AI-for-science debate: phenotype readouts matter more than gene-by-gene reconstruction
fabian_theis · x · 2026-10-10
Computational biologist Fabian Theis and Stanford professor Anshul Kundaje debate training objectives for perturbation-prediction models. Theis argues the phenotypic readout h does much of the work—genes irrelevant to the measured phenotype don't need accurate reconstruction—though generating realistic perturbed cells acts as a regularizer. Kundaje calls this better-defined than raw perturbation prediction and suggests modeling in latent space, since single-cell measurements are so noisy.
Related event: Theis and Kundaje Debate Phenotype-First Perturbation Modeling(4 posts)→
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