arXiv:2505.20131cs.LGq-bio.QM2025-05被引 2

用离散扩散与强化学习实现精准分子编辑,保持结构不变同时优化化学属性。

MolEditRL: Structure-Preserving Molecular Editing via Discrete Diffusion and Reinforcement Learning

  • 基于离散图扩散模型生成分子,结合自然语言指令进行结构重建。
  • 通过强化学习优化编辑决策,在10种化学属性上实现74%成功率提升。
  • 适合药物设计与分子工程领域,参数量减少98%仍保持高性能。

分子编辑旨在修改现有分子以优化特定化学性质,同时保持结构相似性。然而,现有方法多依赖字符串或连续表示,难以捕捉分子的离散图结构特征,导致结构保真度低且控制能力差。本文提出MolEditRL框架,显式融合结构约束与精确属性优化。该框架包含两阶段:(1) 预训练的离散图扩散模型,根据源结构和自然语言指令重建目标分子;(2) 编辑感知的强化学习微调阶段,通过在图约束下优化编辑决策,进一步提升属性匹配与结构保留。为全面评估,我们构建了目前最大、最丰富的分子编辑数据集MolEdit-Instruct,包含300万条多样化样本,覆盖10种化学属性的单/多属性任务。实验表明,MolEditRL在属性优化准确率和结构保真度上显著优于当前最优方法,编辑成功率提升74%,同时仅使用98%更少的参数。

原文摘要 · Abstract (English)

Molecular editing aims to modify a given molecule to optimize desired chemical properties while preserving structural similarity. However, current approaches typically rely on string-based or continuous representations, which fail to adequately capture the discrete, graph-structured nature of molecules, resulting in limited structural fidelity and poor controllability. In this paper, we propose MolEditRL, a molecular editing framework that explicitly integrates structural constraints with precise property optimization. Specifically, MolEditRL consists of two stages: (1) a discrete graph diffusion model pretrained to reconstruct target molecules conditioned on source structures and natural language instructions; (2) an editing-aware reinforcement learning fine-tuning stage that further enhances property alignment and structural preservation by explicitly optimizing editing decisions under graph constraints. For comprehensive evaluation, we construct MolEdit-Instruct, the largest and most property-rich molecular editing dataset, comprising 3 million diverse examples spanning single- and multi-property tasks across 10 chemical attributes. Experimental results demonstrate that MolEditRL significantly outperforms state-of-the-art methods in both property optimization accuracy and structural fidelity, achieving a 74\% improvement in editing success rate while using 98\% fewer parameters.

分子编辑扩散模型强化学习药物设计

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