Association Pattern-enhanced Molecular Representation Learning

Abstract The applicability of drug molecules in various clinical scenarios is significantly influenced by a diverse range of molecular properties. By leveraging self-supervised conditions such as atom attributes and interatomic bonds, existing advanced molecular foundation models can generate expressive representations of these molecules. However, such models often overlook the fixed association patterns within molecules that influence physiological or chemical properties. In this paper, we introduce a novel association pattern-aware message passing method, which can serve as an effective yet general plug-and-play plugin, thereby enhancing the atom representations generated by molecular foundation models without requiring additional pretraining. Additionally, molecular property-specific pattern libraries are constructed to collect the generated interpretable common patterns that bind to these properties. Extensive experiments conducted on 11 benchmark molecular property prediction tasks across 8 advanced molecular foundation models demonstrate significant superiority of the proposed method, with performance improvements of up to approximately 20%. Furthermore, a property-specific pattern library is tailored for blood-brain barrier penetration, which has undergone corresponding mechanistic validation.