ChemHGNN: A Hierarchical Hypergraph Neural Network for Reaction Virtual Screening and Discovery

Abstract

Reaction virtual screening and discovery are fundamental challenges in chemistry and material science, where traditional graph neural networks (GNNs) struggle to model multi-reactant interactions. In this work, we propose ChemHGNN, a hypergraph neural network (HGNN) framework that effectively captures high-order relationships in reaction networks. Unlike GNNs, which require constructing complete graphs for multi-reactant reactions, ChemHGNN naturally models multi-reactant reactions through hyperedges, enabling more expressive reaction representations. To address key challenges—such as combinatorial explosion, model collapse, and chemically invalid negative samples—we introduce a reaction center-aware negative sampling strategy (RCNS) and a hierarchical embedding approach combining molecule, reaction and hypergraph level features. Experiments on the USPTO dataset demonstrate that ChemHGNN significantly outperforms HGNN and GNN baselines, particularly in large-scale settings, while maintaining interpretability and chemical plausibility. Our work establishes ChemHGNN as a superior alternative for reaction virtual screening and discovery, offering a chemically informed framework for accelerating reaction discovery. Click here for GitHub repository.