Bi-level Contrastive Learning for Knowledge-Enhanced Molecule Representations

Molecular representation learning is vital for various downstream applications, including the analysis and prediction of molecular properties and side effects. While Graph Neural Networks (GNNs) have been a popular framework for modeling molecular data, they often struggle to capture the full complexity of molecular representations. In this paper, we introduce a novel method called GODE, which accounts for the dual-level structure inherent in molecules. Molecules possess an intrinsic graph structure and simultaneously function as nodes within a broader molecular knowledge graph. GODE integrates individual molecular graph representations with multi-domain biochemical data from knowledge graphs. By pre-training two GNNs on different graph structures and employing contrastive learning, GODE effectively fuses molecular structures with their corresponding knowledge graph substructures. This fusion yields a more robust and informative representation, enhancing molecular property predictions by leveraging both chemical and biological information. When fine-tuned across 11 chemical property tasks, our model significantly outperforms existing benchmarks, achieving an average ROC-AUC improvement of 12.7% for classification tasks and an average RMSE/MAE improvement of 34.4% for regression tasks. Notably, GODE surpasses the current leading model in property prediction, with advancements of 2.2% in classification and 7.2% in regression tasks.