Comparisons of computational methods for clustered binary data

Clustered binary data are common in medical research and can be fitted to the logistic regression model with random effects which belongs to a wider class of models called the generalized linear mixed model. The likelihood-based estimation of model parameters often has to handle intractable integration which leads to several estimation methods to overcome such difficulty. The penalized quasi-likelihood (PQL) method is the one that is very popular and computationally efficient in most cases. The expectation–maximization (EM) algorithm allows to estimate maximum-likelihood estimates, but requires to compute possibly intractable integration in the E-step. The variants of the EM algorithm to evaluate the E-step are introduced. The Monte Carlo EM (MCEM) method computes the E-step by approximating the expectation using Monte Carlo samples, while the Modified EM (MEM) method computes the E-step by approximating the expectation using the Laplace's method. All these methods involve several steps of approximation so that corresponding estimates of model parameters contain inevitable errors (large or small) induced by approximation. Understanding and quantifying discrepancy theoretically is difficult due to the complexity of approximations in each method, even though the focus is on clustered binary data. As an alternative competing computational method, we consider a non-parametric maximum-likelihood (NPML) method as well. We review and compare the PQL, MCEM, MEM and NPML methods for clustered binary data via simulation study, which will be useful for researchers when choosing an estimation method for their analysis.     

Analysis of generalized linear mixed models via a stochastic approximation algorithm with Markov chain Monte-Carlo method

In recent years much effort has been devoted to maximum likelihood estimation of generalized linear mixed models. Most of the existing methods use the EM algorithm, with various techniques in handling the intractable E-step. In this paper, a new implementation of a stochastic approximation algorithm with Markov chain Monte Carlo method is investigated. The proposed algorithm is computationally straightforward and its convergence is guaranteed. A simulation and three real data sets, including the challenging salamander data, are used to illustrate the procedure and to compare it with some existing methods. The results indicate that the proposed algorithm is an attractive alternative for problems with a large number of random effects or with high dimensional intractable integrals in the likelihood function.     

Convergence Rate of Strong Consistency of the Maximum Likelihood Estimator in Exponential Family Nonlinear Models

This article proposes some regularity conditions. On the basis of the proposed regularity conditions, we show the strong consistency of the maximum likelihood estimator (MLE) in exponential family nonlinear models (EFNM) and give its convergence rate. In an important case, we obtain the convergence rate O(n ^?1/2(log log n)^1/2)—the rate as that in the Law of the Iterated Logarithm (LIL) for iid partial sums and thus cannot be improved anymore.     

Ascent-based Monte Carlo expectation– maximization

Summary.  The expectation–maximization (EM) algorithm is a popular tool for maximizing likelihood functions in the presence of missing data. Unfortunately, EM often requires the evaluation of analytically intractable and high dimensional integrals. The Monte Carlo EM (MCEM) algorithm is the natural extension of EM that employs Monte Carlo methods to estimate the relevant integrals. Typically, a very large Monte Carlo sample size is required to estimate these integrals within an acceptable tolerance when the algorithm is near convergence. Even if this sample size were known at the onset of implementation of MCEM, its use throughout all iterations is wasteful, especially when accurate starting values are not available. We propose a data-driven strategy for controlling Monte Carlo resources in MCEM. The algorithm proposed improves on similar existing methods by recovering EM's ascent (i.e. likelihood increasing) property with high probability, being more robust to the effect of user-defined inputs and handling classical Monte Carlo and Markov chain Monte Carlo methods within a common framework. Because of the first of these properties we refer to the algorithm as 'ascent-based MCEM'. We apply ascent-based MCEM to a variety of examples, including one where it is used to accelerate the convergence of deterministic EM dramatically.     

Computing probabilites of rectangles in case of multinormal distribution

In several stochastic programming models and statistical problems the computation of probabilities of n-dimensional rectangles is required in case of n-dimensional normal distribution. A recent simulation technique presented by the author for computing values of the distribution function can be modified to yield appropriate procedure for computing probabilities of rectangles. Some numerical work is provided to illustrate the use of the new algorithm.     

An augmented data scoring algorithm for maximum likelihood

The expectation-maximization (EM) method facilitates computation of max¬imum likelihood (ML) and maximum penalized likelihood (MPL) solutions. The procedure requires specification of unobservabie complete data which augment the measured or incomplete data. This specification defines a conditional expectation of the complete data log-likelihood function which is computed in the E-stcp. The EM algorithm is most effective when maximizing the iunction Q{0) denned in the F-stnp is easier than maximizing the likelihood function.

The Monte Carlo EM (MCEM) algorithm of Wei & Tanner (1990) was introduced for problems where computation of Q is difficult or intractable. However Monte Carlo can he computationally expensive, e.g. in signal processing applications involving large numbers of parameters. We provide another approach: a modification of thc standard EM algorithm avoiding computation of conditional expectations.     

An asymptotic approximation for the permanent of a doubly stochastic matrix

A determinantal approximation is obtained for the permanent of a doubly stochastic matrix. For moderate-deviation matrix sequences, the asymptotic relative error is of order O(n^?1).     

Numerical maximum likelihood estimation for the g-and-k and generalized g-and-h distributions

Continuing increases in computing power and availability mean that many maximum likelihood estimation (MLE) problems previously thought intractable or too computationally difficult can now be tackled numerically. However, ML parameter estimation for distributions whose only analytical expression is as quantile functions has received little attention. Numerical MLE procedures for parameters of new families of distributions, the g-and-k and the generalized g-and-h distributions, are presented and investigated here. Simulation studies are included, and the appropriateness of using asymptotic methods examined. Because of the generality of these distributions, the investigations are not only into numerical MLE for these distributions, but are also an initial investigation into the performance and problems for numerical MLE applied to quantile-defined distributions in general. Datasets are also fitted using the procedures here. Results indicate that sample sizes significantly larger than 100 should be used to obtain reliable estimates through maximum likelihood.     

Generalized bartlett correction

This paper provides a general method of modifying a statistic of interest in such a way that the distribution of the modified statistic can be approximated by an arbitrary reference distribution to an order of accuracy of O(n ^-1/2) or even O(n ^-1). The reference distribution is usually the asymptotic distribution of the original statistic. We prove that the multiplication of the statistic by a suitable stochastic correction improves the asymptotic approximation to its distribution. This paper extends the results of the closely related paper by Cordeiro and Ferrari (1991) to cope with several other statistical tests. The resulting expression for the adjustment factor requires knowledge of the Edgeworth-type expansion to order O(n^-1) for the distribution of the unmodified statistic. In practice its functional form involves some derivatives of the reference distribution. Certain difference between the cumulants of appropriate order in n of the unmodified statistic and those of its first-order approximation, and the unmodified statistic itself. Some applications are discussed.     

Quantile Regression via the EM Algorithm

The three-parameter asymmetric Laplace distribution (ALD) has received increasing attention in the field of quantile regression due to an important feature between its location and asymmetric parameters. On the basis of the representation of the ALD as a normal-variance–mean mixture with an exponential mixing distribution, this article develops EM and generalized EM algorithms, respectively, for computing regression quantiles of linear and nonlinear regression models. It is interesting to show that the proposed EM algorithm and the MM (Majorization–Minimization) algorithm for quantile regressions are really the same in terms of computation, since the updating formula of them are the same. This provides a good example that connects the EM and MM algorithms. Simulation studies show that the EM algorithm can successfully recover the true parameters in quantile regressions.     

AN ALTERNATIVE PARAMETRIC APPROACH FOR DISCRETE MISSING DATA PROBLEMS

We propose an iterative method of estimation for discrete missing data problems that is conceptually different from the Expectation–Maximization (EM) algorithm and that does not in general yield the observed data maximum likelihood estimate (MLE). The proposed approach is based conceptually upon weighting the set of possible complete-data MLEs. Its implementation avoids the expectation step of EM, which can sometimes be problematic. In the simple case of Bernoulli trials missing completely at random, the iterations of the proposed algorithm are equivalent to the EM iterations. For a familiar genetics-oriented multinomial problem with missing count data and for the motivating example with epidemiologic applications that involves a mixture of a left censored normal distribution with a point mass at zero, we investigate the finite sample performance of the proposed estimator and find it to be competitive with that of the MLE. We give some intuitive justification for the method, and we explore an interesting connection between our algorithm and multiple imputation in order to suggest an approach for estimating standard errors.     

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.     

Approximate and estimated saddlepoint approximations

Classical saddlepoint methods, which assume that the cumulant generating function is known, result in an approximation to the distribution that achieves an error of order O(n^?1). The authors give a general theorem to address the accuracy of saddlepoint approximations in which the cumulant generating function has been estimated or approximated. In practice, the resulting saddlepoint approximations are typically of the order O(n^?1/2). The authors give simulation results for small sample examples to compare estimated saddlepoint approximations.     

Discretisation for inference on normal mixture models

The problem of inference in Bayesian Normal mixture models is known to be difficult. In particular, direct Bayesian inference (via quadrature) suffers from a combinatorial explosion in having to consider every possible partition of n observations into k mixture components, resulting in a computation time which is O(k ⁿ). This paper explores the use of discretised parameters and shows that for equal-variance mixture models, direct computation time can be reduced to O(D ^k n ^k), where relevant continuous parameters are each divided into D regions. As a consequence, direct inference is now possible on genuine data sets for small k, where the quality of approximation is determined by the level of discretisation. For large problems, where the computational complexity is still too great in O(D ^k n ^k) time, discretisation can provide a convergence diagnostic for a Markov chain Monte Carlo analysis.     

Parameter Estimation for Bivariate Shock Models with Singular Distribution for Censored Data with Concomitant Order Statistics

When two‐component parallel systems are tested, the data consist of Type‐II censored data X_(i), i= 1, n, from one component, and their concomitants Y _[i] randomly censored at X_(r), the stopping time of the experiment. Marshall & Olkin's (1967) bivariate exponential distribution is used to illustrate statistical inference procedures developed for this data type. Although this data type is motivated practically, the likelihood is complicated, and maximum likelihood estimation is difficult, especially in the case where the parameter space is a non‐open set. An iterative algorithm is proposed for finding maximum likelihood estimates. This article derives several properties of the maximum likelihood estimator (MLE) including existence, uniqueness, strong consistency and asymptotic distribution. It also develops an alternative estimation method with closed‐form expressions based on marginal distributions, and derives its asymptotic properties. Compared with variances of the MLEs in the finite and large sample situations, the alternative estimator performs very well, especially when the correlation between X and Y is small.     

Statistical inference for start-up demonstration tests with rejection of units upon observing d failures

In this paper, we consider the statistical inference for the success probability in the case of start-up demonstration tests in which rejection of units is possible when a pre-fixed number of failures is observed before the required number of consecutive successes are achieved for acceptance of the unit. Since the expected value of the stopping time is not a monotone function of the unknown parameter, the method of moments is not useful in this situation. Therefore, we discuss two estimation methods for the success probability: (1) the maximum likelihood estimation (MLE) via the expectation-maximization (EM) algorithm and (2) Bayesian estimation with a beta prior. We examine the small-sample properties of the MLE and Bayesian estimator. Finally, we present an example to illustrate the method of inference discussed here.     

Fisher Information for a partially observable simple birth process

ABSTRACT

In this paper, we study the Fisher Information for the birth rate of a partially observable simple birth process involving n observations. We suppose that at each observation time, each individual in the population can be observed independently with known fixed probability p. Finding an analytical form of the Fisher Information in general appears intractable. Nonetheless, we find a very good approximation for the Fisher Information by exploiting the probabilistic properties of the underlying stochastic process. Both numerical and theoretical results strongly support the latter approximation and confirm its high level of accuracy.     

Reduction of bias and skewness with applications to second order accuracy

Suppose [^(q)]{\widehat{\theta}} is an estimator of θ in \mathbbR{\mathbb{R}} that satisfies the central limit theorem. In general, inferences on θ are based on the central limit approximation. These have error O(n ^−1/2), where n is the sample size. Many unsuccessful attempts have been made at finding transformations which reduce this error to O(n ⁻¹). The variance stabilizing transformation fails to achieve this. We give alternative transformations that have bias O(n ⁻²), and skewness O(n ⁻³). Examples include the binomial, Poisson, chi-square and hypergeometric distributions.     

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.     

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.