On the Application of Markov Chain Monte Carlo Methods to Genetic Analyses on Complex Pedigrees

Markov chain Monte Carlo methods are frequently used in the analyses of genetic data on pedigrees for the estimation of probabilities and likelihoods which cannot be calculated by existing exact methods. In the case of discrete data, the underlying Markov chain may be reducible and care must be taken to ensure that reliable estimates are obtained. Potential reducibility thus has implications for the analysis of the mixed inheritance model, for example, where genetic variation is assumed to be due to one single locus of large effect and many loci each with a small effect. Similarly, reducibility arises in the detection of quantitative trait loci from incomplete discrete marker data. This paper aims to describe the estimation problem in terms of simple discrete genetic models and the single-site Gibbs sampler. Reducibility of the Gibbs sampler is discussed and some current methods for circumventing the problem outlined.     

What are the advantages of MCMC based inference in latent variable models?

Recent developments in Markov chain Monte Carlo [MCMC] methods have increased the popularity of Bayesian inference in many fields of research in economics, such as marketing research and financial econometrics. Gibbs sampling in combination with data augmentation allows inference in statistical/econometric models with many unobserved variables. The likelihood functions of these models may contain many integrals, which often makes a standard classical analysis difficult or even unfeasible. The advantage of the Bayesian approach using MCMC is that one only has to consider the likelihood function conditional on the unobserved variables. In many cases this implies that Bayesian parameter estimation is faster than classical maximum likelihood estimation. In this paper we illustrate the computational advantages of Bayesian estimation using MCMC in several popular latent variable models.     

A direct Monte Carlo approach for Bayesian analysis of the seemingly unrelated regression model

Computationally efficient methods for Bayesian analysis of seemingly unrelated regression (SUR) models are described and applied that involve the use of a direct Monte Carlo (DMC) approach to calculate Bayesian estimation and prediction results using diffuse or informative priors. This DMC approach is employed to compute Bayesian marginal posterior densities, moments, intervals and other quantities, using data simulated from known models and also using data from an empirical example involving firms’ sales. The results obtained by the DMC approach are compared to those yielded by the use of a Markov Chain Monte Carlo (MCMC) approach. It is concluded from these comparisons that the DMC approach is worthwhile and applicable to many SUR and other problems.     

Parametric Inference for Diffusion Processes Observed at Discrete Points in Time: a Survey

This paper is a survey of estimation techniques for stationary and ergodic diffusion processes observed at discrete points in time. The reader is introduced to the following techniques: (i) estimating functions with special emphasis on martingale estimating functions and so-called simple estimating functions; (ii) analytical and numerical approximations of the likelihood function which can in principle be made arbitrarily accurate; (iii) Bayesian analysis and MCMC methods; and (iv) indirect inference and EMM which both introduce auxiliary (but wrong) models and correct for the implied bias by simulation.     

Analysis of high dimensional multivariate stochastic volatility models

This paper is concerned with the Bayesian estimation and comparison of flexible, high dimensional multivariate time series models with time varying correlations. The model proposed and considered here combines features of the classical factor model with that of the heavy tailed univariate stochastic volatility model. A unified analysis of the model, and its special cases, is developed that encompasses estimation, filtering and model choice. The centerpieces of the estimation algorithm (which relies on MCMC methods) are: (1) a reduced blocking scheme for sampling the free elements of the loading matrix and the factors and (2) a special method for sampling the parameters of the univariate SV process. The resulting algorithm is scalable in terms of series and factors and simulation-efficient. Methods for estimating the log-likelihood function and the filtered values of the time-varying volatilities and correlations are also provided. The performance and effectiveness of the inferential methods are extensively tested using simulated data where models up to 50 dimensions and 688 parameters are fit and studied. The performance of our model, in relation to various multivariate GARCH models, is also evaluated using a real data set of weekly returns on a set of 10 international stock indices. We consider the performance along two dimensions: the ability to correctly estimate the conditional covariance matrix of future returns and the unconditional and conditional coverage of the 5% and 1% value-at-risk (VaR) measures of four pre-defined portfolios.     

Linkage Disequilibrium Mapping of Disease Susceptibility Genes in Human Populations

The paper reviews recent work on statistical methods for using linkage disequilibrium to locate disease susceptibility genes, given a set of marker genes at known positions in the genome. The paper starts by considering a simple deterministic model for linkage disequilibrium and discusses recent attempts to elaborate it to include the effects of stochastic influences, of "drift", by the use of either Writht-Fisher models or by approaches based on the coalescence of the genealogy of the sample of disease chromosomes. Most of this first part of the paper concerns a series of diallelic markers and, in this case, the models so far proposed are hierarchical probability models for multivariate binary data. Likelihoods are intractable and most approaches to linkage disequilibrium mapping amount to marginal models for pairwise associations between individual markers and the disease susceptibility locus. Approaches to evalutation of a full likelihood require Monte Carlo methods in order to integrate over the large number of unknowns. The fact that the initial state of the stochastic process which has led to present-day allele frequencies is unknown is noted and its implications for the hierarchical probability model is discussed. Difficulties and opportunities arising as a result of more polymorphic markers and extended marker haplotypes are indicated. Connections between the hierarchical modelling approach and methods based upon identity by descent and haplotype sharing by seemingly unrelated case are explored. Finally problems resulting from unknown modes of inheritance, incomplete penetrance, and "phenocopies" are briefly reviewed.     

Bayesian and Frequentist Inference for Ecological Inference: The R×C Case

In this paper we propose Bayesian and frequentist approaches to ecological inference, based on R × C contingency tables, including a covariate. The proposed Bayesian model extends the binomial-beta hierarchical model developed by K ing , R osen and T anner (1999) from the 2×2 case to the R × C case. As in the 2×2 case, the inferential procedure employs Markov chain Monte Carlo (MCMC) methods. As such, the resulting MCMC analysis is rich but computationally intensive. The frequentist approach, based on first moments rather than on the entire likelihood, provides quick inference via nonlinear least-squares, while retaining good frequentist properties. The two approaches are illustrated with simulated data, as well as with real data on voting patterns in Weimar Germany. In the final section of the paper we provide an overview of a range of alternative inferential approaches which trade-off computational intensity for statistical efficiency.     

Bayesian analysis of the ordered probit model with endogenous selection

This paper presents a Bayesian analysis of an ordered probit model with endogenous selection. The model can be applied when analyzing ordered outcomes that depend on endogenous covariates that are discrete choice indicators modeled by a multinomial probit model. The model is illustrated by analyzing the effects of different types of medical insurance plans on the level of hospital utilization, allowing for potential endogeneity of insurance status. The estimation is performed using the Markov chain Monte Carlo (MCMC) methods to approximate the posterior distribution of the parameters in the model.     

On the Stability of the Excess Sensitivity of Aggregate Consumption Growth in the USA

This paper investigates whether there is time variation in the excess sensitivity of aggregate consumption growth to anticipated aggregate disposable income growth using quarterly US data over the period 1953–2014. Our empirical framework contains the possibility of stickiness in aggregate consumption growth and takes into account measurement error and time aggregation. Our empirical specification is cast into a Bayesian state‐space model and estimated using Markov chain Monte Carlo (MCMC) methods. We use a Bayesian model selection approach to deal with the non‐regular test for the null hypothesis of no time variation in the excess sensitivity parameter. Anticipated disposable income growth is calculated by incorporating an instrumental variables estimation approach into our MCMC algorithm. Our results suggest that the excess sensitivity parameter in the USA is stable at around 0.23 over the entire sample period. Copyright © 2016 John Wiley & Sons, Ltd.     

Bayesian stochastic frontier analysis using WinBUGS

Markov chain Monte Carlo (MCMC) methods have become a ubiquitous tool in Bayesian analysis. This paper implements MCMC methods for Bayesian analysis of stochastic frontier models using the WinBUGS package, a freely available software. General code for cross-sectional and panel data are presented and various ways of summarizing posterior inference are discussed. Several examples illustrate that analyses with models of genuine practical interest can be performed straightforwardly and model changes are easily implemented. Although WinBUGS may not be that efficient for more complicated models, it does make Bayesian inference with stochastic frontier models easily accessible for applied researchers and its generic structure allows for a lot of flexibility in model specification.      

An overview of variance component estimation

Variance components estimation originated with estimating error variance in analysis of variance by equating error mean square to its expected value. This equating procedure was then extended to random effects models, first for balanced data (for which minimum variance properties were subsequently established) and later for unbalanced data. Unfortunately, this ANOVA methodology yields no optimum properties (other than unbiasedness) for estimation from unbalanced data. Today it is being replaced by maximum likelihood (ML) and restricted maximum likelihood (REML) based on normality assumptions and involving nonlinear equations that have to be solved numerically. There is also minimum norm quadratic unbiased estimation (MINQUE) which is closely related to REML but with fewer advantages.An invited paper for the ProbaStat '94 conference, Smolenice, Slovakia, May 30–June 3, 1994 Paper number BU-677 in the Biometrics Unit. Cornell University Ithaca NY     

基于SV模型的上海股市波动性实证分析

利用标准SV(SV-N)模型、厚尾SV(SV-T)模型对上证综合指数数据进行实证分析,采用MCMC方法及Gibbs抽样,应用WinBUGS软件对参数进行估计,比较参数估计值及DIC值,研究表明上证指数表现出强的波动持续性,SV模型能够很好地刻画出它的波动特征,且SV-T模型较优。     

Bayesian estimation of transition probabilities from repeated cross sections

This paper discusses some simple practical advantages of Markov chain Monte Carlo (MCMC) methods in estimating entry and exit transition probabilities from repeated independent surveys. Simulated data are used to illustrate the usefulness of MCMC methods when the likelihood function has multiple local maxima. Actual data on the evaluation of an HIV prevention intervention program among drug users are used to demonstrate the advantage of using prior information to enhance parameter identificaiton. The latter example also demonstrates an important strength of the MCMC approach, namely the ability to make inferences on arbitrary functions of model parameters.     

带未知异方差广义空间模型的有效估计

空间单元大小以及其它的经济特征上的差异,常常会导致空间异方差问题。本文给出了广义空间模型异方差问题的三种不同估计方法。第一种方法是将异方差形式参数化,来克服自由度的不足,使用ML估计进行实现。而针对异方差形式未知时,分别采用了基于2SLS的迭代GMM估计和更加直接的MCMC抽样方法加以解决,特别是MCMC方法表现得更加优美。蒙特卡罗模拟表明,给定异方差形式条件下, ML估计通过异方差参数化的方法依然可以获得较好的估计效果。而异方差形式未知的情况下,另外两种方法随着样本数的增大时也可以与ML的估计结果趋于一致。     

A Bayesian Multiple Comparison Procedure for Order-Restricted Mixed Models

A Bayesian hierarchical mixed model is developed for multiple comparisons under a simple order restriction. The model facilitates inferences on the successive differences of the population means, for which we choose independent prior distributions that are mixtures of an exponential distribution and a discrete distribution with its entire mass at zero. We employ Markov Chain Monte Carlo (MCMC) techniques to obtain parameter estimates and estimates of the posterior probabilities that any two of the means are equal. The latter estimates allow one both to determine if any two means are significantly different and to test the homogeneity of all of the means. We investigate the performance of the model-based inferences with simulated data sets, focusing on parameter estimation and successive-mean comparisons using posterior probabilities. We then illustrate the utility of the model in an application based on data from a study designed to reduce lead blood concentrations in children with elevated levels. Our results show that the proposed hierarchical model can effectively unify parameter estimation, tests of hypotheses and multiple comparisons in one setting.     

A comparison of multiple imputation with EM algorithm and MCMC method for quality of life missing data

This study investigated the performance of multiple imputations with Expectation-Maximization (EM) algorithm and Monte Carlo Markov chain (MCMC) method in missing data imputation. We compared the accuracy of imputation based on some real data and set up two extreme scenarios and conducted both empirical and simulation studies to examine the effects of missing data rates and number of items used for imputation. In the empirical study, the scenario represented item of highest missing rate from a domain with fewest items. In the simulation study, we selected a domain with most items and the item imputed has lowest missing rate. In the empirical study, the results showed there was no significant difference between EM algorithm and MCMC method for item imputation, and number of items used for imputation has little impact, either. Compared with the actual observed values, the middle responses of 3 and 4 were over-imputed, and the extreme responses of 1, 2 and 5 were under-represented. The similar patterns occurred for domain imputation, and no significant difference between EM algorithm and MCMC method and number of items used for imputation has little impact. In the simulation study, we chose environmental domain to examine the effect of the following variables: EM algorithm and MCMC method, missing data rates, and number of items used for imputation. Again, there was no significant difference between EM algorithm and MCMC method. The accuracy rates did not significantly reduce with increase in the proportions of missing data. Number of items used for imputation has some contribution to accuracy of imputation, but not as much as expected.     

Forecasting correlated time series with exponential smoothing models

This paper presents the Bayesian analysis of a general multivariate exponential smoothing model that allows us to forecast time series jointly, subject to correlated random disturbances. The general multivariate model, which can be formulated as a seemingly unrelated regression model, includes the previously studied homogeneous multivariate Holt-Winters’ model as a special case when all of the univariate series share a common structure. MCMC simulation techniques are required in order to approach the non-analytically tractable posterior distribution of the model parameters. The predictive distribution is then estimated using Monte Carlo integration. A Bayesian model selection criterion is introduced into the forecasting scheme for selecting the most adequate multivariate model for describing the behaviour of the time series under study. The forecasting performance of this procedure is tested using some real examples.     

贝叶斯视角下时变参数VAR建模——兼论“斜率之谜”

中国渐进式的改革实践要求中国宏观时间序列的建模能够允许参数平滑变化,而传统的VAR模型对此无能为力。本文详细阐述了在贝叶斯估计框架下,如何利用MCMC算法,建立时变参数VAR模型的过程,并利用该模型对徐高(2008)的数据重新进行了拟合,发现其文中提出的斜率之谜现象不复存在,因此时变参数VAR模型在拟合中国宏观时间序列方面更为精准。     

Bayes model averaging of cyclical decompositions in economic time series

A flexible decomposition of a time series into stochastic cycles under possible non‐stationarity is specified, providing both a useful data analysis tool and a very wide model class. A Bayes procedure using Markov Chain Monte Carlo (MCMC) is introduced with a model averaging approach which explicitly deals with the uncertainty on the appropriate number of cycles. The convergence of the MCMC method is substantially accelerated through a convenient reparametrization based on a hierarchical structure of variances in a state space model. The model and corresponding inferential procedure are applied to simulated data and to cyclical economic time series like US industrial production and unemployment. We derive the implied posterior distributions of model parameters and some relevant functions thereof, shedding light on several key features of economic time series. Copyright © 2006 John Wiley & Sons, Ltd.     

Stick-breaking autoregressive processes

This paper considers the problem of defining a time-dependent nonparametric prior for use in Bayesian nonparametric modelling of time series. A recursive construction allows the definition of priors whose marginals have a general stick-breaking form. The processes with Poisson-Dirichlet and Dirichlet process marginals are investigated in some detail. We develop a general conditional Markov Chain Monte Carlo (MCMC) method for inference in the wide subclass of these models where the parameters of the marginal stick-breaking process are nondecreasing sequences. We derive a generalised Pólya urn scheme type representation of the Dirichlet process construction, which allows us to develop a marginal MCMC method for this case. We apply the proposed methods to financial data to develop a semi-parametric stochastic volatility model with a time-varying nonparametric returns distribution. Finally, we present two examples concerning the analysis of regional GDP and its growth.