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 …

Computational optimal transport: With applications to data science

G Peyré, M Cuturi - Foundations and Trends® in Machine …, 2019 - nowpublishers.com
Optimal transport (OT) theory can be informally described using the words of the French
mathematician Gaspard Monge (1746–1818): A worker with a shovel in hand has to move a …

Banmo: Building animatable 3d neural models from many casual videos

G Yang, M Vo, N Neverova… - Proceedings of the …, 2022 - openaccess.thecvf.com
Prior work for articulated 3D shape reconstruction often relies on specialized multi-view and
depth sensors or pre-built deformable 3D models. Such methods do not scale to diverse sets …

A generalized loss function for crowd counting and localization

J Wan, Z Liu, AB Chan - … of the IEEE/CVF conference on …, 2021 - openaccess.thecvf.com
Previous work shows that a better density map representation can improve the performance
of crowd counting. In this paper, we investigate learning the density map representation …

Pot: Python optimal transport

R Flamary, N Courty, A Gramfort, MZ Alaya… - Journal of Machine …, 2021 - jmlr.org
Optimal transport has recently been reintroduced to the machine learning community thanks
in part to novel efficient optimization procedures allowing for medium to large scale …

Optimal transport minimization: Crowd localization on density maps for semi-supervised counting

W Lin, AB Chan - Proceedings of the IEEE/CVF Conference …, 2023 - openaccess.thecvf.com
The accuracy of crowd counting in images has improved greatly in recent years due to the
development of deep neural networks for predicting crowd density maps. However, most …

Unbalanced minibatch optimal transport; applications to domain adaptation

K Fatras, T Séjourné, R Flamary… - … on Machine Learning, 2021 - proceedings.mlr.press
Optimal transport distances have found many applications in machine learning for their
capacity to compare non-parametric probability distributions. Yet their algorithmic complexity …

Domain adaptation for time series under feature and label shifts

H He, O Queen, T Koker, C Cuevas… - International …, 2023 - proceedings.mlr.press
Unsupervised domain adaptation (UDA) enables the transfer of models trained on source
domains to unlabeled target domains. However, transferring complex time series models …

Alignment and integration of spatial transcriptomics data

R Zeira, M Land, A Strzalkowski, BJ Raphael - Nature Methods, 2022 - nature.com
Spatial transcriptomics (ST) measures mRNA expression across thousands of spots from a
tissue slice while recording the two-dimensional (2D) coordinates of each spot. We …

Reconstructing animatable categories from videos

G Yang, C Wang, ND Reddy… - Proceedings of the …, 2023 - openaccess.thecvf.com
Building animatable 3D models is challenging due to the need for 3D scans, laborious
registration, and manual rigging. Recently, differentiable rendering provides a pathway to …