Learning Population Dynamics with Variational Doob-Wasserstein Flow

The dynamics of cells, organisms, and fluids are often modeled as probability distributions evolving over time. Reconstructing and extrapolating this evolution from unpaired snapshots requires assumptions about the underlying process. Wasserstein gradient flows are a common choice, but they cannot describe conservative or periodic dynamics. Lagrangian mechanics in Wasserstein space covers both, but existing methods for learning it are simulation-based: they run a numerical solver at every training step, which makes training expensive. We propose Double-Stitch, a simulation-free method that learns these mechanics by penalizing the residual of the equation of motion along a learned population path. We derive this equation from a Clebsch variational principle that does not require gradient velocities, and show that the residual vanishes exactly when the equation holds. We test Double-Stitch on synthetic, single-cell and ocean vortex datasets and find that it matches or outperforms gradient-flow methods and simulation-based WLM on most tasks, while training $4$-$14$ times faster than WLM. We provide a JAX implementation of Double-Stitch at https://github.com/BasisResearch/stitching.

Reconstructing population dynamics is a central problem in the physical and data sciences. Often, the dynamics are modeled as a Wasserstein gradient flow (WGF): a curve of distributions driven by an energy functional. Though there are multiple mathematical characterizations of a WGF, the dominant algorithmic approach relies on the Jordan--Kinderlehrer--Otto (JKO) scheme. JKO-based methods are inflexible to time discretisation and require solving costly optimal transport problems. We take a residual approach, enforcing the continuity equations via a non-negative loss function whose minimum is the WGF. Combined with a data-fitting divergence, this gives a single global objective. This perspective unifies several existing methods and leads to a new particle-based method, stitching, that is simulation-free and robust to large gaps between observations. We demonstrate that the stitching method achieves state-of-the-art performance across trajectory inference benchmarks. For code see github.com/BasisResearch/wasserstein-residuals.

The population dynamics of molecules, cells, and organisms are governed by a number of unknown forces. In the last decade, population dynamics have predominantly been modeled with Wasserstein gradient flows. However, since gradient flows minimize free energy, they fail to capture important dynamical properties, such as periodicity. In this work, we propose a change in perspective by considering dynamics that minimize a population-level action under a damped Wasserstein Lagrangian. By deriving the corresponding Hamiltonian equations of motion, we formalize Wasserstein Lagrangian Mechanics, a structured class of second-order dynamics that encompasses classical mechanics, quantum mechanics, and gradient flows. We then propose WLM as the first algorithm that learns these second-order dynamics from observed marginals, without specifying the Lagrangian. By directly learning the population mechanics, WLM can both forecast and interpolate unseen marginals, and outperforms existing gradient flow and flow matching methods across a wide range of dynamics, including vortex dynamics, embryonic development, and flocking.