Peer-reviewed paper questions whether gene expression model benchmarks are informative
simocristea · x · 2026-10-02
A newly peer-reviewed paper formalizes a pointed question: are the benchmarks used to evaluate foundation models on gene expression data actually informative? Common evaluations rely on arithmetic-mean baselines averaged over thousands of genes, most irrelevant to the phenotype of interest — largely because real measurements of the target phenotype are often unavailable. A systematic critique of benchmark design for bio foundation models.
Related event: Nature Biotechnology paper challenges gene perturbation model benchmarks(2 posts)→
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