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cs.LG2026
Retrieval-Augmented Foundation Models for Matched Molecular Pair Transformations to Recapitulate Medicinal Chemistry Intuition
Bo Pan, Peter Zhiping Zhang, Hao-Wei Pang +4
Matched molecular pairs (MMPs) capture the local chemical edits that medicinal chemists routinely use to design analogs, but existing ML approaches either operate at the whole-mole…
cs.LG2025
PepEVOLVE: Position-Aware Dynamic Peptide Optimization via Group-Relative Advantage
Trieu Nguyen, Hao-Wei Pang, Shasha Feng
Macrocyclic peptides are an emerging modality that combines biologics-like affinity with small-molecule-like developability, but their vast combinatorial space and multi-parameter…
cs.LG2025★ 3 cited
PepThink-R1: LLM for Interpretable Cyclic Peptide Optimization with CoT SFT and Reinforcement Learning
Ruheng Wang, Hang Zhang, Trieu Nguyen +5
Designing therapeutic peptides with tailored properties is hindered by the vastness of sequence space, limited experimental data, and poor interpretability of current generative mo…