Comparison of Bayesian models for production efficiency

In this paper, we use Markov Chain Monte Carlo (MCMC) methods in order to estimate and compare stochastic production frontier models from a Bayesian perspective. We consider a number of competing models in terms of different production functions and the distribution of the asymmetric error term. All MCMC simulations are done using the package JAGS (Just Another Gibbs Sampler), a clone of the classic BUGS package which works closely with the R package where all the statistical computations and graphics are done.     

A Bayesian random effects model for analyzing mixed negative binomial and continuous longitudinal responses

ABSTRACT

A general Bayesian random effects model for analyzing longitudinal mixed correlated continuous and negative binomial responses with and without missing data is presented. This Bayesian model, given some random effects, uses a normal distribution for the continuous response and a negative binomial distribution for the count response. A Markov Chain Monte Carlo sampling algorithm is described for estimating the posterior distribution of the parameters. This Bayesian model is illustrated by a simulation study. For sensitivity analysis to investigate the change of parameter estimates with respect to the perturbation from missing at random to not missing at random assumption, the use of posterior curvature is proposed. The model is applied to a medical data, obtained from an observational study on women, where the correlated responses are the negative binomial response of joint damage and continuous response of body mass index. The simultaneous effects of some covariates on both responses are also investigated.     

Sampling-based Inference of Time Deformation Models with Heavy Tail Distributions

This article focuses on simulation-based inference for the time-deformation models directed by a duration process. In order to better capture the heavy tail property of the time series of financial asset returns, the innovation of the observation equation is subsequently assumed to have a Student-t distribution. Suitable Markov chain Monte Carlo (MCMC) algorithms, which are hybrids of Gibbs and slice samplers, are proposed for estimation of the parameters of these models. In the algorithms, the parameters of the models can be sampled either directly from known distributions or through an efficient slice sampler. The states are simulated one at a time by using a Metropolis-Hastings method, where the proposal distributions are sampled through a slice sampler. Simulation studies conducted in this article suggest that our extended models and accompanying MCMC algorithms work well in terms of parameter estimation and volatility forecast.     

Bayesian quantile regression for longitudinal data models

In this paper, we discuss a fully Bayesian quantile inference using Markov Chain Monte Carlo (MCMC) method for longitudinal data models with random effects. Under the assumption of error term subject to asymmetric Laplace distribution, we establish a hierarchical Bayesian model and obtain the posterior distribution of unknown parameters at τ-th level. We overcome the current computational limitations using two approaches. One is the general MCMC technique with Metropolis–Hastings algorithm and another is the Gibbs sampling from the full conditional distribution. These two methods outperform the traditional frequentist methods under a wide array of simulated data models and are flexible enough to easily accommodate changes in the number of random effects and in their assumed distribution. We apply the Gibbs sampling method to analyse a mouse growth data and some different conclusions from those in the literatures are obtained.     

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.     

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.     

Efficient Bayesian inference in generalized inverse gamma processes for stochastic volatility

This paper develops a novel and efficient algorithm for Bayesian inference in inverse Gamma stochastic volatility models. It is shown that by conditioning on auxiliary variables, it is possible to sample all the volatilities jointly directly from their posterior conditional density, using simple and easy to draw from distributions. Furthermore, this paper develops a generalized inverse gamma process with more flexible tails in the distribution of volatilities, which still allows for simple and efficient calculations. Using several macroeconomic and financial datasets, it is shown that the inverse gamma and generalized inverse gamma processes can greatly outperform the commonly used log normal volatility processes with Student’s t errors or jumps in the mean equation.     

Assessing convergence diagnostic tests for Bayesian Cox regression

The Markov chain Monte Carlo (MCMC) method generates samples from the posterior distribution and uses these samples to approximate expectations of quantities of interest. For the process, researchers have to decide whether the Markov chain has reached the desired posterior distribution. Using convergence diagnostic tests are very important to decide whether the Markov chain has reached the target distribution. Our interest in this study was to compare the performances of convergence diagnostic tests for all parameters of Bayesian Cox regression model with different number of iterations by using a simulation and a real lung cancer dataset.     

Efficient sampling schemes for Bayesian MARS models with many predictors

Multivariate adaptive regression spline fitting or MARS (Friedman 1991) provides a useful methodology for flexible adaptive regression with many predictors. The MARS methodology produces an estimate of the mean response that is a linear combination of adaptively chosen basis functions. Recently, a Bayesian version of MARS has been proposed (Denison, Mallick and Smith 1998a, Holmes and Denison, 2002) combining the MARS methodology with the benefits of Bayesian methods for accounting for model uncertainty to achieve improvements in predictive performance. In implementation of the Bayesian MARS approach, Markov chain Monte Carlo methods are used for computations, in which at each iteration of the algorithm it is proposed to change the current model by either (a) Adding a basis function (birth step) (b) Deleting a basis function (death step) or (c) Altering an existing basis function (change step). In the algorithm of Denison, Mallick and Smith (1998a), when a birth step is proposed, the type of basis function is determined by simulation from the prior. This works well in problems with a small number of predictors, is simple to program, and leads to a simple form for Metropolis-Hastings acceptance probabilities. However, in problems with very large numbers of predictors where many of the predictors are useless it may be difficult to find interesting interactions with such an approach. In the original MARS algorithm of Friedman (1991) a heuristic is used of building up higher order interactions from lower order ones, which greatly reduces the complexity of the search for good basis functions to add to the model. While we do not exactly follow the intuition of the original MARS algorithm in this paper, we nevertheless suggest a similar idea in which the Metropolis-Hastings proposals of Denison, Mallick and Smith (1998a) are altered to allow dependence on the current model. Our modification allows more rapid identification and exploration of important interactions, especially in problems with very large numbers of predictor variables and many useless predictors. Performance of the algorithms is compared in simulation studies.     

Steady-state Gibbs sampler estimation for lung cancer data

This paper is based on the application of a Bayesian model to a clinical trial study to determine a more effective treatment to lower mortality rates and consequently to increase survival times among patients with lung cancer. In this study, Qian et al. [13 J. Qian, D.K. Stangl, and S. George, A Weibull model for survival data: Using prediction to decide when to stop a clinical trial, in Bayesian Biostatistics, D. Berry and D. Stangl, eds., Marcel Dekker, New York, 1996, pp. 187–205. [Google Scholar]] strived to determine if a Weibull survival model can be used to decide whether to stop a clinical trial. The traditional Gibbs sampler was used to estimate the model parameters. This paper proposes to use the independent steady-state Gibbs sampling (ISSGS) approach, introduced by Dunbar et al. [3 M. Dunbar, H.M. Samawi, R. Vogel, and L. Yu, A more efficient Gibbs sampler estimation using steady state simulation: Application to public health studies, J. Stat. Simul. Comput. 10.1080/00949655.2013.770857.[Taylor &; Francis Online] , [Google Scholar]], to improve the original Gibbs sampler in multidimensional problems. It is demonstrated that ISSGS provides accuracy with unbiased estimation and improves the performance and convergence of the Gibbs sampler in this application.     

Bayesian Inference for a Stochastic Epidemic Model with Uncertain Numbers of Susceptibles of Several Types

A stochastic epidemic model with several kinds of susceptible is used to analyse temporal disease outbreak data from a Bayesian perspective. Prior distributions are used to model uncertainty in the actual numbers of susceptibles initially present. The posterior distribution of the parameters of the model is explored via Markov chain Monte Carlo methods. The methods are illustrated using two datasets, and the results are compared where possible to results obtained by previous analyses.     

Bayesian Estimation of Stochastic Frontier Models with Multivariate Skew t Error Terms

The study of proportions is a common topic in many fields of study. The standard beta distribution or the inflated beta distribution may be a reasonable choice to fit a proportion in most situations. However, they do not fit well variables that do not assume values in the open interval (0, c), 0 < c < 1. For these variables, the authors introduce the truncated inflated beta distribution (TBEINF). This proposed distribution is a mixture of the beta distribution bounded in the open interval (c, 1) and the trinomial distribution. The authors present the moments of the distribution, its scoring vector, and Fisher information matrix, and discuss estimation of its parameters. The properties of the suggested estimators are studied using Monte Carlo simulation. In addition, the authors present an application of the TBEINF distribution for unemployment insurance data.     

Parameter Estimation for Hidden Markov Models with Intractable Likelihoods

Approximate Bayesian computation (ABC) is a popular technique for analysing data for complex models where the likelihood function is intractable. It involves using simulation from the model to approximate the likelihood, with this approximate likelihood then being used to construct an approximate posterior. In this paper, we consider methods that estimate the parameters by maximizing the approximate likelihood used in ABC. We give a theoretical analysis of the asymptotic properties of the resulting estimator. In particular, we derive results analogous to those of consistency and asymptotic normality for standard maximum likelihood estimation. We also discuss how sequential Monte Carlo methods provide a natural method for implementing our likelihood‐based ABC procedures.     

Partially Collapsed Gibbs Sampling for Linear Mixed-effects Models

This article presents a novel Bayesian analysis for linear mixed-effects models. The analysis is based on the method of partial collapsing that allows some components to be partially collapsed out of a model. The resulting partially collapsed Gibbs (PCG) sampler constructed to fit linear mixed-effects models is expected to exhibit much better convergence properties than the corresponding Gibbs sampler. In order to construct the PCG sampler without complicating component updates, we consider the reparameterization of model components by expressing a between-group variance in terms of a within-group variance in a linear mixed-effects model. The proposed method of partial collapsing with reparameterization is applied to the Merton’s jump diffusion model as well as general linear mixed-effects models with proper prior distributions and illustrated using simulated data and longitudinal data on sleep deprivation.     

Flexible Threshold Models for Modelling Interest Rate Volatility

This paper focuses on interest rate models with regime switching and extends previous nonlinear threshold models by relaxing the assumption of a fixed number of regimes. Instead we suggest automatic model determination through Bayesian inference via the reversible jump Markov Chain Monte Carlo (MCMC) algorithm. Moreover, we allow the thresholds in the volatility to be driven not only by the interest rate but also by other economic factors. We illustrate our methodology by applying it to interest rates and other economic factors of the American economy.     

Flexible Threshold Models for Modelling Interest Rate Volatility

This paper focuses on interest rate models with regime switching and extends previous nonlinear threshold models by relaxing the assumption of a fixed number of regimes. Instead we suggest automatic model determination through Bayesian inference via the reversible jump Markov Chain Monte Carlo (MCMC) algorithm. Moreover, we allow the thresholds in the volatility to be driven not only by the interest rate but also by other economic factors. We illustrate our methodology by applying it to interest rates and other economic factors of the American economy.     

Analysis of the Gibbs sampler for a model related to James-Stein estimators

We analyse a hierarchical Bayes model which is related to the usual empirical Bayes formulation of James-Stein estimators. We consider running a Gibbs sampler on this model. Using previous results about convergence rates of Markov chains, we provide rigorous, numerical, reasonable bounds on the running time of the Gibbs sampler, for a suitable range of prior distributions. We apply these results to baseball data from Efron and Morris (1975). For a different range of prior distributions, we prove that the Gibbs sampler will fail to converge, and use this information to prove that in this case the associated posterior distribution is non-normalizable.     

基于吉伯斯样本生成器的向量自回归模型选择

内容提要：向量自回归模型是多元时间序列分析中最常用的方法之一。在建立模型的过程中模型选择是非常重要的一个环节,如果候选模型不是很多时,可以通过比较每个模型的准则值如AIC、AICc、BIC或HQ进行模型选择。可是,当存在大量候选模型时,我们无法一一比较每个模型的准则值。为了解决这个问题,本文提出一个基于吉伯斯样本生成器的向量自回归模型选择方法,结果表明应用该方法能够从大量候选模型中准确、高效地确认准则值最小的模型。     

Bayesian mixture models for complex high dimensional count data in phage display experiments

Summary.  Phage display is a biological process that is used to screen random peptide libraries for ligands that bind to a target of interest with high affinity. On the basis of a count data set from an innovative multistage phage display experiment, we propose a class of Bayesian mixture models to cluster peptide counts into three groups that exhibit different display patterns across stages. Among the three groups, the investigators are particularly interested in that with an ascending display pattern in the counts, which implies that the peptides are likely to bind to the target with strong affinity. We apply a Bayesian false discovery rate approach to identify the peptides with the strongest affinity within the group. A list of peptides is obtained, among which important ones with meaningful functions are further validated by biologists. To examine the performance of the Bayesian model, we conduct a simulation study and obtain desirable results.     

Bayesian neural networks for nonlinear time series forecasting

In this article, we apply Bayesian neural networks (BNNs) to time series analysis, and propose a Monte Carlo algorithm for BNN training. In addition, we go a step further in BNN model selection by putting a prior on network connections instead of hidden units as done by other authors. This allows us to treat the selection of hidden units and the selection of input variables uniformly. The BNN model is compared to a number of competitors, such as the Box-Jenkins model, bilinear model, threshold autoregressive model, and traditional neural network model, on a number of popular and challenging data sets. Numerical results show that the BNN model has achieved a consistent improvement over the competitors in forecasting future values. Insights on how to improve the generalization ability of BNNs are revealed in many respects of our implementation, such as the selection of input variables, the specification of prior distributions, and the treatment of outliers.