Trajectory inference aims at recovering the dynamics of a population from snapshots of its temporal marginals.

Trajectory inference seeks to recover the temporal dynamics of a population from snapshots of its (uncoupled) temporal marginals, i.e. where observed particles are not tracked over time. Lavenant et al. arXiv:2102.09204 addressed this challenging problem under a stochastic differential equation (SDE) model with a gradient-driven drift in the observed space, introducing a minimum entropy estimator relative to the Wiener measure. Chizat et al. arXiv:2205.07146 then provided a practical grid-free mean-field Langevin (MFL) algorithm using Schr\"odinger bridges. Motivated by the overwhelming success of observable state space models in the traditional paired trajectory inference problem (e.g. target tracking), we extend the above framework to a class of latent SDEs in the form of observable state space models. In this setting, we use partial observations to infer trajectories in the latent space under a specified dynamics model (e.g. the constant velocity/acceleration models from target tracking). We introduce PO-MFL to solve this latent trajectory inference problem and provide theoretical guarantees by extending the results of arXiv:2102.09204 to the partially observed setting. We leverage the MFL framework of arXiv:2205.07146, yielding an algorithm based on entropic OT between dynamics-adjusted adjacent time marginals. Experiments validate the robustness of our method and the exponential convergence of the MFL dynamics, and demonstrate significant outperformance over the latent-free method of arXiv:2205.07146 in key scenarios.

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 by Lavenant et al. arXiv:2102.09204, 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 Schr\"odinger 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.

We study the long time behavior of an underdamped mean-field Langevin (MFL) equation, and provide a general convergence as well as an exponential convergence rate result under different conditions. The results on the MFL equation can be applied to study the convergence of the Hamiltonian gradient descent algorithm for the overparametrized optimization. We then provide a numerical example of the algorithm to train a generative adversarial networks (GAN).