11 papers
TracingFlow: A Simulation-Free Trajectory Inference Framework Based on Second-Order Dynamics
Yuhao Sun, Zekun Wu, Zixun Huang +1
Inferring continuous system evolution from sparse temporal snapshots is a key challenge in generative modeling and single-cell omics. While Optimal Transport (OT) is popular, exist…
Beyond Continuity: Simulation-free Reconstruction of Discrete Branching Dynamics from Single-cell Snapshots
Junda Ying, Yuxuan Wang, Bowen Yang +2
Inferring cellular trajectories from destructive snapshots is complicated by the challenges of stochasticity and non-conservative mass dynamics such as cell proliferation and apopt…
Multiscale Supervised Unbalanced Optimal Transport Flow Matching
Qiangwei Peng, Lezhi Chen, Peijie Zhou
Unbalanced optimal transport (UOT) provides a principled framework for modeling single-cell transitions and birth-death dynamics, but its high computational cost limits scalability…
WFR-FM: Simulation-Free Dynamic Unbalanced Optimal Transport
Qiangwei Peng, Zihan Wang, Junda Ying +5
The Wasserstein-Fisher-Rao (WFR) metric extends dynamic optimal transport (OT) by coupling displacement with change of mass, providing a principled geometry for modeling unbalanced…
WFR-MFM: One-Step Inference for Dynamic Unbalanced Optimal Transport
Xinyu Wang, Ruoyu Wang, Qiangwei Peng +2
Reconstructing dynamical evolution from limited observations is a fundamental challenge in single-cell biology, where dynamic unbalanced optimal transport provides a principled fra…
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…