A Markov chain Monte Carlo Expectation Maximization Algorithm for Statistical Analysis of DNA Sequence Evolution with Neighbor-Dependent Substitution Rates

The evolution of DNA sequences can be described by discrete state continuous time Markov processes on a phylogenetic tree. We consider neighbor-dependent evolutionary models where the instantaneous rate of substitution at a site depends on the states of the neighboring sites. Neighbor-dependent substitution models are analytically intractable and must be analyzed using either approximate or simulation-based methods. We describe statistical inference of neighbor-dependent models using a Markov chain Monte Carlo expectation maximization (MCMC-EM) algorithm. In the MCMC-EM algorithm, the high-dimensional integrals required in the EM algorithm are estimated using MCMC sampling. The MCMC sampler requires simulation of sample paths from a continuous time Markov process, conditional on the beginning and ending states and the paths of the neighboring sites. An exact path sampling algorithm is developed for this purpose.     

Prediction and Inference for Truncated Spatial Data

Abstract

Spatial data in mining, hydrology, and pollution monitoring commonly have a substantial proportion of zeros. One way to model such data is to suppose that some pointwise transformation of the observations follows the law of a truncated Gaussian random field. This article considers Monte Carlo methods for prediction and inference problems based on this model. In particular, a method for computing the conditional distribution of the random field at an unobserved location, given the data, is described. These results are compared to those obtained by simple kriging and indicator cokriging. Simple kriging is shown to give highly misleading results about conditional distributions; indicator cokriging does quite a bit better but still can give answers that are substantially different from the conditional distributions. A slight modification of this basic technique is developed for calculating the likelihood function for such models, which provides a method for computing maximum likelihood estimates of unknown parameters and Bayesian predictive distributions for values of the process at unobserved locations.     

Bayesian Inference in Hidden Markov Random Fields for Binary Data Defined on Large Lattices

Hidden Markov random fields represent a complex hierarchical model, where the hidden latent process is an undirected graphical structure. Performing inference for such models is difficult primarily because the likelihood of the hidden states is often unavailable. The main contribution of this article is to present approximate methods to calculate the likelihood for large lattices based on exact methods for smaller lattices. We introduce approximate likelihood methods by relaxing some of the dependencies in the latent model, and also by extending tractable approximations to the likelihood, the so-called pseudolikelihood approximations, for a large lattice partitioned into smaller sublattices. Results are presented based on simulated data as well as inference for the temporal-spatial structure of the interaction between up- and down-regulated states within the mitochondrial chromosome of the Plasmodium falciparum organism. Supplemental material for this article is available online.     

Likelihood Inference under Generalized Hybrid Censoring Scheme with Comp eting Risks

Statistical inference is developed for the analysis of generalized type-II hybrid censoring data under exponential competing risks model. In order to solve the problem that approximate methods make unsatisfactory performances in the case of small sample size, we establish the exact conditional distributions of estimators for parameters by conditional moment generating function(CMGF). Furthermore, confidence intervals(CIs) are constructed by exact distributions, approximate distributions as well as bootstrap method respectively, and their performances are evaluated by Monte Carlo simulations. And finally, a real data set is analyzed to illustrate all the methods developed here.     

Semiparametric quantile regression with random censoring

This paper considers estimation and inference in semiparametric quantile regression models when the response variable is subject to random censoring. The paper considers both the cases of independent and dependent censoring and proposes three iterative estimators based on inverse probability weighting, where the weights are estimated from the censoring distribution using the Kaplan–Meier, a fully parametric and the conditional Kaplan–Meier estimators. The paper proposes a computationally simple resampling technique that can be used to approximate the finite sample distribution of the parametric estimator. The paper also considers inference for both the parametric and nonparametric components of the quantile regression model. Monte Carlo simulations show that the proposed estimators and test statistics have good finite sample properties. Finally, the paper contains a real data application, which illustrates the usefulness of the proposed methods.

     

一类小样本的统计方法建模及其可视化

针对一类高维小样本数据,利用统计方法的非参数检验与偏最小二乘回归(PLS)构造小样本预测模型,实现基于Wilcoxon秩和检验的变量选择与基于PLS的变量压缩降维.并通过DNA序列分类问题实现基于统计方法的小样本数据建模与可视化,计算结果表明方法对小样本具有可行性、有效性.     

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 Computation of Software Reliability

Abstract

Bayesian methods for the Jelinski and Moranda and the Littlewood and Verrall models in software reliability are studied. A Gibbs sampling approach is employed to compute the Bayes estimates. In addition, prediction of future failure times and future reliabilities is examined. Model selection based on the mean squared prediction error and the prequential likelihood of the conditional predictive ordinates is developed.     

Confidence Intervals of Variance Functions in Generalized Linear Model

In this paper we introduce an appealing nonparametric method for estimating variance and conditional variance functions in generalized linear models （GLMs）, when designs are fixed points and random variables respectively, Bias-corrected confidence bands are proposed for the （conditional） variance by local linear smoothers. Nonparametric techniques are developed in deriving the bias-corrected confidence intervals of the （conditional） variance. The asymptotic distribution of the proposed estimator is established and show that the bias-corrected confidence bands asymptotically have the correct coverage properties. A small simulation is performed when unknown regression parameter is estimated by nonparametric quasi-likelihood. The results are also applicable to nonparamctric autoregressive times series model with heteroscedastic conditional variance.     

Discussion of “human life is unlimited-but short” by H Rootzén and D Zholud

The statistical paper human life is short-but unlimited is briefly discussed. The possibilities and limitations of statistical inference concerning very long human life spans are considered. The restricted models of tail distributions that arise from assumption of renormalized convergence of max- or conditional peaks over thresholds-distributions are questioned in the application context of the reviewed paper. The restrictions of natural systems designs on possibilities of extreme life spans, and the potential to adopt modified extreme value models, allowing seasonal variation of death rates, are also pointed out.     

A Non-Linear Filter

Abstract

Using a measure change related to Bayes' rule recursive estimates are obtained for an approximate conditional density where a state process has deterministic dynamics and it is observed in additive Gaussian noise.     

Shooting Methods for Numerical Solution of Stochastic Boundary-Value Problems

Abstract

In the present investigation, numerical methods are developed for approximate solution of stochastic boundary-value problems. In particular, shooting methods are examined for numerically solving systems of Stratonovich boundary-value problems. It is proved that these methods accurately approximate the solutions of stochastic boundary-value problems. An error analysis of these methods is performed. Computational simulations are given.     

Logarithmic Pooling of Priors Linked by a Deterministic Simulation Model

Abstract

We consider Bayesian inference when priors and likelihoods are both available for inputs and outputs of a deterministic simulation model. This problem is fundamentally related to the issue of aggregating (i.e., pooling) expert opinion. We survey alternative strategies for aggregation, then describe computational approaches for implementing pooled inference for simulation models. Our approach (1) numerically transforms all priors to the same space; (2) uses log pooling to combine priors; and (3) then draws standard Bayesian inference. We use importance sampling methods, including an iterative, adaptive approach that is more flexible and has less bias in some instances than a simpler alternative. Our exploratory examples are the first steps toward extension of the approach for highly complex and even noninvertible models.     

Conditioning exceedances on covariate processes

This article concerns the statistical inference for the upper tail of the conditional distribution of a response variable Y given a covariate X = x based on n random vectors within the parametric extreme value framework. Pioneering work in this field was done by Smith (Stat Sci 4:367–393, 1989) and Smith and Shively (Atmos Environ 29:3489–3499, 1995). We propose to base the inference on a conditional distribution of the point process of exceedances given the point process of covariates. It is of importance that the conditional distribution merely depends on the conditional distribution of the response variable given the covariates. In the special case of Poisson processes such a result may be found in Reiss (1993). Our results are valid within the broader model where the response variables are conditionally independent given the covariates. It is numerically exemplified that the maximum likelihood principle leads to more accurate estimators within the conditional approach than in the previous one.     

Quasi-Monte Carlo for Highly Structured Generalised Response Models

Highly structured generalised response models, such as generalised linear mixed models and generalised linear models for time series regression, have become an indispensable vehicle for data analysis and inference in many areas of application. However, their use in practice is hindered by high-dimensional intractable integrals. Quasi-Monte Carlo (QMC) is a dynamic research area in the general problem of high-dimensional numerical integration, although its potential for statistical applications is yet to be fully explored. We survey recent research in QMC, particularly lattice rules, and report on its application to highly structured generalised response models. New challenges for QMC are identified and new methodologies are developed. QMC methods are seen to provide significant improvements compared with ordinary Monte Carlo methods.      

Applications of the representative points in statistical simulations

The paper gives a new approach to statistical simulation and resampling by the use of number-theoretic methods and representative points. Resempling techniques take samples from an approximate population. The bootstrap suggests to use a random sample to form an approximate population. We propose to construct some approximate population distribution by the use of two kinds of representative points, and samples are taken from these approximate distributions. The statistical inference is based on those samples. The statistical inference in this paper involves estimation of mean, variance, skewness, kurtosis, quantile and density of the population distribution. Our results show that the new method can significantly improve the results by the use of Monte Carlo methods.     

Variational Bayes With Intractable Likelihood

Variational Bayes (VB) is rapidly becoming a popular tool for Bayesian inference in statistical modeling. However, the existing VB algorithms are restricted to cases where the likelihood is tractable, which precludes their use in many interesting situations such as in state--space models and in approximate Bayesian computation (ABC), where application of VB methods was previously impossible. This article extends the scope of application of VB to cases where the likelihood is intractable, but can be estimated unbiasedly. The proposed VB method therefore makes it possible to carry out Bayesian inference in many statistical applications, including state--space models and ABC. The method is generic in the sense that it can be applied to almost all statistical models without requiring too much model-based derivation, which is a drawback of many existing VB algorithms. We also show how the proposed method can be used to obtain highly accurate VB approximations of marginal posterior distributions. Supplementary material for this article is available online.     

A Bayesian analysis for the seismic data on Taiwan

A Bayesian approach is used to analyze the seismic events with magnitudes at least 4.7 on Taiwan. Following the idea proposed by Ogata (1988,Journal of the American Statistical Association,83, 9–27), an epidemic model for the process of occurrence times given the observed magnitude values is considered, incorporated with gamma prior distributions for the parameters in the model, while the hyper-parameters of the prior are essentially determined by the seismic data in an earlier period. Bayesian inference is made on the conditional intensity function via Markov chain Monte Carlo method. The results yield acceptable accuracies in predicting large earthquake events within short time periods.     

Falling and explosive,dormant, and rising markets via multiple‐regime financial time series models

A multiple‐regime threshold nonlinear financial time series model, with a fat‐tailed error distribution, is discussed and Bayesian estimation and inference are considered. Furthermore, approximate Bayesian posterior model comparison among competing models with different numbers of regimes is considered which is effectively a test for the number of required regimes. An adaptive Markov chain Monte Carlo (MCMC) sampling scheme is designed, while importance sampling is employed to estimate Bayesian residuals for model diagnostic testing. Our modeling framework provides a parsimonious representation of well‐known stylized features of financial time series and facilitates statistical inference in the presence of high or explosive persistence and dynamic conditional volatility. We focus on the three‐regime case where the main feature of the model is to capturing of mean and volatility asymmetries in financial markets, while allowing an explosive volatility regime. A simulation study highlights the properties of our MCMC estimators and the accuracy and favourable performance as a model selection tool, compared with a deviance criterion, of the posterior model probability approximation method. An empirical study of eight international oil and gas markets provides strong support for the three‐regime model over its competitors, in most markets, in terms of model posterior probability and in showing three distinct regime behaviours: falling/explosive, dormant and rising markets. Copyright © 2009 John Wiley & Sons, Ltd.     

Pair-Copula Bayesian Networks

Pair-copula Bayesian networks (PCBNs) are a novel class of multivariate statistical models, which combine the distributional flexibility of pair-copula constructions (PCCs) with the parsimony of conditional independence models associated with directed acyclic graphs (DAGs). We are first to provide generic algorithms for random sampling and likelihood inference in arbitrary PCBNs as well as for selecting orderings of the parents of the vertices in the underlying graphs. Model selection of the DAG is facilitated using a version of the well-known PC algorithm that is based on a novel test for conditional independence of random variables tailored to the PCC framework. A simulation study shows the PC algorithm’s high aptitude for structure estimation in non-Gaussian PCBNs. The proposed methods are finally applied to modeling financial return data. Supplementary materials for this article are available online.