Following a moving target—Monte Carlo inference for dynamic Bayesian models

Markov chain Monte Carlo (MCMC) sampling is a numerically intensive simulation technique which has greatly improved the practicality of Bayesian inference and prediction. However, MCMC sampling is too slow to be of practical use in problems involving a large number of posterior (target) distributions, as in dynamic modelling and predictive model selection. Alternative simulation techniques for tracking moving target distributions, known as particle filters, which combine importance sampling, importance resampling and MCMC sampling, tend to suffer from a progressive degeneration as the target sequence evolves. We propose a new technique, based on these same simulation methodologies, which does not suffer from this progressive degeneration.     

Markov chain importance sampling with applications to rare event probability estimation

We present a versatile Monte Carlo method for estimating multidimensional integrals, with applications to rare-event probability estimation. The method fuses two distinct and popular Monte Carlo simulation methods—Markov chain Monte Carlo and importance sampling—into a single algorithm. We show that for some applied numerical examples the proposed Markov Chain importance sampling algorithm performs better than methods based solely on importance sampling or MCMC.     

An efficient Monte Carlo EM algorithm for Bayesian lasso

The lasso is a popular technique of simultaneous estimation and variable selection in many research areas. The marginal posterior mode of the regression coefficients is equivalent to estimates given by the non-Bayesian lasso when the regression coefficients have independent Laplace priors. Because of its flexibility of statistical inferences, the Bayesian approach is attracting a growing body of research in recent years. Current approaches are primarily to either do a fully Bayesian analysis using Markov chain Monte Carlo (MCMC) algorithm or use Monte Carlo expectation maximization (MCEM) methods with an MCMC algorithm in each E-step. However, MCMC-based Bayesian method has much computational burden and slow convergence. Tan et al. [An efficient MCEM algorithm for fitting generalized linear mixed models for correlated binary data. J Stat Comput Simul. 2007;77:929–943] proposed a non-iterative sampling approach, the inverse Bayes formula (IBF) sampler, for computing posteriors of a hierarchical model in the structure of MCEM. Motivated by their paper, we develop this IBF sampler in the structure of MCEM to give the marginal posterior mode of the regression coefficients for the Bayesian lasso, by adjusting the weights of importance sampling, when the full conditional distribution is not explicit. Simulation experiments show that the computational time is much reduced with our method based on the expectation maximization algorithm and our algorithms and our methods behave comparably with other Bayesian lasso methods not only in prediction accuracy but also in variable selection accuracy and even better especially when the sample size is relatively large.     

Bayesian inference for pairwise interacting point processes

Pairwise interacting point processes are commonly used to model spatial point patterns. To perform inference, the established frequentist methods can produce good point estimates when the interaction in the data is moderate, but some methods may produce severely biased estimates when the interaction in strong. Furthermore, because the sampling distributions of the estimates are unclear, interval estimates are typically obtained by parametric bootstrap methods. In the current setting however, the behavior of such estimates is not well understood. In this article we propose Bayesian methods for obtaining inferences in pairwise interacting point processes. The requisite application of Markov chain Monte Carlo (MCMC) techniques is complicated by an intractable function of the parameters in the likelihood. The acceptance probability in a Metropolis-Hastings algorithm involves the ratio of two likelihoods evaluated at differing parameter values. The intractable functions do not cancel, and hence an intractable ratio r must be estimated within each iteration of a Metropolis-Hastings sampler. We propose the use of importance sampling techniques within MCMC to address this problem. While r may be estimated by other methods, these, in general, are not readily applied in a Bayesian setting. We demonstrate the validity of our importance sampling approach with a small simulation study. Finally, we analyze the Swedish pine sapling dataset (Strand 1972) and contrast the results with those in the literature.     

Adaptive evolutionary Monte Carlo algorithm for optimization with applications to sensor placement problems

In this paper, we present an adaptive evolutionary Monte Carlo algorithm (AEMC), which combines a tree-based predictive model with an evolutionary Monte Carlo sampling procedure for the purpose of global optimization. Our development is motivated by sensor placement applications in engineering, which requires optimizing certain complicated “black-box” objective function. The proposed method is able to enhance the optimization efficiency and effectiveness as compared to a few alternative strategies. AEMC falls into the category of adaptive Markov chain Monte Carlo (MCMC) algorithms and is the first adaptive MCMC algorithm that simulates multiple Markov chains in parallel. A theorem about the ergodicity property of the AEMC algorithm is stated and proven. We demonstrate the advantages of the proposed method by applying it to a sensor placement problem in a manufacturing process, as well as to a standard Griewank test function.     

A Hellinger distance approach to MCMC diagnostics

Bayesian analysis often requires the researcher to employ Markov Chain Monte Carlo (MCMC) techniques to draw samples from a posterior distribution which in turn is used to make inferences. Currently, several approaches to determine convergence of the chain as well as sensitivities of the resulting inferences have been developed. This work develops a Hellinger distance approach to MCMC diagnostics. An approximation to the Hellinger distance between two distributions f and g based on sampling is introduced. This approximation is studied via simulation to determine the accuracy. A criterion for using this Hellinger distance for determining chain convergence is proposed as well as a criterion for sensitivity studies. These criteria are illustrated using a dataset concerning the Anguilla australis, an eel native to New Zealand.     

Cross-entropy method for estimation of posterior expectation in Bayesian VAR models

In this article, an importance sampling (IS) method for the posterior expectation of a non linear function in a Bayesian vector autoregressive (VAR) model is developed. Most Bayesian inference problems involve the evaluation of the expectation of a function of interest, usually a non linear function of the model parameters, under the posterior distribution. Non linear functions in Bayesian VAR setting are difficult to estimate and usually require numerical methods for their evaluation. A weighted IS estimator is used for the evaluation of the posterior expectation. With the cross-entropy (CE) approach, the IS density is chosen from a specified family of densities such that the CE distance or the Kullback–Leibler divergence between the optimal IS density and the importance density is minimal. The performance of the proposed algorithm is assessed in an iterated multistep forecasting of US macroeconomic time series.     

Layered adaptive importance sampling

Monte Carlo methods represent the de facto standard for approximating complicated integrals involving multidimensional target distributions. In order to generate random realizations from the target distribution, Monte Carlo techniques use simpler proposal probability densities to draw candidate samples. The performance of any such method is strictly related to the specification of the proposal distribution, such that unfortunate choices easily wreak havoc on the resulting estimators. In this work, we introduce a layered (i.e., hierarchical) procedure to generate samples employed within a Monte Carlo scheme. This approach ensures that an appropriate equivalent proposal density is always obtained automatically (thus eliminating the risk of a catastrophic performance), although at the expense of a moderate increase in the complexity. Furthermore, we provide a general unified importance sampling (IS) framework, where multiple proposal densities are employed and several IS schemes are introduced by applying the so-called deterministic mixture approach. Finally, given these schemes, we also propose a novel class of adaptive importance samplers using a population of proposals, where the adaptation is driven by independent parallel or interacting Markov chain Monte Carlo (MCMC) chains. The resulting algorithms efficiently combine the benefits of both IS and MCMC methods.     

Fully Bayesian logistic regression with hyper-LASSO priors for high-dimensional feature selection

Feature selection arises in many areas of modern science. For example, in genomic research, we want to find the genes that can be used to separate tissues of different classes (e.g. cancer and normal). One approach is to fit regression/classification models with certain penalization. In the past decade, hyper-LASSO penalization (priors) have received increasing attention in the literature. However, fully Bayesian methods that use Markov chain Monte Carlo (MCMC) for regression/classification with hyper-LASSO priors are still in lack of development. In this paper, we introduce an MCMC method for learning multinomial logistic regression with hyper-LASSO priors. Our MCMC algorithm uses Hamiltonian Monte Carlo in a restricted Gibbs sampling framework. We have used simulation studies and real data to demonstrate the superior performance of hyper-LASSO priors compared to LASSO, and to investigate the issues of choosing heaviness and scale of hyper-LASSO priors.     

Markov chain Monte Carlo algorithms with sequential proposals

We explore a general framework in Markov chain Monte Carlo (MCMC) sampling where sequential proposals are tried as a candidate for the next state of the Markov chain. This sequential-proposal framework can be applied to various existing MCMC methods, including Metropolis–Hastings algorithms using random proposals and methods that use deterministic proposals such as Hamiltonian Monte Carlo (HMC) or the bouncy particle sampler. Sequential-proposal MCMC methods construct the same Markov chains as those constructed by the delayed rejection method under certain circumstances. In the context of HMC, the sequential-proposal approach has been proposed as extra chance generalized hybrid Monte Carlo (XCGHMC). We develop two novel methods in which the trajectories leading to proposals in HMC are automatically tuned to avoid doubling back, as in the No-U-Turn sampler (NUTS). The numerical efficiency of these new methods compare favorably to the NUTS. We additionally show that the sequential-proposal bouncy particle sampler enables the constructed Markov chain to pass through regions of low target density and thus facilitates better mixing of the chain when the target density is multimodal.

     

Bayesian model selection in linear mixed effects models with autoregressive(p) errors using mixture priors

In this article, we apply the Bayesian approach to the linear mixed effect models with autoregressive(p) random errors under mixture priors obtained with the Markov chain Monte Carlo (MCMC) method. The mixture structure of a point mass and continuous distribution can help to select the variables in fixed and random effects models from the posterior sample generated using the MCMC method. Bayesian prediction of future observations is also one of the major concerns. To get the best model, we consider the commonly used highest posterior probability model and the median posterior probability model. As a result, both criteria tend to be needed to choose the best model from the entire simulation study. In terms of predictive accuracy, a real example confirms that the proposed method provides accurate results.     

Adaptive smoothing in associated kernel discrete functions estimation using Bayesian approach

This paper demonstrates that cross-validation (CV) and Bayesian adaptive bandwidth selection can be applied in the estimation of associated kernel discrete functions. This idea is originally proposed by Brewer [A Bayesian model for local smoothing in kernel density estimation, Stat. Comput. 10 (2000), pp. 299–309] to derive variable bandwidths in adaptive kernel density estimation. Our approach considers the adaptive binomial kernel estimator and treats the variable bandwidths as parameters with beta prior distribution. The best variable bandwidth selector is estimated by the posterior mean in the Bayesian sense under squared error loss. Monte Carlo simulations are conducted to examine the performance of the proposed Bayesian adaptive approach in comparison with the performance of the Asymptotic mean integrated squared error estimator and CV technique for selecting a global (fixed) bandwidth proposed in Kokonendji and Senga Kiessé [Discrete associated kernels method and extensions, Stat. Methodol. 8 (2011), pp. 497–516]. The Bayesian adaptive bandwidth estimator performs better than the global bandwidth, in particular for small and moderate sample sizes.     

Importance sampling type estimators based on approximate marginal Markov chain Monte Carlo

We consider importance sampling (IS) type weighted estimators based on Markov chain Monte Carlo (MCMC) targeting an approximate marginal of the target distribution. In the context of Bayesian latent variable models, the MCMC typically operates on the hyperparameters, and the subsequent weighting may be based on IS or sequential Monte Carlo (SMC), but allows for multilevel techniques as well. The IS approach provides a natural alternative to delayed acceptance (DA) pseudo-marginal/particle MCMC, and has many advantages over DA, including a straightforward parallelization and additional flexibility in MCMC implementation. We detail minimal conditions which ensure strong consistency of the suggested estimators, and provide central limit theorems with expressions for asymptotic variances. We demonstrate how our method can make use of SMC in the state space models context, using Laplace approximations and time-discretized diffusions. Our experimental results are promising and show that the IS-type approach can provide substantial gains relative to an analogous DA scheme, and is often competitive even without parallelization.     

Bayesian analysis of complementary Poisson rate parameters with data subject to misclassification

We formulate closed-form Bayesian estimators for two complementary Poisson rate parameters using double sampling with data subject to misclassification and error free data. We also derive closed-form Bayesian estimators for two misclassification parameters in the modified Poisson model we assume. We use our results to determine credible sets for the rate and misclassification parameters. Additionally, we use MCMC methods to determine Bayesian estimators for three or more rate parameters and the misclassification parameters. We also perform a limited Monte Carlo simulation to examine the characteristics of these estimators. We demonstrate the efficacy of the new Bayesian estimators and highest posterior density regions with examples using two real data sets.     

Generalised additive mixed models analysis via gammSlice

We demonstrate the use of our R package, gammSlice, for Bayesian fitting and inference in generalised additive mixed model analysis. This class of models includes generalised linear mixed models and generalised additive models as special cases. Accurate Bayesian inference is achievable via sufficiently large Markov chain Monte Carlo (MCMC) samples. Slice sampling is a key component of the MCMC scheme. Comparisons with existing generalised additive mixed model software shows that gammSlice offers improved inferential accuracy, albeit at the cost of longer computational time.     

Prediction Intervals for Future Order Statistics from a Generalized Modified Weibull

Viewing the future order statistics as latent variables at each Gibbs sampling iteration, several Bayesian approaches to predict future order statistics based on type-II censored order statistics, X₍₁₎, X₍₂₎, …, X_(r), of a size n( > r) random sample from a four-parameter generalized modified Weibull (GMW) distribution, are studied. Four parameters of the GMW distribution are first estimated via simulation study. Then various Bayesian approaches, which include the plug-in method, the Monte Carlo method, the Gibbs sampling scheme, and the MCMC procedure, are proposed to develop the prediction intervals of unobserved order statistics. Finally, four type-II censored samples are utilized to investigate the predictions.     

Bayesian variable selection in a finite mixture of linear mixed-effects models

Mixture of linear mixed-effects models has received considerable attention in longitudinal studies, including medical research, social science and economics. The inferential question of interest is often the identification of critical factors that affect the responses. We consider a Bayesian approach to select the important fixed and random effects in the finite mixture of linear mixed-effects models. To accomplish our goal, latent variables are introduced to facilitate the identification of influential fixed and random components and to classify the membership of observations in the longitudinal data. A spike-and-slab prior for the regression coefficients is adopted to sidestep the potential complications of highly collinear covariates and to handle large p and small n issues in the variable selection problems. Here we employ Markov chain Monte Carlo (MCMC) sampling techniques for posterior inferences and explore the performance of the proposed method in simulation studies, followed by an actual psychiatric data analysis concerning depressive disorder.     

Classical and Bayesian Analysis of Univariate and Multivariate Stochastic Volatility Models

In this paper, efficient importance sampling (EIS) is used to perform a classical and Bayesian analysis of univariate and multivariate stochastic volatility (SV) models for financial return series. EIS provides a highly generic and very accurate procedure for the Monte Carlo (MC) evaluation of high-dimensional interdependent integrals. It can be used to carry out ML-estimation of SV models as well as simulation smoothing where the latent volatilities are sampled at once. Based on this EIS simulation smoother, a Bayesian Markov chain Monte Carlo (MCMC) posterior analysis of the parameters of SV models can be performed.     

Classical and Bayesian Analysis of Univariate and Multivariate Stochastic Volatility Models

In this paper, efficient importance sampling (EIS) is used to perform a classical and Bayesian analysis of univariate and multivariate stochastic volatility (SV) models for financial return series. EIS provides a highly generic and very accurate procedure for the Monte Carlo (MC) evaluation of high-dimensional interdependent integrals. It can be used to carry out ML-estimation of SV models as well as simulation smoothing where the latent volatilities are sampled at once. Based on this EIS simulation smoother, a Bayesian Markov chain Monte Carlo (MCMC) posterior analysis of the parameters of SV models can be performed.     

Inference for a Class of Stochastic Volatility Models Using Option and Spot Prices: Application of a Bivariate Kalman Filter

In this paper Bayesian methods are applied to a stochastic volatility model using both the prices of the asset and the prices of options written on the asset. Posterior densities for all model parameters, latent volatilities and the market price of volatility risk are produced via a Markov Chain Monte Carlo (MCMC) sampling algorithm. Candidate draws for the unobserved volatilities are obtained in blocks by applying the Kalman filter and simulation smoother to a linearization of a nonlinear state space representation of the model. Crucially, information from both the spot and option prices affects the draws via the specification of a bivariate measurement equation, with implied Black–Scholes volatilities used to proxy observed option prices in the candidate model. Alternative models nested within the Heston (1993) framework are ranked via posterior odds ratios, as well as via fit, predictive and hedging performance. The method is illustrated using Australian News Corporation spot and option price data.