# Integrating Dynamical Systems Modeling with Spatiotemporal scRNA-seq Data Analysis

arXiv: https://arxiv.org/abs/2503.11347 · HTML: https://mlsanity.com/paper/2503.11347/

## Key facts

- Cited by 9 papers in the map (data through 14 Oct 2026).
- Builds on 52 of its 207 references that are in the map.
- First posted on arXiv 14 Mar 2025.

## Builds on (most cited first, 30 of 52)

- [Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2006.11239/) (2020)
- [Score-Based Generative Modeling through Stochastic Differential Equations](https://mlsanity.com/paper/2011.13456/) (2020)
- [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)
- [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)
- [Building Normalizing Flows with Stochastic Interpolants](https://mlsanity.com/paper/2209.15571/) (2022)
- [Stochastic Interpolants: A Unifying Framework for Flows and Diffusions](https://mlsanity.com/paper/2303.08797/) (2023)
- [Improving and generalizing flow-based generative models with minibatch optimal transport](https://mlsanity.com/paper/2302.00482/) (2023)
- [Computational Optimal Transport](https://mlsanity.com/paper/1803.00567/) (2018)
- [Diffusion Schr"odinger Bridge with Applications to Score-Based Generative Modeling](https://mlsanity.com/paper/2106.01357/) (2021)
- [A survey of the Schr"odinger problem and some of its connections with optimal transport](https://mlsanity.com/paper/1308.0215/) (2013)
- [Likelihood Training of Schr"odinger Bridge using Forward-Backward SDEs Theory](https://mlsanity.com/paper/2110.11291/) (2021)
- [I2SB: Image-to-Image Schr"odinger Bridge](https://mlsanity.com/paper/2302.05872/) (2023)
- [Denoising Diffusion Bridge Models](https://mlsanity.com/paper/2309.16948/) (2023)
- [Optimal Transport for structured data with application on graphs](https://mlsanity.com/paper/1805.09114/) (2018)
- [TrajectoryNet: A Dynamic Optimal Transport Network for Modeling Cellular Dynamics](https://mlsanity.com/paper/2002.04461/) (2020)
- [Diffusion Schr"odinger Bridge Matching](https://mlsanity.com/paper/2303.16852/) (2023)
- [Deep Generative Learning via Schr"odinger Bridge](https://mlsanity.com/paper/2106.10410/) (2021)
- [On the relation between optimal transport and Schr"odinger bridges: A stochastic control viewpoint](https://mlsanity.com/paper/1412.4430/) (2014)
- [Action Matching: Learning Stochastic Dynamics from Samples](https://mlsanity.com/paper/2210.06662/) (2022)
- [A Machine Learning Framework for Solving High-Dimensional Mean Field Game and Mean Field Control Problems](https://mlsanity.com/paper/1912.01825/) (2019)
- [Simulation-free Schr"odinger bridges via score and flow matching](https://mlsanity.com/paper/2307.03672/) (2023)
- [Manifold Interpolating Optimal-Transport Flows for Trajectory Inference](https://mlsanity.com/paper/2206.14928/) (2022)
- [The Schr"odinger Bridge between Gaussian Measures has a Closed Form](https://mlsanity.com/paper/2202.05722/) (2022)
- [Deep Generalized Schr"odinger Bridge](https://mlsanity.com/paper/2209.09893/) (2022)
- [A Computational Framework for Solving Wasserstein Lagrangian Flows](https://mlsanity.com/paper/2310.10649/) (2023)
- [Convergence of flow-based generative models via proximal gradient descent in Wasserstein space](https://mlsanity.com/paper/2310.17582/) (2023)
- [Unbalancedness in Neural Monge Maps Improves Unpaired Domain Translation](https://mlsanity.com/paper/2311.15100/) (2023)
- [Learning stochastic dynamics from snapshots through regularized unbalanced optimal transport](https://mlsanity.com/paper/2410.00844/) (2024)

## Built on by (most cited first, 9 of 9)

- [Joint Velocity-Growth Flow Matching for Single-Cell Dynamics Modeling](https://mlsanity.com/paper/2505.13413/) (2025)
- [Modeling Cell Dynamics and Interactions with Unbalanced Mean Field Schr"odinger Bridge](https://mlsanity.com/paper/2505.11197/) (2025)
- [Variational Regularized Unbalanced Optimal Transport: Single Network, Least Action](https://mlsanity.com/paper/2505.11823/) (2025)
- [Learning of Population Dynamics: Inverse Optimization Meets JKO Scheme](https://mlsanity.com/paper/2506.01502/) (2025)
- [WFR-FM: Simulation-Free Dynamic Unbalanced Optimal Transport](https://mlsanity.com/paper/2601.06810/) (2026)
- [CellStream: Dynamical Optimal Transport Informed Embeddings for Reconstructing Cellular Trajectories from Snapshots Data](https://mlsanity.com/paper/2511.13786/) (2025)
- [TracingFlow: A Simulation-Free Trajectory Inference Framework Based on Second-Order Dynamics](https://mlsanity.com/paper/2608.21070/) (2026)
- [Cell-cell Communication Inference and Analysis: Biological Mechanisms, Computational Approaches, and Future Opportunities](https://mlsanity.com/paper/2512.03497/) (2025)
- [Multiscale Supervised Unbalanced Optimal Transport Flow Matching](https://mlsanity.com/paper/2605.16529/) (2026)

## Abstract (arXiv)

Understanding the dynamic nature of biological systems is fundamental to deciphering cellular behavior, developmental processes, and disease progression. Single-cell RNA sequencing (scRNA-seq) has provided static snapshots of gene expression, offering valuable insights into cellular states at a single time point. Recent advancements in temporally resolved scRNA-seq, spatial transcriptomics (ST), and time-series spatial transcriptomics (temporal-ST) have further revolutionized our ability to study the spatiotemporal dynamics of individual cells. These technologies, when combined with computational frameworks such as Markov chains, stochastic differential equations (SDEs), and generative models like optimal transport and Schr"odinger bridges, enable the reconstruction of dynamic cellular trajectories and cell fate decisions. This review discusses how these dynamical system approaches offer new opportunities to model and infer cellular dynamics from a systematic perspective.