教语言模型理解反应机理,让化学合成预测更可解释、更准确。
Teaching Language Models Mechanistic Explainability Through MechSMILES
- 用箭头推移法编码电子流动,训练语言模型预测反应机理。
- 在复杂任务中路径召回率达93.2%(FlowER)和73.3%(mech-USPTO-31k)。
- 适合需要可解释性与机理验证的药物研发与合成规划人员。
化学反应机理是化学家评估反应活性与可行性的重要基础,但现有计算机辅助合成规划(CASP)系统缺乏此类机理推理。本文提出一种计算框架,通过箭头推移形式(arrow-pushing formalism)教导语言模型预测反应机理,该符号体系百年来用于追踪电子流动并遵守质量与电荷守恒。该机理理解使系统具备三项当前方法难以实现的能力:对CASP建议进行后验验证,重构物理上合理的电子路径;实现涵盖氢原子在内的全原子映射;提取区分催化剂与旁观物种的催化感知反应模板。核心是MechSMILES——一种紧凑的文本格式,通过三种箭头类型编码分子结构与电子流动,基于Python环境设计,强制遵守守恒定律,杜绝原子幻觉。我们在四个逐步增加复杂度的机理预测任务上训练并基准测试模型,使用文献中的主流机理数据集。在最挑战性的任务中,仅凭反应物、条件与目标产物预测完整机理,模型在FlowER和mech-USPTO-31k数据集上的路径召回率分别达到93.2%和73.3%,前3名召回率分别为97.6%和86.5%。此外,框架能快速学习新反应类,仅需40个样本即可对臭氧裂解和Suzuki偶联反应生成强机理预测。通过将预测建立在物理上可解释的电子运动基础上,本工作为更可解释、更化学有效的CASP提供了架构无关、开源的基础。
原文摘要 · Abstract (English)
Chemical reaction mechanisms are the foundation of how chemists evaluate reactivity and feasibility, yet current Computer-Assisted Synthesis Planning (CASP) systems operate without this mechanistic reasoning. We introduce a computational framework that teaches language models to predict reaction mechanisms through arrow-pushing formalism, a century-old notation that tracks electron flow while enforcing conservation of mass and charge. This mechanistic understanding enables three capabilities that are difficult or impossible with current methods: post-hoc validation of CASP proposals by reconstructing physically plausible electron pathways, holistic atom-to-atom mapping that tracks all atoms including hydrogens, and extraction of catalyst-aware reaction templates that distinguish recycled catalysts from spectator species. Central to our approach is MechSMILES, a compact textual format encoding molecular structure and electron flow through three arrow types, designed within a Python-based environment that enforces conservation laws and eliminates the possibility of atom hallucination. We trained and benchmarked models on four mechanism prediction tasks of increasing complexity using the main mechanistic datasets in the literature. On our most challenging task, predicting complete mechanisms given only reactants, conditions, and the desired product, our models achieve 93.2\% and 73.3\% pathway retrieval on the FlowER and mech-USPTO-31k datasets respectively, with top-3 retrieval reaching 97.6\% and 86.5\%. Furthermore, the framework rapidly learns new reaction classes, with strong mechanistic predictions for ozonolysis and Suzuki cross-coupling emerging from as few as 40 training examples each. By grounding predictions in physically meaningful electron movements, this work provides an architecture-agnostic, open-source foundation for more explainable and chemically valid CASP.
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