A Monte Carlo EM algorithm for random-coefficient-based dropout models

Longitudinal studies of neurological disorders suffer almost inevitably from non-compliance, which is likely to be non-ignorable. It is important in these cases to model the response variable and the dropout mechanism jointly. In this article we propose a Monte Carlo version of the EM algorithm that can be used to fit random-coefficient-based dropout models. A linear mixed model is assumed for the response variable and a discrete-time proportional hazards model for the dropout mechanism; these share a common set of random coefficients. The ideas are illustrated using data from a five-year trial assessing the efficacy of two drugs in the treatment of patients in the early stages of Parkinson's disease.     

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.     

An automated (Markov chain) Monte Carlo EM algorithm

We present an automated Monte Carlo EM (MCEM) algorithm which efficiently assesses Monte Carlo error in the presence of dependent Monte Carlo, particularly Markov chain Monte Carlo, E-step samples and chooses an appropriate Monte Carlo sample size to minimize this Monte Carlo error with respect to progressive EM step estimates. Monte Carlo error is gauged though an application of the central limit theorem during renewal periods of the MCMC sampler used in the E-step. The resulting normal approximation allows us to construct a rigorous and adaptive rule for updating the Monte Carlo sample size each iteration of the MCEM algorithm. We illustrate our automated routine and compare the performance with competing MCEM algorithms in an analysis of a data set fit by a generalized linear mixed model.     

Maximizing generalized linear mixed model likelihoods with an automated Monte Carlo EM algorithm

Two new implementations of the EM algorithm are proposed for maximum likelihood fitting of generalized linear mixed models. Both methods use random (independent and identically distributed) sampling to construct Monte Carlo approximations at the E-step. One approach involves generating random samples from the exact conditional distribution of the random effects (given the data) by rejection sampling, using the marginal distribution as a candidate. The second method uses a multivariate t importance sampling approximation. In many applications the two methods are complementary. Rejection sampling is more efficient when sample sizes are small, whereas importance sampling is better with larger sample sizes. Monte Carlo approximation using random samples allows the Monte Carlo error at each iteration to be assessed by using standard central limit theory combined with Taylor series methods. Specifically, we construct a sandwich variance estimate for the maximizer at each approximate E-step. This suggests a rule for automatically increasing the Monte Carlo sample size after iterations in which the true EM step is swamped by Monte Carlo error. In contrast, techniques for assessing Monte Carlo error have not been developed for use with alternative implementations of Monte Carlo EM algorithms utilizing Markov chain Monte Carlo E-step approximations. Three different data sets, including the infamous salamander data of McCullagh and Nelder, are used to illustrate the techniques and to compare them with the alternatives. The results show that the methods proposed can be considerably more efficient than those based on Markov chain Monte Carlo algorithms. However, the methods proposed may break down when the intractable integrals in the likelihood function are of high dimension.     

Monte Carlo approximation of likelihood function in spatial GLMMs through an empirical Bayes method

In spatial generalized linear mixed models (SGLMMs), statistical inference encounters problems, since random effects in the model imply high-dimensional integrals to calculate the marginal likelihood function. In this article, we temporarily treat parameters as random variables and express the marginal likelihood function as a posterior expectation. Hence, the marginal likelihood function is approximated using the obtained samples from the posterior density of the latent variables and parameters given the data. However, in this setting, misspecification of prior distribution of correlation function parameter and problems associated with convergence of Markov chain Monte Carlo (MCMC) methods could have an unpleasant influence on the likelihood approximation. To avoid these challenges, we utilize an empirical Bayes approach to estimate prior hyperparameters. We also use a computationally efficient hybrid algorithm by combining inverse Bayes formula (IBF) and Gibbs sampler procedures. A simulation study is conducted to assess the performance of our method. Finally, we illustrate the method applying a dataset of standard penetration test of soil in an area in south of Iran.     

Stochastic approximation Monte Carlo EM for change-point analysis

In the expectation–maximization (EM) algorithm for maximum likelihood estimation from incomplete data, Markov chain Monte Carlo (MCMC) methods have been used in change-point inference for a long time when the expectation step is intractable. However, the conventional MCMC algorithms tend to get trapped in local mode in simulating from the posterior distribution of change points. To overcome this problem, in this paper we propose a stochastic approximation Monte Carlo version of EM (SAMCEM), which is a combination of adaptive Markov chain Monte Carlo and EM utilizing a maximum likelihood method. SAMCEM is compared with the stochastic approximation version of EM and reversible jump Markov chain Monte Carlo version of EM on simulated and real datasets. The numerical results indicate that SAMCEM can outperform among the three methods by producing much more accurate parameter estimates and the ability to achieve change-point positions and estimates simultaneously.     

Nesting Monte Carlo EM for high-dimensional item factor analysis

The item factor analysis model for investigating multidimensional latent spaces has proved to be useful. Parameter estimation in this model requires computationally demanding high-dimensional integrations. While several approaches to approximate such integrations have been proposed, they suffer various computational difficulties. This paper proposes a Nesting Monte Carlo Expectation-Maximization (MCEM) algorithm for item factor analysis with binary data. Simulation studies and a real data example suggest that the Nesting MCEM approach can significantly improve computational efficiency while also enjoying the good properties of stable convergence and easy implementation.     

The Monte Carlo EM method for estimating multivariate tobit latent variable models

We propose a multivariate tobit (MT) latent variable model that is defined by a confirmatory factor analysis with covariates for analysing the mixed type data, which is inherently non-negative and sometimes has a large proportion of zeros. Some useful MT models are special cases of our proposed model. To obtain maximum likelihood estimates, we use the expectation maximum algorithm with its E-step via the Gibbs sampler made feasible by Monte Carlo simulation and its M-step greatly simplified by a sequence of conditional maximization. Standard errors are evaluated by inverting a Monte Carlo approximation of the information matrix using Louis's method. The methodology is illustrated with a simulation study and a real example.     

Publication bias and meta-analysis for 2×2 tables: an average Markov chain Monte Carlo EM algorithm

Summary. A major difficulty in meta-analysis is publication bias . Studies with positive outcomes are more likely to be published than studies reporting negative or inconclusive results. Correcting for this bias is not possible without making untestable assumptions. In this paper, a sensitivity analysis is discussed for the meta-analysis of 2×2 tables using exact conditional distributions. A Markov chain Monte Carlo EM algorithm is used to calculate maximum likelihood estimates. A rule for increasing the accuracy of estimation and automating the choice of the number of iterations is suggested.     

Marginal maximum a posteriori estimation using Markov chain Monte Carlo

Markov chain Monte Carlo (MCMC) methods, while facilitating the solution of many complex problems in Bayesian inference, are not currently well adapted to the problem of marginal maximum a posteriori (MMAP) estimation, especially when the number of parameters is large. We present here a simple and novel MCMC strategy, called State-Augmentation for Marginal Estimation (SAME), which leads to MMAP estimates for Bayesian models. We illustrate the simplicity and utility of the approach for missing data interpolation in autoregressive time series and blind deconvolution of impulsive processes.     

Maximum Likelihood Inference for Multivariate Frailty Models Using an Automated Monte Carlo EM Algorithm

We present a maximum likelihood estimation procedure for the multivariate frailty model. The estimation is based on a Monte Carlo EM algorithm. The expectation step is approximated by averaging over random samples drawn from the posterior distribution of the frailties using rejection sampling. The maximization step reduces to a standard partial likelihood maximization. We also propose a simple rule based on the relative change in the parameter estimates to decide on sample size in each iteration and a stopping time for the algorithm. An important new concept is acquiring absolute convergence of the algorithm through sample size determination and an efficient sampling technique. The method is illustrated using a rat carcinogenesis dataset and data on vase lifetimes of cut roses. The estimation results are compared with approximate inference based on penalized partial likelihood using these two examples. Unlike the penalized partial likelihood estimation, the proposed full maximum likelihood estimation method accounts for all the uncertainty while estimating standard errors for the parameters.     

Structural comparative calibration using the EM algorithm

The problem of comparing the linear calibration equations of several measuring methods, each designed to measure the same characteristic on a common group of individuals, is discussed. We consider the factor analysis version of the model and propose to estimate the model parameters using the EM algorithm. The equations that define the 'M' step are simple to implement and computationally in expensive, requiring no additional maximization procedures. The derivation of the complete data log-likelihood function makes it possible to obtain the expected and observed information matrices for any number p(> 3) of instruments in closed form, upon which large sample inference on the parameters can be based. Re-analysis of two actual data sets is presented.     

Multiple Monte Carlo testing,with applications in spatial point processes

The rank envelope test (Myllymäki et al. in J R Stat Soc B, doi: 10.1111/rssb.12172, 2016) is proposed as a solution to the multiple testing problem for Monte Carlo tests. Three different situations are recognized: (1) a few univariate Monte Carlo tests, (2) a Monte Carlo test with a function as the test statistic, (3) several Monte Carlo tests with functions as test statistics. The rank test has correct (global) type I error in each case and it is accompanied with a p-value and with a graphical interpretation which determines subtests and distances of the used test function(s) which lead to the rejection at the prescribed significance level of the test. Examples of null hypotheses from point process and random set statistics are used to demonstrate the strength of the rank envelope test. The examples include goodness-of-fit test with several test functions, goodness-of-fit test for a group of point patterns, test of dependence of components in a multi-type point pattern, and test of the Boolean assumption for random closed sets. A power comparison to the classical multiple testing procedures is given.     

Climate regime shift detection with a trans‐dimensional,sequential Monte Carlo,variational Bayes method

We present an application study which exemplifies a cutting edge statistical approach for detecting climate regime shifts. The algorithm uses Bayesian computational techniques that make time‐efficient analysis of large volumes of climate data possible. Output includes probabilistic estimates of the number and duration of regimes, the number and probability distribution of hidden states, and the probability of a regime shift in any year of the time series. Analysis of the Pacific Decadal Oscillation (PDO) index is provided as an example. Two states are detected: one is associated with positive values of the PDO and presents lower interannual variability, while the other corresponds to negative values of the PDO and greater variability. We compare this approach with existing alternatives from the literature and highlight the potential for ours to unlock features hidden in climate data.     

Estimation in a truncated bivariate poisson distribution using the EM algorithm

An EM algorithm (Dempster et al., 1977) is derived for the estimation of parameters of the truncated bivariate Poisson distribution with zeros rnissing from both margins. The observed inforrnation matrix is obtained and a numerical exarnple is given where the convergence of the EM algorithm is accelerated by the methods of Louis (1982) and conjugate gradients (Jamshidian antl Jennrich, 1993).     

Markov chain Monte Carlo methods for family trees using a parallel processor

A 1024 CPU parallel computer is used to obtain simulated genotypes in the Tristan da Cunha pedigree using random local updating methods. A four-colour theorem is invoked to justify simultaneous updating. Multiple copies of the program are run simultaneously. These results are used to infer the source of the B allele of the ABO blood group that is present in the population.     

A Monte Carlo Markov chain algorithm for a class of mixture time series models

This article generalizes the Monte Carlo Markov Chain (MCMC) algorithm, based on the Gibbs weighted Chinese restaurant (gWCR) process algorithm, for a class of kernel mixture of time series models over the Dirichlet process. This class of models is an extension of Lo’s (Ann. Stat. 12:351–357, 1984) kernel mixture model for independent observations. The kernel represents a known distribution of time series conditional on past time series and both present and past latent variables. The latent variables are independent samples from a Dirichlet process, which is a random discrete (almost surely) distribution. This class of models includes an infinite mixture of autoregressive processes and an infinite mixture of generalized autoregressive conditional heteroskedasticity (GARCH) processes.     

Decrypting classical cipher text using Markov chain Monte Carlo

We investigate the use of Markov Chain Monte Carlo (MCMC) methods to attack classical ciphers. MCMC has previously been used to break simple substitution ciphers. Here, we extend this approach to transposition ciphers and to substitution-plus-transposition ciphers. Our algorithms run quickly and perform fairly well even for key lengths as high as 40.     

Fitting finite mixture models using iterative Monte Carlo classification

Parameters of a finite mixture model are often estimated by the expectation–maximization (EM) algorithm where the observed data log-likelihood function is maximized. This paper proposes an alternative approach for fitting finite mixture models. Our method, called the iterative Monte Carlo classification (IMCC), is also an iterative fitting procedure. Within each iteration, it first estimates the membership probabilities for each data point, namely the conditional probability of a data point belonging to a particular mixing component given that the data point value is obtained, it then classifies each data point into a component distribution using the estimated conditional probabilities and the Monte Carlo method. It finally updates the parameters of each component distribution based on the classified data. Simulation studies were conducted to compare IMCC with some other algorithms for fitting mixture normal, and mixture t, densities.