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

arXiv: https://arxiv.org/abs/2302.10907 · HTML: https://mlsanity.com/paper/2302.10907/

## Key facts

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

## 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 71)

- [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)
- [Diffusion Models Beat GANs on Image Synthesis](https://mlsanity.com/paper/2105.05233/) (2021)
- [Hierarchical Text-Conditional Image Generation with CLIP Latents](https://mlsanity.com/paper/2204.06125/) (2022)
- [Photorealistic Text-to-Image Diffusion Models with Deep Language Understanding](https://mlsanity.com/paper/2205.11487/) (2022)
- [Generative Adversarial Networks](https://mlsanity.com/paper/2203.00667/) (2022)
- [Generative Modeling by Estimating Gradients of the Data Distribution](https://mlsanity.com/paper/1907.05600/) (2019)
- [Auto-Encoding Variational Bayes](https://mlsanity.com/paper/1312.6114/) (2013)
- [Elucidating the Design Space of Diffusion-Based Generative Models](https://mlsanity.com/paper/2206.00364/) (2022)
- [Video Diffusion Models](https://mlsanity.com/paper/2204.03458/) (2022)
- [DPM-Solver: A Fast ODE Solver for Diffusion Probabilistic Model Sampling in Around 10 Steps](https://mlsanity.com/paper/2206.00927/) (2022)
- [Structured Denoising Diffusion Models in Discrete State-Spaces](https://mlsanity.com/paper/2107.03006/) (2021)
- [Image Super-Resolution via Iterative Refinement](https://mlsanity.com/paper/2104.07636/) (2021)
- [DiffWave: A Versatile Diffusion Model for Audio Synthesis](https://mlsanity.com/paper/2009.09761/) (2020)
- [Normalizing Flows for Probabilistic Modeling and Inference](https://mlsanity.com/paper/1912.02762/) (2019)
- [Cascaded Diffusion Models for High Fidelity Image Generation](https://mlsanity.com/paper/2106.15282/) (2021)
- [Variational Diffusion Models](https://mlsanity.com/paper/2107.00630/) (2021)
- [Improved Techniques for Training Score-Based Generative Models](https://mlsanity.com/paper/2006.09011/) (2020)
- [Diffusion-LM Improves Controllable Text Generation](https://mlsanity.com/paper/2205.14217/) (2022)
- [Conditional Image Generation with PixelCNN Decoders](https://mlsanity.com/paper/1606.05328/) (2016)
- [Pseudo Numerical Methods for Diffusion Models on Manifolds](https://mlsanity.com/paper/2202.09778/) (2022)
- [Maximum Likelihood Training of Score-Based Diffusion Models](https://mlsanity.com/paper/2101.09258/) (2021)
- [Score-based Generative Modeling in Latent Space](https://mlsanity.com/paper/2106.05931/) (2021)
- [WaveGrad: Estimating Gradients for Waveform Generation](https://mlsanity.com/paper/2009.00713/) (2020)
- [CSDI: Conditional Score-based Diffusion Models for Probabilistic Time Series Imputation](https://mlsanity.com/paper/2107.03502/) (2021)
- [Argmax Flows and Multinomial Diffusion: Learning Categorical Distributions](https://mlsanity.com/paper/2102.05379/) (2021)
- [GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation](https://mlsanity.com/paper/2203.02923/) (2022)
- [Label-Efficient Semantic Segmentation with Diffusion Models](https://mlsanity.com/paper/2112.03126/) (2021)
- [SRDiff: Single Image Super-Resolution with Diffusion Probabilistic Models](https://mlsanity.com/paper/2104.14951/) (2021)

## Built on by (most cited first, 15 of 15)

- [An Overview of Diffusion Models: Applications, Guided Generation, Statistical Rates and Optimization](https://mlsanity.com/paper/2404.07771/) (2024)
- [Gradient Guidance for Diffusion Models: An Optimization Perspective](https://mlsanity.com/paper/2404.14743/) (2024)
- [On the Design Fundamentals of Diffusion Models: A Survey](https://mlsanity.com/paper/2306.04542/) (2023)
- [Enhancing Deep Reinforcement Learning: A Tutorial on Generative Diffusion Models in Network Optimization](https://mlsanity.com/paper/2308.05384/) (2023)
- [Convergence Analysis of Discrete Diffusion Model: Exact Implementation through Uniformization](https://mlsanity.com/paper/2402.08095/) (2024)
- [A Survey of Generative AI for de novo Drug Design: New Frontiers in Molecule and Protein Generation](https://mlsanity.com/paper/2402.08703/) (2024)
- [Convergence of Score-Based Discrete Diffusion Models: A Discrete-Time Analysis](https://mlsanity.com/paper/2410.02321/) (2024)
- [Almost Linear Convergence under Minimal Score Assumptions: Quantized Transition Diffusion](https://mlsanity.com/paper/2505.21892/) (2025)
- [Diffusion Transformer Captures Spatial-Temporal Dependencies: A Theory for Gaussian Process Data](https://mlsanity.com/paper/2407.16134/) (2024)
- [scRDiT: Generating single-cell RNA-seq data by diffusion transformers and accelerating sampling](https://mlsanity.com/paper/2404.06153/) (2024)
- [Diffusion Models for Reinforcement Learning: Foundations, Taxonomy, and Development](https://mlsanity.com/paper/2510.12253/) (2025)
- [Temporal Evolution of Knee Osteoarthritis: A Diffusion-based Morphing Model for X-ray Medical Image Synthesis](https://mlsanity.com/paper/2408.00891/) (2024)
- [White-Box Diffusion Transformer for single-cell RNA-seq generation](https://mlsanity.com/paper/2411.06785/) (2024)
- [Denoising diffusion models for high-resolution microscopy image restoration](https://mlsanity.com/paper/2409.12078/) (2024)
- [DiffEx: Explaining a Classifier with Diffusion Models to Identify Microscopic Cellular Variations](https://mlsanity.com/paper/2502.09663/) (2025)

## 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.