arXiv:2608.21070v1 Announce Type: cross
Abstract: Inferring continuous system evolution from sparse temporal snapshots is a key challenge in generative modeling and single-cell omics. While Optimal T...
By Yuhao Sun, Zekun Wu, Zixun Huang, Peijie Zhou
arXiv:2605. 00545v2 Announce Type: replace-cross Abstract: Inferring cellular trajectories from destructive snapshots is complicated by the challenges of stochasticity and non-conservative mass dynamics such as cell proliferation and apoptosis.
By Junda Ying, Yuxuan Wang, Bowen Yang, Peijie Zhou, Lei Zhang
Multiscale Supervised Unbalanced Optimal Transport Flow Matching (MUST‑FM) is a simulation‑free framework that scales unbalanced optimal transport (UOT) for single‑cell trajectory inference by exploiting hierarchical data structure. It optionally incorporates supervised transition priors, such as cell lineages, to guide displacement fields and mass variations. Experiments demonstrate reduced computational overhead and robust, biologically meaningful trajectory inference on atlas‑scale single‑cell datasets.
By Qiangwei Peng, Lezhi Chen, Peijie Zhou
arXiv:2606. 11286v1 Announce Type: cross Abstract: High-content imaging assays quantify cellular responses to chemical and genetic perturbations, yet continuous trajectories of individual cells are unobservable because cells are chemically fixed at acquisition.
By Xurui Wang, Qin Ren, Jun Ma, Haibin Ling, Chenyu You
The paper introduces Finsler Flow Matching (FFM), a method for learning continuous stochastic dynamics from discrete Markov transition graphs in single‑cell snapshot data. FFM constructs a Finsler geometry using first and second local moments, learns directed geodesics via neural networks, and employs these to build geometry‑aware stochastic paths that can be simulated without explicit score or flow matching. Benchmark tests show that FFM better recovers intermediate cellular states, especially when dynamics are directional or anisotropic.
By Niklas Canova, Jonas Simon Fleck
The paper introduces SUDO, a simulation‑free framework for unbalanced dynamic optimal transport (UDOT) that supports general convex growth penalties beyond the quadratic Wasserstein‑Fisher‑Rao case. By showing that concave penalties lead to degenerate solutions, the authors focus on convex penalties, learning conditional paths and transport costs to solve a semi‑coupling problem and then applying unbalanced flow matching. On benchmark datasets, SUDO matches the accuracy of analytical WFR solvers while being faster than simulation‑based methods, and it also handles asymmetric penalties that better reflect proliferation‑dominant biological priors.
By Junda Ying, Yuxuan Wang, Bowen Yang, Peijie Zhou, Lei Zhang