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Equi-mRNA: the first codon-level equivariant mRNA language model

Our paper encodes synonymous-codon symmetry directly into the representation as SO(2) cyclic subgroups, rather than leaving a language model to infer it from data.

DDeepBio ScientificDeepBio ScientificAug 21, 2025 · 1 min read

Equi-mRNA is a codon-level equivariant language model for mRNA. Synonymous codons are mapped to cyclic subgroups of SO(2), so codon substitutions that preserve amino-acid identity become rotations the model is equivariant to by construction, held in place by an auxiliary equivariance loss and symmetry-aware pooling.

The paper is on arXiv (2508.15103). Architecture, benchmarks against named baselines and the biological interpretability analyses are on the model card.

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