We propose the linear barycentric coding model (LBCM) which utilizes the linear optimal transport (LOT) metric for analysis and synthesis of probability measures. We provide a closed-form solution to the variational problem characterizing the probability measures in the LBCM and establish equivalence of the LBCM to the set of 2-Wasserstein barycenters in the special case of compatible measures. Computational methods for synthesizing and analyzing measures in the LBCM are developed with finite sample guarantees. One of our main theoretical contributions is to identify an LBCM, expressed in terms of a simple family, which is sufficient to express all probability measures on the closed unit interval. We show that a natural analogous construction of an LBCM in 2 dimensions fails, and we leave it as an open problem to identify the proper extension in more than 1 dimension. We conclude by demonstrating the utility of LBCM for covariance estimation and data imputation.

Despite the success of deep learning-based algorithms, it is widely known that neural networks may fail to be robust. A popular paradigm to enforce robustness is adversarial training (AT), however, this introduces many computational and theoretical difficulties. Recent works have developed a connection between AT in the multiclass classification setting and multimarginal optimal transport (MOT), unlocking a new set of tools to study this problem. In this paper, we leverage the MOT connection to propose computationally tractable numerical algorithms for computing universal lower bounds on the optimal adversarial risk and identifying optimal classifiers. We propose two main algorithms based on linear programming (LP) and entropic regularization (Sinkhorn). Our key insight is that one can harmlessly truncate the higher order interactions between classes, preventing the combinatorial run times typically encountered in MOT problems. We validate these results with experiments on MNIST and CIFAR-$10$, which demonstrate the tractability of our approach.

This paper considers the use of recently proposed optimal transport-based multivariate goodness-of-fit (GoF) test statistics, namely rank energy and its variant the soft rank energy derived from entropy-regularized optimal transport, for unsupervised non-parametric change point detection (CPD) in multivariate time series data. We show that the soft rank energy enjoys both fast rates of statistical convergence and robust continuity properties which lead to strong performance on real datasets. Our analyses remove the need for resampling and out-of-sample extensions previously required to obtain such rates. Our theoretical results show that the rank energy suffers from the curse of dimensionality in statistical estimation and moreover can signal a change point from arbitrarily small perturbations, which leads to a high rate of false alarms in CPD. Additionally, under mild regularity conditions, we quantify the discrepancy between soft rank energy and rank energy in terms of the regularization parameter. Finally, we show our approach performs favorably in numerical experiments compared to several other optimal transport-based methods as well as maximum mean discrepancy (MMD), which is a popular multivariate GoF statistic.

The framework of optimal transport has been leveraged to extend the notion of rank to the multivariate setting as corresponding to an optimal transport map, while preserving desirable properties of the resulting goodness-of-fit (GoF) statistics. In particular, the rank energy (RE) and rank maximum mean discrepancy (RMMD) are distribution-free under the null, exhibit high power in statistical testing, and are robust to outliers. In this paper, we point to and alleviate some of the shortcomings of these GoF statistics that are of practical significance, namely high computational cost, curse of dimensionality in statistical sample complexity, and lack of differentiability with respect to the data. We show that all these issues are addressed by defining multivariate rank as an entropic transport map derived from the entropic regularization of the optimal transport problem, which we refer to as the soft rank. We consequently propose two new statistics, the soft rank energy (sRE) and soft rank maximum mean discrepancy (sRMMD). Given n sample data points, we provide non-asymptotic convergence rates for the sample estimate of the entropic transport map to its population version that are essentially of the order n^(-1/2) when the source measure is subgaussian and the target measure has compact support. This result is novel compared to existing results which achieve a rate of n^(-1) but crucially rely on both measures having compact support. In contrast, the corresponding convergence rate of estimating an optimal transport map, and hence the rank map, is exponential in the data dimension. We leverage these fast convergence rates to show that the sample estimates of sRE and sRMMD converge rapidly to their population versions. Combined with the computational efficiency of methods in solving the entropy-regularized optimal transport problem, these results enable efficient rank-based GoF statistical computation, even in high dimensions. Furthermore, the sample estimates of sRE and sRMMD are differentiable with respect to the data and amenable to popular machine learning frameworks that rely on gradient methods. We leverage these properties towards showcasing their utility for generative modeling on two important problems: image generation and generating valid knockoffs for controlled feature selection.

This paper considers the problem of measure estimation under the barycentric coding model (BCM), in which an unknown measure is assumed to belong to the set of Wasserstein-2 barycenters of a finite set of known measures. Estimating a measure under this model is equivalent to estimating the unknown barycentric coordinates. We provide novel geometrical, statistical, and computational insights for measure estimation under the BCM, consisting of three main results. Our first main result leverages the Riemannian geometry of Wasserstein-2 space to provide a procedure for recovering the barycentric coordinates as the solution to a quadratic optimization problem assuming access to the true reference measures. The essential geometric insight is that the parameters of this quadratic problem are determined by inner products between the optimal displacement maps from the given measure to the reference measures defining the BCM. Our second main result then establishes an algorithm for solving for the coordinates in the BCM when all the measures are observed empirically via i.i.d. samples. We prove precise rates of convergence for this algorithm—determined by the smoothness of the underlying measures and their dimensionality—thereby guaranteeing its statistical consistency. Finally, we demonstrate the utility of the BCM and associated estimation procedures in three application areas: (i) covariance estimation for Gaussian measures; (ii) image processing; and (iii) natural language processing.

MOTIVATION: Protein function prediction, based on the patterns of connection in a protein-protein interaction (or association) network, is perhaps the most studied of the classical, fundamental inference problems for biological networks. A highly successful set of recent approaches use random walk-based low-dimensional embeddings that tend to place functionally similar proteins into coherent spatial regions. However, these approaches lose valuable local graph structure from the network when considering only the embedding. We introduce GLIDER, a method that replaces a protein-protein interaction or association network with a new graph-based similarity network. GLIDER is based on a variant of our previous GLIDE method, which was designed to predict missing links in protein-protein association networks, capturing implicit local and global (i.e. embedding-based) graph properties. RESULTS: GLIDER outperforms competing methods on the task of predicting GO functional labels in cross-validation on a heterogeneous collection of four human protein-protein association networks derived from the 2016 DREAM Disease Module Identification Challenge, and also on three different protein-protein association networks built from the STRING database. We show that this is due to the strong functional enrichment that is present in the local GLIDER neighborhood in multiple different types of protein-protein association networks. Furthermore, we introduce the GLIDER graph neighborhood as a way for biologists to visualize the local neighborhood of a disease gene. As an application, we look at the local GLIDER neighborhoods of a set of known Parkinson's Disease GWAS genes, rediscover many genes which have known involvement in Parkinson's disease pathways, plus suggest some new genes to study. AVAILABILITY AND IMPLEMENTATION: All code is publicly available and can be accessed here: https://github.com/kap-devkota/GLIDER. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.