GPU-Powered Shotgun Stochastic Search for Dirichlet Process Mixtures of Gaussian Graphical Models

Gaussian graphical models (GGMs) are popular for modeling high-dimensional multivariate data with sparse conditional dependencies. A mixture of GGMs extends this model to the more realistic scenario where observations come from a heterogenous population composed of a small number of homogeneous subgroups. In this article, we present a novel stochastic search algorithm for finding the posterior mode of high-dimensional Dirichlet process mixtures of decomposable GGMs. Further, we investigate how to harness the massive thread-parallelization capabilities of graphical processing units to accelerate computation. The computational advantages of our algorithms are demonstrated with various simulated data examples in which we compare our stochastic search with a Markov chain Monte Carlo (MCMC) algorithm in moderate dimensional data examples. These experiments show that our stochastic search largely outperforms the MCMC algorithm in terms of computing-times and in terms of the quality of the posterior mode discovered. Finally, we analyze a gene expression dataset in which MCMC algorithms are too slow to be practically useful.     

Optimal control and numerical methods for hybrid stochastic SIS models

This work focuses on optimal controls of a class of stochastic SIS epidemic models under regime switching. By assuming that a decision maker can influence the infectivity period, our aim is to minimize the expected discounted cost due to illness, medical treatment, and the adverse effect on the society. In addition, a model with the incorporation of vaccination is proposed. Numerical schemes are developed by approximating the continuous-time dynamics using Markov chain approximation methods. It is demonstrated that the approximation schemes converge to the optimal strategy as the mesh size goes to zero. Numerical examples are provided to illustrate our results.     

Bayesian estimation of stochastic volatility models based on OU processes with marginal Gamma law

This paper discusses practical Bayesian estimation of stochastic volatility models based on OU processes with marginal Gamma laws. Estimation is based on a parameterization which is derived from the Rosiński representation, and has the advantage of being a non-centered parameterization. The parameterization is based on a marked point process, living on the positive real line, with uniformly distributed marks. We define a Markov chain Monte Carlo (MCMC) scheme which enables multiple updates of the latent point process, and generalizes single updating algorithm used earlier. At each MCMC draw more than one point is added or deleted from the latent point process. This is particularly useful for high intensity processes. Furthermore, the article deals with superposition models, where it discuss how the identifiability problem inherent in the superposition model may be avoided by the use of a Markov prior. Finally, applications to simulated data as well as exchange rate data are discussed.     

Generalized Nonparametric Mixed Effects Models

Generalized linear mixed effects models (GLMM) provide useful tools for correlated and/or over-dispersed non-Gaussian data. This article considers generalized nonparametric mixed effects models (GNMM), which relax the rigid linear assumption on the conditional predictor in a GLMM. We use smoothing splines to model fixed effects. The random effects are general and may also contain stochastic processes corresponding to smoothing splines. We show how to construct smoothing spline ANOVA (SS ANOVA) decompositions for the predictor function. Components in a SS ANOVA decomposition have nice interpretations as main effects and interactions. Experimental design considerations help determine which components are fixed or random. We estimate all parameters and spline functions using stochastic approximation with Markov chain Monte Carlo (MCMC). As iteration increases we increase the MCMC sample size and decrease the step-size of the parameter update. This approach guarantees convergence of the estimates to the expected fixed points. We evaluate our methods through a simulation study.     

MCMC calibration of spot‐prices models in electricity markets

The calibration of some stochastic differential equation used to model spot prices in electricity markets is investigated. As an alternative to relying on standard likelihood maximization, the adoption of a fully Bayesian paradigm is explored, that relies on Markov chain Monte Carlo (MCMC) stochastic simulation and provides the posterior distributions of the model parameters. The proposed method is applied to one‐ and two‐factor stochastic models, using both simulated and real data. The results demonstrate good agreement between the maximum likelihood and MCMC point estimates. The latter approach, however, provides a more complete characterization of the model uncertainty, an information that can be exploited to obtain a more realistic assessment of the forecasting error. In order to further validate the MCMC approach, the posterior distribution of the Italian electricity price volatility is explored for different maturities and compared with the corresponding maximum likelihood estimates.     

The Alive Particle Filter and Its Use in Particle Markov Chain Monte Carlo

In the following article, we investigate a particle filter for approximating Feynman–Kac models with indicator potentials and we use this algorithm within Markov chain Monte Carlo (MCMC) to learn static parameters of the model. Examples of such models include approximate Bayesian computation (ABC) posteriors associated with hidden Markov models (HMMs) or rare-event problems. Such models require the use of advanced particle filter or MCMC algorithms to perform estimation. One of the drawbacks of existing particle filters is that they may “collapse,” in that the algorithm may terminate early, due to the indicator potentials. In this article, using a newly developed special case of the locally adaptive particle filter, we use an algorithm that can deal with this latter problem, while introducing a random cost per-time step. In particular, we show how this algorithm can be used within MCMC, using particle MCMC. It is established that, when not taking into account computational time, when the new MCMC algorithm is applied to a simplified model it has a lower asymptotic variance in comparison to a standard particle MCMC algorithm. Numerical examples are presented for ABC approximations of HMMs.     

Markov Chain Monte Carlo Convergence Assessment via Two-Way Analysis of Variance

Abstract

In this article we discuss the problem of assessing the performance of Markov chain Monte Carlo (MCMC) algorithms on the basis of simulation output. In essence, we extend the original ideas of Gelman and Rubin and, more recently, Brooks and Gelman, to problems where we are able to split the variation inherent within the MCMC simulation output into two distinct groups. We show how such a diagnostic may be useful in assessing the performance of MCMC samplers addressing model choice problems, such as the reversible jump MCMC algorithm. In the model choice context, we show how the reversible jump MCMC simulation output for parameters that retain a coherent interpretation throughout the simulation, can be used to assess convergence. By considering various decompositions of the sampling variance of this parameter, we can assess the performance of our MCMC sampler in terms of its mixing properties both within and between models and we illustrate our approach in both the graphical Gaussian models and normal mixtures context. Finally, we provide an example of the application of our diagnostic to the assessment of the influence of different starting values on MCMC simulation output, thereby illustrating the wider utility of our method beyond the Bayesian model choice and reversible jump MCMC context.     

有缺失数据的META-MARKOV模型的局部计算

根据meta Markov模型的特征,本文提出了有缺失数据的meta Markov模型的局部计算方法．由于最小可压缩集与局部计算关系密切,本文给出了一种搜索包含预先给定的子集的最小可压缩集的算法．     

Randomized approximation scheme and perfect sampler for closed Jackson networks with multiple servers

In this paper, we propose a fully polynomial-time randomized approximation scheme (FPRAS) for a closed Jackson network. Our algorithm is based on the Markov chain Monte Carlo (MCMC) method. Thus our scheme returns an approximate solution, for which the size of the error satisfies a given bound. To our knowledge, this algorithm is the first polynomial time MCMC algorithm for closed Jackson networks with multiple servers. We propose two new ergodic Markov chains, both of which have a unique stationary distribution that is the product form solution for closed Jackson networks. One of them is for an approximate sampler, and we show that it mixes rapidly. The other is for a perfect sampler based on the monotone coupling from the past (CFTP) algorithm proposed by Propp and Wilson, and we show that it has a monotone update function.     

Bayesian Semiparametric Regression Analysis of Multicategorical Time-Space Data

We present a unified semiparametric Bayesian approach based on Markov random field priors for analyzing the dependence of multicategorical response variables on time, space and further covariates. The general model extends dynamic, or state space, models for categorical time series and longitudinal data by including spatial effects as well as nonlinear effects of metrical covariates in flexible semiparametric form. Trend and seasonal components, different types of covariates and spatial effects are all treated within the same general framework by assigning appropriate priors with different forms and degrees of smoothness. Inference is fully Bayesian and uses MCMC techniques for posterior analysis. The approach in this paper is based on latent semiparametric utility models and is particularly useful for probit models. The methods are illustrated by applications to unemployment data and a forest damage survey.     

Implementations of the Monte Carlo EM Algorithm

The Monte Carlo EM (MCEM) algorithm is a modification of the EM algorithm where the expectation in the E-step is computed numerically through Monte Carlo simulations. The most exible and generally applicable approach to obtaining a Monte Carlo sample in each iteration of an MCEM algorithm is through Markov chain Monte Carlo (MCMC) routines such as the Gibbs and Metropolis–Hastings samplers. Although MCMC estimation presents a tractable solution to problems where the E-step is not available in closed form, two issues arise when implementing this MCEM routine: (1) how do we minimize the computational cost in obtaining an MCMC sample? and (2) how do we choose the Monte Carlo sample size? We address the first question through an application of importance sampling whereby samples drawn during previous EM iterations are recycled rather than running an MCMC sampler each MCEM iteration. The second question is addressed through an application of regenerative simulation. We obtain approximate independent and identical samples by subsampling the generated MCMC sample during different renewal periods. Standard central limit theorems may thus be used to gauge Monte Carlo error. In particular, we apply an automated rule for increasing the Monte Carlo sample size when the Monte Carlo error overwhelms the EM estimate at any given iteration. We illustrate our MCEM algorithm through analyses of two datasets fit by generalized linear mixed models. As a part of these applications, we demonstrate the improvement in computational cost and efficiency of our routine over alternative MCEM strategies.     

流行病灭绝时间和费用估计随机模型

本文用具有吸收状态的生灭马氏过程建立了流行病随机模型,研究了灭绝之前生灭过程的分布,发现初始分布是拟平稳分布时,其灭绝时间服从指数分布,并得到了灭绝时间与状态概率的关系式和费用估计的期望值.应用模型给出了一个固定人口为N的流行病灭绝时间和平均费用的数值模拟结果.     

Estimation of Semiparametric Models in the Presence of Endogeneity and Sample Selection

We analyze a semiparametric model for data that suffer from the problems of sample selection, where some of the data are observed for only part of the sample with a probability that depends on a selection equation, and of endogeneity, where a covariate is correlated with the disturbance term. The introduction of nonparametric functions in the model permits great flexibility in the way covariates affect response variables. We present an efficient Bayesian method for the analysis of such models that allows us to consider general systems of outcome variables and endogenous regressors that are continuous, binary, censored, or ordered. Estimation is by Markov chain Monte Carlo (MCMC) methods. The algorithm we propose does not require simulation of the outcomes that are missing due to the selection mechanism, which reduces the computational load and improves the mixing of the MCMC chain. The approach is applied to a model of women’s labor force participation and log-wage determination. Data and computer code used in this article are available online.     

A Generalized Markov Sampler

A recent development of the Markov chain Monte Carlo (MCMC) technique is the emergence of MCMC samplers that allow transitions between different models. Such samplers make possible a range of computational tasks involving models, including model selection, model evaluation, model averaging and hypothesis testing. An example of this type of sampler is the reversible jump MCMC sampler, which is a generalization of the Metropolis–Hastings algorithm. Here, we present a new MCMC sampler of this type. The new sampler is a generalization of the Gibbs sampler, but somewhat surprisingly, it also turns out to encompass as particular cases all of the well-known MCMC samplers, including those of Metropolis, Barker, and Hastings. Moreover, the new sampler generalizes the reversible jump MCMC. It therefore appears to be a very general framework for MCMC sampling. This paper describes the new sampler and illustrates its use in three applications in Computational Biology, specifically determination of consensus sequences, phylogenetic inference and delineation of isochores via multiple change-point analysis.     

Spatiotemporal Models for Gaussian Areal Data

We introduce a class of spatiotemporal models for Gaussian areal data. These models assume a latent random field process that evolves through time with random field convolutions; the convolving fields follow proper Gaussian Markov random field (PGMRF) processes. At each time, the latent random field process is linearly related to observations through an observational equation with errors that also follow a PGMRF. The use of PGMRF errors brings modeling and computational advantages. With respect to modeling, it allows more flexible model structures such as different but interacting temporal trends for each region, as well as distinct temporal gradients for each region. Computationally, building upon the fact that PGMRF errors have proper density functions, we have developed an efficient Bayesian estimation procedure based on Markov chain Monte Carlo with an embedded forward information filter backward sampler (FIFBS) algorithm. We show that, when compared with the traditional one-at-a-time Gibbs sampler, our novel FIFBS-based algorithm explores the posterior distribution much more efficiently. Finally, we have developed a simulation-based conditional Bayes factor suitable for the comparison of nonnested spatiotemporal models. An analysis of the number of homicides in Rio de Janeiro State illustrates the power of the proposed spatiotemporal framework.

Supplemental materials for this article are available online in the journal’s webpage.     

Efficient Bayesian Inference for Multivariate Factor Stochastic Volatility Models

We discuss efficient Bayesian estimation of dynamic covariance matrices in multivariate time series through a factor stochastic volatility model. In particular, we propose two interweaving strategies to substantially accelerate convergence and mixing of standard MCMC approaches. Similar to marginal data augmentation techniques, the proposed acceleration procedures exploit nonidentifiability issues which frequently arise in factor models. Our new interweaving strategies are easy to implement and come at almost no extra computational cost; nevertheless, they can boost estimation efficiency by several orders of magnitude as is shown in extensive simulation studies. To conclude, the application of our algorithm to a 26-dimensional exchange rate dataset illustrates the superior performance of the new approach for real-world data. Supplementary materials for this article are available online.     

Sparse Variational Analysis of Linear Mixed Models for Large Data Sets

It is increasingly common to be faced with longitudinal or multi-level data sets that have large numbers of predictors and/or a large sample size. Current methods of fitting and inference for mixed effects models tend to perform poorly in such settings. When there are many variables, it is appealing to allow uncertainty in subset selection and to obtain a sparse characterization of the data. Bayesian methods are available to address these goals using Markov chain Monte Carlo (MCMC), but MCMC is very computationally expensive and can be infeasible in large p and/or large n problems. As a fast approximate Bayes solution, we recommend a novel approximation to the posterior relying on variational methods. Variational methods are used to approximate the posterior of the parameters in a decomposition of the variance components, with priors chosen to obtain a sparse solution that allows selection of random effects. The method is evaluated through a simulation study, and applied to an epidemiological application.     

Bayesian total loss estimation using shared random effects

The pricing of insurance policies requires estimates of the total loss. The traditional compound model imposes an independence assumption on the number of claims and their individual sizes. Bivariate models, which model both variables jointly, eliminate this assumption. A regression approach allows policy holder characteristics and product features to be included in the model. This article presents a bivariate model that uses joint random effects across both response variables to induce dependence effects. Bayesian posterior estimation is done using Markov Chain Monte Carlo (MCMC) methods. A real data example demonstrates that our proposed model exhibits better fitting and forecasting capabilities than existing models.     

Stochastic volatility Gaussian Heath-Jarrow-Morton models

This paper extends the class of deterministic volatility Heath-Jarrow-Morton models to a Markov chain stochastic volatility framework allowing for jump discontinuities and a variety of deformations of the term structure of forward rate volatilities. Analytical solutions for the dynamics of the volatility term structure are obtained. Semimartingale decompositions of the interest rates under a spot and forward martingale measures are identified. Stochastic volatility versions of the continuous time Ho-Lee and Hull-White extended Vasicek models are obtained. Introducing a regime shift in volatility that is an exponential function of time to maturity leads to a Vasicek dynamics with regime switching coefficients of the short rate.