arXiv subjects

David B Dunson

Publications and source records attributed to David B Dunson.

15 recordsLinked to original sources

arXiv2026

Inferring manifolds using Gaussian processes

It is often of interest to infer lower-dimensional structure underlying complex data. As a flexible class of non-linear structures, it is common to focus on Riemannian manifolds. Most existing manifold learning algorithms replace the original data with lower-dimensional coordinates without providing an estimate of the manifold or using the manifold to denoise the original data. This article proposes a new methodology to address these problems, allowing interpolation of the estimated manifold between the fitted data points. The proposed approach is motivated by the novel theoretical properties of local covariance matrices constructed from samples near a manifold. Our results enable us to turn a global manifold reconstruction problem into a local regression problem, allowing for the application of Gaussian processes for probabilistic manifold reconstruction. In addition to the theory justifying our methodology, we provide simulated and real data examples to illustrate the performance.

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arXiv2024

Targeted stochastic gradient Markov chain Monte Carlo for hidden Markov models with rare latent states

Markov chain Monte Carlo (MCMC) algorithms for hidden Markov models often rely on the forward-backward sampler. This makes them computationally slow as the length of the time series increases, motivating the development of sub-sampling-based approaches. These approximate the full posterior by using small random subsequences of the data at each MCMC iteration within stochastic gradient MCMC. In the presence of imbalanced data resulting from rare latent states, subsequences often exclude rare latent state data, leading to inaccurate inference and prediction/detection of rare events. We propose a targeted sub-sampling (TASS) approach that over-samples observations corresponding to rare latent states when calculating the stochastic gradient of parameters associated with them. TASS uses an initial clustering of the data to construct subsequence weights that reduce the variance in gradient estimation. This leads to improved sampling efficiency, in particular in settings where the rare latent states correspond to extreme observations. We demonstrate substantial gains in predictive and inferential accuracy on real and synthetic examples.

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arXiv2022

Tree Representations of Brain Structural Connectivity via Persistent Homology

The brain structural connectome is generated by a collection of white matter fiber bundles constructed from diffusion weighted MRI (dMRI), acting as highways for neural activity. There has been abundant interest in studying how the structural connectome varies across individuals in relation to their traits, ranging from age and gender to neuropsychiatric outcomes. After applying tractography to dMRI to get white matter fiber bundles, a key question is how to represent the brain connectome to facilitate statistical analyses relating connectomes to traits. The current standard divides the brain into regions of interest (ROIs), and then relies on an adjacency matrix (AM) representation. Each cell in the AM is a measure of connectivity, e.g., number of fiber curves, between a pair of ROIs. Although the AM representation is intuitive, a disadvantage is the high-dimensionality due to the large number of cells in the matrix. This article proposes a simpler tree representation of the brain connectome, which is motivated by ideas in computational topology and takes topological and biological information on the cortical surface into consideration. We demonstrate that our tree representation preserves useful information and interpretability, while reducing dimensionality to improve statistical and computational efficiency. Applications to data from the Human Connectome Project (HCP) are considered and code is provided for reproducing our analyses.

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arXiv2022

Bayesian inferences on uncertain ranks and orderings: Application to ranking players and lineups

It is common to be interested in rankings or order relationships among entities. In complex settings where one does not directly measure a univariate statistic upon which to base ranks, such inferences typically rely on statistical models having entity-specific parameters. These can be treated as random effects in hierarchical models characterizing variation among the entities. In this paper, we are particularly interested in the problem of ranking basketball players in terms of their contribution to team performance. Using data from the United States National Basketball Association (NBA), we find that many players have similar latent ability levels, making any single estimated ranking highly misleading. The current literature fails to provide summaries of order relationships that adequately account for uncertainty. Motivated by this, we propose a Bayesian strategy for characterizing uncertainty in inferences on order relationships among players and lineups. Our approach adapts to scenarios in which uncertainty in ordering is high by producing more conservative results that improve interpretability. This is achieved through a reward function within a decision theoretic framework. We apply our approach to data from the 2009-10 NBA season.

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arXiv2021

Graph Based Gaussian Processes on Restricted Domains

In nonparametric regression, it is common for the inputs to fall in a restricted subset of Euclidean space. Typical kernel-based methods that do not take into account the intrinsic geometry of the domain across which observations are collected may produce sub-optimal results. In this article, we focus on solving this problem in the context of Gaussian process (GP) models, proposing a new class of Graph Laplacian based GPs (GL-GPs), which learn a covariance that respects the geometry of the input domain. As the heat kernel is intractable computationally, we approximate the covariance using finitely-many eigenpairs of the Graph Laplacian (GL). The GL is constructed from a kernel which depends only on the Euclidean coordinates of the inputs. Hence, we can benefit from the full knowledge about the kernel to extend the covariance structure to newly arriving samples by a Nyström type extension. We provide substantial theoretical support for the GL-GP methodology, and illustrate performance gains in various applications.

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arXiv2021

Spectral Convergence of Graph Laplacian and Heat Kernel Reconstruction in $L^\infty$ from Random Samples

In the manifold setting, we provide a series of spectral convergence results quantifying how the eigenvectors and eigenvalues of the graph Laplacian converge to the eigenfunctions and eigenvalues of the Laplace-Beltrami operator in the $L^\infty$ sense. The convergence rate is also provided. Based on these results, convergence of the proposed heat kernel approximation algorithm, as well as the convergence rate, to the exact heat kernel is guaranteed. To our knowledge, this is the first work exploring the spectral convergence in the $L^\infty$ sense and providing a numerical heat kernel reconstruction from the point cloud with theoretical guarantees.

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arXiv2020

Nonparametric graphical model for counts

Although multivariate count data are routinely collected in many application areas, there is surprisingly little work developing flexible models for characterizing their dependence structure. This is particularly true when interest focuses on inferring the conditional independence graph. In this article, we propose a new class of pairwise Markov random field-type models for the joint distribution of a multivariate count vector. By employing a novel type of transformation, we avoid restricting to non-negative dependence structures or inducing other restrictions through truncations. Taking a Bayesian approach to inference, we choose a Dirichlet process prior for the distribution of a random effect to induce great flexibility in the specification. An efficient Markov chain Monte Carlo (MCMC) algorithm is developed for posterior computation. We prove various theoretical properties, including posterior consistency, and show that our COunt Nonparametric Graphical Analysis (CONGA) approach has good performance relative to competitors in simulation studies. The methods are motivated by an application to neuron spike count data in mice.

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arXiv2020

Geodesic Distance Estimation with Spherelets

Many statistical and machine learning approaches rely on pairwise distances between data points. The choice of distance metric has a fundamental impact on performance of these procedures, raising questions about how to appropriately calculate distances. When data points are real-valued vectors, by far the most common choice is the Euclidean distance. This article is focused on the problem of how to better calculate distances taking into account the intrinsic geometry of the data, assuming data are concentrated near an unknown subspace or manifold. The appropriate geometric distance corresponds to the length of the shortest path along the manifold, which is the geodesic distance. When the manifold is unknown, it is challenging to accurately approximate the geodesic distance. Current algorithms are either highly complex, and hence often impractical to implement, or based on simple local linear approximations and shortest path algorithms that may have inadequate accuracy. We propose a simple and general alternative, which uses pieces of spheres, or spherelets, to locally approximate the unknown subspace and thereby estimate the geodesic distance through paths over spheres. Theory is developed showing lower error for many manifolds, with applications in clustering, conditional density estimation and mean regression. The conclusion is supported through multiple simulation examples and real data sets.

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arXiv2020

Bayesian Factor Analysis for Inference on Interactions

This article is motivated by the problem of inference on interactions among chemical exposures impacting human health outcomes. Chemicals often co-occur in the environment or in synthetic mixtures and as a result exposure levels can be highly correlated. We propose a latent factor joint model, which includes shared factors in both the predictor and response components while assuming conditional independence. By including a quadratic regression in the latent variables in the response component, we induce flexible dimension reduction in characterizing main effects and interactions. We propose a Bayesian approach to inference under this Factor analysis for INteractions (FIN) framework. Through appropriate modifications of the factor modeling structure, FIN can accommodate higher order interactions and multivariate outcomes. We provide theory on posterior consistency and the impact of misspecifying the number of factors. We evaluate the performance using a simulation study and data from the National Health and Nutrition Examination Survey (NHANES). Code is available on GitHub.

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arXiv2019

Consistent Entropy Estimation for Stationary Time Series

Entropy estimation, due in part to its connection with mutual information, has seen considerable use in the study of time series data including causality detection and information flow. In many cases, the entropy is estimated using $k$-nearest neighbor (Kozachenko-Leonenko) based methods. However, analytic results on this estimator are limited to independent data. In the article, we show rigorous bounds on the rate of decay of the bias in the number of samples, $N$, assuming they are drawn from a stationary process which satisfies a suitable mixing condition. Numerical examples are presented which demonstrate the efficiency of the estimator when applied to a Markov process with stationary Gaussian density. These results support the asymptotic rates derived in the theoretical work.

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arXiv2019

Estimating densities with nonlinear support using Fisher-Gaussian kernels

Current tools for multivariate density estimation struggle when the density is concentrated near a nonlinear subspace or manifold. Most approaches require choice of a kernel, with the multivariate Gaussian by far the most commonly used. Although heavy-tailed and skewed extensions have been proposed, such kernels cannot capture curvature in the support of the data. This leads to poor performance unless the sample size is very large relative to the dimension of the data. This article proposes a novel generalization of the Gaussian distribution, which includes an additional curvature parameter. We refer to the proposed class as Fisher-Gaussian (FG) kernels, since they arise by sampling from a von Mises-Fisher density on the sphere and adding Gaussian noise. The FG density has an analytic form, and is amenable to straightforward implementation within Bayesian mixture models using Markov chain Monte Carlo. We provide theory on large support, and illustrate gains relative to competitors in simulated and real data applications.

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arXiv2019

Bayesian Distance Clustering

Model-based clustering is widely-used in a variety of application areas. However, fundamental concerns remain about robustness. In particular, results can be sensitive to the choice of kernel representing the within-cluster data density. Leveraging on properties of pairwise differences between data points, we propose a class of Bayesian distance clustering methods, which rely on modeling the likelihood of the pairwise distances in place of the original data. Although some information in the data is discarded, we gain substantial robustness to modeling assumptions. The proposed approach represents an appealing middle ground between distance- and model-based clustering, drawing advantages from each of these canonical approaches. We illustrate dramatic gains in the ability to infer clusters that are not well represented by the usual choices of kernel. A simulation study is included to assess performance relative to competitors, and we apply the approach to clustering of brain genome expression data. Keywords: Distance-based clustering; Mixture model; Model-based clustering; Model misspecification; Pairwise distance matrix; Partial likelihood; Robustness.

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arXiv2019

Bayesian time-aligned factor analysis of paired multivariate time series

Many modern data sets require inference methods that can estimate the shared and individual-specific components of variability in collections of matrices that change over time. Promising methods have been developed to analyze these types of data in static cases, but very few approaches are available for dynamic settings. To address this gap, we consider novel models and inference methods for pairs of matrices in which the columns correspond to multivariate observations at different time points. In order to characterize common and individual features, we propose a Bayesian dynamic factor modeling framework called Time Aligned Common and Individual Factor Analysis (TACIFA) that includes uncertainty in time alignment through an unknown warping function. We provide theoretical support for the proposed model, showing identifiability and posterior concentration. The structure enables efficient computation through a Hamiltonian Monte Carlo (HMC) algorithm. We show excellent performance in simulations, and illustrate the method through application to a social synchrony experiment.

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arXiv2019

Classification via local manifold approximation

Classifiers label data as belonging to one of a set of groups based on input features. It is challenging to obtain accurate classification performance when the feature distributions in the different classes are complex, with nonlinear, overlapping and intersecting supports. This is particularly true when training data are limited. To address this problem, this article proposes a new type of classifier based on obtaining a local approximation to the support of the data within each class in a neighborhood of the feature to be classified, and assigning the feature to the class having the closest support. This general algorithm is referred to as LOcal Manifold Approximation (LOMA) classification. As a simple and theoretically supported special case having excellent performance in a broad variety of examples, we use spheres for local approximation, obtaining a SPherical Approximation (SPA) classifier. We illustrate substantial gains for SPA over competitors on a variety of challenging simulated and real data examples.

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arXiv2018

Bayesian Constraint Relaxation

Prior information often takes the form of parameter constraints. Bayesian methods include such information through prior distributions having constrained support. By using posterior sampling algorithms, one can quantify uncertainty without relying on asymptotic approximations. However, sharply constrained priors are (a) not necessary in some settings; and (b) tend to limit modeling scope to a narrow set of distributions that are tractable computationally. Inspired by the vast literature that replaces the slab-and-spike prior with a continuous approximation, we propose to replace the sharp indicator function of the constraint with an exponential kernel, thereby creating a close-to-constrained neighborhood within the Euclidean space in which the constrained subspace is embedded. This kernel decays with distance from the constrained space at a rate depending on a relaxation hyperparameter. By avoiding the sharp constraint, we enable use of off-the-shelf posterior sampling algorithms, such as Hamiltonian Monte Carlo, facilitating automatic computation in broad models. We study the constrained and relaxed distributions under multiple settings, and theoretically quantify their differences. We illustrate the method through multiple novel modeling examples.

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