Entropic Wasserstein Gradient Flows

This article details a novel numerical scheme to approximate gradient flows for optimal transport (i.e. Wasserstein) metrics. These flows have proved useful to tackle theoretically and numerically non-linear diffusion equations that model for instance porous media or crowd evolutions. These gradient flows define a suitable notion of weak solutions for these evolutions and they can be approximated in a stable way using discrete flows. These discrete flows are implicit Euler time stepping according to the Wasserstein metric. A bottleneck of these approaches is the high computational load induced by the resolution of each step. Indeed, this corresponds to the resolution of a convex optimization problem involving a Wasserstein distance to the previous iterate. Following several recent works on the approximation of Wasserstein distances, we consider a discrete flow induced by an entropic regularization of the transportation coupling. This entropic regularization allows one to trade the initial Wasserstein fidelity term for a Kulback-Leibler divergence, which is easier to deal with numerically. We show how KL proximal schemes, and in particular Dykstra's algorithm, can be used to compute each step of the regularized flow. The resulting algorithm is both fast, parallelizable and versatile, because it only requires multiplications by a Gibbs kernel. On Euclidean domains discretized on an uniform grid, this corresponds to a linear filtering (for instance a Gaussian filtering when $c$ is the squared Euclidean distance) which can be computed in nearly linear time. On more general domains, such as (possibly non-convex) shapes or on manifolds discretized by a triangular mesh, following a recently proposed numerical scheme for optimal transport, this Gibbs kernel multiplication is approximated by a short-time heat diffusion

A Riemannian approach to strain measures in nonlinear elasticity

The isotropic Hencky strain energy appears naturally as a distance measure of the deformation gradient to the set SO(n) of rigid rotations in the canonical left-invariant Riemannian metric on the general linear group GL(n). Objectivity requires the Riemannian metric to be left-GL(n)-invariant, isotropy requires the Riemannian metric to be right-O(n)-invariant. The latter two conditions are satisfied for a three-parameter family of Riemannian metrics on the tangent space of GL(n). Surprisingly, the final result is basically independent of the chosen parameters. In deriving the result, geodesics on GL(n) have to be parametrized and a novel minimization problem, involving the matrix logarithm for non-symmetric arguments, has to be solved

Active skeleton for bacteria modeling

The investigation of spatio-temporal dynamics of bacterial cells and their molecular components requires automated image analysis tools to track cell shape properties and molecular component locations inside the cells. In the study of bacteria aging, the molecular components of interest are protein aggregates accumulated near bacteria boundaries. This particular location makes very ambiguous the correspondence between aggregates and cells, since computing accurately bacteria boundaries in phase-contrast time-lapse imaging is a challenging task. This paper proposes an active skeleton formulation for bacteria modeling which provides several advantages: an easy computation of shape properties (perimeter, length, thickness, orientation), an improved boundary accuracy in noisy images, and a natural bacteria-centered coordinate system that permits the intrinsic location of molecular components inside the cell. Starting from an initial skeleton estimate, the medial axis of the bacterium is obtained by minimizing an energy function which incorporates bacteria shape constraints. Experimental results on biological images and comparative evaluation of the performances validate the proposed approach for modeling cigar-shaped bacteria like Escherichia coli. The Image-J plugin of the proposed method can be found online at http://fluobactracker.inrialpes.fr.Comment: Published in Computer Methods in Biomechanics and Biomedical Engineering: Imaging and Visualizationto appear i