X, what happens?", ExPert solves the inverse: given a disease state, infer what perturbation drove it.
- Inverts the problem: identifies causal perturbations from measured cell states across genes, combinations, donor tissue, and drug-screen contexts.
- Architecture combines knowledge-graph priors (UniProt, PPI, depmap) for zero-shot encoding with a prototype-based encoder-decoder.
- Demonstrated on real cases: tracing patient cells to hidden liver-disease biology and mitochondrial defects underlying blood phenotypes.
- Authors report utility on unseen measured states with increasing difficulty.
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