Robust Heterogeneous Graph Classification for Molecular Property Prediction with Information Bottleneck

Zhibin Ni, Chang Liu, Hai Wan, Xibin Zhao

Abstract: Heterogeneous Graph Neural Networks (HGNNs) have achieved state-of-the-art performance in classifying molecular graphs, capitalizing on their ability to capture rich semantics. However, HGNNs for molecule property prediction exhibit significant susceptibility to adversarial attacks—a challenge that prior research has entirely overlooked. To fill this gap, this paper introduces the first study focused on robust graph-level representation learning tailored for heterogeneous molecular graphs. To achieve this goal, we propose a comprehensive Robust Heterogeneous Graph Classification (RHGC) framework grounded in the Information Bottleneck principle, which aims to identify the most informative and least noisy heterogeneous subgraphs to derive robust, holistic representations. This is specifically accomplished through a dedicated Node Semantic Purifier, which enhances node-level and semantic-level robustness by eliminating label-irrelevant interference using graph stochastic attention and the Hilbert-Schmidt Independence Criterion, along with a Global Graph Disentanglement method, which improves graph-level robustness by addressing information leak. Experiments on three molecular benchmarks demonstrate that RHGC enhances accuracy by an average of 5.06% under all three attack settings and meanwhile by 4.33% on clean data.