Objective Bayes Covariate‐Adjusted Sparse Graphical Model Selection

We present an objective Bayes method for covariance selection in Gaussian multivariate regression models having a sparse regression and covariance structure, the latter being Markov with respect to a directed acyclic graph (DAG). Our procedure can be easily complemented with a variable selection step, so that variable and graphical model selection can be performed jointly. In this way, we offer a solution to a problem of growing importance especially in the area of genetical genomics (eQTL analysis). The input of our method is a single default prior, essentially involving no subjective elicitation, while its output is a closed form marginal likelihood for every covariate‐adjusted DAG model, which is constant over each class of Markov equivalent DAGs; our procedure thus naturally encompasses covariate‐adjusted decomposable graphical models. In realistic experimental studies, our method is highly competitive, especially when the number of responses is large relative to the sample size.     

Parametric Inference in Stationary Time Series Models with Dependent Errors

This article is concerned with inference for the parameter vector in stationary time series models based on the frequency domain maximum likelihood estimator. The traditional method consistently estimates the asymptotic covariance matrix of the parameter estimator and usually assumes the independence of the innovation process. For dependent innovations, the asymptotic covariance matrix of the estimator depends on the fourth‐order cumulants of the unobserved innovation process, a consistent estimation of which is a difficult task. In this article, we propose a novel self‐normalization‐based approach to constructing a confidence region for the parameter vector in such models. The proposed procedure involves no smoothing parameter, and is widely applicable to a large class of long/short memory time series models with weakly dependent innovations. In simulation studies, we demonstrate favourable finite sample performance of our method in comparison with the traditional method and a residual block bootstrap approach.     

Generalized M-estimation for the accelerated failure time model

The accelerated failure time (AFT) model is an important regression tool to study the association between failure time and covariates. In this paper, we propose a robust weighted generalized M (GM) estimation for the AFT model with right-censored data by appropriately using the Kaplan–Meier weights in the GM–type objective function to estimate the regression coefficients and scale parameter simultaneously. This estimation method is computationally simple and can be implemented with existing software. Asymptotic properties including the root-n consistency and asymptotic normality are established for the resulting estimator under suitable conditions. We further show that the method can be readily extended to handle a class of nonlinear AFT models. Simulation results demonstrate satisfactory finite sample performance of the proposed estimator. The practical utility of the method is illustrated by a real data example.     

Estimating the variance for heterogeneity in arm‐based network meta‐analysis

Network meta‐analysis can be implemented by using arm‐based or contrast‐based models. Here we focus on arm‐based models and fit them using generalized linear mixed model procedures. Full maximum likelihood (ML) estimation leads to biased trial‐by‐treatment interaction variance estimates for heterogeneity. Thus, our objective is to investigate alternative approaches to variance estimation that reduce bias compared with full ML. Specifically, we use penalized quasi‐likelihood/pseudo‐likelihood and hierarchical (h) likelihood approaches. In addition, we consider a novel model modification that yields estimators akin to the residual maximum likelihood estimator for linear mixed models. The proposed methods are compared by simulation, and 2 real datasets are used for illustration. Simulations show that penalized quasi‐likelihood/pseudo‐likelihood and h‐likelihood reduce bias and yield satisfactory coverage rates. Sum‐to‐zero restriction and baseline contrasts for random trial‐by‐treatment interaction effects, as well as a residual ML‐like adjustment, also reduce bias compared with an unconstrained model when ML is used, but coverage rates are not quite as good. Penalized quasi‐likelihood/pseudo‐likelihood and h‐likelihood are therefore recommended.     

Variance Estimation under Two‐Phase Sampling

We consider the variance estimation of the weighted likelihood estimator (WLE) under two‐phase stratified sampling without replacement. Asymptotic variance of the WLE in many semiparametric models contains unknown functions or does not have a closed form. The standard method of the inverse probability weighted (IPW) sample variances of an estimated influence function is then not available in these models. To address this issue, we develop the variance estimation procedure for the WLE in a general semiparametric model. The phase I variance is estimated by taking a numerical derivative of the IPW log likelihood. The phase II variance is estimated based on the bootstrap for a stratified sample in a finite population. Despite a theoretical difficulty of dependent observations due to sampling without replacement, we establish the (bootstrap) consistency of our estimators. Finite sample properties of our method are illustrated in a simulation study.     

Orthogonality of the mean and error distribution in generalized linear models

We show that the mean-model parameter is always orthogonal to the error distribution in generalized linear models. Thus, the maximum likelihood estimator of the mean-model parameter will be asymptotically efficient regardless of whether the error distribution is known completely, known up to a finite vector of parameters, or left completely unspecified, in which case the likelihood is taken to be an appropriate semiparametric likelihood. Moreover, the maximum likelihood estimator of the mean-model parameter will be asymptotically independent of the maximum likelihood estimator of the error distribution. This generalizes some well-known results for the special cases of normal, gamma, and multinomial regression models, and, perhaps more interestingly, suggests that asymptotically efficient estimation and inferences can always be obtained if the error distribution is non parametrically estimated along with the mean. In contrast, estimation and inferences using misspecified error distributions or variance functions are generally not efficient.     

Focused information criteria for copulas

In this paper, we extend the focused information criterion (FIC) to copula models. Copulas are often used for applications where the joint tail behavior of the variables is of particular interest, and selecting a copula that captures this well is then essential. Traditional model selection methods such as the Akaike information criterion (AIC) and the Bayesian information criterion (BIC) aim at finding the overall best‐fitting model, which is not necessarily the one best suited for the application at hand. The FIC, on the other hand, evaluates and ranks candidate models based on the precision of their point estimates of a context‐given focus parameter. This could be any quantity of particular interest, for example, the mean, a correlation, conditional probabilities, or measures of tail dependence. We derive FIC formulae for the maximum likelihood estimator, the two‐stage maximum likelihood estimator, and the so‐called pseudo‐maximum‐likelihood (PML) estimator combined with parametric margins. Furthermore, we confirm the validity of the AIC formula for the PML estimator combined with parametric margins. To study the numerical behavior of FIC, we have carried out a simulation study, and we have also analyzed a multivariate data set pertaining to abalones. The results from the study show that the FIC successfully ranks candidate models in terms of their performance, defined as how well they estimate the focus parameter. In terms of estimation precision, FIC clearly outperforms AIC, especially when the focus parameter relates to only a specific part of the model, such as the conditional upper‐tail probability.     

Relative risk regression for current status data in case‐cohort studies

We propose using the weighted likelihood method to fit a general relative risk regression model for the current status data with missing data as arise, for example, in case‐cohort studies. The missingness probability is either known or can be reasonably estimated. Asymptotic properties of the weighted likelihood estimators are established. For the case of using estimated weights, we construct a general theorem that guarantees the asymptotic normality of the M‐estimator of a finite dimensional parameter in a class of semiparametric models, where the infinite dimensional parameter is allowed to converge at a slower than parametric rate, and some other parameters in the objective function are estimated a priori. The weighted bootstrap method is employed to estimate the variances. Simulations show that the proposed method works well for finite sample sizes. A motivating example of the case‐cohort study from an HIV vaccine trial is used to demonstrate the proposed method. The Canadian Journal of Statistics 39: 557–577; 2011. © 2011 Statistical Society of Canada     

Robust estimation of linear state space models

The model parameters of linear state space models are typically estimated with maximum likelihood estimation, where the likelihood is computed analytically with the Kalman filter. Outliers can deteriorate the estimation. Therefore we propose an alternative estimation method. The Kalman filter is replaced by a robust version and the maximum likelihood estimator is robustified as well. The performance of the robust estimator is investigated in a simulation study. Robust estimation of time varying parameter regression models is considered as a special case. Finally, the methodology is applied to real data.     

Case-cohort analysis with semiparametric transformation models

Semiparametric transformation models provide flexible regression models for survival analysis, including the Cox proportional hazards and the proportional odds models as special cases. We consider the application of semiparametric transformation models in case-cohort studies, where the covariate data are observed only on cases and on a subcohort randomly sampled from the full cohort. We first propose an approximate profile likelihood approach with full-cohort data, which amounts to the pseudo-partial likelihood approach of Zucker [2005. A pseudo-partial likelihood method for semiparametric survival regression with covariate errors. J. Amer. Statist. Assoc. 100, 1264–1277]. Simulation results show that our proposal is almost as efficient as the nonparametric maximum likelihood estimator. We then extend this approach to the case-cohort design, applying the Horvitz–Thompson weighting method to the estimating equations from the approximated profile likelihood. Two levels of weights can be utilized to achieve unbiasedness and to gain efficiency. The resulting estimator has a closed-form asymptotic covariance matrix, and is found in simulations to be substantially more efficient than the estimator based on martingale estimating equations. The extension to left-truncated data will be discussed. We illustrate the proposed method on data from a cardiovascular risk factor study conducted in Taiwan.     

Pseudo‐likelihood estimation in ARCH models

The author presents asymptotic results for the class of pseudo‐likelihood estimators in the autoregressive conditional heteroscedastic models introduced by Engle (1982). Unlike what is required for the quasi‐likelihood estimator, some estimators in the class he considers do not require the finiteness of the fourth moment of the error density. Thus his method is applicable to heavy‐tailed error distributions for which moments higher than two may not exist.     

Maximum penalized likelihood estimation of mixed proportional hazard models

Unobservable individual effects in models of duration will cause estimation bias that include the structural parameters as well as the duration dependence. The maximum penalized likelihood estimator is examined as an estimator for the survivor model with heterogeneity. Proofs of the existence and uniqueness of the maximum penalized likelihood estimator in duration model with general forms of unobserved heterogeneity are provided. Some small sample evidence on the behavior of the maximum penalized likelihood estimator is given. The maximum penalized likelihood estimator is shown to be computationally feasible and to provide reasonable estimates in most cases.     

Statistical Inference and Applications of Mixture of Varying Coefficient Models

In this paper, we consider a new mixture of varying coefficient models, in which each mixture component follows a varying coefficient model and the mixing proportions and dispersion parameters are also allowed to be unknown smooth functions. We systematically study the identifiability, estimation and inference for the new mixture model. The proposed new mixture model is rather general, encompassing many mixture models as its special cases such as mixtures of linear regression models, mixtures of generalized linear models, mixtures of partially linear models and mixtures of generalized additive models, some of which are new mixture models by themselves and have not been investigated before. The new mixture of varying coefficient model is shown to be identifiable under mild conditions. We develop a local likelihood procedure and a modified expectation–maximization algorithm for the estimation of the unknown non‐parametric functions. Asymptotic normality is established for the proposed estimator. A generalized likelihood ratio test is further developed for testing whether some of the unknown functions are constants. We derive the asymptotic distribution of the proposed generalized likelihood ratio test statistics and prove that the Wilks phenomenon holds. The proposed methodology is illustrated by Monte Carlo simulations and an analysis of a CO₂‐GDP data set.     

Empirical Uncertain Bayes Methods in Area‐level Models

Random effects model can account for the lack of fitting a regression model and increase precision of estimating area‐level means. However, in case that the synthetic mean provides accurate estimates, the prior distribution may inflate an estimation error. Thus, it is desirable to consider the uncertain prior distribution, which is expressed as the mixture of a one‐point distribution and a proper prior distribution. In this paper, we develop an empirical Bayes approach for estimating area‐level means, using the uncertain prior distribution in the context of a natural exponential family, which we call the empirical uncertain Bayes (EUB) method. The regression model considered in this paper includes the Poisson‐gamma and the binomial‐beta, and the normal‐normal (Fay–Herriot) model, which are typically used in small area estimation. We obtain the estimators of hyperparameters based on the marginal likelihood by using a well‐known expectation‐maximization algorithm and propose the EUB estimators of area means. For risk evaluation of the EUB estimator, we derive a second‐order unbiased estimator of a conditional mean squared error by using some techniques of numerical calculation. Through simulation studies and real data applications, we evaluate a performance of the EUB estimator and compare it with the usual empirical Bayes estimator.     

空间回归模型估计中的最小二乘法

空间回归模型由于引入了空间地理信息而使得其参数估计变得复杂,因为主要采用最大似然法,致使一般人认为在空间回归模型参数估计中不存在最小二乘法。通过分析空间回归模型的参数估计技术,研究发现,最小二乘法和最大似然法分别用于估计空间回归模型的不同的参数,只有将两者结合起来才能快速有效地完成全部的参数估计。数理论证结果表明,空间回归模型参数最小二乘估计量是最佳线性无偏估计量。空间回归模型的回归参数可以在估计量为正态性的条件下而实施显著性检验,而空间效应参数则不可以用此方法进行检验。     

An improved SAEM algorithm for maximum likelihood estimation in mixtures of non linear mixed effects models

We propose a new methodology for maximum likelihood estimation in mixtures of non linear mixed effects models (NLMEM). Such mixtures of models include mixtures of distributions, mixtures of structural models and mixtures of residual error models. Since the individual parameters inside the NLMEM are not observed, we propose to combine the EM algorithm usually used for mixtures models when the mixture structure concerns an observed variable, with the Stochastic Approximation EM (SAEM) algorithm, which is known to be suitable for maximum likelihood estimation in NLMEM and also has nice theoretical properties. The main advantage of this hybrid procedure is to avoid a simulation step of unknown group labels required by a “full” version of SAEM. The resulting MSAEM (Mixture SAEM) algorithm is now implemented in the Monolix software. Several criteria for classification of subjects and estimation of individual parameters are also proposed. Numerical experiments on simulated data show that MSAEM performs well in a general framework of mixtures of NLMEM. Indeed, MSAEM provides an estimator close to the maximum likelihood estimator in very few iterations and is robust with regard to initialization. An application to pharmacokinetic (PK) data demonstrates the potential of the method for practical applications.     

Frequentist model averaging for envelope models

The envelope method produces efficient estimation in multivariate linear regression, and is widely applied in biology, psychology, and economics. This paper estimates parameters through a model averaging methodology and promotes the predicting abilities of the envelope models. We propose a frequentist model averaging method by minimizing a cross-validation criterion. When all the candidate models are misspecified, the proposed model averaging estimator is proved to be asymptotically optimal. When correct candidate models exist, the coefficient estimator is proved to be consistent, and the sum of the weights assigned to the correct models, in probability, converges to one. Simulations and an empirical application demonstrate the effectiveness of the proposed method.     

Focused information criterion and model averaging based on weighted composite quantile regression

We study the focused information criterion and frequentist model averaging and their application to post‐model‐selection inference for weighted composite quantile regression (WCQR) in the context of the additive partial linear models. With the non‐parametric functions approximated by polynomial splines, we show that, under certain conditions, the asymptotic distribution of the frequentist model averaging WCQR‐estimator of a focused parameter is a non‐linear mixture of normal distributions. This asymptotic distribution is used to construct confidence intervals that achieve the nominal coverage probability. With properly chosen weights, the focused information criterion based WCQR estimators are not only robust to outliers and non‐normal residuals but also can achieve efficiency close to the maximum likelihood estimator, without assuming the true error distribution. Simulation studies and a real data analysis are used to illustrate the effectiveness of the proposed procedure.     

Semiparametric Density Deconvolution

Abstract.  A new semiparametric method for density deconvolution is proposed, based on a model in which only the ratio of the unconvoluted to convoluted densities is specified parametrically. Deconvolution results from reweighting the terms in a standard kernel density estimator, where the weights are defined by the parametric density ratio. We propose that in practice, the density ratio be modelled on the log-scale as a cubic spline with a fixed number of knots. Parameter estimation is based on maximization of a type of semiparametric likelihood. The resulting asymptotic properties for our deconvolution estimator mirror the convergence rates in standard density estimation without measurement error when attention is restricted to our semiparametric class of densities. Furthermore, numerical studies indicate that for practical sample sizes our weighted kernel estimator can provide better results than the classical non-parametric kernel estimator for a range of densities outside the specified semiparametric class.     

Indirect inference for fractional time series models

In this paper we present an indirect estimation procedure for (ARFIMA) fractional time series models.The estimation method is based on an ‘incorrect’criterion which does not directly provide a consistent estimator of the parameters of interest,but leads to correct inference by using simulations.

The main steps are the following. First,we consider an auxiliary model which can be easily estimated.Specifically,we choose the finite lag Autoregressive model.Then, this is estimated on the observations and simulated values drawn from the ARFIMA model associated with a given value of the parameters of interest.Finally,the latter is calibrated in order to obtain close values of the two estimators of the auxiliary parameters.

In this article,we describe the estimation procedure and compare the performance of the indirect estimator with some alternative estimators based on the likelihood function by a Monte Carlo study.