These notes recapitulate the high level mathematical principles behind different techniques for generative modeling. I show the connections between optimal transport and standard techniques such as Schr{ö}dinger bridge and flow matching.

Optimal Transport (OT) has attracted significant interest in the machine learning community, not only for its ability to define meaningful distances between probability distributions - such as the Wasserstein distance - but also for its formulation of OT plans. Its computational complexity remains a bottleneck, though, and slicing techniques have been developed to scale OT to large datasets. Recently, a novel slicing scheme, dubbed min-SWGG, lifts a single one-dimensional plan back to the original multidimensional space, finally selecting the slice that yields the lowest Wasserstein distance as an approximation of the full OT plan. Despite its computational and theoretical advantages, min-SWGG inherits typical limitations of slicing methods: (i) the number of required slices grows exponentially with the data dimension, and (ii) it is constrained to linear projections. Here, we reformulate min-SWGG as a bilevel optimization problem and propose a differentiable approximation scheme to efficiently identify the optimal slice, even in high-dimensional settings. We furthermore define its generalized extension for accommodating to data living on manifolds. Finally, we demonstrate the practical value of our approach in various applications, including gradient flows on manifolds and highdimensional spaces, as well as a novel sliced OT-based conditional flow matching for image generation - where fast computation of transport plans is essential.

This paper investigates the connections between rectified flows, flow matching, and optimal transport. Flow matching is a recent approach to learning generative models by estimating velocity fields that guide transformations from a source to a target distribution. Rectified flow matching aims to straighten the learned transport paths, yielding more direct flows between distributions. Our first contribution is a set of invariance properties of rectified flows and explicit velocity fields. In addition, we also provide explicit constructions and analysis in the Gaussian (not necessarily independent) and Gaussian mixture settings and study the relation to optimal transport. Our second contribution addresses recent claims suggesting that rectified flows, when constrained such that the learned velocity field is a gradient, can yield (asymptotically) solutions to optimal transport problems. We study the existence of solutions for this problem and demonstrate that they only relate to optimal transport under assumptions that are significantly stronger than those previously acknowledged. In particular, we present several counterexamples that invalidate earlier equivalence results in the literature, and we argue that enforcing a gradient constraint on rectified flows is, in general, not a reliable method for computing optimal transport maps.

Learning the underlying dynamics of single cells from snapshot data has gained increasing attention in scientific and machine learning research.

Adding entropic regularization to Optimal Transport (OT) problems has become a standard approach for designing efficient and scalable solvers. However, regularization introduces a bias from the true solution. To mitigate this bias while still benefiting from the acceleration provided by regularization, a natural solver would adaptively decrease the regularization as it approaches the solution. Although some algorithms heuristically implement this idea, their theoretical guarantees and the extent of their acceleration compared to using a fixed regularization remain largely open. In the setting of semi-discrete OT, where the source measure is continuous and the target is discrete, we prove that decreasing the regularization can indeed accelerate convergence. To this end, we introduce DRAG: Decreasing (entropic) Regularization Averaged Gradient, a stochastic gradient descent algorithm where the regularization decreases with the number of optimization steps. We provide a theoretical analysis showing that DRAG benefits from decreasing regularization compared to a fixed scheme, achieving an unbiased O(1/t)sample and iteration complexity for both the OT cost and the potential estimation, and a O(1/ t) rate for the OT map. Our theoretical findings are supported by numerical experiments that validate the effectiveness of DRAG and highlight its practical advantages.

Modeling the dynamics from sparsely time-resolved snapshot data is crucial for understanding complex cellular processes and behavior.

Recent advances in flow-based generative modelling have provided scalable methods for computing the Schr odinger Bridge (SB) between distributions, a dynamic form of entropy-regularised Optimal Transport (OT) for the quadratic cost. The successful Iterative Markovian Fitting (IMF) procedure solves the SB problem via sequential bridge-matching steps, presenting an elegant and practical approach with many favourable properties over the more traditional Iterative Proportional Fitting (IPF) procedure. Beyond the standard setting, optimal transport can be generalised to the multi-marginal case in which the objective is to minimise a cost defined over several marginal distributions. Of particular importance are costs defined over a tree structure, from which Wasserstein barycentres can be recovered as a special case. In this work, we extend the IMF procedure to solve for the tree-structured SB problem. Our resulting algorithm inherits the many advantages of IMF over IPF approaches in the tree-based setting. In the case of Wasserstein barycentres, our approach can be viewed as extending the widely used fixed-point approach to use flow-based entropic OT solvers, while requiring only simple bridge-matching steps at each iteration.

In this paper, we propose a flow-based method for learning all-to-all transfer maps among conditional distributions that approximates pairwise optimal transport. The proposed method addresses the challenge of handling the case of continuous conditions, which often involve a large set of conditions with sparse empirical observations per condition. We introduce a novel cost function that enables simultaneous learning of optimal transports for all pairs of conditional distributions. Our method is supported by a theoretical guarantee that, in the limit, it converges to the pairwise optimal transports among infinite pairs of conditional distributions. The learned transport maps are subsequently used to couple data points in conditional flow matching. We demonstrate the effectiveness of this method on synthetic and benchmark datasets, as well as on chemical datasets in which continuous physical properties are defined as conditions.

Optimal transport between graphs, based on Gromov-Wasserstein and other extensions, is a powerful tool for comparing and aligning graph structures. However, solving the associated non-convex optimization problems is computationally expensive, which limits the scalability of these methods to large graphs. In this work, we present Unbalanced Learning of Optimal Transport (ULOT), a deep learning method that predicts optimal transport plans between two graphs. Our method is trained by minimizing the fused unbalanced Gromov-Wasserstein (FUGW) loss. We propose a novel neural architecture with cross-attention that is conditioned on the FUGW tradeoff hyperparameters. We evaluate ULOT on synthetic stochastic block model (SBM) graphs and on real cortical surface data obtained from fMRI. ULOT predicts transport plans with competitive loss up to two orders of magnitude faster than classical solvers. Furthermore, the predicted plan can be used as a warm start for classical solvers to accelerate their convergence. Finally, the predicted transport plan is fully differentiable with respect to the graph inputs and FUGW hyperparameters, enabling the optimization of functionals of the ULOT plan.

Distributionally Robust Optimization (DRO) offers a promising framework by optimizing worst-case performance over a set of candidate distributions, referred to as the uncertainty set. However, the efficacy of DRO heavily depends on the design of the uncertainty set, and existing methods often perform suboptimally due to an inappropriate or inflexible uncertainty set. In this work, we first propose a novel perspective that casts entropy-regularized Wasserstein DRO as a dynamic process of distributional exploration and semantic alignment, both driven by optimal transport (OT). This unified viewpoint yields two key new techniques: semantic calibration, which bootstraps semantically meaningful transport costs via inverse OT, and adaptive refinement, which adjusts uncertainty set using OT-driven feedback. Together, these components form an exploration-and-feedback system, where the transport costs and uncertainty set evolve jointly during training, enabling the model to better adapt to potential distribution shifts. Moreover, we provide an in-depth analysis of this adaptive process and prove theoretical guarantees of convergence. Finally, we present our experimental results across diverse distribution shift scenarios, which demonstrate that our approach significantly outperforms existing methods, achieving state-ofthe-art robustness.