Manifold Learning with Sparse Regularised Optimal Transport

Manifold learning is a central task in modern statistics and data science. Many datasets (cells, documents, images, molecules) can be represented as point clouds embedded in a high dimensional ambient space, however the degrees of freedom intrinsic to the data are usually far fewer than the number of ambient dimensions. The task of detecting a latent manifold along which the data are embedded is a prerequisite for a wide family of downstream analyses. Real-world datasets are subject to noisy observations and sampling, so that distilling information about the underlying manifold is a major challenge. We propose a method for manifold learning that utilises a symmetric version of optimal transport with a quadratic regularisation that constructs a sparse and adaptive affinity matrix, that can be interpreted as a generalisation of the bistochastic kernel normalisation. We prove that the resulting kernel is consistent with a Laplace-type operator in the continuous limit, establish robustness to heteroskedastic noise and exhibit these results in simulations. We identify a highly efficient computational scheme for computing this optimal transport for discrete data and demonstrate that it outperforms competing methods in a set of examples.

Quadratically Regularized Optimal Transport: nearly optimal potentials and convergence of discrete Laplace operators

We consider the conjecture proposed in Matsumoto, Zhang and Schiebinger (2022) suggesting that optimal transport with quadratic regularisation can be used to construct a graph whose discrete Laplace operator converges to the Laplace--Beltrami operator. We derive first order optimal potentials for the problem under consideration and find that the resulting solutions exhibit a surprising resemblance to the well-known Barenblatt--Prattle solution of the porous medium equation. Then, relying on these first order optimal potentials, we derive the pointwise $L^2$-limit of such discrete operators built from an i.i.d. random sample on a smooth compact manifold. Simulation results complementing the limiting distribution results are also presented.