References¶

If you find this package helpful in your research, we would greatly appreciate it if you could consider citing our following work.

The first two papers are our surveys, in which we originally proposed the concept of this package.

Zhenyi Zhang, Zihan Wang, Yuhao Sun, Jiantao Shen, Qiangwei Peng, Tiejun Li, and Peijie Zhou. “Deciphering cell-fate trajectories using spatiotemporal single-cell transcriptomic data“. npj Syst Biol Appl 2025. (https://www.nature.com/articles/s41540-025-00624-9)
Zhenyi Zhang, Yuhao Sun, Qiangwei Peng, Tiejun Li, and Peijie Zhou. “Integrating Dynamical Systems Modeling with Spatiotemporal scRNA-Seq Data Analysis”. In: Entropy 27.5, 2025b. ISSN: 1099-4300.

These paper present the core algorithm on which this package is built.

Zhenyi Zhang, Tiejun Li, and Peijie Zhou. “Learning stochastic dynamics from snapshots through regularized unbalanced optimal transport”. In: ICLR 2025 Oral.
Zhenyi Zhang, Zihan Wang, Yuhao Sun, Tiejun Li, and Peijie Zhou. “Modeling Cell Dynamics and Interactions with Unbalanced Mean Field Schrödinger Bridge”. In: NeurIPS 2025.
Dongyi Wang, Yuanwei Jiang, Zhenyi Zhang, Xiang Gu, Peijie Zhou, and Jian Sun. “Joint Velocity-Growth Flow Matching for Single-Cell Dynamics Modeling”. In: NeurIPS 2025.

Additional related papers may be cited as needed.

Yuhao Sun, Zhenyi Zhang, Zihan Wang, Tiejun Li, and Peijie Zhou. “Variational Regularized Unbalanced Optimal Transport: Single Network, Least Action”. In: NeurIPS 2025.
Qiangwei Peng, Peijie Zhou, and Tiejun Li. “stVCR: Reconstructing spatio-temporal dynamics of cell development using optimal transport”. In: Nature Methods.

We would also like to acknowledge our other package, as many implementations in the current framework are built upon it.