Hyperbolic Graph Diffusion Model (2306.07618v3)
Abstract: Diffusion generative models (DMs) have achieved promising results in image and graph generation. However, real-world graphs, such as social networks, molecular graphs, and traffic graphs, generally share non-Euclidean topologies and hidden hierarchies. For example, the degree distributions of graphs are mostly power-law distributions. The current latent diffusion model embeds the hierarchical data in a Euclidean space, which leads to distortions and interferes with modeling the distribution. Instead, hyperbolic space has been found to be more suitable for capturing complex hierarchical structures due to its exponential growth property. In order to simultaneously utilize the data generation capabilities of diffusion models and the ability of hyperbolic embeddings to extract latent hierarchical distributions, we propose a novel graph generation method called, Hyperbolic Graph Diffusion Model (HGDM), which consists of an auto-encoder to encode nodes into successive hyperbolic embeddings, and a DM that operates in the hyperbolic latent space. HGDM captures the crucial graph structure distributions by constructing a hyperbolic potential node space that incorporates edge information. Extensive experiments show that HGDM achieves better performance in generic graph and molecule generation benchmarks, with a $48\%$ improvement in the quality of graph generation with highly hierarchical structures.
- Search in power-law networks. Physical review E, 64(4): 046135.
- Tree-like structure in large social and information networks. In 2013 IEEE 13th international conference on data mining, 1–10. IEEE.
- Graph neural network: A comprehensive review on non-euclidean space. IEEE Access, 9: 60588–60606.
- Riemannian adaptive optimization methods. arXiv preprint arXiv:1810.00760.
- Hyperbolic graph convolutional neural networks. Advances in neural information processing systems, 32.
- Graph representation learning: a survey. APSIPA Transactions on Signal and Information Processing, 9: e15.
- Fully hyperbolic neural networks. arXiv preprint arXiv:2105.14686.
- Modeling scale-free graphs with hyperbolic geometry for knowledge-aware recommendation. In Proceedings of the Fifteenth ACM International Conference on Web Search and Data Mining, 94–102.
- Fast neighborhood subgraph pairwise distance kernel. In Proceedings of the 26th International Conference on Machine Learning, 255–262. Omnipress; Madison, WI, USA.
- A hyperbolic-to-hyperbolic graph convolutional network. In Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, 154–163.
- Riemannian score-based generative modeling. arXiv preprint arXiv:2202.02763.
- MolGAN: An implicit generative model for small molecular graphs. arXiv preprint arXiv:1805.11973.
- Graph neural networks for social recommendation. In The world wide web conference, 417–426.
- Hyperbolic neural networks. Advances in neural information processing systems, 31.
- Deep residual learning for image recognition. In Proceedings of the IEEE conference on computer vision and pattern recognition, 770–778.
- Denoising diffusion probabilistic models. Advances in Neural Information Processing Systems, 33: 6840–6851.
- Equivariant diffusion for molecule generation in 3d. In International Conference on Machine Learning, 8867–8887. PMLR.
- Riemannian diffusion models. Advances in Neural Information Processing Systems, 35: 2750–2761.
- ZINC: a free tool to discover chemistry for biology. Journal of chemical information and modeling, 52(7): 1757–1768.
- Denoising Diffusion Implicit Models. arXiv preprint arXiv:2010.02502.
- Torsional diffusion for molecular conformer generation. arXiv preprint arXiv:2206.01729.
- Torsional Diffusion for Molecular Conformer Generation. arXiv preprint arXiv:2206.01729.
- Score-based generative modeling of graphs via the system of stochastic differential equations. In International Conference on Machine Learning, 10362–10383. PMLR.
- Geoopt: Riemannian optimization in pytorch. arXiv preprint arXiv:2005.02819.
- Landrum, G.; et al. 2016. Rdkit: Open-source cheminformatics software. 2016. URL http://www. rdkit. org/, https://github. com/rdkit/rdkit, 149(150): 650.
- Learning deep generative models of graphs. arXiv preprint arXiv:1803.03324.
- The geometry of graphs and some of its algorithmic applications. Combinatorica, 15: 215–245.
- Graph normalizing flows. Advances in Neural Information Processing Systems, 32.
- Graphebm: Molecular graph generation with energy-based models. arXiv preprint arXiv:2102.00546.
- Hyperbolic graph neural networks. Advances in neural information processing systems, 32.
- Graphdf: A discrete flow model for molecular graph generation. In International Conference on Machine Learning, 7192–7203. PMLR.
- Continuous hierarchical representations with poincaré variational auto-encoders. Advances in neural information processing systems, 32.
- Munzner, T. 1997. H3: Laying out large directed graphs in 3D hyperbolic space. In Proceedings of VIZ’97: Visualization Conference, Information Visualization Symposium and Parallel Rendering Symposium, 2–10. IEEE.
- A wrapped normal distribution on hyperbolic space for gradient-based learning. In International Conference on Machine Learning, 4693–4702. PMLR.
- Learning continuous hierarchies in the lorentz model of hyperbolic geometry. In International conference on machine learning, 3779–3788. PMLR.
- Permutation invariant graph generation via score-based generative modeling. In International Conference on Artificial Intelligence and Statistics, 4474–4484. PMLR.
- Unsupervised hyperbolic representation learning via message passing auto-encoders. In Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, 5516–5526.
- Pytorch: An imperative style, high-performance deep learning library. Advances in neural information processing systems, 32.
- Fréchet ChemNet distance: a metric for generative models for molecules in drug discovery. Journal of chemical information and modeling, 58(9): 1736–1741.
- Quantum chemistry structures and properties of 134 kilo molecules. Scientific data, 1(1): 1–7.
- High-resolution image synthesis with latent diffusion models. In Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, 10684–10695.
- BRENDA, the enzyme database: updates and major new developments. Nucleic acids research, 32(suppl_1): D431–D433.
- Collective classification in network data. AI magazine, 29(3): 93–93.
- Graphaf: a flow-based autoregressive model for molecular graph generation. arXiv preprint arXiv:2001.09382.
- Graphvae: Towards generation of small graphs using variational autoencoders. In Artificial Neural Networks and Machine Learning–ICANN 2018: 27th International Conference on Artificial Neural Networks, Rhodes, Greece, October 4-7, 2018, Proceedings, Part I 27, 412–422. Springer.
- Generative modeling by estimating gradients of the data distribution. Advances in neural information processing systems, 32.
- Score-based generative modeling through stochastic differential equations. arXiv preprint arXiv:2011.13456.
- Thornber, C. 1979. Isosterism and molecular modification in drug design. Chemical Society Reviews, 8(4): 563–580.
- Ungar, A. A. 2007. The hyperbolic square and mobius transformations. Banach Journal of Mathematical Analysis, 1(1): 101–116.
- Ungar, A. A. 2008. A gyrovector space approach to hyperbolic geometry. Synthesis Lectures on Mathematics and Statistics, 1(1): 1–194.
- Graph attention networks. arXiv preprint arXiv:1710.10903.
- Top-n: Equivariant set and graph generation without exchangeability. arXiv preprint arXiv:2110.02096.
- Hyperbolic relational graph convolution networks plus: a simple but highly efficient QSAR-modeling method. Briefings in Bioinformatics, 22(5): bbab112.
- GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation. arXiv preprint arXiv:2203.02923.
- A neural network approach to jointly modeling social networks and mobile trajectories. ACM Transactions on Information Systems (TOIS), 35(4): 1–28.
- Hicf: Hyperbolic informative collaborative filtering. In Proceedings of the 28th ACM SIGKDD Conference on Knowledge Discovery and Data Mining, 2212–2221.
- HRCF: Enhancing collaborative filtering via hyperbolic geometric regularization. In Proceedings of the ACM Web Conference 2022, 2462–2471.
- Graphrnn: Generating realistic graphs with deep auto-regressive models. In International conference on machine learning, 5708–5717. PMLR.
- MoFlow: an invertible flow model for generating molecular graphs. In Proceedings of the 26th ACM SIGKDD International Conference on Knowledge Discovery & Data Mining, 617–626.