arXiv:2603.11703 · v3
EvoFlows: Evolutionary Edit-Based Flow-Matching for Protein Engineering
摘要
Protein optimization improves an existing protein through targeted mutations, but existing protein language models are poorly suited to it: autoregressive models require full sequence generation, masked language and discrete diffusion models rely on pre-specified mutation locations, and none naturally support insertions and deletions relative to a template. We introduce EvoFlows, a variable-length sequence-to-sequence approach that learns mutational trajectories between evolutionarily related proteins via edit flows, predicting not only _which_ mutation to perform, but also _where_ and _how many_ should occur. Across diverse protein families from UniRef and OAS, EvoFlows generates variants that remain consistent with natural families while exploring farther from the template than leading baselines. _In vitro_ validation of a VHH binder and an enzyme confirms that the large majority of generated variants remain functional and stable without computational downselection.
作者备注：Accepted at Workshop on Foundation Models for Science: Real-World Impact and Science-First Design, ICLR 2026; Published at the 21st Machine Learning in Computational Biology (MLCB 2026)