Incorporating Retrieval-based Causal Learning with Information Bottlenecks for Interpretable Molecular Graph Learning

Graph Neural Networks (GNNs) have gained considerable traction for modeling molecular structures and predicting properties, but their interpretability remains a significant challenge in understanding chemical behaviors. Current interpretation methods often rely on post-hoc explanations, which aim to provide transparency in GNN decisions. However, these approaches struggle with interpreting complex subgraphs and fail to leverage explanations to enhance predictive capabilities. While transparent methods can enhance GNN predictions, they typically compromise on explanation precision. This limitation underscores the need for a new strategy that effectively integrates GNN explanations and predictions. In this study, we have developed a novel interpretable causal GNN framework that combines retrieval-based causal learning with Graph Information Bottleneck (GIB) theory. Our framework semi-parametrically identifies crucial subgraphs through GIB and compresses explanatory subgraphs using a causal module. The framework consistently outperformed state-of-the-art methods, achieving a 32.72% increase in precision for scientific explanation tasks involving diverse substructures. More importantly, the learned explanations were also shown to be able to improve GNN prediction performance. This advancement is particularly vital for molecular graph learning, as it addresses the critical need to interpret how molecular structures influence predicted properties, thereby aiding drug discovery and materials science by providing insights into chemical mechanisms.