mlsanityData to 7 Oct 2026

Diffusion Models in Bioinformatics: A New Wave of Deep Learning Revolution in Action

arXiv 2302.10907 ↗First posted 13 Feb 2023cs.LG cs.AI q-bio.QMcited by 15

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

Abstract (arXiv)

Denoising diffusion models have emerged as one of the most powerful generative models in recent years. They have achieved remarkable success in many fields, such as computer vision, natural language processing (NLP), and bioinformatics. Although there are a few excellent reviews on diffusion models and their applications in computer vision and NLP, there is a lack of an overview of their applications in bioinformatics. This review aims to provide a rather thorough overview of the applications of diffusion models in bioinformatics to aid their further development in bioinformatics and computational biology. We start with an introduction of the key concepts and theoretical foundations of three cornerstone diffusion modeling frameworks (denoising diffusion probabilistic models, noise-conditioned scoring networks, and stochastic differential equations), followed by a comprehensive description of diffusion models employed in the different domains of bioinformatics, including cryo-EM data enhancement, single-cell data analysis, protein design and generation, drug and small molecule design, and protein-ligand interaction. The review is concluded with a summary of the potential new development and applications of diffusion models in bioinformatics.

Key facts. Cited by 15 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 71 of its 97 references that are in the map. First posted on arXiv 13 Feb 2023.

Builds on

71 of 97 references.

Closest ancestors · 9

Same direction, newest first

  1. 2022Latent Space Diffusion Models of Cryo-EM Structures25 Nov
  2. 2022Structure-based Drug Design with Equivariant Diffusion Models24 Oct
  3. 2022Equivariant 3D-Conditional Diffusion Models for Molecular Linker Design11 Oct
  4. 2022Protein structure generation via folding diffusion30 Sep
  5. 2022Diffusion probabilistic modeling of protein backbones in 3D for the motif-scaffolding problem8 Jun
  6. 2022Protein Structure and Sequence Generation with Equivariant Denoising Diffusion Probabilistic Models26 May
  7. 2022GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation6 Mar
  8. 2022Score-based Generative Modeling of Graphs via the System of Stochastic Differential Equations5 Feb
  9. 2021CSDI: Conditional Score-based Diffusion Models for Probabilistic Time Series Imputation7 Jul

Other references · 62

  1. 2020Denoising Diffusion Probabilistic Modelscited by 20,851
  2. 2020Denoising Diffusion Implicit Modelscited by 9,655
  3. 2020Score-Based Generative Modeling through Stochastic Differential Equationscited by 8,964
  4. 2021Diffusion Models Beat GANs on Image Synthesiscited by 8,185
  5. 2022Hierarchical Text-Conditional Image Generation with CLIP Latentscited by 6,539
  6. 2022Photorealistic Text-to-Image Diffusion Models with Deep Language Understandingcited by 6,322
  7. 2022Generative Adversarial Networkscited by 5,603
  8. 2019Generative Modeling by Estimating Gradients of the Data Distributioncited by 4,067
  9. 2013Auto-Encoding Variational Bayescited by 3,980
  10. 2022Elucidating the Design Space of Diffusion-Based Generative Modelscited by 2,994
  11. 2022Video Diffusion Modelscited by 2,280
  12. 2022DPM-Solver: A Fast ODE Solver for Diffusion Probabilistic Model Sampling in Around 10 Stepscited by 1,961
38 more
  1. 2021Structured Denoising Diffusion Models in Discrete State-Spacescited by 1,665
  2. 2021Image Super-Resolution via Iterative Refinementcited by 1,506
  3. 2020DiffWave: A Versatile Diffusion Model for Audio Synthesiscited by 1,339
  4. 2019Normalizing Flows for Probabilistic Modeling and Inferencecited by 1,315
  5. 2021Cascaded Diffusion Models for High Fidelity Image Generationcited by 1,155
  6. 2021Variational Diffusion Modelscited by 1,145
  7. 2020Improved Techniques for Training Score-Based Generative Modelscited by 1,036
  8. 2022Diffusion-LM Improves Controllable Text Generationcited by 1,006
  9. 2016Conditional Image Generation with PixelCNN Decoderscited by 859
  10. 2022Pseudo Numerical Methods for Diffusion Models on Manifoldscited by 695
  11. 2021Maximum Likelihood Training of Score-Based Diffusion Modelscited by 670
  12. 2021Score-based Generative Modeling in Latent Spacecited by 634
  13. 2020WaveGrad: Estimating Gradients for Waveform Generationcited by 620
  14. 2021Argmax Flows and Multinomial Diffusion: Learning Categorical Distributionscited by 566
  15. 2021Label-Efficient Semantic Segmentation with Diffusion Modelscited by 495
  16. 2021SRDiff: Single Image Super-Resolution with Diffusion Probabilistic Modelscited by 415
  17. 2022Analytic-DPM: an Analytic Estimate of the Optimal Reverse Variance in Diffusion Probabilistic Modelscited by 331
  18. 2021Score-based diffusion models for accelerated MRIcited by 308
  19. 2022DiffDock: Diffusion Steps, Twists, and Turns for Molecular Dockingcited by 307
  20. 2021SegDiff: Image Segmentation with Diffusion Probabilistic Modelscited by 279
  21. 2022Cold Diffusion: Inverting Arbitrary Image Transforms Without Noisecited by 275
  22. 2022Torsional Diffusion for Molecular Conformer Generationcited by 262
  23. 2021Gotta Go Fast When Generating Data with Score-Based Modelscited by 218
  24. 2022Riemannian Score-Based Generative Modellingcited by 216
  25. 2021Autoregressive Diffusion Modelscited by 208
  26. 2022Diffusion-GAN: Training GANs with Diffusioncited by 203
  27. 2022Diffusion-based Time Series Imputation and Forecasting with Structured State Space Modelscited by 195
  28. 2022Unsupervised Medical Image Translation with Adversarial Diffusion Modelscited by 191
  29. 2021A Variational Perspective on Diffusion-Based Generative Models and Score Matchingcited by 182
  30. 2022EGSDE: Unpaired Image-to-Image Translation via Energy-Guided Stochastic Differential Equationscited by 172
  31. 2021On Fast Sampling of Diffusion Probabilistic Modelscited by 170
  32. 2022Lossy Image Compression with Conditional Diffusion Modelscited by 165
  33. 2020Multivariate Probabilistic Time Series Forecasting via Conditioned Normalizing Flowscited by 142
  34. 2022Adaptive Diffusion Priors for Accelerated MRI Reconstructioncited by 117
  35. 2022Diffusion-based Molecule Generation with Informative Prior Bridgescited by 104
  36. 2022DiffuseVAE: Efficient, Controllable and High-Fidelity Generation from Low-Dimensional Latentscited by 103
  37. 2021Step-unrolled Denoising Autoencoders for Text Generationcited by 102
  38. 2021A Conditional Point Diffusion-Refinement Paradigm for 3D Point Cloud Completioncited by 100

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Citing papers per year: 2023: 2; 2024: 10; 2025: 3.

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  1. 2024An Overview of Diffusion Models: Applications, Guided Generation, Statistical Rates and Optimizationcited by 72
  2. 2023On the Design Fundamentals of Diffusion Models: A Surveycited by 59
  3. 2024Gradient Guidance for Diffusion Models: An Optimization Perspectivecited by 59
  4. 2023Enhancing Deep Reinforcement Learning: A Tutorial on Generative Diffusion Models in Network Optimizationcited by 56
  5. 2024Convergence Analysis of Discrete Diffusion Model: Exact Implementation through Uniformizationcited by 44
  6. 2024A Survey of Generative AI for de novo Drug Design: New Frontiers in Molecule and Protein Generationcited by 29
  7. 2024Convergence of Score-Based Discrete Diffusion Models: A Discrete-Time Analysiscited by 24
  8. 2025Almost Linear Convergence under Minimal Score Assumptions: Quantized Transition Diffusioncited by 6
  9. 2024Diffusion Transformer Captures Spatial-Temporal Dependencies: A Theory for Gaussian Process Datacited by 5
  10. 2024scRDiT: Generating single-cell RNA-seq data by diffusion transformers and accelerating samplingcited by 3
  11. 2025Diffusion Models for Reinforcement Learning: Foundations, Taxonomy, and Developmentcited by 2
  12. 2024Temporal Evolution of Knee Osteoarthritis: A Diffusion-based Morphing Model for X-ray Medical Image Synthesiscited by 1
3 more
  1. 2024White-Box Diffusion Transformer for single-cell RNA-seq generationcited by 1
  2. 2024Denoising diffusion models for high-resolution microscopy image restorationcited by 0
  3. 2025DiffEx: Explaining a Classifier with Diffusion Models to Identify Microscopic Cellular Variationscited by 0

Similar, not cited

Close in wording, no citation either way

  1. 2024Sifting through the Noise: A Survey of Diffusion Probabilistic Models and Their Applications to Biomolecules
  2. 2025Learning Diffusion Models with Flexible Representation Guidance
  3. 2022Diffusion Models: A Comprehensive Survey of Methods and Applications
  4. 2022Diffusion Models in Vision: A Survey
  5. 2023Generative Diffusion Models on Graphs: Methods and Applications
  6. 2024Steering Masked Discrete Diffusion Models via Discrete Denoising Posterior Prediction
  7. 2022Diffusion Models for Medical Image Analysis: A Comprehensive Survey
  8. 2023Denoising Diffusion Probabilistic Models for Generation of Realistic Fully-Annotated Microscopy Image Data Sets