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 …

The emergence of reproducibility and consistency in diffusion models

H Zhang, J Zhou, Y Lu, M Guo, P Wang… - Forty-first International …, 2023 - openreview.net
In this work, we investigate an intriguing and prevalent phenomenon of diffusion models
which we term as" consistent model reproducibility'': given the same starting noise input and …

Inversion by direct iteration: An alternative to denoising diffusion for image restoration

M Delbracio, P Milanfar - arXiv preprint arXiv:2303.11435, 2023 - arxiv.org
Inversion by Direct Iteration (InDI) is a new formulation for supervised image restoration that
avoids the so-called" regression to the mean" effect and produces more realistic and …

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

A Tong, 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 …

Sampling thermodynamic ensembles of molecular systems with generative neural networks: Will integrating physics-based models close the generalization gap?

GM Rotskoff - Current Opinion in Solid State and Materials Science, 2024 - Elsevier
If the promise of generative modeling techniques is realized, it may fundamentally change
how we carry out molecular simulation. The suite of techniques and models collectively …

Learning single-cell perturbation responses using neural optimal transport

C Bunne, SG Stark, G Gut, JS Del Castillo… - Nature …, 2023 - nature.com
Understanding and predicting molecular responses in single cells upon chemical, genetic or
mechanical perturbations is a core question in biology. Obtaining single-cell measurements …

Action matching: Learning stochastic dynamics from samples

K Neklyudov, R Brekelmans… - … on machine learning, 2023 - proceedings.mlr.press
Learning the continuous dynamics of a system from snapshots of its temporal marginals is a
problem which appears throughout natural sciences and machine learning, including in …

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

N Ma, M Goldstein, MS Albergo, NM Boffi… - arXiv preprint arXiv …, 2024 - arxiv.org
We present Scalable Interpolant Transformers (SiT), a family of generative models built on
the backbone of Diffusion Transformers (DiT). The interpolant framework, which allows for …

Uncertainty quantification via neural posterior principal components

E Nehme, O Yair, T Michaeli - Advances in Neural …, 2023 - proceedings.neurips.cc
Uncertainty quantification is crucial for the deployment of image restoration models in safety-
critical domains, like autonomous driving and biological imaging. To date, methods for …

Denoising diffusion bridge models

L Zhou, A Lou, S Khanna, S Ermon - arXiv preprint arXiv:2309.16948, 2023 - arxiv.org
Diffusion models are powerful generative models that map noise to data using stochastic
processes. However, for many applications such as image editing, the model input comes …