arXiv subjects

Sharvaj Kubal

Publications and source records attributed to Sharvaj Kubal.

4 recordsLinked to original sources

arXiv2025

Optimal sequencing depth for single-cell RNA-sequencing in Wasserstein space

How many samples should one collect for an empirical distribution to be as close as possible to the true population? This question is not trivial in the context of single-cell RNA-sequencing. With limited sequencing depth, profiling more cells comes at the cost of fewer reads per cell. Therefore, one must strike a balance between the number of cells sampled and the accuracy of each measured gene expression profile. In this paper, we analyze an empirical distribution of cells and obtain upper and lower bounds on the Wasserstein distance to the true population. Our analysis holds for general, non-parametric distributions of cells, and is validated by simulation experiments on a real single-cell dataset.

math.ST↗

arXiv2025

STARK denoises spatial transcriptomics images via adaptive regularization

We present an approach to denoising spatial transcriptomics images that is particularly effective for uncovering cell identities in the regime of ultra-low sequencing depths, and also allows for interpolation of gene expression. The method -- Spatial Transcriptomics via Adaptive Regularization and Kernels (STARK) -- augments kernel ridge regression with an incrementally adaptive graph Laplacian regularizer. In each iteration, we (1) perform kernel ridge regression with a fixed graph to update the image, and (2) update the graph based on the new image. The kernel ridge regression step involves reducing the infinite dimensional problem on a space of images to finite dimensions via a modified representer theorem. Starting with a purely spatial graph, and updating it as we improve our image makes the graph more robust to noise in low sequencing depth regimes. We show that the aforementioned approach optimizes a block-convex objective through an alternating minimization scheme wherein the sub-problems have closed form expressions that are easily computed. This perspective allows us to prove convergence of the iterates to a stationary point of this non-convex objective. Statistically, such stationary points converge to the ground truth with rate $\mathcal{O}(R^{-1/2})$ where $R$ is the number of reads. In numerical experiments on real spatial transcriptomics data, the denoising performance of STARK, evaluated in terms of label transfer accuracy, shows consistent improvement over the competing methods tested.

stat.ML↗

arXiv2025

Average-case thresholds for exact regularization of linear programs

Small regularizers can preserve linear programming solutions exactly. This paper provides the first average-case analysis of exact regularization: with a standard Gaussian cost vector and fixed constraint set, bounds are established for the probability that exact regularization succeeds as a function of regularization strength. Failure is characterized via the Gaussian measure of inner cones, controlled by novel two-sided bounds on the measure of shifted cones. Results reveal dimension-dependent scaling laws and connect exact regularization of linear programs to their polyhedral geometry via the normal fan and the Gaussian (solid-angle) measure of its cones. Computable bounds are obtained in several canonical settings, including regularized optimal transport. Numerical experiments corroborate the predicted scalings and thresholds.

math.OC↗

arXiv2024

Log-concave Density Estimation with Independent Components

We propose a method for estimating a log-concave density on $\mathbb R^d$ from samples, under the assumption that there exists an orthogonal transformation that makes the components of the random vector independent. While log-concave density estimation is hard both computationally and statistically, the independent components assumption alleviates both issues, while still maintaining a large non-parametric class. We prove that under mild conditions, at most $\tilde{\mathcal{O}}(ε^{-4})$ samples (suppressing constants and log factors) suffice for our proposed estimator to be within $ε$ of the original density in squared Hellinger distance. On the computational front, while the usual log-concave maximum likelihood estimate can be obtained via a finite-dimensional convex program, it is slow to compute -- especially in higher dimensions. We demonstrate through numerical experiments that our estimator can be computed efficiently, making it more practical to use.

math.ST↗