Hyperbolic Graph Diffusion Model for Molecule Generation

Recently, diffusion models have achieved remarkable performance in data generation, e.g., generating high-quality images. Nevertheless, chemistry molecules often have complex non-Euclidean spatial structures, with the behavior changing dynamically and unpredictably. Most existing diffusion models highly rely on computing the probability distribution, i.e., Gaussian distribution, in Euclidean space, which cannot capture internal non-Euclidean structures of molecules, especially the hierarchical structures of the implicit manifold surface represented by molecules. It has been observed that the complex hierarchical structures in hyperbolic embedding space become more prominent and easier to be captured. In order to leverage both the data generation power of diffusion models and the strong capability to extract complex geometric features of hyperbolic embedding, we propose to extend the diffusion model to hyperbolic manifolds for molecule generation, namely, Hyperbolic Graph Diffusion Model (HGDM). The proposed HGDM employs a hyperbolic variational autoencoder to generate the hyperbolic hidden representation of nodes and then a score-based hyperbolic graph neural network is used to learn the distribution in hyperbolic space. Numerical experimental results show that the proposed HGDM achieves higher performance on several molecular datasets, compared with state-of-the-art methods.