Sparse Training of Discrete Diffusion Models for Graph Generation
On the map: Diffusion models → Flow matching, time series and science
Abstract (arXiv)
Generative graph models struggle to scale due to the need to predict the existence or type of edges between all node pairs. To address the resulting quadratic complexity, existing scalable models often impose restrictive assumptions such as a cluster structure within graphs, thus limiting their applicability. To address this, we introduce SparseDiff, a novel diffusion model based on the observation that almost all large graphs are sparse. By selecting a subset of edges, SparseDiff effectively leverages sparse graph representations both during the noising process and within the denoising network, which ensures that space complexity scales linearly with the number of chosen edges. During inference, SparseDiff progressively fills the adjacency matrix with the selected subsets of edges, mirroring the training process. Our model demonstrates state-of-the-art performance across multiple metrics on both small and large datasets, confirming its effectiveness and robustness across varying graph sizes. It also ensures faster convergence, particularly on larger graphs, achieving a fourfold speedup on the large Ego dataset compared to dense models, thereby paving the way for broader applications.
Key facts. Cited by 26 papers in the map (data through 7 Oct 2026). Placed in Flow matching, time series and science, one of 14 directions in Diffusion models. Builds on 43 of its 56 references that are in the map. First posted on arXiv 3 Nov 2023.
Builds on
43 of 56 references.
Closest ancestors · 8
Same direction, newest first
- 2023Autoregressive Diffusion Model for Graph Generation17 Jul
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- 2023MiDi: Mixed Graph and 3D Denoising Diffusion for Molecule Generation17 Feb
- 2022Diffusion Models for Graphs Benefit From Discrete State Spaces4 Oct
- 2022DiGress: Discrete Denoising diffusion for graph generation29 Sep
- 2022Score-based Generative Modeling of Graphs via the System of Stochastic Differential Equations5 Feb
- 2020Permutation Invariant Graph Generation via Score-Based Generative Modeling2 Mar
Other references · 35
- 2020Denoising Diffusion Probabilistic Modelscited by 20,851
- 2020Denoising Diffusion Implicit Modelscited by 9,655
- 2017Graph Attention Networkscited by 8,854
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- 2017Neural Message Passing for Quantum Chemistrycited by 3,460
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- 2017FiLM: Visual Reasoning with a General Conditioning Layercited by 2,286
- 2022Imagen Video: High Definition Video Generation with Diffusion Modelscited by 1,765
- 2021Structured Denoising Diffusion Models in Discrete State-Spacescited by 1,665
- 2020DiffWave: A Versatile Diffusion Model for Audio Synthesiscited by 1,339
- 2017MoleculeNet: A Benchmark for Molecular Machine Learningcited by 1,037
- 2018Link Prediction Based on Graph Neural Networkscited by 829
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- 2018Junction Tree Variational Autoencoder for Molecular Graph Generationcited by 647
- 2020On the Bottleneck of Graph Neural Networks and its Practical Implicationscited by 624
- 2020Masked Label Prediction: Unified Message Passing Model for Semi-Supervised Classificationcited by 500
- 2020Principal Neighbourhood Aggregation for Graph Netscited by 477
- 2021Understanding over-squashing and bottlenecks on graphs via curvaturecited by 471
- 2018GraphRNN: Generating Realistic Graphs with Deep Auto-regressive Modelscited by 406
- 2018MolGAN: An implicit generative model for small molecular graphscited by 392
- 2018GraphVAE: Towards Generation of Small Graphs Using Variational Autoencoderscited by 375
- 2018Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Modelscited by 270
- 2019Deep Graph Library: A Graph-Centric, Highly-Performant Package for Graph Neural Networkscited by 241
- 2020Can Graph Neural Networks Count Substructures?cited by 235
- 2019Efficient Graph Generation with Graph Recurrent Attention Networkscited by 231
- 2020Hierarchical Generation of Molecular Graphs using Structural Motifscited by 204
- 2018Fr'echet ChemNet Distance: A metric for generative models for molecules in drug discoverycited by 191
- 2018Constrained Graph Variational Autoencoders for Molecule Designcited by 182
- 2023On Over-Squashing in Message Passing Neural Networks: The Impact of Width, Depth, and Topologycited by 163
- 2019GraphNVP: An Invertible Flow Model for Generating Molecular Graphscited by 115
- 2022SPECTRE: Spectral Conditioning Helps to Overcome the Expressivity Limits of One-shot Graph Generatorscited by 96
- 2022Graph Neural Networks for Link Prediction with Subgraph Sketchingcited by 81
- 2021Learning to Extend Molecular Scaffolds with Structural Motifscited by 70
- 2020Scalable Deep Generative Modeling for Sparse Graphscited by 63
- 2022On Evaluation Metrics for Graph Generative Modelscited by 44
- 2023HiGen: Hierarchical Graph Generative Networkscited by 5
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Citing papers per year: 2024: 8; 2025: 10; 2026: 8.
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- 2024Generative Flows on Discrete State-Spaces: Enabling Multimodal Flows with Applications to Protein Co-Designcited by 294
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- 2025Fast Solvers for Discrete Diffusion Models: Theory and Applications of High-Order Algorithmscited by 47
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- 2024Generative Modelling of Structurally Constrained Graphscited by 17
- 2025Simple and Critical Iterative Denoising: A Recasting of Discrete Diffusion in Graph Generationcited by 9
- 2025FragFM: Hierarchical Framework for Efficient Molecule Generation via Fragment-Level Discrete Flow Matchingcited by 5
- 2025TFG-Flow: Training-free Guidance in Multimodal Generative Flowcited by 4
- 2025Discrete State Diffusion Models: A Sample Complexity Perspectivecited by 4
- 2026Unrestrained Simplex Denoising for Discrete Data. A Non-Markovian Approach Applied to Graph Generationcited by 2
- 2026Principled Latent Diffusion for Graphs via Laplacian Autoencoderscited by 1
- 2026Hierarchical Discrete Flow Matching for Graph Generationcited by 1
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- 2026From Graphs to Feeders: Constraint-Guided Diffusion for Rule-Compliant Feeder Generation24 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 State Diffusion Models: A Sample Complexity Perspective12 Oct 2025
- 2025A collaborative constrained graph diffusion model for the generation of realistic synthetic molecules22 May 2025
- 2025Simple and Critical Iterative Denoising: A Recasting of Discrete Diffusion in Graph Generation27 Mar 2025
- 2025FragFM: Hierarchical Framework for Efficient Molecule Generation via Fragment-Level Discrete Flow Matching19 Feb 2025
- 2025Fast Solvers for Discrete Diffusion Models: Theory and Applications of High-Order Algorithms1 Feb 2025
- 2025TFG-Flow: Training-free Guidance in Multimodal Generative Flow24 Jan 2025
- 2024How Discrete and Continuous Diffusion Meet: Comprehensive Analysis of Discrete Diffusion Models via a Stochastic Integral Framework4 Oct 2024
12 newest of 15 All 15 (JSON)
- 2024Unlocking Guidance for Discrete State-Space Diffusion and Flow Modelscited by 124
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- 2025FreeScene: Mixed Graph Diffusion for 3D Scene Synthesis from Free Promptscited by 8
- 2025Scalable Generative Modeling of Weighted Graphscited by 2
- 2024GraphRCG: Self-Conditioned Graph Generationcited by 1
- 2024Heterogeneous Graph Generation: A Hierarchical Approach using Node Feature Poolingcited by 0
- 2025SynCircuit: Automated Generation of New Synthetic RTL Circuits Can Enable Big Data in Circuitscited by 0
- 2025CoPHo: Classifier-guided Conditional Topology Generation with Persistent Homologycited by 0
- 2026Local Message-Passing for Discrete Graph Generationcited by 0
- 2026DBMol: Design of High-Affinity, Target-Specific Small Molecules through Structure Prediction Modelscited by 0
- 2026Partially Observed Sparse Graphs: The Unknown Sampling Rate is a Tail Indexcited by 0
- 2026Partially Observed Sparse Graphs: The Unknown Sampling Rate is a Tail Index14 Aug 2026
- 2026DBMol: Design of High-Affinity, Target-Specific Small Molecules through Structure Prediction Models21 Jul 2026
- 2026Local Message-Passing for Discrete Graph Generation9 Mar 2026
- 2025CoPHo: Classifier-guided Conditional Topology Generation with Persistent Homology17 Dec 2025
- 2025SynCircuit: Automated Generation of New Synthetic RTL Circuits Can Enable Big Data in Circuits26 Aug 2025
- 2025Scalable Generative Modeling of Weighted Graphs30 Jul 2025
- 2025FreeScene: Mixed Graph Diffusion for 3D Scene Synthesis from Free Prompts3 Jun 2025
- 2024Heterogeneous Graph Generation: A Hierarchical Approach using Node Feature Pooling15 Oct 2024
- 2024Unlocking Guidance for Discrete State-Space Diffusion and Flow Models3 Jun 2024
- 2024GLAD: Improving Latent Graph Generative Modeling with Simple Quantization25 Mar 2024
- 2024GraphRCG: Self-Conditioned Graph Generation2 Mar 2024
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