The paper introduces TP‑DATE, a dynamic framework that extends Gromov–Wasserstein optimal transport (GW‑OT) to reconstruct continuous trajectories without simulation. It formulates a broad class of static and dynamic Quadratic‑form OT (QOT) via path actions, proving static‑dynamic equivalence, and develops travelling‑pair flow matching to capture interacting conditional paths in a single vector field. Experiments on synthetic and real spatial transcriptomics data show that TP‑DATE better preserves spatial structure and improves 3D dynamics reconstruction.
By Junda Ying, Zhiwei Zeng, Peijie Zhou, Lei Zhang
arXiv:2608. 15306v1 Announce Type: cross Abstract: High-throughput single-cell and spatial transcriptomic technologies provide high-resolution snapshots of heterogeneous cellular states, but their destructive nature prevents repeated measurements of the same cells over time.
By Mary Chriselda Antony Oliver, Kaitlyn Hohmeier, Tuyen Tran, Alejandra Castillo, Caroline Moosm\"uller, Shiying Li
arXiv:2510. 01894v3 Announce Type: replace Abstract: Many natural dynamic processes -- such as in vivo cellular differentiation or disease progression -- can only be observed through the lens of static sample snapshots.
By Thomas Gravier, Thomas Boyer, Auguste Genovesio
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
Reconstructing population dynamics is a central problem in the physical and data sciences. Often, the dynamics are modeled as a Wasserstein gradient flow (WGF): a curve of distributions driven by an energy functional.
arXiv:2607. 04738v1 Announce Type: cross Abstract: Reconstructing population dynamics is a central problem in the physical and data sciences.
By Markus Heinonen, Yair Shenfeld, Ricardo Baptista, Daniel Waxman, Dmitry Batenkov, Tim Cooijmans, Eli Bingham
arXiv:2609.25659v1 Announce Type: new
Abstract: Many scientific datasets, such as molecular conformational ensembles or single-cell tissue measurements, are naturally modeled as meta-distributions: d...
By Doron Haviv, Edward De Brouwer, Rishabh Anand, Rex Ying, A\"icha Bentaieb, Gabriele Scalia, Hector Corrada Bravo
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
The paper introduces a new framework for learning continuous-time diffeomorphic image registration by modeling a non-autonomous ODE as a two-parameter flow map. By enforcing cocycle consistency, the method learns flow maps without time discretization or velocity integration during training, enabling efficient inference with few compositions. Experiments on nine datasets show consistent alignment improvements, including a 2.1% Dice gain on brain MRI, 12% TRE reduction on lung CT, and 2.6% Dice improvement on cardiac MRI and ultrasound.
By Mohammadjavad Matinkia, Nilanjan Ray
We introduce Potential Matching Optimal Transport (PMOT), a potential-flow framework for general $p$-cost optimal transport with $c_p(x,y)=\|x-y\|^p$. PMOT parameterizes the CNF velocity field with a scalar potential in the generalized Benamou--Brenier form for the chosen exponent $p$.
arXiv:2608. 04234v1 Announce Type: cross Abstract: We study the problem of aligning data from multiple modalities into a shared representation space, focusing on settings where strong pretrained unimodal encoders are available but cross-modal paired data are scarce.
By Yixuan Florence Wu, Yilun Zhu, Naichen Shi
arXiv:2606. 05327v1 Announce Type: new Abstract: Flow matching (FM) has emerged as a powerful framework for learning dynamic transport maps between two empirical distributions.
By Raghav Kansal, David Crair, Nghia Nguyen, Scott Pope, Bradley Parry