Modeling Cell Dynamics and Interactions with Unbalanced Mean Field Schrödinger Bridge

Zhenyi Zhang, Zihan Wang, Yuhao Sun, Tiejun Li, Peijie Zhou

Keywords: optimal transport, Schrödinger bridge, trajectory inference, single-cell

TL;DR: We introduce CytoBridge, a new deep learning approach that models unbalanced stochastic cellular dynamics and interactions from snapshot data.

Abstract: Modeling the dynamics from sparsely time-resolved snapshot data is crucial for understanding complex cellular processes and behavior. Existing methods leverage optimal transport, Schrödinger bridge theory, or their variants to simultaneously infer stochastic, unbalanced dynamics from snapshot data. However, these approaches remain limited in their ability to account for cell-cell interactions. This integration is essential in real-world scenarios since intercellular communications are fundamental life processes and can influence cell state-transition dynamics. To address this challenge, we formulate the Unbalanced Mean-Field Schrödinger Bridge (UMFSB) framework to model unbalanced stochastic interaction dynamics from snapshot data. Inspired by this framework, we further propose CytoBridge, a deep learning algorithm designed to approximate the UMFSB problem. By explicitly modeling cellular transitions, proliferation, and interactions through neural networks, CytoBridge offers the flexibility to learn these processes directly from data. The effectiveness of our method has been extensively validated using both synthetic gene regulatory data and real scRNA-seq datasets. Compared to existing methods, CytoBridge identifies growth, transition, and interaction patterns, eliminates false transitions, and reconstructs the developmental landscape with greater accuracy. Code is available at: https://github.com/zhenyiizhang/CytoBridge-NeurIPS.

Primary Area: Machine learning for sciences (e.g. climate, health, life sciences, physics, social sciences)

Submission Number: 8055