Motif-Based Graph Learning for Synthetic Reaction Condition Prediction

Abstract

Organic synthetic reactions form the foundation of industrial manufacturing. It is crucial to develop advanced predictive models for synthetic reaction conditions to support the optimization of organic reactions. Synthetic reaction condition is closely related to the molecular motifs (substructures or functional groups), which traditional molecular graphs are unable or difficult to capture. However, many existing studies overlook the significance of motif-level graphs. To address this issue, we propose a novel method for predicting reaction conditions in organic synthesis. First, we extract the chemical features of the reactants and products at both the atom and motif levels, and then uses two branches in the encoder to separately capture local and global contexts and then integrate them. Next, a cross-attention module is employed to learn the latent relationships between the reactants and products, enriching the reaction representation. Experimental results demonstrate that our method outperforms the strongest baseline with up to 30% improvement in Top-10 accuracy on the USPTO_CONDITION data set. Attention analysis further reveals that our method effectively captures critical motifs closely related to synthetic reaction conditions and exhibits interpretable capabilities. The code for MGLSRC is available at: https://github.com/Z-dot-max/MGLSRC.