Bayesian factor models in characterizing molecular adaptation

Assessing the selective influence of amino acid properties is important in understanding evolution at the molecular level. A collection of methods and models has been developed in recent years to determine if amino acid sites in a given DNA sequence alignment display substitutions that are altering or conserving a prespecified set of amino acid properties. Residues showing an elevated number of substitutions that favorably alter a physicochemical property are considered targets of positive natural selection. Such approaches usually perform independent analyses for each amino acid property under consideration, without taking into account the fact that some of the properties may be highly correlated. We propose a Bayesian hierarchical regression model with latent factor structure that allows us to determine which sites display substitutions that conserve or radically change a set of amino acid properties, while accounting for the correlation structure that may be present across such properties. We illustrate our approach by analyzing simulated data sets and an alignment of lysin sperm DNA.     

Estimation under modified Weibull distribution based on right censored generalized order statistics

In this paper, the maximum likelihood (ML) and Bayes, by using Markov chain Monte Carlo (MCMC), methods are considered to estimate the parameters of three-parameter modified Weibull distribution (MWD(β, τ, λ)) based on a right censored sample of generalized order statistics (gos). Simulation experiments are conducted to demonstrate the efficiency of the proposed methods. Some comparisons are carried out between the ML and Bayes methods by computing the mean squared errors (MSEs), Akaike's information criteria (AIC) and Bayesian information criteria (BIC) of the estimates to illustrate the paper. Three real data sets from Weibull(α, β) distribution are introduced and analyzed using the MWD(β, τ, λ) and also using the Weibull(α, β) distribution. A comparison is carried out between the mentioned models based on the corresponding Kolmogorov–Smirnov (K–S) test statistic, {AIC and BIC} to emphasize that the MWD(β, τ, λ) fits the data better than the other distribution. All parameters are estimated based on type-II censored sample, censored upper record values and progressively type-II censored sample which are generated from the real data sets.     

Nonparametric Bayes factors based on empirical likelihood ratios

Bayes methodology provides posterior distribution functions based on parametric likelihoods adjusted for prior distributions. A distribution-free alternative to the parametric likelihood is use of empirical likelihood (EL) techniques, well known in the context of nonparametric testing of statistical hypotheses. Empirical likelihoods have been shown to exhibit many of the properties of conventional parametric likelihoods. In this paper, we propose and examine Bayes factors (BF) methods that are derived via the EL ratio approach. Following Kass and Wasserman (1995), we consider Bayes factors type decision rules in the context of standard statistical testing techniques. We show that the asymptotic properties of the proposed procedure are similar to the classical BF's asymptotic operating characteristics. Although we focus on hypothesis testing, the proposed approach also yields confidence interval estimators of unknown parameters. Monte Carlo simulations were conducted to evaluate the theoretical results as well as to demonstrate the power of the proposed test.     

Extended BIC for linear regression models with diverging number of relevant features and high or ultra-high feature spaces

In many conventional scientific investigations with high or ultra-high dimensional feature spaces, the relevant features, though sparse, are large in number compared with classical statistical problems, and the magnitude of their effects tapers off. It is reasonable to model the number of relevant features as a diverging sequence when sample size increases. In this paper, we investigate the properties of the extended Bayes information criterion (EBIC) (Chen and Chen, 2008) for feature selection in linear regression models with diverging number of relevant features in high or ultra-high dimensional feature spaces. The selection consistency of the EBIC in this situation is established. The application of EBIC to feature selection is considered in a SCAD cum EBIC procedure. Simulation studies are conducted to demonstrate the performance of the SCAD cum EBIC procedure in finite sample cases.     

指数族分布中参数的经验贝叶斯估计

指数族分布是一类应用广泛的分布类,包括了泊松分布、Gamma分布、Beta分布、二项分布等常见分布.在非寿险中,索赔额或索赔次数过程常常被假定服从指数族分布,由于风险的非齐次性,指数族分布中的参数θ也为随机变量,假定服从指数族共轭先验分布.此时风险参数的估计落入了Bayes框架,风险参数θ的Bayes估计被表达“信度”形式.然而,在实际运用中,由于先验分布与样本分布中仍然含有结构参数,根据样本的边际分布的似然函数估计结构参数,从而获得风险参数的经验Bayes估计,最后证明了该经验Bayes估计是渐近最优的.     

Reliability estimation in stress–strength models: an MCMC approach

In this paper, we consider the estimation of the stress–strength parameter R=P(Y<X) when X and Y are independent and both are modified Weibull distributions with the common two shape parameters but different scale parameters. The Markov Chain Monte Carlo sampling method is used for posterior inference of the reliability of the stress–strength model. The maximum-likelihood estimator of R and its asymptotic distribution are obtained. Based on the asymptotic distribution, the confidence interval of R can be obtained using the delta method. We also propose a bootstrap confidence interval of R. The Bayesian estimators with balanced loss function, using informative and non-informative priors, are derived. Different methods and the corresponding confidence intervals are compared using Monte Carlo simulations.     

Bayes sequential estimation for a Poisson process under a LINEX loss function

In this paper, within the framework of a Bayesian model, we consider the problem of sequentially estimating the intensity parameter of a homogeneous Poisson process with a linear exponential (LINEX) loss function and a fixed cost per unit time. An asymptotically pointwise optimal (APO) rule is proposed. It is shown to be asymptotically optimal for the arbitrary priors and asymptotically non-deficient for the conjugate priors in a similar sense of Bickel and Yahav [Asymptotically pointwise optimal procedures in sequential analysis, in Proceedings of the Fifth Berkeley Symposium on Mathematical Statistics and Probability, Vol. 1, University of California Press, Berkeley, CA, 1967, pp. 401–413; Asymptotically optimal Bayes and minimax procedures in sequential estimation, Ann. Math. Statist. 39 (1968), pp. 442–456] and Woodroofe [A.P.O. rules are asymptotically non-deficient for estimation with squared error loss, Z. Wahrsch. verw. Gebiete 58 (1981), pp. 331–341], respectively. The proposed APO rule is illustrated using a real data set.     

Partially Accelerated Life Tests for the Weibull Distribution Under Multiply Censored Data

This article aims to estimate the parameters of the Weibull distribution in step-stress partially accelerated life tests under multiply censored data. The step partially acceleration life test is that all test units are first run simultaneously under normal conditions for a pre-specified time, and the surviving units are then run under accelerated conditions until a predetermined censoring time. The maximum likelihood estimates are used to obtaining the parameters of the Weibull distribution and the acceleration factor under multiply censored data. Additionally, the confidence intervals for the estimators are obtained. Simulation results show that the maximum likelihood estimates perform well in most cases in terms of the mean bias, errors in the root mean square and the coverage rate. An example is used to illustrate the performance of the proposed approach.     

Bayes Estimation Based on Joint Progressive Type II Censored Data Under LINEX Loss Function

In the lifetime experiments, the joint censoring scheme is useful for planning comparative purposes of two identical products manufactured coming from different lines. In this article, we will confine ourselves to the data obtained by conducting a joint progressive Type II censoring scheme on the basis of the two combined samples selected from the two lines. Moreover, it is supposed that the distributions of lifetimes of the two products satisfy in a proportional hazard model. A general form for the distributions is considered, and we tackle the problem of obtaining Bayes estimates under the squared error and linear-exponential (LINEX) loss functions. As a special case, the Weibull distribution is discussed in more detail. Finally, the estimated risks of the various estimators obtained are compared using the Monte Carlo method.     

Case–control genome-wide joint association study using semiparametric empirical model and approximate Bayes factor

We propose a semiparametric approach for the analysis of case–control genome-wide association study. Parametric components are used to model both the conditional distribution of the case status given the covariates and the distribution of genotype counts, whereas the distribution of the covariates are modelled nonparametrically. This yields a direct and joint modelling of the case status, covariates and genotype counts, and gives a better understanding of the disease mechanism and results in more reliable conclusions. Side information, such as the disease prevalence, can be conveniently incorporated into the model by an empirical likelihood approach and leads to more efficient estimates and a powerful test in the detection of disease-associated SNPs. Profiling is used to eliminate a nuisance nonparametric component, and the resulting profile empirical likelihood estimates are shown to be consistent and asymptotically normal. For the hypothesis test on disease association, we apply the approximate Bayes factor (ABF) which is computationally simple and most desirable in genome-wide association studies where hundreds of thousands to a million genetic markers are tested. We treat the approximate Bayes factor as a hybrid Bayes factor which replaces the full data by the maximum likelihood estimates of the parameters of interest in the full model and derive it under a general setting. The deviation from Hardy–Weinberg Equilibrium (HWE) is also taken into account and the ABF for HWE using cases is shown to provide evidence of association between a disease and a genetic marker. Simulation studies and an application are further provided to illustrate the utility of the proposed methodology.