A hierarchical interaction message net for accurate molecular property prediction

Discovering molecules with desirable molecular properties, including ADMET profiles, is of great importance in drug discovery. Existing approaches typically employ deep learning models, such as Graph Neural Networks and Transformers, to predict these molecular properties by learning from diverse chemical information. However, these models often lack mechanisms for effective interaction among multi-level features. To address these limitations, we propose a Hierarchical Interaction Message Passing Mechanism, which serves as the foundation of our model, the Hierarchical Interaction Message Net (HimNet). Our method enables interaction-aware representation learning across atomic, motif, and molecular levels via hierarchical attention-guided message passing. This design allows HimNet to effectively balance global and local information, ensuring rich and task-relevant feature extraction for downstream property prediction tasks. We systematically evaluate HimNet on eleven datasets, including eight widely-used MoleculeNet benchmarks and three challenging, high-value datasets for metabolic stability, malaria activity, and liver microsomal clearance, covering a broad range of pharmacologically relevant properties. Extensive experiments demonstrate that HimNet achieves the best or near-best performance in most molecular property prediction tasks. We believe that HimNet offers an accurate and efficient solution for molecular activity and ADMET property prediction, contributing significantly to advanced decision-making in the early stages of drug discovery. Accurate prediction of molecular properties is crucial for drug discovery, yet existing models often struggle with multi-level feature interaction. Here, the authors introduce the hierarchical interaction message net (HimNet), which enhances representation learning across atomic, motif, and molecular levels, achieving superior performance in property prediction tasks.