arXiv:2608.27429cs.AI2026-08

用电子分布流动匹配预测反应机理,可自动推导化学路径并预测副产物。

Mechanistic Reaction Prediction via Discrete Flow Matching on Graph-Structured Electron Occupation

论文配图:Mechanistic Reaction Prediction via Discrete Flow Matching on Graph-Structured Electron Occupation
图 1 · 摘自论文原文
  • 将反应建模为电子占据向量上的离散流匹配,基于最优传输插值电子移动路径。
  • 在USPTO-480K上表现优于主流模型,且在复杂结构和新反应类型上更稳健。
  • 无需标注基元步骤即可生成符合化学常识的反应机理,适合机理研究者使用。

化学反应本质上是电子空间的转变,但多数机器学习方法要么从头生成产物分子,要么通过启发式图编辑直接操作分子拓扑。本文提出MAELLE(MechAnistic Edit Flow-matching on Electron Rearrangements),将反应建模为图结构整数电子占据空间上的离散流匹配。具体地,将反应物到产物的映射定义为连续时间马尔可夫链(CTMC),作用于所有成键、非成键及氢原子位点的电子占据空间。为构建反应物与产物间的插值路径,将离散流匹配的混合路径推广为基于编辑的公式,利用最优传输插值电子迁移,生成类似机理的移动序列,无需基元步骤标注。MAELLE在USPTO-480K基准上达到领先性能;在结构复杂性和反应类型两类分布外设置下评估鲁棒性,发现其性能优于现有方法。由于学习的流覆盖全电子重分布,MAELLE可自然恢复与已知化学一致的机理轨迹,并预测反应副产物。

原文摘要 · Abstract (English)

Chemical reactions are fundamentally transformations in electron space, yet most machine learning approaches model them either through de novo generation of product molecules or through heuristic graph edits that operate directly on molecular topology. We introduce MAELLE (MechAnistic Edit fLow-matching on eLectron rEarrangements), which instead models reactions as discrete flow matching over electron occupation vectors. Concretely, we formulate the reactant-to-product mapping as a Continuous-time Markov Chain (CTMC) over the graph-structured integer-valued electron occupation space defined on all bonding, non-bonding, and hydrogen sites. To construct the interpolants between the reactants and products, we generalize the discrete flow matching mixture path to an edit-based formulation, where the electron moves are interpolated using Optimal Transport, yielding a mechanism-like set of moves without elementary step annotations. MAELLE achieves competitive performance on the USPTO-480K benchmark compared with leading reaction prediction models. Beyond in-distribution learning, we evaluate robustness across two out-of-distribution settings - structural complexity and reaction type - and find that MAELLE maintains strong performance where existing methods degrade. Finally, because the learned flow operates over the full electron redistribution, MAELLE naturally recovers mechanistic trajectories that align with known chemistry and can predict side products of a reaction.

反应预测电子分布流匹配机理生成

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