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Shuangjia Zheng

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#machine learning Preprint Sep 2026

M3OS: A Monte Carlo Graph Search-Orchestrated Multi-Agent LLM System for Evidence-Traced Molecular Optimization

M3OS is presented, a multi-agent LLM system that decouples molecular-design reasoning from optimization-state management through Monte Carlo graph search, and achieves higher success rates than baselines, supporting the integration of persistent search state, specialized agents and controlled execution for multi-constr...

Jun-Jie Wang, Yao-Wei Jin, Ruo-Hui Tang et al. · 0 citations
Jul 2026

EnerBridge-DPO: Energy-Aware Markov Bridge Inverse Folding for Protein Sequence Design

EnerBridge-DPO, an energy-aware inverse folding framework that integrates Markov bridge sequence generation with preference optimization for protein complex design, suggests that incorporating energy-related preferences into Markov bridge inverse folding can improve computationally predicted energetic profiles.

Dingyi Rong, Haotian Lu, Xupeng Zhang et al. · 0 citations

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