Inferring spatial and signaling relationships between cells from single cell transcriptomic data.

Single-cell RNA sequencing (scRNA-seq) provides details for individual cells; however, crucial spatial information is often lost. We present SpaOTsc, a method relying on structured optimal transport to recover spatial properties of scRNA-seq data by utilizing spatial measurements of a relatively small number of genes. A spatial metric for individual cells in scRNA-seq data is first established based on a map connecting it with the spatial measurements. The cell-cell communications are then obtained by "optimally transporting" signal senders to target signal receivers in space. Using partial information decomposition, we next compute the intercellular gene-gene information flow to estimate the spatial regulations between genes across cells. Four datasets are employed for cross-validation of spatial gene expression prediction and comparison to known cell-cell communications. SpaOTsc has broader applications, both in integrating non-spatial single-cell measurements with spatial data, and directly in spatial single-cell transcriptomics data to reconstruct spatial cellular dynamics in tissues

Minimax estimation of smooth optimal transport maps

Brenier's theorem is a cornerstone of optimal transport that guarantees the existence of an optimal transport map $T$ between two probability distributions $P$ and $Q$ over $\mathbb{R}^d$ under certain regularity conditions. The main goal of this work is to establish the minimax estimation rates for such a transport map from data sampled from $P$ and $Q$ under additional smoothness assumptions on $T$. To achieve this goal, we develop an estimator based on the minimization of an empirical version of the semi-dual optimal transport problem, restricted to truncated wavelet expansions. This estimator is shown to achieve near minimax optimality using new stability arguments for the semi-dual and a complementary minimax lower bound. Furthermore, we provide numerical experiments on synthetic data supporting our theoretical findings and highlighting the practical benefits of smoothness regularization. These are the first minimax estimation rates for transport maps in general dimension.Comment: 53 pages, 6 figure

Fully Probabilistic Design for Optimal Transport

The goal of this paper is to introduce a new theoretical framework for Optimal Transport (OT), using the terminology and techniques of Fully Probabilistic Design (FPD). Optimal Transport is the canonical method for comparing probability measures and has been successfully applied in a wide range of areas (computer vision Rubner et al. [2004], computer graphics Solomon et al. [2015], natural language processing Kusner et al. [2015], etc.). However, we argue that the current OT framework suffers from two shortcomings: first, it is hard to induce generic constraints and probabilistic knowledge in the OT problem; second, the current formalism does not address the question of uncertainty in the marginals, lacking therefore the mechanisms to design robust solutions. By viewing the OT problem as the optimal design of a probability density function with marginal constraints, we prove that OT is an instance of the more generic FPD framework. In this new setting, we can furnish the OT framework with the necessary mechanisms for processing probabilistic constraints and deriving uncertainty quantifiers, hence establishing a new extended framework, called FPD-OT. Our main contribution in this paper is to establish the connection between OT and FPD, providing new theoretical insights for both. This will lay the foundations for the application of FPD-OT in a subsequent work, notably in processing more sophisticated knowledge constraints, as well as in designing robust solutions in the case of uncertain marginals.Comment: Keywords: Optimal Transport, Fully Probabilistic Design, Convex optimizatio

Optimal Transport vs Many-to-many assignment for Graph Matching

National audienceGraph matching for shape comparison or network analysis is a challenging issue in machine learning and computer vision. Gener-ally, this problem is formulated as an assignment task, where we seek the optimal matching between the vertices that minimizes the differencebetween the graphs. We compare a standard approach to perform graph matching, to a slightly-adapted version of regularized optimal transport,initially conceived to obtain the Gromov-Wassersein distance between structured objects (e.g. graphs) with probability masses associated to thenodes. We adapt the latter formulation to undirected and unlabeled graphs of different dimensions, by adding dummy vertices to cast the probleminto an assignment framework. The experiments are performed on randomly generated graphs onto which different spatial transformations areapplied. The results are compared with respect to the matching cost and execution time, showcasing the different limitations and/or advantagesof using these techniques for the comparison of graph networks

InfoOT: Information Maximizing Optimal Transport

Optimal transport aligns samples across distributions by minimizing the transportation cost between them, e.g., the geometric distances. Yet, it ignores coherence structure in the data such as clusters, does not handle outliers well, and cannot integrate new data points. To address these drawbacks, we propose InfoOT, an information-theoretic extension of optimal transport that maximizes the mutual information between domains while minimizing geometric distances. The resulting objective can still be formulated as a (generalized) optimal transport problem, and can be efficiently solved by projected gradient descent. This formulation yields a new projection method that is robust to outliers and generalizes to unseen samples. Empirically, InfoOT improves the quality of alignments across benchmarks in domain adaptation, cross-domain retrieval, and single-cell alignment