SOTA perturb models struggle to generalize beyond training perturbations, says Kundaje

anshulkundaje · x · 2026-10-06

In post 9 of his scFM critique thread, Anshul Kundaje writes that SOTA perturbation models continue to struggle to generalize beyond the range of their perturbation training data and prior knowledge. He says this is fine but important to recognize given the learning strategy used — building on his earlier point that the models' predictive power largely comes from prior knowledge rather than learned causal mechanisms.

Related event: Stanford's Kundaje Attacks Single-Cell Foundation Models and 'Virtual Cell' Hype in 12-Tweet Thread(12 posts)→

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