Questions and Answers

In addition to his contributions to biostatistics and clinical trials, Paul Meier had a long-term interest in the legal applications of statistics. As part of this, he had extensive experience as a statistical consultant. Legal consulting can be a minefield, but as a result of his background, Paul had excellent advice to give to those starting out on how to function successfully in this environment.     

A Second-order Adjustment to the Profile Likelihood in the Case of a Multidimensional Parameter of Interest

Inference in the presence of nuisance parameters is often carried out by using the χ²-approximation to the profile likelihood ratio statistic. However, in small samples, the accuracy of such procedures may be poor, in part because the profile likelihood does not behave as a true likelihood, in particular having a profile score bias and information bias which do not vanish. To account better for nuisance parameters, various researchers have suggested that inference be based on an additively adjusted version of the profile likelihood function. Each of these adjustments to the profile likelihood generally has the effect of reducing the bias of the associated profile score statistic. However, these adjustments are not applicable outside the specific parametric framework for which they were developed. In particular, it is often difficult or even impossible to apply them where the parameter about which inference is desired is multidimensional. In this paper, we propose a new adjustment function which leads to an adjusted profile likelihood having reduced score and information biases and is readily applicable to a general parametric framework, including the case of vector-valued parameters of interest. Examples are given to examine the performance of the new adjusted profile likelihood in small samples, and also to compare its performance with other adjusted profile likelihoods.     

Updating Schemes, Correlation Structure, Blocking and Parameterization for the Gibbs Sampler

In this paper many convergence issues concerning the implementation of the Gibbs sampler are investigated. Exact computable rates of convergence for Gaussian target distributions are obtained. Different random and non-random updating strategies and blocking combinations are compared using the rates. The effect of dimensionality and correlation structure on the convergence rates are studied. Some examples are considered to demonstrate the results. For a Gaussian image analysis problem several updating strategies are described and compared. For problems in Bayesian linear models several possible parameterizations are analysed in terms of their convergence rates characterizing the optimal choice.     

Effects of temporal resolution adjustments on dynamic sexual contact models

Simulation and inferential modeling of sexual contact dynamics can be used to help predict the propagation of sexually transmitted infections (STI) such as HIV, by providing information on both cross-sectional network structure and how that structure changes over time. Researchers’ choices regarding the temporal resolution of such network models is often driven by the resolution of the data collected to support model fitting and evaluation. These inherited temporal resolutions can become problematic if they differ from the resolution of other processes to which the network must be related. In such cases, a model “correction” is necessary: specifically, we would like to have a systematic method for adjusting a fitted model to allow it to make predictions at a different timescale than the one on which it was initially based. Here, we introduce a basic set of desiderata for such adjustments, and assess three very simple approaches to timescale adjustments for models of sexual contact networks (SCNs), with focus on models parameterized within the separable temporal exponential family random graph model (STERGM) framework. We also examine the impact of time-scale changes on SCN characteristics themselves, and outline a set of desiderata for what an adjustment strategy may be expected to achieve. Our findings have implications both for timescale correction of dynamic network models, and for dynamic network data collection.     

On convergence of the EM algorithmand the Gibbs sampler

In this article we investigate the relationship between the EM algorithm and the Gibbs sampler. We show that the approximate rate of convergence of the Gibbs sampler by Gaussian approximation is equal to that of the corresponding EM-type algorithm. This helps in implementing either of the algorithms as improvement strategies for one algorithm can be directly transported to the other. In particular, by running the EM algorithm we know approximately how many iterations are needed for convergence of the Gibbs sampler. We also obtain a result that under certain conditions, the EM algorithm used for finding the maximum likelihood estimates can be slower to converge than the corresponding Gibbs sampler for Bayesian inference. We illustrate our results in a number of realistic examples all based on the generalized linear mixed models.     

Comparisons of Three Approaches for Discrete Conditional Models

This article describes three methods for computing a discrete joint density from full conditional densities. They are the Gibbs sampler, a hybrid method, and an interaction-based method. The hybrid method uses the iterative proportional fitting algorithm, and it is derived from the mixed parameterization of a contingency table. The interaction-based approach is derived from the canonical parameters, while the Gibbs sampler can be regarded as based on the mean parameters. In short, different approaches are motivated by different parameterizations. The setting of a bivariate conditionally specified distribution is used as the premise for comparing the numerical accuracy of the three methods. Detailed comparisons of marginal distributions, odds ratios and expected values are reported. We give theoretical justifications as to why the hybrid method produces better approximation than the Gibbs sampler. Generalizations to more than two variables are discussed. In practice, Gibbs sampler has certain advantages: it is conceptually easy to understand and there are many software tools available. Nevertheless, the hybrid method and the interaction-based method are accurate and simple alternatives when the Gibbs sampler results in a slowly mixing chain and requires substantial simulation efforts.     

Specifying a Gaussian Markov Random Field by a Sparse Cholesky Triangle

ABSTRACT

This note discusses the approach of specifying a Gaussian Markov random field (GMRF) by the Cholesky triangle of the precision matrix. A such representation can be made extremely sparse using numerical techniques for incomplete sparse Cholesky factorization, and provide very computational efficient representation for simulating from the GMRF. However, we provide theoretical and empirical justification showing that the sparse Cholesky triangle representation is fragile when conditioning a GMRF on a subset of the variables or observed data, meaning that the computational cost increases.