Atomic and Subgraph-aware Bilateral Aggregation for Molecular Representation Learning

Abstract

Molecular representation learning is a crucial task in predicting molecular properties. Molecules are often modeled as graphs where atoms and chemical bonds are represented as nodes and edges, respectively, and Graph Neural Networks (GNNs) have been commonly utilized to predict atom-related properties, such as reactivity and solubility. However, functional groups (subgraphs) are closely related to some chemical properties of molecules, such as efficacy, and metabolic properties, which cannot be solely determined by individual atoms. In this paper, we introduce a new model for molecular representation learning called the Atomic and Subgraph-aware Bilateral Aggregation (ASBA), which addresses the limitations of previous atom-wise and subgraph-wise models by incorporating both types of information. ASBA consists of two branches, one for atom-wise information and the other for subgraph-wise information. Considering existing atom-wise GNNs cannot properly extract invariant subgraph features, we propose a decomposition-polymerization GNN architecture for the subgraph-wise branch. Furthermore, we propose cooperative node-level and graph-level self-supervised learning strategies for ASBA to improve its generalization. Our method offers a more comprehensive way to learn representations for molecular property prediction and has broad potential in drug and material discovery applications. Extensive experiments have demonstrated the effectiveness of our method.