Bootstrap and Bayesian bootstrap clones for censored Markov chains

This is a study of the behaviors of the naive bootstrap and the Bayesian bootstrap clones designed to approximate the sampling distribution of the Aalen–Johansen estimator of a non-homogeneous censored Markov chain. The study shows that the approximations based on the Bayesian bootstrap clones and the naive bootstrap are first-order asymptotically equivalent. The two bootstrap methods are illustrated by a marketing example, and their performance is validated by a Monte Carlo experiment.     

Asymptotic bootstrap validity for finite markov chains

Two methods of bootstrap, viz., standard, and conditional, are presented for estimating the transition probabilities of a finite state Markov chain. Asymptotic validity of the bootstrap estimates are established for both methods. An applica- tion to a bootstrapped statistic for testing independence is briefly discussed together with some simulation results.     

Markov Poisson regression models for discrete time series. Part 1: Methodology

This paper proposes and investigates a class of Markov Poisson regression models in which Poisson rate functions of covariates are conditional on unobserved states which follow a finite-state Markov chain. Features of the proposed model, estimation, inference, bootstrap confidence intervals, model selection and other implementation issues are discussed. Monte Carlo studies suggest that the proposed estimation method is accurate and reliable for single- and multiple-subject time series data; the choice of starting probabilities for the Markov process has little eff ect on the parameter estimates; and penalized likelihood criteria are reliable for determining the number of states. Part 2 provides applications of the proposed model.     

Testing a markov chain for independence

A bootstrap procedure is proposed for testing whether an observed Markov chain is actually an independent process, based on the observed transition probability matrix. The results of simulations showing the power and size of the bootstrap test are presented. The asymptotic distribution of the non-unit eigenvalues is given under the null hypothesis.     

Randomized nomination sampling for finite populations

We propose a randomized minima–maxima nomination (RMMN) sampling design for use in finite populations. We derive the first- and second-order inclusion probabilities for both with and without replacement variations of the design. The inclusion probabilities for the without replacement variation are derived using a non-homogeneous Markov process. The design is simple to implement and results in simple and easy to calculate estimators and variances. It generalizes maxima nomination sampling for use in finite populations and includes some other sampling designs as special cases. We provide some optimality results and show that, in the context of finite population sampling, maxima nomination sampling is not generally the optimum design to follow. We also show, through numerical examples and a case study, that the proposed design can result in significant improvements in efficiency compared to simple random sampling without replacement designs for a wide choice of population types. Finally, we describe a bootstrap method for choosing values of the design parameters.     

Monte Carlo integration with Markov chain

There are two conceptually distinct tasks in Markov chain Monte Carlo (MCMC): a sampler is designed for simulating a Markov chain and then an estimator is constructed on the Markov chain for computing integrals and expectations. In this article, we aim to address the second task by extending the likelihood approach of Kong et al. for Monte Carlo integration. We consider a general Markov chain scheme and use partial likelihood for estimation. Basically, the Markov chain scheme is treated as a random design and a stratified estimator is defined for the baseline measure. Further, we propose useful techniques including subsampling, regulation, and amplification for achieving overall computational efficiency. Finally, we introduce approximate variance estimators for the point estimators. The method can yield substantially improved accuracy compared with Chib's estimator and the crude Monte Carlo estimator, as illustrated with three examples.     

Maximum likelihood estimation of bivariate circular hidden Markov models from incomplete data

In this paper, we propose a hidden Markov model for the analysis of the time series of bivariate circular observations, by assuming that the data are sampled from bivariate circular densities, whose parameters are driven by the evolution of a latent Markov chain. The model segments the data by accounting for redundancies due to correlations along time and across variables. A computationally feasible expectation maximization (EM) algorithm is provided for the maximum likelihood estimation of the model from incomplete data, by treating the missing values and the states of the latent chain as two different sources of incomplete information. Importance-sampling methods facilitate the computation of bootstrap standard errors of the estimates. The methodology is illustrated on a bivariate time series of wind and wave directions and compared with popular segmentation models for bivariate circular data, which ignore correlations across variables and/or along time.     

A New Markov Binomial Distribution

In this article, we introduce a two-state homogeneous Markov chain and define a geometric distribution related to this Markov chain. We define also the negative binomial distribution similar to the classical case and call it NB related to interrupted Markov chain. The new binomial distribution is related to the interrupted Markov chain. Some characterization properties of the geometric distributions are given. Recursion formulas and probability mass functions for the NB distribution and the new binomial distribution are derived.     

Testing lumpability for marginal discrete hidden Markov models

When some states of a Markov chain are aggregated (or lumped) and the new process, with lumped states, inherits the Markov property, the original chain is said to be lumpable. We discuss the notion of lumpability for discrete hidden Markov models (DHMMs) and we explain why, in general, testing this hypothesis leads to non-standard problems. Nevertheless, we present a case where lumpability in DHMMs is a regular problem of comparing nested models. Finally, some simulation results assessing the performance of the proposed test and an application to two real data sets are given.     

A Strong Law of Large Numbers for Strongly Mixing Processes

We prove a strong law of large numbers for a class of strongly mixing processes. Our result rests on recent advances in understanding of concentration of measure. It is simple to apply and gives finite-sample (as opposed to asymptotic) bounds, with readily computable rate constants. In particular, this makes it suitable for analysis of inhomogeneous Markov processes. We demonstrate how it can be applied to establish an almost-sure convergence result for a class of models that includes as a special case a class of adaptive Markov chain Monte Carlo algorithms.     

Markov chain Monte Carlo algorithms with sequential proposals

We explore a general framework in Markov chain Monte Carlo (MCMC) sampling where sequential proposals are tried as a candidate for the next state of the Markov chain. This sequential-proposal framework can be applied to various existing MCMC methods, including Metropolis–Hastings algorithms using random proposals and methods that use deterministic proposals such as Hamiltonian Monte Carlo (HMC) or the bouncy particle sampler. Sequential-proposal MCMC methods construct the same Markov chains as those constructed by the delayed rejection method under certain circumstances. In the context of HMC, the sequential-proposal approach has been proposed as extra chance generalized hybrid Monte Carlo (XCGHMC). We develop two novel methods in which the trajectories leading to proposals in HMC are automatically tuned to avoid doubling back, as in the No-U-Turn sampler (NUTS). The numerical efficiency of these new methods compare favorably to the NUTS. We additionally show that the sequential-proposal bouncy particle sampler enables the constructed Markov chain to pass through regions of low target density and thus facilitates better mixing of the chain when the target density is multimodal.

     

Parallel tempering for dynamic generalized linear models

ABSTRACT

Markov chain Monte Carlo (MCMC) methods can be used for statistical inference. The methods are time-consuming due to time-vary. To resolve these problems, parallel tempering (PT), as a parallel MCMC method, is tried, for dynamic generalized linear models (DGLMs), as well as the several optimal properties of our proposed method. In PT, two or more samples are drawn at the same time, and samples can exchange information with each other. We also present some simulations of the DGLMs in the case and provide two applications of Poisson-type DGLMs in financial research.     

A block bootstrap comparison for sparse chains

In this paper we apply the sequential bootstrap method proposed by Collet et al. [Bootstrap Central Limit theorem for chains of infinite order via Markov approximations, Markov Processes and Related Fields 11(3) (2005), pp. 443–464] to estimate the variance of the empirical mean of a special class of chains of infinite order called sparse chains. For this process, we show that we are able to compute numerically the true value of the standard error with any fixed error.

Our main goal is to present a comparison, for sparse chains, among sequential bootstrap, the block bootstrap method proposed by Künsch [The jackknife and the Bootstrap for general stationary observations, Ann. Statist. 17 (1989), pp. 1217–1241] and improved by Liu and Singh [Moving blocks jackknife and Bootstrap capture week dependence, in Exploring the limits of the Bootstrap, R. Lepage and L. Billard, eds., Wiley, New York, 1992, pp. 225–248] and the bootstrap method proposed by Bühlmann [Blockwise bootstrapped empirical process for stationary sequences, Ann. Statist. 22 (1994), pp. 995–1012].     

Non parametric resampling for stationary Markov processes: The local grid bootstrap approach

A new resampling technique, referred as “local grid bootstrap” (LGB), based on nonparametric local bootstrap and applicable to a wide range of stationary general space Markov processes is proposed. This nonparametric technique resamples local neighborhoods defined around the true samples of the observed multivariate time serie. The asymptotic behavior of this resampling procedure is studied in detail. Applications to linear and nonlinear (in particular chaotic) simulated time series are presented, and compared to Paparoditis and Politis [2002. J. Statist. Plan. Inf. 108, 301–328] approach, referred as “local bootstrap” (LB) and developed in earlier similar works. The method shows to be efficient and robust even when the length of the observed time series is reasonably small.     

Central Limit Theorem approximations for the number of runs in Markov-dependent binary sequences

We consider Markov-dependent binary sequences and study various types of success runs (overlapping, non-overlapping, exact, etc.) by examining additive functionals based on state visits and transitions in an appropriate Markov chain. We establish a multivariate Central Limit Theorem for the number of these types of runs and obtain its covariance matrix by means of the recurrent potential matrix of the Markov chain. Explicit expressions for the covariance matrix are given in the Bernoulli and a simple Markov-dependent case by expressing the recurrent potential matrix in terms of the stationary distribution and the mean transition times in the chain. We also obtain a multivariate Central Limit Theorem for the joint number of non-overlapping runs of various sizes and give its covariance matrix in explicit form for Markov dependent trials.     

Introducing model uncertainty by moving blocks bootstrap

It is common in parametric bootstrap to select the model from the data, and then treat as if it were the true model. Chatfield (1993, 1996) has shown that ignoring the model uncertainty may seriously undermine the coverage accuracy of prediction intervals. In this paper, we propose a method based on moving block bootstrap for introducing the model selection step in the resampling algorithm. We present a Monte Carlo study comparing the finite sample properties of the proposel method with those of alternative methods in the case of prediction intervas.     

Minimum variance unbiased estimation based on bootstrap iterations

Practical computation of the minimum variance unbiased estimator (MVUE) is often a difficult, if not impossible, task, even though general theory assures its existence under regularity conditions. We propose a new approach based on iterative bootstrap bias correction of the maximum likelihood estimator to accurately approximate the MVUE. Viewing bootstrap iteration as a Markov process, we develop a computational algorithm for bias correction based on arbitrarily many bootstrap iterations. The algorithm, when applied parametrically to finite sample spaces, does not involve Monte Carlo simulation. For infinite sample spaces, a nonparametric version of the algorithm is combined with a preliminary round of Monte Carlo simulation to yield an approximate MVUE. Both algorithms are computationally more efficient and stable than conventional simulation-based bootstrap iterations. Examples are given of both finite and infinite sample spaces to illustrate the effectiveness of our new approach. Supported by a grant from the Research Grants Council of the Hong Kong Special Administrative Region, China (Project No. HKU 7026/97P).     

A comparison of bootstrap approaches for estimating uncertainty of parameters in linear mixed‐effects models

A version of the nonparametric bootstrap, which resamples the entire subjects from original data, called the case bootstrap, has been increasingly used for estimating uncertainty of parameters in mixed‐effects models. It is usually applied to obtain more robust estimates of the parameters and more realistic confidence intervals (CIs). Alternative bootstrap methods, such as residual bootstrap and parametric bootstrap that resample both random effects and residuals, have been proposed to better take into account the hierarchical structure of multi‐level and longitudinal data. However, few studies have been performed to compare these different approaches. In this study, we used simulation to evaluate bootstrap methods proposed for linear mixed‐effect models. We also compared the results obtained by maximum likelihood (ML) and restricted maximum likelihood (REML). Our simulation studies evidenced the good performance of the case bootstrap as well as the bootstraps of both random effects and residuals. On the other hand, the bootstrap methods that resample only the residuals and the bootstraps combining case and residuals performed poorly. REML and ML provided similar bootstrap estimates of uncertainty, but there was slightly more bias and poorer coverage rate for variance parameters with ML in the sparse design. We applied the proposed methods to a real dataset from a study investigating the natural evolution of Parkinson's disease and were able to confirm that the methods provide plausible estimates of uncertainty. Given that most real‐life datasets tend to exhibit heterogeneity in sampling schedules, the residual bootstraps would be expected to perform better than the case bootstrap. Copyright © 2013 John Wiley & Sons, Ltd.     

Using a Markov Chain to Construct a Tractable Approximation of an Intractable Probability Distribution

Abstract.  Let π denote an intractable probability distribution that we would like to explore. Suppose that we have a positive recurrent, irreducible Markov chain that satisfies a minorization condition and has π as its invariant measure. We provide a method of using simulations from the Markov chain to construct a statistical estimate of π from which it is straightforward to sample. We show that this estimate is 'strongly consistent' in the sense that the total variation distance between the estimate and π converges to 0 almost surely as the number of simulations grows. Moreover, we use some recently developed asymptotic results to provide guidance as to how much simulation is necessary. Draws from the estimate can be used to approximate features of π or as intelligent starting values for the original Markov chain. We illustrate our methods with two examples.