7 papers
Entropy production in Knudsen thermodynamics of compartmented systems
Timothy Chumley, Renato Feres, Zhenyi Zhang
We investigate entropy production and nonequilibrium transport in a class of random dynamical systems modeling a Knudsen gas confined to a compartmented container. The system consi…
CellStream: Dynamical Optimal Transport Informed Embeddings for Reconstructing Cellular Trajectories from Snapshots Data
Yue Ling, Peiqi Zhang, Zhenyi Zhang +1
Single-cell RNA sequencing (scRNA-seq), especially temporally resolved datasets, enables genome-wide profiling of gene expression dynamics at single-cell resolution across discrete…
Joint Velocity-Growth Flow Matching for Single-Cell Dynamics Modeling
Dongyi Wang, Yuanwei Jiang, Zhenyi Zhang +3
Learning the underlying dynamics of single cells from snapshot data has gained increasing attention in scientific and machine learning research. The destructive measurement techniq…
Variational Regularized Unbalanced Optimal Transport: Single Network, Least Action
Yuhao Sun, Zhenyi Zhang, Zihan Wang +2
Recovering the dynamics from a few snapshots of a high-dimensional system is a challenging task in statistical physics and machine learning, with important applications in computat…
Modeling Cell Dynamics and Interactions with Unbalanced Mean Field Schrödinger Bridge
Zhenyi Zhang, Zihan Wang, Yuhao Sun +2
Modeling the dynamics from sparsely time-resolved snapshot data is crucial for understanding complex cellular processes and behavior. Existing methods leverage optimal transport, S…
Learning stochastic dynamics from snapshots through regularized unbalanced optimal transport
Zhenyi Zhang, Tiejun Li, Peijie Zhou
Reconstructing dynamics using samples from sparsely time-resolved snapshots is an important problem in both natural sciences and machine learning. Here, we introduce a new deep lea…