Author

Mingrui Li

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Preprint Jul 2026

Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs

Experiments show that AP-REASONER outperforms baseline subsamplers on structure-sensitive downstream tasks and enables controllable recovery of alternative protein conformations, highlighting the value of modeling MSA subsampling as a controllable optimization problem, where factor-graph reasoning offers an effective alternative to heuristic selection.

Zhangzhi Xiong, Minzhang Li, Hao Yu et al. · 0 citations