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 …

Sit: Exploring flow and diffusion-based generative models with scalable interpolant transformers

N Ma, M Goldstein, MS Albergo, NM Boffi… - … on Computer Vision, 2024 - Springer
Abstract We present Scalable Interpolant Transformers (SiT), a family of generative models
built on the backbone of Diffusion Transformers (DiT). The interpolant framework, which …

Improving and generalizing flow-based generative models with minibatch optimal transport

A Tong, K Fatras, N Malkin, G Huguet, Y Zhang… - arxiv preprint arxiv …, 2023 - arxiv.org
Continuous normalizing flows (CNFs) are an attractive generative modeling technique, but
they have thus far been held back by limitations in their simulation-based maximum …

Diffusion schrödinger bridge matching

Y Shi, V De Bortoli, A Campbell… - Advances in Neural …, 2023 - 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 …

Discrete flow matching

I Gat, T Remez, N Shaul, F Kreuk… - Advances in …, 2025 - proceedings.neurips.cc
Abstract Despite Flow Matching and diffusion models having emerged as powerful
generative paradigms for continuous variables such as images and videos, their application …

Equivariant flow matching

L Klein, A Krämer, F Noé - Advances in Neural Information …, 2023 - proceedings.neurips.cc
Normalizing flows are a class of deep generative models that are especially interesting for
modeling probability distributions in physics, where the exact likelihood of flows allows …

AlphaFold meets flow matching for generating protein ensembles

B **g, B Berger, T Jaakkola - arxiv preprint arxiv:2402.04845, 2024 - arxiv.org
The biological functions of proteins often depend on dynamic structural ensembles. In this
work, we develop a flow-based generative modeling approach for learning and sampling the …

Equivariant flow matching with hybrid probability transport for 3d molecule generation

Y Song, J Gong, M Xu, Z Cao, Y Lan… - Advances in …, 2023 - proceedings.neurips.cc
The generation of 3D molecules requires simultaneously deciding the categorical features
(atom types) and continuous features (atom coordinates). Deep generative models …

Perflow: Piecewise rectified flow as universal plug-and-play accelerator

H Yan, X Liu, J Pan, JH Liew… - Advances in Neural …, 2025 - proceedings.neurips.cc
Abstract We present Piecewise Rectified Flow (PeRFlow), a flow-based method for
accelerating diffusion models. PeRFlow divides the sampling process of generative flows …

Fast protein backbone generation with se (3) flow matching

J Yim, A Campbell, AYK Foong, M Gastegger… - arxiv preprint arxiv …, 2023 - arxiv.org
We present FrameFlow, a method for fast protein backbone generation using SE (3) flow
matching. Specifically, we adapt FrameDiff, a state-of-the-art diffusion model, to the flow …