Trajectory inference aims at recovering the dynamics of a population from snapshots of its temporal marginals. To solve this task, a min-entropy estimator relative to the Wiener measure in path space was introduced in [Lavenant et al., 2021], and shown to consistently recover the dynamics of a large class of drift-diffusion processes from the solution of an infinite dimensional convex optimization problem. In this paper, we introduce a grid-free algorithm to compute this estimator. Our method consists in a family of point clouds (one per snapshot) coupled via Schrödinger bridges which evolve with noisy gradient descent. We study the mean-field limit of the dynamics and prove its global convergence to the desired estimator. Overall, this leads to an inference method with end-to-end theoretical guarantees that solves an interpretable model for trajectory inference. We also present how to adapt the method to deal with mass variations, a useful extension when dealing with single cell RNA-sequencing data where cells can branch and die.

This paper introduces a new nonlinear dictionary learning method for histograms in the probability simplex. The method leverages optimal transport theory, in the sense that our aim is to reconstruct histograms using so-called displacement interpolations (a.k.a. Wasserstein barycenters) between dictionary atoms; such atoms are themselves synthetic histograms in the probability simplex. Our method simultaneously estimates such atoms and, for each datapoint, the vector of weights that can optimally reconstruct it as an optimal transport barycenter of such atoms. Our method is computationally tractable thanks to the addition of an entropic regularization to the usual optimal transportation problem, leading to an approximation scheme that is efficient, parallel, and simple to differentiate. Both atoms and weights are learned using a gradient-based descent method. Gradients are obtained by automatic differentiation of the generalized Sinkhorn iterations that yield barycenters with entropic smoothing. Because of its formulation relying on Wasserstein barycenters instead of the usual matrix product between dictionary and codes, our method allows for nonlinear relationships between atoms and the reconstruction of input data. We illustrate its application in several different image processing settings.