# Discrete-state Continuous-time Diffusion for Graph Generation

arXiv: https://arxiv.org/abs/2405.11416 · HTML: https://mlsanity.com/paper/2405.11416/

## Key facts

- Cited by 76 papers in the map (data through 14 Oct 2026).
- Placed in Flow matching, time series and science, one of 14 directions in Diffusion models.
- Builds on 59 of its 87 references that are in the map.
- First posted on arXiv 19 May 2024.

## Placed in

- Diffusion models / [Flow matching, time series and science](https://mlsanity.com/diffusion/flow-matching-time-series-and-science/)

## Builds on (most cited first, 30 of 59)

- [Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2006.11239/) (2020)
- [Denoising Diffusion Implicit Models](https://mlsanity.com/paper/2010.02502/) (2020)
- [Score-Based Generative Modeling through Stochastic Differential Equations](https://mlsanity.com/paper/2011.13456/) (2020)
- [Deep Unsupervised Learning using Nonequilibrium Thermodynamics](https://mlsanity.com/paper/1503.03585/) (2015)
- [Generative Modeling by Estimating Gradients of the Data Distribution](https://mlsanity.com/paper/1907.05600/) (2019)
- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (2017)
- [FiLM: Visual Reasoning with a General Conditioning Layer](https://mlsanity.com/paper/1709.07871/) (2017)
- [Structured Denoising Diffusion Models in Discrete State-Spaces](https://mlsanity.com/paper/2107.03006/) (2021)
- [Variational Diffusion Models](https://mlsanity.com/paper/2107.00630/) (2021)
- [Diffusion Models: A Comprehensive Survey of Methods and Applications](https://mlsanity.com/paper/2209.00796/) (2022)
- [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)
- [Argmax Flows and Multinomial Diffusion: Learning Categorical Distributions](https://mlsanity.com/paper/2102.05379/) (2021)
- [DiGress: Discrete Denoising diffusion for graph generation](https://mlsanity.com/paper/2209.14734/) (2022)
- [GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation](https://mlsanity.com/paper/2203.02923/) (2022)
- [Principal Neighbourhood Aggregation for Graph Nets](https://mlsanity.com/paper/2004.05718/) (2020)
- [A Continuous Time Framework for Discrete Denoising Models](https://mlsanity.com/paper/2205.14987/) (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)
- [GraphVAE: Towards Generation of Small Graphs Using Variational Autoencoders](https://mlsanity.com/paper/1802.03480/) (2018)
- [Understanding Diffusion Objectives as the ELBO with Simple Data Augmentation](https://mlsanity.com/paper/2303.00848/) (2023)
- [GuacaMol: Benchmarking Models for De Novo Molecular Design](https://mlsanity.com/paper/1811.09621/) (2018)
- [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)
- [Permutation Invariant Graph Generation via Score-Based Generative Modeling](https://mlsanity.com/paper/2003.00638/) (2020)
- [Torsional Diffusion for Molecular Conformer Generation](https://mlsanity.com/paper/2206.01729/) (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)
- [Identity-aware Graph Neural Networks](https://mlsanity.com/paper/2101.10320/) (2021)

## Built on by (most cited first, 30 of 76)

- [Categorical Flow Maps](https://mlsanity.com/paper/2602.12233/) (2026)
- [How Efficient is LLM-Generated Code? A Rigorous & High-Standard Benchmark](https://mlsanity.com/paper/2406.06647/) (2024)
- [Cometh: A continuous-time discrete-state graph diffusion model](https://mlsanity.com/paper/2406.06449/) (2024)
- [Diffuse Everything: Multimodal Diffusion Models on Arbitrary State Spaces](https://mlsanity.com/paper/2506.07903/) (2025)
- [MDNS: Masked Diffusion Neural Sampler via Stochastic Optimal Control](https://mlsanity.com/paper/2508.10684/) (2025)
- [SelfElicit: Your Language Model Secretly Knows Where is the Relevant Evidence](https://mlsanity.com/paper/2502.08767/) (2025)
- [Graph Generative Pre-trained Transformer](https://mlsanity.com/paper/2501.01073/) (2025)
- [Pave Your Own Path: Graph Gradual Domain Adaptation on Fused Gromov-Wasserstein Geodesics](https://mlsanity.com/paper/2505.12709/) (2025)
- [Can Graph Neural Networks Learn Language with Extremely Weak Text Supervision?](https://mlsanity.com/paper/2412.08174/) (2024)
- [Flatten Graphs as Sequences: Transformers are Scalable Graph Generators](https://mlsanity.com/paper/2502.02216/) (2025)
- [Gradient Compressed Sensing: A Query-Efficient Gradient Estimator for High-Dimensional Zeroth-Order Optimization](https://mlsanity.com/paper/2405.16805/) (2024)
- [Breaking Silos: Adaptive Model Fusion Unlocks Better Time Series Forecasting](https://mlsanity.com/paper/2505.18442/) (2025)
- [Dynamic Generation of Multi-LLM Agents Communication Topologies with Graph Diffusion Models](https://mlsanity.com/paper/2510.07799/) (2025)
- [Ask, and it shall be given: On the Turing completeness of prompting](https://mlsanity.com/paper/2411.01992/) (2024)
- [Improving Molecular Graph Generation with Flow Matching and Optimal Transport](https://mlsanity.com/paper/2411.05676/) (2024)
- [Simple and Critical Iterative Denoising: A Recasting of Discrete Diffusion in Graph Generation](https://mlsanity.com/paper/2503.21592/) (2025)
- [PLANETALIGN: A Comprehensive Python Library for Benchmarking Network Alignment](https://mlsanity.com/paper/2505.21366/) (2025)
- [Hierarchical LoRA MoE for Efficient CTR Model Scaling](https://mlsanity.com/paper/2510.10432/) (2025)
- [Prune as You Generate: Online Rollout Pruning for Faster and Better RLVR](https://mlsanity.com/paper/2603.24840/) (2026)
- [Bures-Wasserstein Flow Matching for Graph Generation](https://mlsanity.com/paper/2506.14020/) (2025)
- [InterFormer: Effective Heterogeneous Interaction Learning for Click-Through Rate Prediction](https://mlsanity.com/paper/2411.09852/) (2024)
- [HOG-Diff: Higher-Order Guided Diffusion for Graph Generation](https://mlsanity.com/paper/2502.04308/) (2025)
- [FragFM: Hierarchical Framework for Efficient Molecule Generation via Fragment-Level Discrete Flow Matching](https://mlsanity.com/paper/2502.15805/) (2025)
- [Learning Flexible Forward Trajectories for Masked Molecular Diffusion](https://mlsanity.com/paper/2505.16790/) (2025)
- [Graph Data Selection for Domain Adaptation: A Model-Free Approach](https://mlsanity.com/paper/2505.17293/) (2025)
- [PowerGrow: Feasible Co-Growth of Structures and Dynamics for Power Grid Synthesis](https://mlsanity.com/paper/2509.12212/) (2025)
- [Graph-GRPO: Training Graph Flow Models with Reinforcement Learning](https://mlsanity.com/paper/2603.10395/) (2026)
- [Principled Latent Diffusion for Graphs via Laplacian Autoencoders](https://mlsanity.com/paper/2601.13780/) (2026)
- [Backdoor Attacks on Discrete Graph Diffusion Models](https://mlsanity.com/paper/2503.06340/) (2025)
- [Recent Developments in GNNs for Drug Discovery](https://mlsanity.com/paper/2506.01302/) (2025)

## Abstract (arXiv)

Graph is a prevalent discrete data structure, whose generation has wide applications such as drug discovery and circuit design. Diffusion generative models, as an emerging research focus, have been applied to graph generation tasks. Overall, according to the space of states and time steps, diffusion generative models can be categorized into discrete-/continuous-state discrete-/continuous-time fashions. In this paper, we formulate the graph diffusion generation in a discrete-state continuous-time setting, which has never been studied in previous graph diffusion models. The rationale of such a formulation is to preserve the discrete nature of graph-structured data and meanwhile provide flexible sampling trade-offs between sample quality and efficiency. Analysis shows that our training objective is closely related to generation quality, and our proposed generation framework enjoys ideal invariant/equivariant properties concerning the permutation of node ordering. Our proposed model shows competitive empirical performance against state-of-the-art graph generation solutions on various benchmarks and, at the same time, can flexibly trade off the generation quality and efficiency in the sampling phase.