# Discrete Graph Auto-Encoder

arXiv: https://arxiv.org/abs/2306.07735 · HTML: https://mlsanity.com/paper/2306.07735/

## 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 (most cited first, 30 of 41)

- [Batch Normalization: Accelerating Deep Network Training by Reducing Internal Covariate Shift](https://mlsanity.com/paper/1502.03167/) (2015)
- [Neural Discrete Representation Learning](https://mlsanity.com/paper/1711.00937/) (2017)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [Generating Diverse High-Fidelity Images with VQ-VAE-2](https://mlsanity.com/paper/1906.00446/) (2019)
- [Variational Graph Auto-Encoders](https://mlsanity.com/paper/1611.07308/) (2016)
- [Deeper Insights into Graph Convolutional Networks for Semi-Supervised Learning](https://mlsanity.com/paper/1801.07606/) (2018)
- [Automatic chemical design using a data-driven continuous representation of molecules](https://mlsanity.com/paper/1610.02415/) (2016)
- [Equivariant Diffusion for Molecule Generation in 3D](https://mlsanity.com/paper/2203.17003/) (2022)
- [Junction Tree Variational Autoencoder for Molecular Graph Generation](https://mlsanity.com/paper/1802.04364/) (2018)
- [DiGress: Discrete Denoising diffusion for graph generation](https://mlsanity.com/paper/2209.14734/) (2022)
- [GraphRNN: Generating Realistic Graphs with Deep Auto-regressive Models](https://mlsanity.com/paper/1802.08773/) (2018)
- [MolGAN: An implicit generative model for small molecular graphs](https://mlsanity.com/paper/1805.11973/) (2018)
- [Provably Powerful Graph Networks](https://mlsanity.com/paper/1905.11136/) (2019)
- [GraphVAE: Towards Generation of Small Graphs Using Variational Autoencoders](https://mlsanity.com/paper/1802.03480/) (2018)
- [GraphAF: a Flow-based Autoregressive Model for Molecular Graph Generation](https://mlsanity.com/paper/2001.09382/) (2020)
- [Grammar Variational Autoencoder](https://mlsanity.com/paper/1703.01925/) (2017)
- [Score-based Generative Modeling of Graphs via the System of Stochastic Differential Equations](https://mlsanity.com/paper/2202.02514/) (2022)
- [Can Graph Neural Networks Count Substructures?](https://mlsanity.com/paper/2002.04025/) (2020)
- [Efficient Graph Generation with Graph Recurrent Attention Networks](https://mlsanity.com/paper/1910.00760/) (2019)
- [Learning Deep Generative Models of Graphs](https://mlsanity.com/paper/1803.03324/) (2018)
- [Hierarchical Generation of Molecular Graphs using Structural Motifs](https://mlsanity.com/paper/2002.03230/) (2020)
- [What graph neural networks cannot learn: depth vs width](https://mlsanity.com/paper/1907.03199/) (2019)
- [Fr'echet ChemNet Distance: A metric for generative models for molecules in drug discovery](https://mlsanity.com/paper/1803.09518/) (2018)
- [Geometric Latent Diffusion Models for 3D Molecule Generation](https://mlsanity.com/paper/2305.01140/) (2023)
- [Constrained Graph Variational Autoencoders for Molecule Design](https://mlsanity.com/paper/1805.09076/) (2018)
- [MoFlow: An Invertible Flow Model for Generating Molecular Graphs](https://mlsanity.com/paper/2006.10137/) (2020)
- [GraphDF: A Discrete Flow Model for Molecular Graph Generation](https://mlsanity.com/paper/2102.01189/) (2021)
- [Scene Graph Generation from Objects, Phrases and Region Captions](https://mlsanity.com/paper/1707.09700/) (2017)
- [GraphNVP: An Invertible Flow Model for Generating Molecular Graphs](https://mlsanity.com/paper/1905.11600/) (2019)
- [Fast Decoding in Sequence Models using Discrete Latent Variables](https://mlsanity.com/paper/1803.03382/) (2018)

## Built on by (most cited first, 10 of 10)

- [Learning the Language of Protein Structure](https://mlsanity.com/paper/2405.15840/) (2024)
- [Simple and Critical Iterative Denoising: A Recasting of Discrete Diffusion in Graph Generation](https://mlsanity.com/paper/2503.21592/) (2025)
- [GLAD: Improving Latent Graph Generative Modeling with Simple Quantization](https://mlsanity.com/paper/2403.16883/) (2024)
- [mCLM: A Modular Chemical Language Model that Generates Functional and Makeable Molecules](https://mlsanity.com/paper/2505.12565/) (2025)
- [Discrete Tokenization for Multimodal LLMs: A Comprehensive Survey](https://mlsanity.com/paper/2507.22920/) (2025)
- [Principled Latent Diffusion for Graphs via Laplacian Autoencoders](https://mlsanity.com/paper/2601.13780/) (2026)
- [Unrestrained Simplex Denoising for Discrete Data. A Non-Markovian Approach Applied to Graph Generation](https://mlsanity.com/paper/2603.28572/) (2026)
- [Hierarchical Discrete Flow Matching for Graph Generation](https://mlsanity.com/paper/2604.00236/) (2026)
- [Synergistic Dual Spatial-aware Generation of Image-to-Text and Text-to-Image](https://mlsanity.com/paper/2410.15312/) (2024)
- [Embedded Graph Flows for Categorical Graph Generation](https://mlsanity.com/paper/2609.05328/) (2026)

## 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.