We consider the problem of combining opinions from different experts in an explicitly model-based way to construct a valid subjective prior in a Bayesian statistical approach. We propose a generic approach by considering a hierarchical model accounting for various sources of variation as well as accounting for potential dependence between experts. We apply this approach to two problems. The first problem deals with a food risk assessment problem involving modelling dose-response for Listeria monocytogenes contamination of mice. Two hierarchical levels of variation are considered (between and within experts) with a complex mathematical situation due to the use of an indirect probit regression. The second concerns the time taken by PhD students to submit their thesis in a particular school. It illustrates a complex situation where three hierarchical levels of variation are modelled but with a simpler underlying probability distribution (log-Normal).

The problem of matching unlabeled point sets using Bayesian inference is considered. Two recently proposed models for the likelihood are compared, based on the Procrustes size-and-shape and the full configuration. Bayesian inference is carried out for matching point sets using Markov chain Monte Carlo simulation. An improvement to the existing Procrustes algorithm is proposed which improves convergence rates, using occasional large jumps in the burn-in period. The Procrustes and configuration methods are compared in a simulation study and using real data, where it is of interest to estimate the strengths of matches between protein binding sites. The performance of both methods is generally quite similar, and a connection between the two models is made using a Laplace approximation.

In this paper, we develop a simulation-based framework for regularized logistic regression, exploiting two novel results for scale mixtures of normals. By carefully choosing a hierarchical model for the likelihood by one type of mixture, and implementing regularization with another, we obtain new MCMC schemes with varying efficiency depending on the data type (binary v. binomial, say) and the desired estimator (maximum likelihood, maximum a posteriori, posterior mean). Advantages of our omnibus approach include flexibility, computational efficiency, applicability in $p\gg n$ settings, uncertainty estimates, variable selection, and assessing the optimal degree of regularization. We compare our methodology to modern alternatives on both synthetic and real data. An R package called reglogit is available on CRAN.

Prior effective sample size (ESS) of a Bayesian parametric model was defined by Morita, et al. (2008, Biometrics, 64, 595-602). Starting with an $\varepsilon$-information prior defined to have the same means and correlations as the prior but to be vague in a suitable sense, the ESS is the required sample size to obtain a hypothetical posterior very close to the prior. In this paper, we present two alternative definitions for the prior ESS that are suitable for a conditionally independent hierarchical model. The two definitions focus on either the first level prior or second level prior. The proposed methods are applied to important examples to verify that each of the two types of prior ESS matches the intuitively obvious answer where it exists. We illustrate the method with applications to several motivating examples, including a single-arm clinical trial to evaluate treatment response probabilities across different disease subtypes, a dose-finding trial based on toxicity in this setting, and a multicenter randomized trial of treatments for affective disorders.

Individual-level models (ILMs), as defined by Deardon et al. (2010), are a class of models originally designed to model the spread of infectious disease. However, they can also be considered as a tool for modelling the spatio-temporal dynamics of fire. We consider the much simplified problem of modelling the combustion dynamics on a piece of wax paper under relatively controlled conditions. The models are fitted in a Bayesian framework using Markov chain Monte Carlo (MCMC) methods. The focus here is on choosing a model that best fits the combustion pattern.

Assessing between-study variability in the context of conventional random-effects meta-analysis is notoriously difficult when incorporating data from only a small number of historical studies. In order to borrow strength, historical and current data are often assumed to be fully homogeneous, but this can have drastic consequences for power and Type I error if the historical information is biased. In this paper, we propose empirical and fully Bayesian modifications of the commensurate prior model (Hobbs et al. 2011) extending Pocock (1976), and evaluate their frequentist and Bayesian properties for incorporating patient-level historical data using general and generalized linear mixed regression models. Our proposed commensurate prior models lead to preposterior admissible estimators that facilitate alternative bias-variance trade-offs than those offered by pre-existing methodologies for incorporating historical data from a small number of historical studies. We also provide a sample analysis of a colon cancer trial comparing time-to-disease progression using a Weibull regression model.

We propose and develop a novel and effective perfect sampling methodology for simulating from posteriors corresponding to mixtures with either known (fixed) or unknown number of components. For the latter we consider the Dirichlet process-based mixture model developed by these authors, and show that our ideas are applicable to conjugate, and importantly, to non-conjugate cases. As to be expected, and as we show, perfect sampling for mixtures with known number of components can be achieved with much less effort with a simplified version of our general methodology, whether or not conjugate or non-conjugate priors are used. While no special assumption is necessary in the conjugate set-up for our theory to work, we require the assumption of compact parameter space in the non-conjugate set-up. However, we argue, with appropriate analytical, simulation, and real data studies as support, that such compactness assumption is not unrealistic and is not an impediment in practice. Not only do we validate our ideas theoretically and with simulation studies, but we also consider application of our proposal to three real data sets used by several authors in the past in connection with mixture models. The results we achieved in each of our experiments with either simulation study or real data application, are quite encouraging. However, the computation can be extremely burdensome in the case of large number of mixture components and in massive data sets. We discuss the role of parallel processing in mitigating the extreme computational burden.

The emergence of Markov chain Monte Carlo (MCMC) methods has opened a way for Bayesian analysis of complex models. Running MCMC samplers typically requires thousands of model evaluations, which can exceed available computer resources when this evaluation is computationally intensive. We will discuss two generally applicable techniques to improve the efficiency of MCMC. First, we consider a parallel version of the adaptive MCMC algorithm of Haario et al. (2001), implementing the idea of inter-chain adaptation introduced by Craiu et al. (2009). Second, we present an early rejection (ER) approach, where model simulation is stopped as soon as one can conclude that the proposed parameter value will be rejected by the MCMC algorithm.

This work is motivated by practical needs in estimating parameters of climate and Earth system models. These computationally intensive models involve non-linear expressions of the geophysical and biogeochemical processes of the Earth system. Modeling of these processes, especially those operating in scales smaller than the model grid, involves a number of specified parameters, or ‘tunables’. MCMC methods are applicable for estimation of these parameters, but they are computationally very demanding. Efficient MCMC variants are thus needed to obtain reliable results in reasonable time. Here we evaluate the computational gains attainable through parallel adaptive MCMC and Early Rejection using both simple examples and a realistic climate model.

Determining the marginal likelihood from a simulated posterior distribution is central to Bayesian model selection but is computationally challenging. The often-used harmonic mean approximation (HMA) makes no prior assumptions about the character of the distribution but tends to be inconsistent. The Laplace approximation is stable but makes strong, and often inappropriate, assumptions about the shape of the posterior distribution. Here, I argue that the marginal likelihood can be reliably computed from a posterior sample using Lebesgue integration theory in one of two ways: 1) when the HMA integral exists, compute the measure function numerically and analyze the resulting quadrature to control error; 2) compute the measure function numerically for the marginal likelihood integral itself using a space-partitioning tree, followed by quadrature. The first algorithm automatically eliminates the part of the sample that contributes large truncation error in the HMA. Moreover, it provides a simple graphical test for the existence of the HMA integral. The second algorithm uses the posterior sample to assign probability to a partition of the sample space and performs the marginal likelihood integral directly. It uses the posterior sample to discover and tessellate the subset of the sample space that was explored and uses quantiles to compute a representative field value. When integrating directly, this space may be trimmed to remove regions with low probability density and thereby improve accuracy. This second algorithm is consistent for all proper distributions. Error analysis provides some diagnostics on the numerical condition of the results in both cases.