Computing optimal transport distances such as the earth mover's distance is a fundamental problem in machine learning, statistics, and computer vision. Despite the recent introduction of several algorithms with good empirical performance, it is unknown whether general optimal transport distances can be approximated in near-linear time. This paper demonstrates that this ambitious goal is in fact achieved by Cuturi's Sinkhorn Distances. This result relies on a new analysis of Sinkhorn iterations, which also directly suggests a new greedy coordinate descent algorithm Greenkhorn with the same theoretical guarantees. Numerical simulations illustrate that Greenkhorn significantly outperforms the classical Sinkhorn algorithm in practice.

We present an optimal transport framework for learning topics from textual data. While the celebrated Latent Dirichlet allocation (LDA) topic model and its variants have been applied to many disciplines, they mainly focus on wordoccurrences and neglect to incorporate semantic regularities in language.

We propose a new framework for formulating optimal transport distances between Markov chains. Previously known formulations studied couplings between the entire joint distribution induced by the chains, and derived solutions via a reduction to dynamic programming (DP) in an appropriately defined Markov decision process. This formulation has, however, not led to particularly efficient algorithms so far, since computing the associated DP operators requires fully solving a static optimal transport problem, and these operators need to be applied numerous times during the overall optimization process. In this work, we develop an alternative perspective by considering couplings between a ``flattened'' version of the joint distributions that we call discounted occupancy couplings, and show that calculating optimal transport distances in the full space of joint distributions can be equivalently formulated as solving a linear program (LP) in this reduced space. This LP formulation formulation allows us to port several algorithmic ideas from other areas of optimal transport theory. In particular, our formulation makes it possible to introduce an appropriate notion of entropy regularization into the optimization problem, which in turn enables us to directly calculate optimal transport distances via a Sinkhorn-like method we call Sinkhorn Value Iteration (SVI). We show both theoretically and empirically that this method converges quickly to an optimal coupling, essentially at the same computational cost of running vanilla Sinkhorn in each pair of states. Along the way, we point out that our optimal transport distance exactly matches the common notion of bisimulation metrics between Markov chains, and thus our results also apply to computing such metrics, and in fact our algorithm turns out to be significantly more efficient than the best known methods developed so far for this purpose.

Current Graph Neural Networks (GNN) architectures generally rely on two important components: node features embedding through message passing, and aggregation with a specialized form of pooling. The structural (or topological) information is implicitly taken into account in these two steps. We propose in this work a novel point of view, which places distances to some learnable graph templates at the core of the graph representation. This distance embedding is constructed thanks to an optimal transport distance: the Fused Gromov-Wasserstein (FGW) distance, which encodes simultaneously feature and structure dissimilarities by solving a soft graph-matching problem. We postulate that the vector of FGW distances to a set of template graphs has a strong discriminative power, which is then fed to a non-linear classifier for final predictions. Distance embedding can be seen as a new layer, and can leverage on existing message passing techniques to promote sensible feature representations. Interestingly enough, in our work the optimal set of template graphs is also learnt in an end-to-end fashion by differentiating through this layer. After describing the corresponding learning procedure, we empirically validate our claim on several synthetic and real life graph classification datasets, where our method is competitive or surpasses kernel and GNN state-of-the-art approaches.

Optimal Transport (OT) distances are now routinely used as loss functions in ML tasks.

Computing optimal transport distances such as the earth mover's distance is a fundamental problem in machine learning, statistics, and computer vision. Despite the recent introduction of several algorithms with good empirical performance, it is unknown whether general optimal transport distances can be approximated in near-linear time. This paper demonstrates that this ambitious goal is in fact achieved by Cuturi's Sinkhorn Distances. This result relies on a new analysis of Sinkhorn iterations, which also directly suggests a new greedy coordinate descent algorithm Greenkhorn with the same theoretical guarantees. Numerical simulations illustrate that Greenkhorn significantly outperforms the classical Sinkhorn algorithm in practice.

We propose a new framework for formulating optimal transport distances between Markov chains. Previously known formulations studied couplings between the entire joint distribution induced by the chains, and derived solutions via a reduction to dynamic programming (DP) in an appropriately defined Markov decision process. This formulation has, however, not led to particularly efficient algorithms so far, since computing the associated DP operators requires fully solving a static optimal transport problem, and these operators need to be applied numerous times during the overall optimization process. In this work, we develop an alternative perspective by considering couplings between a flattened'' version of the joint distributions that we call discounted occupancy couplings, and show that calculating optimal transport distances in the full space of joint distributions can be equivalently formulated as solving a linear program (LP) in this reduced space. This LP formulation formulation allows us to port several algorithmic ideas from other areas of optimal transport theory.

Biological and artificial neural systems form high-dimensional neural representations that underpin their computational capabilities. Methods for quantifying geometric similarity in neural representations have become a popular tool for identifying computational principles that are potentially shared across neural systems. These methods generally assume that neural responses are deterministic and static. However, responses of biological systems, and some artificial systems, are noisy and dynamically unfold over time. Furthermore, these characteristics can have substantial influence on a system's computational capabilities. Here, we demonstrate that existing metrics can fail to capture key differences between neural systems with noisy dynamic responses. We then propose a metric for comparing the geometry of noisy neural trajectories, which can be derived as an optimal transport distance between Gaussian processes. We use the metric to compare models of neural responses in different regions of the motor system and to compare the dynamics of latent diffusion models for text-to-image synthesis. Biological and artificial neural systems represent their environments and internal states as patterns of neural activity, or "neural representations". In an effort to understand general principals governing these representations, a large body of work has sought to quantify the extent to which they are similar across systems (Klabunde et al., 2023). Most of these existing (dis)similarity measures assume that neural activities are deterministic and static.