Bayes Estimates of Markov Trends in Possibly Cointegrated Series

Stylized facts show that average growth rates of U.S. per capita consumption and income differ in recession and expansion periods. Because a linear combination of such series does not have to be a constant mean process, standard cointegration analysis between the variables to examine the permanent income hypothesis may not be valid. To model the changing growth rates in both series, we introduce a multivariate Markov trend model that accounts for different growth rates in consumption and income during expansions and recessions and across variables within both regimes. The deviations from the multivariate Markov trend are modeled by a vector autoregression (VAR) model. Bayes estimates of this model are obtained using Markov chain Monte Carlo methods. The empirical results suggest the existence of a cointegration relation between U.S. per capita disposable income and consumption, after correction for a multivariate Markov trend. This result is also obtained when per capita investment is added to the VAR.     

Modeling Multilevel Survival Data Using Frailty Models

Often the dependence in multivariate survival data is modeled through an individual level effect called the frailty. Due to its mathematical simplicity, the gamma distribution is often used as the frailty distribution for hazard modeling. However, it is well known that the gamma frailty distribution has many drawbacks. For example, it weakens the effect of covariates. In addition, in the presence of a multilevel model, overall frailty comes from several levels. To overcome such drawbacks, more heavy-tailed distributions are needed to model the frailty distribution in order to incorporate extra variability. In this article, we develop a class of log-skew-t distributions for the frailty. This class includes the log-normal distribution along with many other heavy tailed distributions, e.g., log-Cauchy, log normal, and log-t as special cases.

Conditional on the frailty, the survival times are assumed to be independent with proportional hazard structure. The modeling process is then completed by assuming multilevel frailty-effects. Instead of tuning a strict parameterization of the baseline hazard function, we consider the partial likelihood approach and thus leave the baseline function unspecified. By eliminating the hazard, the pre-specification and computation are simplified considerably.     

A geometric approach to transdimensional markov chain monte carlo

The authors present theoretical results that show how one can simulate a mixture distribution whose components live in subspaces of different dimension by reformulating the problem in such a way that observations may be drawn from an auxiliary continuous distribution on the largest subspace and then transformed in an appropriate fashion. Motivated by the importance of enlarging the set of available Markov chain Monte Carlo (MCMC) techniques, the authors show how their results can be fruitfully employed in problems such as model selection (or averaging) of nested models, or regeneration of Markov chains for evaluating standard deviations of estimated expectations derived from MCMC simulations.     

Equilibrium dynamics of ice streams: a Bayesian statistical analysis

Studies of the behaviors of glaciers, ice sheets, and ice streams rely heavily on both observations and physical models. Data acquired via remote sensing provide critical information on geometry and movement of ice over large sections of Antarctica and Greenland. However, uncertainties are present in both the observations and the models. Hence, there is a need for combining these information sources in a fashion that incorporates uncertainty and quantifies its impact on conclusions. We present a hierarchical Bayesian approach to modeling ice-stream velocities incorporating physical models and observations regarding velocity, ice thickness, and surface elevation from the North East Ice Stream in Greenland. The Bayesian model leads to interesting issues in model assessment and computation.     

Bayes and MCMC for Undergraduates

Students of statistics should be taught the ideas and methods that are widely used in practice and that will help them understand the world of statistics. Today, this means teaching them about Bayesian methods. In this article, I present ideas on teaching an undergraduate Bayesian course that uses Markov chain Monte Carlo and that can be a second course or, for strong students, a first course in statistics.     

Note on posterior inference for the Bingham distribution

The properties of high-dimensional Bingham distributions have been studied by Kume and Walker (2014 Kume, A., and S. G. Walker. 2014. On the Bingham distribution with large dimension. Journal of Multivariate Analysis 124:345–52.[Crossref], [Web of Science ®] , [Google Scholar]). Fallaize and Kypraios (2016 Fallaize, C. J., and T. Kypraios. 2016. Exact Bayesian inference for the Bingham distribution. Statistics and Computing 26:349–60.[Crossref], [Web of Science ®] , [Google Scholar]) propose the Bayesian inference for the Bingham distribution and they use developments in Bayesian computation for distributions with doubly intractable normalizing constants (Møller et al. 2006 Møller, J., A. N. Pettitt, R. Reeves, and K. K. Berthelsen. 2006. An efficient Markov chain Monte Carlo method for distributions with intractable normalising constants. Biometrika 93 (2):451–458.[Crossref], [Web of Science ®] , [Google Scholar]; Murray, Ghahramani, and MacKay 2006 Murray, I., Z. Ghahramani, and D. J. C. MacKay. 2006. MCMC for doubly intractable distributions. In Proceedings of the 22nd annual conference on uncertainty in artificial intelligence (UAI-06), 359–66. AUAI Press. [Google Scholar]). However, they rely heavily on two Metropolis updates that they need to tune. In this article, we propose instead a model selection with the marginal likelihood.     

Binary probability maps using a hidden conditional autoregressive Gaussian process with an application to Finnish common toad data

The Finnish common toad data of Heikkinen and Hogmander are reanalysed using an alternative fully Bayesian model that does not require a pseudolikelihood approximation and an alternative prior distribution for the true presence or absence status of toads in each 10 km×10 km square. Markov chain Monte Carlo methods are used to obtain posterior probability estimates of the square-specific presences of the common toad and these are presented as a map. The results are different from those of Heikkinen and Hogmander and we offer an explanation in terms of the prior used for square-specific presence of the toads. We suggest that our approach is more faithful to the data and avoids unnecessary confounding of effects. We demonstrate how to extend our model efficiently with square-specific covariates and illustrate this by introducing deterministic spatial changes.     

Modeling Endogenous Mobility in Earnings Determination

ABSTRACT

We evaluate the bias from endogenous job mobility in fixed-effects estimates of worker- and firm-specific earnings heterogeneity using longitudinally linked employer–employee data from the LEHD infrastructure file system of the U.S. Census Bureau. First, we propose two new residual diagnostic tests of the assumption that mobility is exogenous to unmodeled determinants of earnings. Both tests reject exogenous mobility. We relax exogenous mobility by modeling the matched data as an evolving bipartite graph using a Bayesian latent-type framework. Our results suggest that allowing endogenous mobility increases the variation in earnings explained by individual heterogeneity and reduces the proportion due to employer and match effects. To assess external validity, we match our estimates of the wage components to out-of-sample estimates of revenue per worker. The mobility-bias-corrected estimates attribute much more of the variation in revenue per worker to variation in match quality and worker quality than the uncorrected estimates. Supplementary materials for this article are available online.     

Bayesian model learning based on a parallel MCMC strategy

We introduce a novel Markov chain Monte Carlo algorithm for estimation of posterior probabilities over discrete model spaces. Our learning approach is applicable to families of models for which the marginal likelihood can be analytically calculated, either exactly or approximately, given any fixed structure. It is argued that for certain model neighborhood structures, the ordinary reversible Metropolis-Hastings algorithm does not yield an appropriate solution to the estimation problem. Therefore, we develop an alternative, non-reversible algorithm which can avoid the scaling effect of the neighborhood. To efficiently explore a model space, a finite number of interacting parallel stochastic processes is utilized. Our interaction scheme enables exploration of several local neighborhoods of a model space simultaneously, while it prevents the absorption of any particular process to a relatively inferior state. We illustrate the advantages of our method by an application to a classification model. In particular, we use an extensive bacterial database and compare our results with results obtained by different methods for the same data.     

Stochastic search variable selection for log-linear models

We develop a Markov chain Monte Carlo algorithm, based on ‘stochastic search variable selection’ (George and McCuUoch, 1993), for identifying promising log-linear models. The method may be used in the analysis of multi-way contingency tables where the set of plausible models is very large.     

On population-based simulation for static inference

In this paper we present a review of population-based simulation for static inference problems. Such methods can be described as generating a collection of random variables {X _n } _n=1,…,N in parallel in order to simulate from some target density π (or potentially sequence of target densities). Population-based simulation is important as many challenging sampling problems in applied statistics cannot be dealt with successfully by conventional Markov chain Monte Carlo (MCMC) methods. We summarize population-based MCMC (Geyer, Computing Science and Statistics: The 23rd Symposium on the Interface, pp. 156–163, 1991; Liang and Wong, J. Am. Stat. Assoc. 96, 653–666, 2001) and sequential Monte Carlo samplers (SMC) (Del Moral, Doucet and Jasra, J. Roy. Stat. Soc. Ser. B 68, 411–436, 2006a), providing a comparison of the approaches. We give numerical examples from Bayesian mixture modelling (Richardson and Green, J. Roy. Stat. Soc. Ser. B 59, 731–792, 1997).     

A Bayesian Approach to Modelling Reticulation Events with Application to the Ribosomal Protein Gene rps11 of Flowering Plants

Traditional phylogenetic inference assumes that the history of a set of taxa can be explained by a tree. This assumption is often violated as some biological entities can exchange genetic material giving rise to non‐treelike events often called reticulations. Failure to consider these events might result in incorrectly inferred phylogenies. Phylogenetic networks provide a flexible tool which allows researchers to model the evolutionary history of a set of organisms in the presence of reticulation events. In recent years, a number of methods addressing phylogenetic network parameter estimation have been introduced. Some of them are based on the idea that a phylogenetic network can be defined as a directed acyclic graph. Based on this definition, we propose a Bayesian approach to the estimation of phylogenetic network parameters which allows for different phylogenies to be inferred at different parts of a multiple DNA alignment. The algorithm is tested on simulated data and applied to the ribosomal protein gene rps11 data from five flowering plants, where reticulation events are suspected to be present. The proposed approach can be applied to a wide variety of problems which aim at exploring the possibility of reticulation events in the history of a set of taxa.     

On cross‐validation of Bayesian models

The authors examine several aspects of cross‐validation for Bayesian models. In particular, they propose a computational scheme which does not require a separate posterior sample for each training sample.     

Estimation and variable selection in nonparametric heteroscedastic regression

The article considers a Gaussian model with the mean and the variance modeled flexibly as functions of the independent variables. The estimation is carried out using a Bayesian approach that allows the identification of significant variables in the variance function, as well as averaging over all possible models in both the mean and the variance functions. The computation is carried out by a simulation method that is carefully constructed to ensure that it converges quickly and produces iterates from the posterior distribution that have low correlation. Real and simulated examples demonstrate that the proposed method works well. The method in this paper is important because (a) it produces more realistic prediction intervals than nonparametric regression estimators that assume a constant variance; (b) variable selection identifies the variables in the variance function that are important; (c) variable selection and model averaging produce more efficient prediction intervals than those obtained by regular nonparametric regression.     

Efficient Semiparametric Bayesian Estimation of Multivariate Discrete Proportional Hazards Model with Random Effects

We incorporate a random effect into a multivariate discrete proportional hazards model and propose an efficient semiparametric Bayesian estimation method. By introducing a prior process for the parameters of baseline hazards, we consider a nonparametric estimation of baseline hazards function. Using a state space representation, we derive a dynamic modeling of baseline hazards function and propose an efficient block sampler for Markov chain Monte Carlo method. A numerical example using kidney patients data is given.     

Bayesian generalized fused lasso modeling via NEG distribution

The fused lasso penalizes a loss function by the L₁ norm for both the regression coefficients and their successive differences to encourage sparsity of both. In this paper, we propose a Bayesian generalized fused lasso modeling based on a normal-exponential-gamma (NEG) prior distribution. The NEG prior is assumed into the difference of successive regression coefficients. The proposed method enables us to construct a more versatile sparse model than the ordinary fused lasso using a flexible regularization term. Simulation studies and real data analyses show that the proposed method has superior performance to the ordinary fused lasso.     

Implementation of a robust bayesian method

In this work we study robustness in Bayesian models through a generalization of the Normal distribution. We show new appropriate techniques in order to deal with this distribution in Bayesian inference. Then we propose two approaches to decide, in some applications, if we should replace the usual Normal model by this generalization. First, we pose this dilemma as a model rejection problem, using diagnostic measures. In the second approach we evaluate the model's predictive efficiency. We illustrate those perspectives with a simulation study, a non linear model and a longitudinal data model.     

Regional source apportionment of PM2.5 in Seoul using Bayesian multivariate receptor model

Seoul, the capital city of Korea with over 10 million residents, has been experiencing serious air pollution problems. Previous studies on source apportionment of PM2.5 in Seoul are based on measurements of chemical compositions of PM2.5 from a single monitoring site. In this paper, we analyse PM2.5 concentration data collected from multiple sites in 24 districts of Seoul and estimate regional source profiles using Bayesian multivariate receptor model. The regional source profiles provide information for the identification of major PM2.5 sources as well as the regions relatively more seriously affected by each source than other regions. These regional characteristics relevant to PM2.5 can help establish effective, customised, region-specific PM2.5 control strategies for each region rather than general strategies that apply to every region of Seoul.     

Bayesian inference for generalized extreme value distributions via Hamiltonian Monte Carlo

In this article, we propose to evaluate and compare Markov chain Monte Carlo (MCMC) methods to estimate the parameters in a generalized extreme value model. We employed the Bayesian approach using traditional Metropolis-Hastings methods, Hamiltonian Monte Carlo (HMC), and Riemann manifold HMC (RMHMC) methods to obtain the approximations to the posterior marginal distributions of interest. Applications to real datasets and simulation studies provide evidence that the extra analytical work involved in Hamiltonian Monte Carlo algorithms is compensated by a more efficient exploration of the parameter space.