arXiv:2411.03320q-bio.BMcs.AI2024-11

用图注意力模型预测化学反应产率,重点分析反应物与试剂的相互作用。

log-RRIM: Yield Prediction via Local-to-global Reaction Representation Learning and Interaction Modeling

  • 通过交叉注意力机制捕捉试剂与反应中心的交互关系。
  • 在中高产率反应上表现优异,准确率显著提升。
  • 适合药物合成和反应优化领域的研究人员使用。

精确预测化学反应产率对优化有机合成至关重要,可减少实验耗时与资源浪费。随着人工智能的发展,基于AI的方法成为加速产率预测的新途径。本文提出log-RRIM,一种基于图变压器的产率预测框架。其核心是引入交叉注意力机制,聚焦试剂与反应中心之间的相互作用,体现化学反应中试剂对键断裂与形成的关键影响。log-RRIM采用局部到全局的反应表征学习策略:先捕获分子级别的细节信息,再建模并聚合分子间相互作用。该分层过程有效揭示不同分子片段对整体产率的贡献,不受尺寸差异影响。实验表明,log-RRIM在中高产率反应上表现优越,证明其作为产率预测工具的可靠性。其对反应物-试剂交互的精细建模及分子片段贡献的精准捕捉,使其成为化学合成反应规划与优化的重要工具。数据与代码已公开于 https://github.com/ninglab/Yield_log_RRIM。

原文摘要 · Abstract (English)

Accurate prediction of chemical reaction yields is crucial for optimizing organic synthesis, potentially reducing time and resources spent on experimentation. With the rise of artificial intelligence (AI), there is growing interest in leveraging AI-based methods to accelerate yield predictions without conducting in vitro experiments. We present log-RRIM, an innovative graph transformer-based framework designed for predicting chemical reaction yields. A key feature of log-RRIM is its integration of a cross-attention mechanism that focuses on the interplay between reagents and reaction centers. This design reflects a fundamental principle in chemical reactions: the crucial role of reagents in influencing bond-breaking and formation processes, which ultimately affect reaction yields. log-RRIM also implements a local-to-global reaction representation learning strategy. This approach initially captures detailed molecule-level information and then models and aggregates intermolecular interactions. Through this hierarchical process, log-RRIM effectively captures how different molecular fragments contribute to and influence the overall reaction yield, regardless of their size variations. log-RRIM shows superior performance in our experiments, especially for medium to high-yielding reactions, proving its reliability as a predictor. The framework's sophisticated modeling of reactant-reagent interactions and precise capture of molecular fragment contributions make it a valuable tool for reaction planning and optimization in chemical synthesis. The data and codes of log-RRIM are accessible through https://github.com/ninglab/Yield_log_RRIM.

化学合成图神经网络产率预测

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