Dynamic Generalized Gromov-Wasserstein Optimal Transport

Single-cell trajectory inference from destructive time-course snapshots is fundamentally ill-posed: neither cross-time cell correspondences nor continuous trajectories are observed, so the snapshot distributions alone do not uniquely determine the underlying dynamics. Existing optimal transport and flow-based methods typically couple cells by Euclidean proximity at observed clock times, which can misalign trajectories when development is asynchronous and cells sampled at the same experimental time occupy different latent pseudotime stages. We propose PACE, a trajectory inference framework that recovers geometry-consistent continuous transport dynamics from destructive time-course snapshots through three coupled components. First, PACE constructs a state- and time-dependent anisotropic Riemannian metric that assigns low transport cost along locally supported tangent directions while penalizing normal velocity components. Second, it alternates between refining cross-time couplings under the induced path-action cost and fitting endpoint-preserving neural bridges between adjacent snapshots. Third, it distills the learned bridge dynamics into a global continuous-time velocity field over cellular states. Across seven controlled and biological datasets covering nine held-out reconstruction experiments, PACE achieves the strongest overall reconstruction performance, reducing MMD, Wasserstein-1 distance, and Wasserstein-2 distance by 23.7% on average relative to the strongest competing baseline. PACE also improves RNA-velocity alignment by 15.4% on an embryoid body differentiation benchmark, without requiring explicit cell pairing, lineage tracing, or RNA-velocity supervision during training. Code is available at https://github.com/AI4Science-WestlakeU/PACE.

We introduce Potential Matching Optimal Transport (PMOT), a potential-flow framework for general $p$-cost optimal transport with $c_p(x,y)=\|x-y\|^p$. PMOT parameterizes the CNF velocity field with a scalar potential in the generalized Benamou--Brenier form for the chosen exponent $p$. It trains the potential gradient with a self-induced matching loss along straight bridges determined by the model's own endpoints, while allowing flexible terminal distribution matching. Our main result establishes zero-loss exactness: under the stated regularity, exact terminal matching, and uniqueness assumptions, any zero-loss solution satisfies the generalized Benamou--Brenier optimality system and recovers the corresponding $p$-optimal transport map and dynamics. On synthetic benchmarks, PMOT learns $p$-specific maps that agree with the corresponding $p$-matched OT references. It also remains competitive as a likelihood-based density model on high-dimensional tabular data, and an MMD-based color transformation experiment demonstrates flexible sample-based terminal matching.

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.