HAGO-Net: Hierarchical Geometric Massage Passing for Molecular Representation Learning

Abstract

Molecular representation learning has emerged as a game-changer at the intersection of AI and chemistry, with great potential in applications such as drug design and materials discovery. A substantial obstacle in successfully applying molecular representation learning is the difficulty of effectively and completely characterizing and learning molecular geometry, which has not been well addressed to date. To overcome this challenge, we propose a novel framework that features a novel geometric graph, termed HAGO-Graph, and a specifically designed geometric graph learning model, HAGO-Net. In the framework, the foundation is HAGO-Graph, which enables a complete characterization of molecular geometry in a hierarchical manner. Specifically, we leverage the concept of n-body in physics to characterize geometric patterns at multiple spatial scales. We then specifically design a message passing scheme, HAGO-MPS, and implement the scheme as a geometric graph neural network, HAGO-Net, to effectively learn the representation of HAGO-Graph by horizontal and vertical aggregation. We further prove DHAGO-Net, the derivative function of HAGO-Net, is an equivariant model. The proposed models are validated by extensive comparisons on four challenging benchmarks. Notably, the models exhibited state-of-the-art performance in molecular chirality identification and property prediction, achieving state-of-the-art performance on five properties of QM9 dataset. The models also achieved competitive results on molecular dynamics prediction task.