Kundaje: unreported baseline tweaks like weighted means could beat fine-tuned scFMs

anshulkundaje · x · 2026-10-06

In post 6 of his scFM critique thread, Anshul Kundaje notes that the paper apparently doesn't report minor baseline improvements — e.g. weighted means, or linear models trained directly on WMSE — which could potentially make these trivial baselines more powerful and further undermine the case for fine-tuned scFMs. He adds he may have missed such reports.

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

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