Discrete Graph Auto-Encoder
Not on the map. Why?
Abstract (arXiv)
Despite advances in generative methods, accurately modeling the distribution of graphs remains a challenging task primarily because of the absence of predefined or inherent unique graph representation. Two main strategies have emerged to tackle this issue: 1) restricting the number of possible representations by sorting the nodes, or 2) using permutation-invariant/equivariant functions, specifically Graph Neural Networks (GNNs). In this paper, we introduce a new framework named Discrete Graph Auto-Encoder (DGAE), which leverages the strengths of both strategies and mitigate their respective limitations. In essence, we propose a strategy in 2 steps. We first use a permutation-equivariant auto-encoder to convert graphs into sets of discrete latent node representations, each node being represented by a sequence of quantized vectors. In the second step, we sort the sets of discrete latent representations and learn their distribution with a specifically designed auto-regressive model based on the Transformer architecture. Through multiple experimental evaluations, we demonstrate the competitive performances of our model in comparison to the existing state-of-the-art across various datasets. Various ablation studies support the interest of our method.
Key facts. Cited by 10 papers in the map (data through 14 Oct 2026). Builds on 41 of its 57 references that are in the map. First posted on arXiv 13 Jun 2023.
Builds on
41 of 57 references.
References · 41
- 2015Batch Normalization: Accelerating Deep Network Training by Reducing Internal Covariate Shiftcited by 7,005
- 2017Neural Discrete Representation Learningcited by 4,712
- 2018How Powerful are Graph Neural Networks?cited by 4,393
- 2019Generating Diverse High-Fidelity Images with VQ-VAE-2cited by 1,387
- 2016Variational Graph Auto-Encoderscited by 1,382
- 2018Deeper Insights into Graph Convolutional Networks for Semi-Supervised Learningcited by 1,102
- 2016Automatic chemical design using a data-driven continuous representation of moleculescited by 765
- 2022Equivariant Diffusion for Molecule Generation in 3Dcited by 677
- 2018Junction Tree Variational Autoencoder for Molecular Graph Generationcited by 652
- 2022DiGress: Discrete Denoising diffusion for graph generationcited by 520
- 2018GraphRNN: Generating Realistic Graphs with Deep Auto-regressive Modelscited by 413
- 2018MolGAN: An implicit generative model for small molecular graphscited by 393
29 more
- 2019Provably Powerful Graph Networkscited by 389
- 2018GraphVAE: Towards Generation of Small Graphs Using Variational Autoencoderscited by 383
- 2020GraphAF: a Flow-based Autoregressive Model for Molecular Graph Generationcited by 305
- 2017Grammar Variational Autoencodercited by 285
- 2022Score-based Generative Modeling of Graphs via the System of Stochastic Differential Equationscited by 283
- 2020Can Graph Neural Networks Count Substructures?cited by 236
- 2019Efficient Graph Generation with Graph Recurrent Attention Networkscited by 234
- 2018Learning Deep Generative Models of Graphscited by 229
- 2020Hierarchical Generation of Molecular Graphs using Structural Motifscited by 208
- 2019What graph neural networks cannot learn: depth vs widthcited by 201
- 2018Fr'echet ChemNet Distance: A metric for generative models for molecules in drug discoverycited by 194
- 2023Geometric Latent Diffusion Models for 3D Molecule Generationcited by 186
- 2018Constrained Graph Variational Autoencoders for Molecule Designcited by 185
- 2020MoFlow: An Invertible Flow Model for Generating Molecular Graphscited by 185
- 2021GraphDF: A Discrete Flow Model for Molecular Graph Generationcited by 180
- 2017Scene Graph Generation from Objects, Phrases and Region Captionscited by 154
- 2019GraphNVP: An Invertible Flow Model for Generating Molecular Graphscited by 116
- 2018Fast Decoding in Sequence Models using Discrete Latent Variablescited by 104
- 2019Graph Normalizing Flowscited by 104
- 2020Building powerful and equivariant graph neural networks with structural message-passingcited by 97
- 2022How Powerful are K-hop Message Passing Graph Neural Networkscited by 90
- 2018NeVAE: A Deep Generative Model for Molecular Graphscited by 67
- 2020GraphGen: A Scalable Approach to Domain-agnostic Labeled Graph Generationcited by 66
- 2018On Weisfeiler-Leman Invariance: Subgraph Counts and Related Graph Propertiescited by 63
- 2018Generative Code Modeling with Graphscited by 60
- 2020Robust Training of Vector Quantized Bottleneck Modelscited by 54
- 2021MolGrow: A Graph Normalizing Flow for Hierarchical Molecular Generationcited by 22
- 2018Sequence-to-Action: End-to-End Semantic Graph Generation for Semantic Parsingcited by 21
- 2018Generating Triples with Adversarial Networks for Scene Graph Constructioncited by 5
Built on by
Citing papers per year: 2024: 3; 2025: 3; 2026: 4.
10 papers.
- 2024Learning the Language of Protein Structurecited by 10
- 2025Simple and Critical Iterative Denoising: A Recasting of Discrete Diffusion in Graph Generationcited by 10
- 2024GLAD: Improving Latent Graph Generative Modeling with Simple Quantizationcited by 8
- 2025mCLM: A Modular Chemical Language Model that Generates Functional and Makeable Moleculescited by 8
- 2025Discrete Tokenization for Multimodal LLMs: A Comprehensive Surveycited by 8
- 2026Principled Latent Diffusion for Graphs via Laplacian Autoencoderscited by 4
- 2026Unrestrained Simplex Denoising for Discrete Data. A Non-Markovian Approach Applied to Graph Generationcited by 2
- 2026Hierarchical Discrete Flow Matching for Graph Generationcited by 2
- 2024Synergistic Dual Spatial-aware Generation of Image-to-Text and Text-to-Imagecited by 1
- 2026Embedded Graph Flows for Categorical Graph Generationcited by 0
- 2026Embedded Graph Flows for Categorical Graph Generation4 Sep 2026
- 2026Hierarchical Discrete Flow Matching for Graph Generation31 Mar 2026
- 2026Unrestrained Simplex Denoising for Discrete Data. A Non-Markovian Approach Applied to Graph Generation30 Mar 2026
- 2026Principled Latent Diffusion for Graphs via Laplacian Autoencoders20 Jan 2026
- 2025Discrete Tokenization for Multimodal LLMs: A Comprehensive Survey21 Jul 2025
- 2025mCLM: A Modular Chemical Language Model that Generates Functional and Makeable Molecules18 May 2025
- 2025Simple and Critical Iterative Denoising: A Recasting of Discrete Diffusion in Graph Generation27 Mar 2025
- 2024Synergistic Dual Spatial-aware Generation of Image-to-Text and Text-to-Image20 Oct 2024
- 2024Learning the Language of Protein Structure24 May 2024
- 2024GLAD: Improving Latent Graph Generative Modeling with Simple Quantization25 Mar 2024
Similar, not cited
Close in wording, no citation either way
- 2025Hierarchical Vector Quantized Graph Autoencoder with Annealing-Based Code Selection
- 2024Preserving Node Distinctness in Graph Autoencoders via Similarity Distillation
- 2024Node Identifiers: Compact, Discrete Representations for Efficient Graph Learning
- 2024Neural Graph Generator: Feature-Conditioned Graph Generation using Latent Diffusion Models
- 2026VecFormer: Towards Efficient and Generalizable Graph Transformer with Graph Token Attention
- 2025Graph Representation Learning with Diffusion Generative Models
- 2020Permutation Invariant Graph Generation via Score-Based Generative Modeling
- 2021VQ-GNN: A Universal Framework to Scale up Graph Neural Networks using Vector Quantization