Molecular hypergraph neural networks

Abstract

Graph neural networks (GNNs) have demonstrated promising performance across various chemistry-related tasks. However, conventional graphs only model the pairwise connectivity in molecules, failing to adequately represent higher order connections, such as multi-center bonds and conjugated structures. To tackle this challenge, we introduce molecular hypergraphs and propose Molecular Hypergraph Neural Networks (MHNNs) to predict the optoelectronic properties of organic semiconductors, where hyperedges represent conjugated structures. A general algorithm is designed for irregular high-order connections, which can efficiently operate on molecular hypergraphs with hyperedges of various orders. The results show that MHNN outperforms all baseline models on most tasks of organic photovoltaic, OCELOT chromophore v1, and PCQM4Mv2 datasets. Notably, MHNN achieves this without any 3D geometric information, surpassing the baseline model that utilizes atom positions. Moreover, MHNN achieves better performance than pretrained GNNs under limited training data, underscoring its excellent data efficiency. This work provides a new strategy for more general molecular representations and property prediction tasks related to high-order connections.