HINPool: A Unified Heterogeneous Graph Pooling Framework for Accurate Molecular and Protein Property Prediction

Abstract Graph pooling has gained significant progress in recent years as an effective solution for graph-level property classification tasks. With the emergence of research on Heterogeneous Information Networks (HINs), this paper argues that graph-level datasets for graph classification should be treated as HINs rather than homogeneous graphs to enhance information aggregation. We propose HINPool, a novel and general graph pooling framework for graph-level property classification with HINs. First, we devise a systematic HIN construction procedure from the original data to capture complex interactions. Next, we introduce a type-aware heterogeneous graph pooling method featuring a Type-Aware Selector (TAS) to select essential nodes and a Readout Aggregator (RA) to fuse critical information into a graph-level representation. Finally, a cross-layer fusion function is applied to combine the output embeddings from each graph pooling layer, creating a final graph representation for downstream classification tasks. Our approach achieves near state-of-the-art performance on widely used graph classification benchmark datasets, demonstrating significant improvements in four out of five datasets. This work redefines the strategy for graph-level property classification with HGNNs and heterogeneous graph pooling to model intricate relationships, enhancing performance without requiring extensive domain-specific knowledge.