Optimal transport for single-cell and spatial omics

C Bunne, G Schiebinger, A Krause, A Regev… - Nature Reviews …, 2024 - nature.com
High-throughput single-cell profiling provides an unprecedented ability to uncover the
molecular states of millions of cells. These technologies are, however, destructive to cells …

Diffusion Schrödinger bridge matching

Y Shi, V De Bortoli, A Campbell… - Advances in Neural …, 2024 - proceedings.neurips.cc
Solving transport problems, ie finding a map transporting one given distribution to another,
has numerous applications in machine learning. Novel mass transport methods motivated …

Generative modeling with phase stochastic bridges

T Chen, J Gu, L Dinh, EA Theodorou… - arxiv preprint arxiv …, 2023 - arxiv.org
Diffusion models (DMs) represent state-of-the-art generative models for continuous inputs.
DMs work by constructing a Stochastic Differential Equation (SDE) in the input space (ie …

A computational framework for solving Wasserstein Lagrangian flows

K Neklyudov, R Brekelmans, A Tong… - arxiv preprint arxiv …, 2023 - arxiv.org
The dynamical formulation of the optimal transport can be extended through various choices
of the underlying geometry ($\textit {kinetic energy} $), and the regularization of density …

Learning diffusion at lightspeed

A Terpin, N Lanzetti, M Gadea, F Dörfler - arxiv preprint arxiv:2406.12616, 2024 - arxiv.org
Diffusion regulates numerous natural processes and the dynamics of many successful
generative models. Existing models to learn the diffusion terms from observational data rely …

Generative modeling for time series via Schr {\" o} dinger bridge

M Hamdouche, P Henry-Labordere, H Pham - arxiv preprint arxiv …, 2023 - arxiv.org
We propose a novel generative model for time series based on Schr {\" o} dinger bridge (SB)
approach. This consists in the entropic interpolation via optimal transport between a …

Quantum state generation with structure-preserving diffusion model

Y Zhu, T Chen, EA Theodorou, X Chen… - arxiv preprint arxiv …, 2024 - arxiv.org
This article considers the generative modeling of the states of quantum systems, and an
approach based on denoising diffusion model is proposed. The key contribution is an …

Correlational Lagrangian Schr\" odinger Bridge: Learning Dynamics with Population-Level Regularization

Y You, R Zhou, Y Shen - arxiv preprint arxiv:2402.10227, 2024 - arxiv.org
Accurate modeling of system dynamics holds intriguing potential in broad scientific fields
including cytodynamics and fluid mechanics. This task often presents significant challenges …

Variational Schr\" odinger Momentum Diffusion

K Rojas, Y Tan, M Tao, Y Nevmyvaka… - arxiv preprint arxiv …, 2025 - arxiv.org
The momentum Schr\" odinger Bridge (mSB) has emerged as a leading method for
accelerating generative diffusion processes and reducing transport costs. However, the lack …

Multi-marginal Schr\" odinger Bridges with Iterative Reference Refinement

Y Shen, R Berlinghieri, T Broderick - arxiv preprint arxiv:2408.06277, 2024 - arxiv.org
Practitioners often aim to infer an unobserved population trajectory using sample snapshots
at multiple time points. Eg, given single-cell sequencing data, scientists would like to learn …