arXiv subjects

Peter D. Hoff

Publications and source records attributed to Peter D. Hoff.

At least 19 recordsLinked to original sources

arXiv2026

Testing Separability of High-Dimensional Covariance Matrices

Due to their parsimony, separable covariance models have been popular in modeling matrix-variate data. However, the inference from such a model may be misleading if the population covariance matrix $Σ$ is actually non-separable, motivating the use of statistical tests of separability. The existing separability tests suffer mainly from two issues: 1) test statistics that are not well-defined in high-dimensional settings, 2) low power for small sample sizes and null distributions that depend on unknown parameters, preventing exact error rate control. To address these issues, we propose novel invariant tests using the core covariance matrix, a complementary notion to a separable covariance matrix. We show that testing separability of $Σ$ is equivalent to testing sphericity of its core component. With this insight, we construct test statistics that are well-defined in high-dimensional settings and have distributions that are invariant under the null hypothesis of separability, allowing for exact simulation of null distributions. We establish the asymptotic properties of some test statistics by proving the asymptotic spectral equivalence between the sample covariance matrix and its core in a $p/n\rightarrowγ\in(0,\infty)$ regime. The large power of our proposed tests relative to existing procedures is demonstrated numerically.

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arXiv2024

Decomposing Network Influence: Social Influence Regression

Understanding network influence and its determinants are key challenges in political science and network analysis. Traditional latent variable models position actors within a social space based on network dependencies but often do not elucidate the underlying factors driving these interactions. To overcome this limitation, we propose the Social Influence Regression (SIR) model, an extension of vector autoregression tailored for relational data that incorporates exogenous covariates into the estimation of influence patterns. The SIR model captures influence dynamics via a pair of $n \times n$ matrices that quantify how the actions of one actor affect the future actions of another. This framework not only provides a statistical mechanism for explaining actor influence based on observable traits but also improves computational efficiency through an iterative block coordinate descent method. We showcase the SIR model's capabilities by applying it to monthly conflict events between countries, using data from the Integrated Crisis Early Warning System (ICEWS). Our findings demonstrate the SIR model's ability to elucidate complex influence patterns within networks by linking them to specific covariates. This paper's main contributions are: (1) introducing a model that explains third-order dependencies through exogenous covariates and (2) offering an efficient estimation approach that scales effectively with large, complex networks.

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arXiv2024

A flexible and interpretable spatial covariance model for data on graphs

Spatial models for areal data are often constructed such that all pairs of adjacent regions are assumed to have near-identical spatial autocorrelation. In practice, data can exhibit dependence structures more complicated than can be represented under this assumption. In this article we develop a new model for spatially correlated data observed on graphs, which can flexibly represented many types of spatial dependence patterns while retaining aspects of the original graph geometry. Our method implies an embedding of the graph into Euclidean space wherein covariance can be modeled using traditional covariance functions, such as those from the Matérn family. We parameterize our model using a class of graph metrics compatible with such covariance functions, and which characterize distance in terms of network flow, a property useful for understanding proximity in many ecological settings. By estimating the parameters underlying these metrics, we recover the "intrinsic distances" between graph nodes, which assist in the interpretation of the estimated covariance and allow us to better understand the relationship between the observed process and spatial domain. We compare our model to existing methods for spatially dependent graph data, primarily conditional autoregressive models and their variants, and illustrate advantages of our method over traditional approaches. We fit our model to bird abundance data for several species in North Carolina, and show how it provides insight into the interactions between species-specific spatial distributions and geography.

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arXiv2024

Incorporating circuit theory into a dynamic model for crowd-sourced observations of migratory birds

While the overarching pattern of biannual avian migration is well understood, there are significant questions pertaining to this phenomenon that invite further study. Necessary to any analysis of these questions is an understanding of how a given species' spatial distribution evolves in time. While studies of animal movement are often conducted using telemetry data, the collection of such data can be time- and resource-intensive, frequently resulting in small sample sizes. Ecological surveys of animal populations are also indicative of species distribution trends, but may be constrained to a limited spatial domain. Within this article we utilize crowd-sourced observations from the eBird database to model the abundance of migratory bird species in space and time. While crowd-sourced observations are individually less reliable than those produced by experts, the sheer size and spatial coverage of the eBird database make it attractive for use in this setting. We introduce a hidden Markov model for observed bird counts utilizing a novel transition structure developed using principles from circuit theory. After illustrating model properties we fit it to observations of Baltimore orioles and yellow-rumped warblers within the eastern United States and discuss insight it provides into the migratory patterns for these species.

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arXiv2024

The multirank likelihood for semiparametric canonical correlation analysis

Many analyses of multivariate data focus on evaluating the dependence between two sets of variables, rather than the dependence among individual variables within each set. Canonical correlation analysis (CCA) is a classical data analysis technique that estimates parameters describing the dependence between such sets. However, inference procedures based on traditional CCA rely on the assumption that all variables are jointly normally distributed. We present a semiparametric approach to CCA in which the multivariate margins of each variable set may be arbitrary, but the dependence between variable sets is described by a parametric model that provides low-dimensional summaries of dependence. While maximum likelihood estimation in the proposed model is intractable, we propose two estimation strategies: one using a pseudolikelihood for the model and one using a Markov chain Monte Carlo (MCMC) algorithm that provides Bayesian estimates and confidence regions for the between-set dependence parameters. The MCMC algorithm is derived from a multirank likelihood function, which uses only part of the information in the observed data in exchange for being free of assumptions about the multivariate margins. We apply the proposed Bayesian inference procedure to Brazilian climate data and monthly stock returns from the materials and communications market sectors.

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arXiv2024

Bayesian Covariance Estimation for Multi-group Matrix-variate Data

Multi-group covariance estimation for matrix-variate data with small within group sample sizes is a key part of many data analysis tasks in modern applications. To obtain accurate group-specific covariance estimates, shrinkage estimation methods which shrink an unstructured, group-specific covariance either across groups towards a pooled covariance or within each group towards a Kronecker structure have been developed. However, in many applications, it is unclear which approach will result in more accurate covariance estimates. In this article, we present a hierarchical prior distribution which flexibly allows for both types of shrinkage. The prior linearly combines shrinkage across groups towards a shared pooled covariance and shrinkage within groups towards a group-specific Kronecker covariance. We illustrate the utility of the proposed prior in speech recognition and an analysis of chemical exposure data.

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arXiv2024

A Latent Variable Model for Relational Events with Multiple Receivers

Directional relational event data, such as email data, often contain unicast messages (i.e., messages of one sender towards one receiver) and multicast messages (i.e., messages of one sender towards multiple receivers). The Enron email data that is the focus in this paper consists of 31% multicast messages. Multicast messages contain important information about the roles of actors in the network, which is needed for better understanding social interaction dynamics. In this paper a multiplicative latent factor model is proposed to analyze such relational data. For a given message, all potential receiver actors are placed on a suitability scale, and the actors are included in the receiver set whose suitability score exceeds a threshold value. Unobserved heterogeneity in the social interaction behavior is captured using a multiplicative latent factor structure with latent variables for actors (which differ for actors as senders and receivers) and latent variables for individual messages. A Bayesian computational algorithm, which relies on Gibbs sampling, is proposed for model fitting. Model assessment is done using posterior predictive checks. Based on our analyses of the Enron email data, a mc-amen model with a 2 dimensional latent variable can accurately capture the empirical distribution of the cardinality of the receiver set and the composition of the receiver sets for commonly observed messages. Moreover the results show that actors have a comparable (but not identical) role as a sender and as a receiver in the network.

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arXiv2023

Frequentist Prediction Sets for Species Abundance using Indirect Information

Citizen science databases that consist of volunteer-led sampling efforts of species communities are relied on as essential sources of data in ecology. Summarizing such data across counties with frequentist-valid prediction sets for each county provides an interpretable comparison across counties of varying size or composition. As citizen science data often feature unequal sampling efforts across a spatial domain, prediction sets constructed with indirect methods that share information across counties may be used to improve precision. In this article, we present a nonparametric framework to obtain precise prediction sets for a multinomial random sample based on indirect information that maintain frequentist coverage guarantees for each county. We detail a simple algorithm to obtain prediction sets for each county using indirect information where the computation time does not depend on the sample size and scales nicely with the number of species considered. The indirect information may be estimated by a proposed empirical Bayes procedure based on information from auxiliary data. Our approach makes inference for under-sampled counties more precise, while maintaining area-specific frequentist validity for each county. Our method is used to provide a useful description of avian species abundance in North Carolina, USA based on citizen science data from the eBird database.

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arXiv2023

Structured Shrinkage Priors

In many regression settings the unknown coefficients may have some known structure, for instance they may be ordered in space or correspond to a vectorized matrix or tensor. At the same time, the unknown coefficients may be sparse, with many nearly or exactly equal to zero. However, many commonly used priors and corresponding penalties for coefficients do not encourage simultaneously structured and sparse estimates. In this paper we develop structured shrinkage priors that generalize multivariate normal, Laplace, exponential power and normal-gamma priors. These priors allow the regression coefficients to be correlated a priori without sacrificing elementwise sparsity or shrinkage. The primary challenges in working with these structured shrinkage priors are computational, as the corresponding penalties are intractable integrals and the full conditional distributions that are needed to approximate the posterior mode or simulate from the posterior distribution may be non-standard. We overcome these issues using a flexible elliptical slice sampling procedure, and demonstrate that these priors can be used to introduce structure while preserving sparsity.

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arXiv2022

Optimal Conformal Prediction for Small Areas

Existing inferential methods for small area data involve a trade-off between maintaining area-level frequentist coverage rates and improving inferential precision via the incorporation of indirect information. In this article, we propose a method to obtain an area-level prediction region for a future observation which mitigates this trade-off. The proposed method takes a conformal prediction approach in which the conformity measure is the posterior predictive density of a working model that incorporates indirect information. The resulting prediction region has guaranteed frequentist coverage regardless of the working model, and, if the working model assumptions are accurate, the region has minimum expected volume compared to other regions with the same coverage rate. When constructed under a normal working model, we prove such a prediction region is an interval and construct an efficient algorithm to obtain the exact interval. We illustrate the performance of our method through simulation studies and an application to EPA radon survey data.

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arXiv2020

Hierarchical Multidimensional Scaling for the Comparison of Musical Performance Styles

Quantification of stylistic differences between musical artists is of academic interest to the music community, and is also useful for other applications such as music information retrieval and recommendation systems. Information about stylistic differences can be obtained by comparing the performances of different artists across common musical pieces. In this article, we develop a statistical methodology for identifying and quantifying systematic stylistic differences among artists that are consistent across audio recordings of a common set of pieces, in terms of several musical features. Our focus is on a comparison of ten different orchestras, based on data from audio recordings of the nine Beethoven symphonies. As generative or fully parametric models of raw audio data can be highly complex, and more complex than necessary for our goal of identifying differences between orchestras, we propose to reduce the data from a set of audio recordings down to pairwise distances between orchestras, based on different musical characteristics of the recordings, such as tempo, dynamics, and timbre. For each of these characteristics, we obtain multiple pairwise distance matrices, one for each movement of each symphony. We develop a hierarchical multidimensional scaling (HMDS) model to identify and quantify systematic differences between orchestras in terms of these three musical characteristics, and interpret the results in the context of known qualitative information about the orchestras. This methodology is able to recover several expected systematic similarities between orchestras, as well as to identify some more novel results. For example, we find that modern recordings exhibit a high degree of similarity to each other, as compared to older recordings.

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arXiv2020

Smaller $p$-values in genomics studies using distilled historical information

Medical research institutions have generated massive amounts of biological data by genetically profiling hundreds of cancer cell lines. In parallel, academic biology labs have conducted genetic screens on small numbers of cancer cell lines under custom experimental conditions. In order to share information between these two approaches to scientific discovery, this article proposes a "frequentist assisted by Bayes" (FAB) procedure for hypothesis testing that allows historical information from massive genomics datasets to increase the power of hypothesis tests in specialized studies. The exchange of information takes place through a novel probability model for multimodal genomics data, which distills historical information pertaining to cancer cell lines and genes across a wide variety of experimental contexts. If the relevance of the historical information for a given study is high, then the resulting FAB tests can be more powerful than the corresponding classical tests. If the relevance is low, then the FAB tests yield as many discoveries as the classical tests. Simulations and practical investigations demonstrate that the FAB testing procedure can increase the number of effects discovered in genomics studies while still maintaining strict control of type I error and false discovery rates.

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arXiv2019

Smaller $p$-values via indirect information

This article develops $p$-values for evaluating means of normal populations that make use of indirect or prior information. A $p$-value of this type is based on a biased test statistic that is optimal on average with respect to a probability distribution that encodes indirect information about the mean parameter, resulting in a smaller $p$-value if the indirect information is accurate. In a variety of multiparameter settings, we show how to adaptively estimate the indirect information for each mean parameter while still maintaining uniformity of the $p$-values under their null hypotheses. This is done using a linking model through which indirect information about the mean of one population may be obtained from the data of other populations. Importantly, the linking model does not need to be correct to maintain the uniformity of the $p$-values under their null hypotheses. This methodology is illustrated in several data analysis scenarios, including small area inference, spatially arranged populations, interactions in linear regression, and generalized linear models.

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arXiv2019

Monte Carlo simulation on the Stiefel manifold via polar expansion

Motivated by applications to Bayesian inference for statistical models with orthogonal matrix parameters, we present $\textit{polar expansion},$ a general approach to Monte Carlo simulation from probability distributions on the Stiefel manifold. To bypass many of the well-established challenges of simulating from the distribution of a random orthogonal matrix $\boldsymbol{Q},$ we construct a distribution for an unconstrained random matrix $\boldsymbol{X}$ such that $\boldsymbol{Q}_X,$ the orthogonal component of the polar decomposition of $\boldsymbol{X},$ is equal in distribution to $\boldsymbol{Q}.$ The distribution of $\boldsymbol{X}$ is amenable to Markov chain Monte Carlo (MCMC) simulation using standard methods, and an approximation to the distribution of $\boldsymbol{Q}$ can be recovered from a Markov chain on the unconstrained space. When combined with modern MCMC software, polar expansion allows for routine and flexible posterior inference in models with orthogonal matrix parameters. We find that polar expansion with adaptive Hamiltonian Monte Carlo is an order of magnitude more efficient than competing MCMC approaches in a benchmark protein interaction network application. We also propose a new approach to Bayesian functional principal components analysis which we illustrate in a meteorological time series application.

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arXiv2019

Lasso ANOVA Decompositions for Matrix and Tensor Data

Consider the problem of estimating the entries of an unknown mean matrix or tensor given a single noisy realization. In the matrix case, this problem can be addressed by decomposing the mean matrix into a component that is additive in the rows and columns, i.e.\ the additive ANOVA decomposition of the mean matrix, plus a matrix of elementwise effects, and assuming that the elementwise effects may be sparse. Accordingly, the mean matrix can be estimated by solving a penalized regression problem, applying a lasso penalty to the elementwise effects. Although solving this penalized regression problem is straightforward, specifying appropriate values of the penalty parameters is not. Leveraging the posterior mode interpretation of the penalized regression problem, moment-based empirical Bayes estimators of the penalty parameters can be defined. Estimation of the mean matrix using these these moment-based empirical Bayes estimators can be called LANOVA penalization, and the corresponding estimate of the mean matrix can be called the LANOVA estimate. The empirical Bayes estimators are shown to be consistent. Additionally, LANOVA penalization is extended to accommodate sparsity of row and column effects and to estimate an unknown mean tensor. The behavior of the LANOVA estimate is examined under misspecification of the distribution of the elementwise effects, and LANOVA penalization is applied to several datasets, including a matrix of microarray data, a three-way tensor of fMRI data and a three-way tensor of wheat infection data.

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arXiv2018

Random orthogonal matrices and the Cayley transform

Random orthogonal matrices play an important role in probability and statistics, arising in multivariate analysis, directional statistics, and models of physical systems, among other areas. Calculations involving random orthogonal matrices are complicated by their constrained support. Accordingly, we parametrize the Stiefel and Grassmann manifolds, represented as subsets of orthogonal matrices, in terms of Euclidean parameters using the Cayley transform. We derive the necessary Jacobian terms for change of variables formulas. Given a density defined on the Stiefel or Grassmann manifold, these allow us to specify the corresponding density for the Euclidean parameters, and vice versa. As an application, we describe and illustrate through examples a Markov chain Monte Carlo approach to simulating from distributions on the Stiefel and Grassmann manifolds. Finally, we establish an asymptotic independent normal approximation for the distribution of the Euclidean parameters which corresponds to the uniform distribution on the Stiefel manifold. This result contributes to the growing literature on normal approximations to the entries of random orthogonal matrices or transformations thereof.

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arXiv2018

Testing Sparsity-Inducing Penalties

Many penalized maximum likelihood estimators correspond to posterior mode estimators under specific prior distributions. Appropriateness of a particular class of penalty functions can therefore be interpreted as the appropriateness of a prior for the parameters. For example, the appropriateness of a lasso penalty for regression coefficients depends on the extent to which the empirical distribution of the regression coefficients resembles a Laplace distribution. We give a testing procedure of whether or not a Laplace prior is appropriate and accordingly, whether or not using a lasso penalized estimate is appropriate. This testing procedure is designed to have power against exponential power priors which correspond to $\ell_q$ penalties. Via simulations, we show that this testing procedure achieves the desired level and has enough power to detect violations of the Laplace assumption when the numbers of observations and unknown regression coefficients are large. We then introduce an adaptive procedure that chooses a more appropriate prior and corresponding penalty from the class of exponential power priors when the null hypothesis is rejected. We show that this can improve estimation of the regression coefficients both when they are drawn from an exponential power distribution and when they are drawn from a spike-and-slab distribution.

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arXiv2018

Inferential Approaches for Network Analyses: AMEN for Latent Factor Models

We introduce a Bayesian approach to conduct inferential analyses on dyadic data while accounting for interdependencies between observations through a set of additive and multiplicative effects (AME). The AME model is built on a generalized linear modeling framework and is thus flexible enough to be applied to a variety of contexts. We contrast the AME model to two prominent approaches in the literature: the latent space model (LSM) and the exponential random graph model (ERGM). Relative to these approaches, we show that the AME approach is a) to be easy to implement; b) interpretable in a general linear model framework; c) computationally straightforward; d) not prone to degeneracy; e) captures 1st, 2nd, and 3rd order network dependencies; and f) notably outperforms ERGMs and LSMs on a variety of metrics and in an out-of-sample context. In summary, AME offers a straightforward way to undertake nuanced, principled inferential network analysis for a wide range of social science questions.

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