Relation-Aware Pretraining and Reaction Center Modeling for Chemical Reaction Graph Representation Learning

Learning informative representations of chemical reactions is crucial for advancing synthesis-related downstream tasks, such as reaction condition prediction and yield prediction. However, existing models often struggle to simultaneously capture the global reactant-product relationships and the localized structural evolutions at the reaction center within a unified framework. To bridge this gap, we propose the Knowledge-Aware Graph Transformer (KAGT), a framework for chemical reaction graph representation learning. KAGT combines a shared graph Transformer encoder with a condition-attributed reaction knowledge graph, in which reactant and product molecular graphs serve as source and target entities and solvent, catalyst, and temperature descriptors define latent relation attributes for relation-aware pretraining. The pretraining strategy further includes masked atom modeling and 3D geometric denoising based on computed molecular conformers. We also introduce an explicit reaction-center modeling mechanism guided by atom mapping to capture fine-grained local transformations. Evaluations across three downstream tasks show that KAGT achieves strong performance relative to existing baselines in reaction classification, reaction condition prediction, and yield prediction. Qualitative case studies further show that the learned center scores concentrate on chemically plausible transformation sites, supporting KAGT as a transferable representation framework for AI-driven chemical synthesis.