arXiv:2509.16084cs.LG2025-09被引 9

通过迭代路径优化,让生成分子真正可合成。

Exploring Synthesizable Chemical Space with Iterative Pathway Refinements

  • 用统一模型双向生成合成路径,支持从底向上和从顶向下推理。
  • 在可合成分子重构任务中,重建率与路径多样性均领先。
  • 适合药物分子设计者探索海量可合成化合物空间。

分子生成模型常产生不可合成的分子。为解决此问题,本文提出ReaSyn框架,通过将输入分子投影到可合成空间,迭代优化合成路径。该框架采用简洁的合成路径表示,支持自回归模型同时生成底向和顶向路径,实现双向子树迭代精炼。此外引入离散流模型,在整条路径层面进行插入、删除、替换操作,完成全局编辑。迭代循环包括:底向解码、顶向解码与整体编辑,构成强大的路径推理策略,有效探索组合爆炸的可合成化学空间。实验显示,ReaSyn在可合成分子重构中达到最高重建率与路径多样性,在目标导向分子优化中表现最优,并显著优于以往可合成投影方法的命中扩展能力。结果表明其在大规模可合成化学空间导航中的卓越性能。

原文摘要 · Abstract (English)

A well-known pitfall of molecular generative models is that they are not guaranteed to generate synthesizable molecules. Existing solutions for this problem often struggle to effectively navigate exponentially large combinatorial space of synthesizable molecules and suffer from poor coverage. To address this problem, we introduce ReaSyn, an iterative generative pathway refinement framework that obtains synthesizable analogs to input molecules by projecting them onto synthesizable space. Specifically, we propose a simple synthetic pathway representation that allows for generating pathways in both bottom-up and top-down traversal of synthetic trees. We design ReaSyn so that both bottom-up and top-down pathways can be sampled with a single unified autoregressive model. ReaSyn can thus iteratively refine subtrees of generated synthetic trees in a bidirectional manner. Further, we introduce a discrete flow model that refines the generated pathway at the entire pathway level with edit operations: insertion, deletion, and substitution. The iterative refinement cycle of (1) bottom-up decoding, (2) top-down decoding, and (3) holistic editing constitutes a powerful pathway reasoning strategy, allowing the model to explore the vast space of synthesizable molecules. Experimentally, ReaSyn achieves the highest reconstruction rate and pathway diversity in synthesizable molecule reconstruction and the highest optimization performance in synthesizable goal-directed molecular optimization, and significantly outperforms previous synthesizable projection methods in synthesizable hit expansion. These results highlight ReaSyn's superior ability to navigate combinatorially-large synthesizable chemical space.

分子生成可合成性路径优化

Thank you to arXiv for use of its open access interoperability. PaperDance 不是 arXiv 官方产品;中文卡片由大模型生成,请以原文为准。