Bayesian analysis of mixture modelling using the multivariate t distribution

A finite mixture model using the multivariate t distribution has been shown as a robust extension of normal mixtures. In this paper, we present a Bayesian approach for inference about parameters of t-mixture models. The specifications of prior distributions are weakly informative to avoid causing nonintegrable posterior distributions. We present two efficient EM-type algorithms for computing the joint posterior mode with the observed data and an incomplete future vector as the sample. Markov chain Monte Carlo sampling schemes are also developed to obtain the target posterior distribution of parameters. The advantages of Bayesian approach over the maximum likelihood method are demonstrated via a set of real data.     

A Bayesian Adjustment for Covariate Misclassification with Correlated Binary Outcome Data

Estimated associations between an outcome variable and misclassified covariates tend to be biased when the methods of estimation that ignore the classification error are applied. Available methods to account for misclassification often require the use of a validation sample (i.e. a gold standard). In practice, however, such a gold standard may be unavailable or impractical. We propose a Bayesian approach to adjust for misclassification in a binary covariate in the random effect logistic model when a gold standard is not available. This Markov Chain Monte Carlo (MCMC) approach uses two imperfect measures of a dichotomous exposure under the assumptions of conditional independence and non-differential misclassification. A simulated numerical example and a real clinical example are given to illustrate the proposed approach. Our results suggest that the estimated log odds of inpatient care and the corresponding standard deviation are much larger in our proposed method compared with the models ignoring misclassification. Ignoring misclassification produces downwardly biased estimates and underestimate uncertainty.     

New methods for fitting multiple sinusoids from irregularly sampled data

A novel framework is proposed for the estimation of multiple sinusoids from irregularly sampled time series. This spectral analysis problem is addressed as an under-determined inverse problem, where the spectrum is discretized on an arbitrarily thin frequency grid. As we focus on line spectra estimation, the solution must be sparse, i.e. the amplitude of the spectrum must be zero almost everywhere. Such prior information is taken into account within the Bayesian framework. Two models are used to account for the prior sparseness of the solution, namely a Laplace prior and a Bernoulli–Gaussian prior, associated to optimization and stochastic sampling algorithms, respectively. Such approaches are efficient alternatives to usual sequential prewhitening methods, especially in case of strong sampling aliases perturbating the Fourier spectrum. Both methods should be intensively tested on real data sets by physicists.     

Bayesian inference for a discretely observed stochastic kinetic model

The ability to infer parameters of gene regulatory networks is emerging as a key problem in systems biology. The biochemical data are intrinsically stochastic and tend to be observed by means of discrete-time sampling systems, which are often limited in their completeness. In this paper we explore how to make Bayesian inference for the kinetic rate constants of regulatory networks, using the stochastic kinetic Lotka-Volterra system as a model. This simple model describes behaviour typical of many biochemical networks which exhibit auto-regulatory behaviour. Various MCMC algorithms are described and their performance evaluated in several data-poor scenarios. An algorithm based on an approximating process is shown to be particularly efficient.     

Higher-order Bayesian Approximations for Pseudo-posterior Distributions

The theory of higher-order asymptotics provides accurate approximations to posterior distributions for a scalar parameter of interest, and to the corresponding tail area, for practical use in Bayesian analysis. The aim of this article is to extend these approximations to pseudo-posterior distributions, e.g., posterior distributions based on a pseudo-likelihood function and a suitable prior, which are proved to be particularly useful when the full likelihood is analytically or computationally infeasible. In particular, from a theoretical point of view, we derive the Laplace approximation for a pseudo-posterior distribution, and for the corresponding tail area, for a scalar parameter of interest, also in the presence of nuisance parameters. From a computational point of view, starting from these higher-order approximations, we discuss the higher-order tail area (HOTA) algorithm useful to approximate marginal posterior distributions, and related quantities. Compared to standard Markov chain Monte Carlo methods, the main advantage of the HOTA algorithm is that it gives independent samples at a negligible computational cost. The relevant computations are illustrated by two examples.     

Marginal likelihood estimation from the Metropolis output: tips and tricks for efficient implementation in generalized linear latent variable models

The marginal likelihood can be notoriously difficult to compute, and particularly so in high-dimensional problems. Chib and Jeliazkov employed the local reversibility of the Metropolis–Hastings algorithm to construct an estimator in models where full conditional densities are not available analytically. The estimator is free of distributional assumptions and is directly linked to the simulation algorithm. However, it generally requires a sequence of reduced Markov chain Monte Carlo runs which makes the method computationally demanding especially in cases when the parameter space is large. In this article, we study the implementation of this estimator on latent variable models which embed independence of the responses to the observables given the latent variables (conditional or local independence). This property is employed in the construction of a multi-block Metropolis-within-Gibbs algorithm that allows to compute the estimator in a single run, regardless of the dimensionality of the parameter space. The counterpart one-block algorithm is also considered here, by pointing out the difference between the two approaches. The paper closes with the illustration of the estimator in simulated and real-life data sets.     

Complex Latent Variable Modeling in Educational Assessment

Bayesian item response theory models have been widely used in different research fields. They support measuring constructs and modeling relationships between constructs, while accounting for complex test situations (e.g., complex sampling designs, missing data, heterogenous population). Advantages of this flexible modeling framework together with powerful simulation-based estimation techniques are discussed. Furthermore, it is shown how the Bayes factor can be used to test relevant hypotheses in assessment using the College Basic Academic Subjects Examination (CBASE) data.     

Bayesian blinded sample size re-estimation

Information before unblinding regarding the success of confirmatory clinical trials is highly uncertain. Current techniques using point estimates of auxiliary parameters for estimating expected blinded sample size: (i) fail to describe the range of likely sample sizes obtained after the anticipated data are observed, and (ii) fail to adjust to the changing patient population. Sequential MCMC-based algorithms are implemented for purposes of sample size adjustments. The uncertainty arising from clinical trials is characterized by filtering later auxiliary parameters through their earlier counterparts and employing posterior distributions to estimate sample size and power. The use of approximate expected power estimates to determine the required additional sample size are closely related to techniques employing Simple Adjustments or the EM algorithm. By contrast with these, our proposed methodology provides intervals for the expected sample size using the posterior distribution of auxiliary parameters. Future decisions about additional subjects are better informed due to our ability to account for subject response heterogeneity over time. We apply the proposed methodologies to a depression trial. Our proposed blinded procedures should be considered for most studies due to ease of implementation.     

Accelerating inference for diffusions observed with measurement error and large sample sizes using approximate Bayesian computation

In recent years, dynamical modelling has been provided with a range of breakthrough methods to perform exact Bayesian inference. However, it is often computationally unfeasible to apply exact statistical methodologies in the context of large data sets and complex models. This paper considers a nonlinear stochastic differential equation model observed with correlated measurement errors and an application to protein folding modelling. An approximate Bayesian computation (ABC)-MCMC algorithm is suggested to allow inference for model parameters within reasonable time constraints. The ABC algorithm uses simulations of ‘subsamples’ from the assumed data-generating model as well as a so-called ‘early-rejection’ strategy to speed up computations in the ABC-MCMC sampler. Using a considerate amount of subsamples does not seem to degrade the quality of the inferential results for the considered applications. A simulation study is conducted to compare our strategy with exact Bayesian inference, the latter resulting two orders of magnitude slower than ABC-MCMC for the considered set-up. Finally, the ABC algorithm is applied to a large size protein data. The suggested methodology is fairly general and not limited to the exemplified model and data.     

Bayesian penalized B-spline estimation approach for epidemic models

Ordinary differential equations (ODEs) are normally used to model dynamic processes in applied sciences such as biology, engineering, physics, and many other areas. In these models, the parameters are usually unknown, and thus they are often specified artificially or empirically. Alternatively, a feasible method is to estimate the parameters based on observed data. In this study, we propose a Bayesian penalized B-spline approach to estimate the parameters and initial values for ODEs used in epidemiology. We evaluated the efficiency of the proposed method based on simulations using the Markov chain Monte Carlo algorithm for the Kermack–McKendrick model. The proposed approach is also illustrated based on a real application to the transmission dynamics of hepatitis C virus in mainland China.