# Flow Matching Meets Biology and Life Science: A Survey

arXiv: https://arxiv.org/abs/2507.17731 · HTML: https://mlsanity.com/paper/2507.17731/

## Key facts

- Cited by 14 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 138 of its 291 references that are in the map.
- First posted on arXiv 23 Jul 2025.

## 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 138)

- [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)
- [Masked Autoencoders Are Scalable Vision Learners](https://mlsanity.com/paper/2111.06377/) (2021)
- [Deep Unsupervised Learning using Nonequilibrium Thermodynamics](https://mlsanity.com/paper/1503.03585/) (2015)
- [Flow Matching for Generative Modeling](https://mlsanity.com/paper/2210.02747/) (2022)
- [Generative Modeling by Estimating Gradients of the Data Distribution](https://mlsanity.com/paper/1907.05600/) (2019)
- [Neural Ordinary Differential Equations](https://mlsanity.com/paper/1806.07366/) (2018)
- [Flow Straight and Fast: Learning to Generate and Transfer Data with Rectified Flow](https://mlsanity.com/paper/2209.03003/) (2022)
- [Variational Inference with Normalizing Flows](https://mlsanity.com/paper/1505.05770/) (2015)
- [Conditional Generative Adversarial Nets](https://mlsanity.com/paper/1411.1784/) (2014)
- [Density estimation using Real NVP](https://mlsanity.com/paper/1605.08803/) (2016)
- [DPM-Solver: A Fast ODE Solver for Diffusion Probabilistic Model Sampling in Around 10 Steps](https://mlsanity.com/paper/2206.00927/) (2022)
- [Consistency Models](https://mlsanity.com/paper/2303.01469/) (2023)
- [Structured Denoising Diffusion Models in Discrete State-Spaces](https://mlsanity.com/paper/2107.03006/) (2021)
- [Glow: Generative Flow with Invertible 1x1 Convolutions](https://mlsanity.com/paper/1807.03039/) (2018)
- [A Survey on Evaluation of Large Language Models](https://mlsanity.com/paper/2307.03109/) (2023)
- [Diffusion Models: A Comprehensive Survey of Methods and Applications](https://mlsanity.com/paper/2209.00796/) (2022)
- [NICE: Non-linear Independent Components Estimation](https://mlsanity.com/paper/1410.8516/) (2014)
- [Diffusion Models in Vision: A Survey](https://mlsanity.com/paper/2209.04747/) (2022)
- [Least Squares Generative Adversarial Networks](https://mlsanity.com/paper/1611.04076/) (2016)
- [An Introduction to Variational Autoencoders](https://mlsanity.com/paper/1906.02691/) (2019)
- [Building Normalizing Flows with Stochastic Interpolants](https://mlsanity.com/paper/2209.15571/) (2022)
- [Improving and generalizing flow-based generative models with minibatch optimal transport](https://mlsanity.com/paper/2302.00482/) (2023)
- [Generalizing to Unseen Domains: A Survey on Domain Generalization](https://mlsanity.com/paper/2103.03097/) (2021)
- [Masked Autoregressive Flow for Density Estimation](https://mlsanity.com/paper/1705.07057/) (2017)
- [Benchmarking Graph Neural Networks](https://mlsanity.com/paper/2003.00982/) (2020)
- [Equivariant Diffusion for Molecule Generation in 3D](https://mlsanity.com/paper/2203.17003/) (2022)
- [Wasserstein GAN](https://mlsanity.com/paper/1701.07875/) (2017)
- [The Medical Segmentation Decathlon](https://mlsanity.com/paper/2106.05735/) (2021)

## Built on by (most cited first, 14 of 14)

- [Learning on the Manifold: Unlocking Standard Diffusion Transformers with Representation Encoders](https://mlsanity.com/paper/2602.10099/) (2026)
- [Hierarchical LoRA MoE for Efficient CTR Model Scaling](https://mlsanity.com/paper/2510.10432/) (2025)
- [SplineFlow: Flow Matching for Dynamical Systems with B-Spline Interpolants](https://mlsanity.com/paper/2601.23072/) (2026)
- [Mixture of Sequence: Theme-Aware Mixture-of-Experts for Long-Sequence Recommendation](https://mlsanity.com/paper/2604.20858/) (2026)
- [Fast Organic Crystal Structure Prediction with Unit Cell Flow Matching](https://mlsanity.com/paper/2606.03199/) (2026)
- [ContextFlow: Context-Aware Flow Matching For Trajectory Inference From Spatial Omics Data](https://mlsanity.com/paper/2510.02952/) (2025)
- [Deep Neural Networks Inspired by Differential Equations](https://mlsanity.com/paper/2510.09685/) (2025)
- [Graph homophily booster: Reimagining the role of discrete features in heterophilic graph learning](https://mlsanity.com/paper/2602.07256/) (2026)
- [Elucidating the Design Space of Flow Matching for Cellular Microscopy](https://mlsanity.com/paper/2603.26790/) (2026)
- [LDDMM stochastic interpolants: an application to domain uncertainty quantification in hemodynamics](https://mlsanity.com/paper/2603.28324/) (2026)
- [Mat'ern Noise for Triangulation-Agnostic Flow Matching on Meshes](https://mlsanity.com/paper/2605.19305/) (2026)
- [Canopy: A Heterograph Foundation Model for Metabolic Engineering](https://mlsanity.com/paper/2607.06224/) (2026)
- [Renormalization Group Flow Matching for Scalable Local Generative Modeling](https://mlsanity.com/paper/2608.23696/) (2026)
- [Stable Transformers for Graph Generation](https://mlsanity.com/paper/2609.39739/) (2026)

## Abstract (arXiv)

Over the past decade, advances in generative modeling, such as generative adversarial networks, masked autoencoders, and diffusion models, have significantly transformed biological research and discovery, enabling breakthroughs in molecule design, protein generation, catalysis discovery, drug discovery, and beyond. At the same time, biological applications have served as valuable testbeds for evaluating the capabilities of generative models. Recently, flow matching has emerged as a powerful and efficient alternative to diffusion-based generative modeling, with growing interest in its application to problems in biology and life sciences. This paper presents the first comprehensive survey of recent developments in flow matching and its applications in biological domains. We begin by systematically reviewing the foundations and variants of flow matching, and then categorize its applications into three major areas: biological sequence modeling, molecule generation and design, and peptide and protein generation. For each, we provide an in-depth review of recent progress. We also summarize commonly used datasets and software tools, and conclude with a discussion of potential future directions. The corresponding curated resources are available at https://github.com/Violet24K/Awesome-Flow-Matching-Meets-Biology.