mlsanityData to 7 Oct 2026

Graph Diffusion Transformers for Multi-Conditional Molecular Generation

arXiv 2401.13858 ↗First posted 24 Jan 2024cs.LG q-bio.BMcited by 44

On the map: Diffusion models → Flow matching, time series and science

Abstract (arXiv)

Inverse molecular design with diffusion models holds great potential for advancements in material and drug discovery. Despite success in unconditional molecular generation, integrating multiple properties such as synthetic score and gas permeability as condition constraints into diffusion models remains unexplored. We present the Graph Diffusion Transformer (Graph DiT) for multi-conditional molecular generation. Graph DiT integrates an encoder to learn numerical and categorical property representations with the Transformer-based denoiser. Unlike previous graph diffusion models that add noise separately on the atoms and bonds in the forward diffusion process, Graph DiT is trained with a novel graph-dependent noise model for accurate estimation of graph-related noise in molecules. We extensively validate Graph DiT for multi-conditional polymer and small molecule generation. Results demonstrate the superiority of Graph DiT across nine metrics from distribution learning to condition control for molecular properties. A polymer inverse design task for gas separation with feedback from domain experts further demonstrates its practical utility.

Key facts. Cited by 44 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 33 of its 50 references that are in the map. First posted on arXiv 24 Jan 2024.

Builds on

33 of 50 references.

Closest ancestors · 7

Same direction, newest first

  1. 2023Geometric Latent Diffusion Models for 3D Molecule Generation2 May
  2. 2023Data-Centric Learning from Unlabeled Graphs with Diffusion Model17 Mar
  3. 2022DiGress: Discrete Denoising diffusion for graph generation29 Sep
  4. 2022Equivariant Diffusion for Molecule Generation in 3D31 Mar
  5. 2022GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation6 Mar
  6. 2022Score-based Generative Modeling of Graphs via the System of Stochastic Differential Equations5 Feb
  7. 2020Permutation Invariant Graph Generation via Score-Based Generative Modeling2 Mar

Other references · 26

  1. 2017Attention Is All You Needcited by 59,932
  2. 2020Denoising Diffusion Probabilistic Modelscited by 20,851
  3. 2021Diffusion Models Beat GANs on Image Synthesiscited by 8,185
  4. 2022Scalable Diffusion Models with Transformerscited by 5,931
  5. 2022Classifier-Free Diffusion Guidancecited by 5,717
  6. 2021Improved Denoising Diffusion Probabilistic Modelscited by 3,736
  7. 2021GLIDE: Towards Photorealistic Image Generation and Editing with Text-Guided Diffusion Modelscited by 3,595
  8. 2017Arbitrary Style Transfer in Real-time with Adaptive Instance Normalizationcited by 1,998
  9. 2021Structured Denoising Diffusion Models in Discrete State-Spacescited by 1,665
  10. 2017MoleculeNet: A Benchmark for Molecular Machine Learningcited by 1,037
  11. 2017Sigmoid-Weighted Linear Units for Neural Network Function Approximation in Reinforcement Learningcited by 935
  12. 2018Junction Tree Variational Autoencoder for Molecular Graph Generationcited by 647
14 more
  1. 2018GuacaMol: Benchmarking Models for De Novo Molecular Designcited by 294
  2. 2018Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Modelscited by 270
  3. 2018Fr'echet ChemNet Distance: A metric for generative models for molecules in drug discoverycited by 191
  4. 2022Sample Efficiency Matters: A Benchmark for Practical Molecular Optimizationcited by 151
  5. 2021MARS: Markov Molecular Sampling for Multi-objective Drug Discoverycited by 125
  6. 2022Exploring Chemical Space with Score-based Out-of-distribution Generationcited by 95
  7. 2021Inverse design of 3d molecular structures with conditional generative neural networkscited by 93
  8. 2022Equivariant Energy-Guided SDE for Inverse Molecular Designcited by 72
  9. 2022Graph Rationalization with Environment-based Augmentationscited by 70
  10. 2021Differentiable Scaffolding Tree for Molecular Optimizationcited by 53
  11. 2023Sample-efficient Multi-objective Molecular Optimization with GFlowNetscited by 48
  12. 2023Genetic algorithms are strong baselines for molecule generationcited by 31
  13. 2023Semi-Supervised Graph Imbalanced Regressioncited by 14
  14. 2020Goal-directed Generation of Discrete Structures with Conditional Generative Modelscited by 8

Built on by

Cited by year (2026 to 7 Oct)

Citing papers per year: 2024: 4; 2025: 21; 2026: 19.

44 papers.

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By area:

  1. 2025Position: Graph Learning Will Lose Relevance Due To Poor Benchmarkscited by 52
  2. 2025Proximal Diffusion Neural Samplercited by 16
  3. 2025A Survey of Graph Transformers: Architectures, Theories and Applicationscited by 12
  4. 2024Learning Molecular Representation in a Cellcited by 8
  5. 2025FreeScene: Mixed Graph Diffusion for 3D Scene Synthesis from Free Promptscited by 8
  6. 2025Learning Flexible Forward Trajectories for Masked Molecular Diffusioncited by 6
  7. 2025MolTextNet: A Two-Million Molecule-Text Dataset for Multimodal Molecular Learningcited by 6
  8. 2025Graph Diffusion Transformers are In-Context Molecular Designerscited by 6
  9. 2025Graph-structured Small Molecule Drug Discovery Through Deep Learning: Progress, Challenges, and Opportunitiescited by 5
  10. 2025PowerGrow: Feasible Co-Growth of Structures and Dynamics for Power Grid Synthesiscited by 5
  11. 2025Controllable Graph Generation with Diffusion Models via Inference-Time Tree Search Guidancecited by 5
  12. 2026Molecular Representations in Implicit Functional Space via Hyper-Networkscited by 5
32 more
  1. 2026GoAgent: Group-of-Agents Communication Topology Generation for LLM-based Multi-Agent Systemscited by 5
  2. 2026RADAR: Redundancy-Aware Diffusion for Multi-Agent Communication Structure Generationcited by 5
  3. 2024Instruction-Based Molecular Graph Generation with Unified Text-Graph Diffusion Modelcited by 3
  4. 2025Backdoor Attacks on Discrete Graph Diffusion Modelscited by 3
  5. 2026Adaptive Diffusion Posterior Sampling for Data and Model Fusion of Complex Nonlinear Dynamical Systemscited by 3
  6. 2024Any-Property-Conditional Molecule Generation with Self-Criticism using Spanning Treescited by 2
  7. 2025Composable Score-based Graph Diffusion Model for Multi-Conditional Molecular Generationcited by 2
  8. 2025PolyGraph Discrepancy: a classifier-based metric for graph generationcited by 2
  9. 2024A General-Purpose Framework for Chemical Reaction Representation with Atomic Correspondence and Flexible Condition Adaptationcited by 1
  10. 2025DMol: A Highly Efficient and Chemical Motif-Preserving Molecule Generation Platformcited by 1
  11. 2025NMIRacle: Multi-modal Generative Molecular Elucidation from IR and NMR Spectracited by 1
  12. 2026NNiT: Width-Agnostic Neural Network Generation with Structurally Aligned Weight Spacescited by 1
  13. 2026FlowMS: Flow Matching for De Novo Structure Elucidation from Mass Spectracited by 1
  14. 2026VQ-SAD: Vector Quantized Structure Aware Diffusion For Molecule Generationcited by 1
  15. 2026Controllable Molecular Generative Foundation Modelscited by 1
  16. 2026From Uniform to Learned Graph Priors: Diffusion for Structure Discoverycited by 1
  17. 2025Learning Repetition-Invariant Representations for Polymer Informaticscited by 0
  18. 2025Cognitive Structure Generation: From Educational Priors to Policy Optimizationcited by 0
  19. 2025Cross-Modality Controlled Molecule Generation with Diffusion Language Modelcited by 0
  20. 2025A Conformation-Centric Generative Foundation Model for Linear Polymer Modeling and Designcited by 0
  21. 2025Scaffold-Aware Generative Augmentation and Reranking for Enhanced Virtual Screeningcited by 0
  22. 2025CoPHo: Classifier-guided Conditional Topology Generation with Persistent Homologycited by 0
  23. 2026Breaking the Bottlenecks: Scalable Diffusion Models for 3D Molecular Generationcited by 0
  24. 2026MolHIT: Advancing Molecular-Graph Generation with Hierarchical Discrete Diffusion Modelscited by 0
  25. 2026One Pass for All: A Discrete Diffusion Model for Knowledge Graph Triple Set Predictioncited by 0
  26. 2026BiMol-Diff: A Unified Diffusion Framework for Molecular Generation and Captioningcited by 0
  27. 2026Fine-Grained Graph Generation through Latent Mixture Schedulingcited by 0
  28. 2026Reading the Cell, Designing the Cure: Perturbation-Conditioned Molecular Diffusion for Function-Oriented Drug Designcited by 0
  29. 2026FLAG: Foundation model representation with Latent diffusion Alignment via Graph for spatial gene expression predictioncited by 0
  30. 2026CoDiffGRN: Rethinking Gene Regulatory Network Inference via the BEELINE-KGC Benchmark and Co-evolutionary Discrete Diffusioncited by 0
  31. 2026Graph Forward Distribution Matching for Molecular Inverse Designcited by 0
  32. 2026Stable Transformers for Graph Generationcited by 0

Similar, not cited

Close in wording, no citation either way

  1. 2023Conditional Diffusion Based on Discrete Graph Structures for Molecular Graph Generation
  2. 2025Graph Diffusion that can Insert and Delete
  3. 2025Sampling 3D Molecular Conformers with Diffusion Transformers
  4. 2025JTreeformer: Graph-Transformer via Latent-Diffusion Model for Molecular Generation
  5. 20243M-Diffusion: Latent Multi-Modal Diffusion for Language-Guided Molecular Structure Generation
  6. 2024Geometric-Facilitated Denoising Diffusion Model for 3D Molecule Generation
  7. 2023GraphGUIDE: interpretable and controllable conditional graph generation with discrete Bernoulli diffusion
  8. 2024Diffusion Models in textitDe Novo Drug Design