A leakage-controlled benchmark shows apparent codon-language-model advantages in synonymous-variant prediction are evaluation artifacts
Synonymous codon choices shape mRNA stability, translation, and folding, and codon language models (cLMs) are increasingly reported to read this biology from sequence. However, when a true signal is thin relative to a confounding one, standard evaluation protocols can manufacture the reported gain rather than measure it, and we show this is what has happened for cLMs on synonymous-variant…
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