# Embedded Graph Flows for Categorical Graph Generation

arXiv: https://arxiv.org/abs/2609.05328 · HTML: https://mlsanity.com/paper/2609.05328/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 17 of its 23 references that are in the map.
- First posted on arXiv 4 Sep 2026.

## Builds on (most cited first, 17 of 17)

- [Flow Matching for Generative Modeling](https://mlsanity.com/paper/2210.02747/) (2022)
- [DiGress: Discrete Denoising diffusion for graph generation](https://mlsanity.com/paper/2209.14734/) (2022)
- [Generative Flows on Discrete State-Spaces: Enabling Multimodal Flows with Applications to Protein Co-Design](https://mlsanity.com/paper/2402.04997/) (2024)
- [Score-based Generative Modeling of Graphs via the System of Stochastic Differential Equations](https://mlsanity.com/paper/2202.02514/) (2022)
- [Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Models](https://mlsanity.com/paper/1811.12823/) (2018)
- [Fr'echet ChemNet Distance: A metric for generative models for molecules in drug discovery](https://mlsanity.com/paper/1803.09518/) (2018)
- [Variational Flow Matching for Graph Generation](https://mlsanity.com/paper/2406.04843/) (2024)
- [DeFoG: Discrete Flow Matching for Graph Generation](https://mlsanity.com/paper/2410.04263/) (2024)
- [Graph Generation with Diffusion Mixture](https://mlsanity.com/paper/2302.03596/) (2023)
- [Mixed Continuous and Categorical Flow Matching for 3D De Novo Molecule Generation](https://mlsanity.com/paper/2404.19739/) (2024)
- [ELF: Embedded Language Flows](https://mlsanity.com/paper/2605.10938/) (2026)
- [Categorical Flow Maps](https://mlsanity.com/paper/2602.12233/) (2026)
- [Exploring Discrete Flow Matching for 3D De Novo Molecule Generation](https://mlsanity.com/paper/2411.16644/) (2024)
- [Discrete Graph Auto-Encoder](https://mlsanity.com/paper/2306.07735/) (2023)
- [Improving Molecular Graph Generation with Flow Matching and Optimal Transport](https://mlsanity.com/paper/2411.05676/) (2024)
- [Catch-Only-One: Non-Transferable Examples for Model-Specific Authorization](https://mlsanity.com/paper/2510.10982/) (2025)
- [Re-Key-Free, Risky-Free: Adaptable Model Usage Control](https://mlsanity.com/paper/2511.18772/) (2025)

## Abstract (arXiv)

Generating categorical graphs requires choosing node and edge types that form a coherent structure without depending on node order. Many graph generators encode categories as fixed one-hot vectors, which can impose an artificial geometry in which categories are equidistant. We propose Embedded Graph Flows (EGF), a generative model that learns continuous embeddings for node and unordered-edge categories and transports Gaussian noise towards these learnt endpoints using a permutation-equivariant graph transformer. A terminal readout maps the embeddings back to discrete graph categories. Across molecular benchmarks, EGF achieved competitive performance. On QM9, EGF gives the best result on all four reported metrics among the three methods, including a Fr'echet ChemNet Distance (FCD) of 0.150, compared with 0.717 for the categorical-diffusion baseline DiGress and 0.812 for the bridge-based baseline GruM. When applied to larger molecules in ZINC250k, EGF retains the lowest maximum mean discrepancy (MMD) using the neighbourhood subgraph pairwise distance kernel (NSPDK), indicating close agreement with the local substructures of the reference molecules. Our code is available at https://github.com/Trusted-System-Lab/EGF.