SE3Set: Harnessing Equivariant Hypergraph Neural Networks for Molecular Representation Learning

In this paper, we develop SE3Set, an SE(3) equivariant hypergraph neural network architecture tailored for advanced molecular representation learning. Hypergraphs are not merely an extension of traditional graphs; they are pivotal for modeling high-order relationships, a capability that conventional equivariant graph-based methods lack due to their inherent limitations in representing intricate many-body interactions. To achieve this, we first construct hypergraphs by proposing a new fragmentation method that considers both chemical and three-dimensional spatial information of the molecular system. We then design SE3Set, which incorporates equivariance into the hypergraph neural network. This ensures that the learned molecular representations are invariant to spatial transformations, thereby providing robustness essential for the accurate prediction of molecular properties. SE3Set has shown performance on par with state-of-the-art (SOTA) models for small molecule datasets like QM9 and MD17. It demonstrates outstanding performance on the MD22 dataset, achieving a remarkable ~20\% improvement in accuracy across all molecules. Furthermore, on the OE62 dataset, SE3Set outperforms all short-range models. We also conducted a detailed analysis of OE62, highlighting the prevalence of complex many-body interactions in large molecules. This exceptional performance of SE3Set across diverse molecular structures underscores its transformative potential in computational chemistry, offering a route to more accurate and physically nuanced modeling. The code of this work is available at https://github.com/Navantock/SE3Set.