General partially linear varying-coefficient transformation model with right censored data

In this paper, a unified maximum marginal likelihood estimation procedure is proposed for the analysis of right censored data using general partially linear varying-coefficient transformation models (GPLVCTM), which are flexible enough to include many survival models as its special cases. Unknown functional coefficients in the models are approximated by cubic B-spline polynomial. We estimate B-spline coefficients and regression parameters by maximizing marginal likelihood function. One advantage of this procedure is that it is free of both baseline and censoring distribution. Through simulation studies and a real data application (VA data from the Veteran's Administration Lung Cancer Study Clinical Trial), we illustrate that the proposed estimation procedure is accurate, stable and practical.     

Testing for constancy in varying coefficient models

We consider varying coefficient models, which are an extension of the classical linear regression models in the sense that the regression coefficients are replaced by functions in certain variables (for example, time), the covariates are also allowed to depend on other variables. Varying coefficient models are popular in longitudinal data and panel data studies, and have been applied in fields such as finance and health sciences. We consider longitudinal data and estimate the coefficient functions by the flexible B-spline technique. An important question in a varying coefficient model is whether an estimated coefficient function is statistically different from a constant (or zero). We develop testing procedures based on the estimated B-spline coefficients by making use of nice properties of a B-spline basis. Our method allows longitudinal data where repeated measurements for an individual can be correlated. We obtain the asymptotic null distribution of the test statistic. The power of the proposed testing procedures are illustrated on simulated data where we highlight the importance of including the correlation structure of the response variable and on real data.     

Bayesian adaptive Lasso for quantile regression models with nonignorably missing response data

Abstract

Handling data with the nonignorably missing mechanism is still a challenging problem in statistics. In this paper, we develop a fully Bayesian adaptive Lasso approach for quantile regression models with nonignorably missing response data, where the nonignorable missingness mechanism is specified by a logistic regression model. The proposed method extends the Bayesian Lasso by allowing different penalization parameters for different regression coefficients. Furthermore, a hybrid algorithm that combined the Gibbs sampler and Metropolis-Hastings algorithm is implemented to simulate the parameters from posterior distributions, mainly including regression coefficients, shrinkage coefficients, parameters in the non-ignorable missing models. Finally, some simulation studies and a real example are used to illustrate the proposed methodology.     

Boosted coefficient models

Regression methods typically construct a mapping from the covariates into the real numbers. Here, however, we consider regression problems where the task is to form a mapping from the covariates into a set of (univariate) real-valued functions. Examples are given by conditional density estimation, hazard regression and regression with a functional response. Our approach starts by modeling the function of interest using a sum of B-spline basis functions. To model dependence on the covariates, the coefficients of this expansion are each modeled as functions of the covariates. We propose to estimate these coefficient functions using boosted tree models. Algorithms are provided for the above three situations, and real data sets are used to investigate their performance. The results indicate that the proposed methodology performs well. In addition, it is both straightforward, and capable of handling a large number of covariates.     

Semiparametric partially linear varying coefficient models with panel count data

This paper studies semiparametric regression analysis of panel count data, which arise naturally when recurrent events are considered. Such data frequently occur in medical follow-up studies and reliability experiments, for example. To explore the nonlinear interactions between covariates, we propose a class of partially linear models with possibly varying coefficients for the mean function of the counting processes with panel count data. The functional coefficients are estimated by B-spline function approximations. The estimation procedures are based on maximum pseudo-likelihood and likelihood approaches and they are easy to implement. The asymptotic properties of the resulting estimators are established, and their finite-sample performance is assessed by Monte Carlo simulation studies. We also demonstrate the value of the proposed method by the analysis of a cancer data set, where the new modeling approach provides more comprehensive information than the usual proportional mean model.     

A flexible semiparametric regression model for bimodal,asymmetric and censored data

In this paper, we propose a new semiparametric heteroscedastic regression model allowing for positive and negative skewness and bimodal shapes using the B-spline basis for nonlinear effects. The proposed distribution is based on the generalized additive models for location, scale and shape framework in order to model any or all parameters of the distribution using parametric linear and/or nonparametric smooth functions of explanatory variables. We motivate the new model by means of Monte Carlo simulations, thus ignoring the skewness and bimodality of the random errors in semiparametric regression models, which may introduce biases on the parameter estimates and/or on the estimation of the associated variability measures. An iterative estimation process and some diagnostic methods are investigated. Applications to two real data sets are presented and the method is compared to the usual regression methods.     

Comparative GMM and GQL logistic regression models on hierarchical data

We often rely on the likelihood to obtain estimates of regression parameters but it is not readily available for generalized linear mixed models (GLMMs). Inferences for the regression coefficients and the covariance parameters are key in these models. We presented alternative approaches for analyzing binary data from a hierarchical structure that do not rely on any distributional assumptions: a generalized quasi-likelihood (GQL) approach and a generalized method of moments (GMM) approach. These are alternative approaches to the typical maximum-likelihood approximation approach in Statistical Analysis System (SAS) such as Laplace approximation (LAP). We examined and compared the performance of GQL and GMM approaches with multiple random effects to the LAP approach as used in PROC GLIMMIX, SAS. The GQL approach tends to produce unbiased estimates, whereas the LAP approach can lead to highly biased estimates for certain scenarios. The GQL approach produces more accurate estimates on both the regression coefficients and the covariance parameters with smaller standard errors as compared to the GMM approach. We found that both GQL and GMM approaches are less likely to result in non-convergence as opposed to the LAP approach. A simulation study was conducted and a numerical example was presented for illustrative purposes.     

Bilinear modulation models for seasonal tables of counts

We propose generalized linear models for time or age-time tables of seasonal counts, with the goal of better understanding seasonal patterns in the data. The linear predictor contains a smooth component for the trend and the product of a smooth component (the modulation) and a periodic time series of arbitrary shape (the carrier wave). To model rates, a population offset is added. Two-dimensional trends and modulation are estimated using a tensor product B-spline basis of moderate dimension. Further smoothness is ensured using difference penalties on the rows and columns of the tensor product coefficients. The optimal penalty tuning parameters are chosen based on minimization of a quasi-information criterion. Computationally efficient estimation is achieved using array regression techniques, avoiding excessively large matrices. The model is applied to female death rate in the US due to cerebrovascular diseases and respiratory diseases.     

Robust estimation for functional coefficient regression models with spatial data

A global smoothing procedure is developed using B-spline function approximation for estimating the unknown functions of a functional coefficient regression model with spatial data. A general formulation is used to treat mean regression, median regression, quantile regression and robust mean regression in one setting. The global convergence rates of the estimators of unknown coefficient functions are established. Various applications of the main results, including estimating conditional quantile coefficient functions and robustifying the mean regression coefficient functions are given. Finite sample properties of our procedures are studied through Monte Carlo simulations. A housing data example is used to illustrate the proposed methodology.     

Stochastic variational inference for large-scale discrete choice models using adaptive batch sizes

Discrete choice models describe the choices made by decision makers among alternatives and play an important role in transportation planning, marketing research and other applications. The mixed multinomial logit (MMNL) model is a popular discrete choice model that captures heterogeneity in the preferences of decision makers through random coefficients. While Markov chain Monte Carlo methods provide the Bayesian analogue to classical procedures for estimating MMNL models, computations can be prohibitively expensive for large datasets. Approximate inference can be obtained using variational methods at a lower computational cost with competitive accuracy. In this paper, we develop variational methods for estimating MMNL models that allow random coefficients to be correlated in the posterior and can be extended easily to large-scale datasets. We explore three alternatives: (1) Laplace variational inference, (2) nonconjugate variational message passing and (3) stochastic linear regression. Their performances are compared using real and simulated data. To accelerate convergence for large datasets, we develop stochastic variational inference for MMNL models using each of the above alternatives. Stochastic variational inference allows data to be processed in minibatches by optimizing global variational parameters using stochastic gradient approximation. A novel strategy for increasing minibatch sizes adaptively within stochastic variational inference is proposed.     

Laplace based approximate posterior inference for differential equation models

Ordinary differential equations are arguably the most popular and useful mathematical tool for describing physical and biological processes in the real world. Often, these physical and biological processes are observed with errors, in which case the most natural way to model such data is via regression where the mean function is defined by an ordinary differential equation believed to provide an understanding of the underlying process. These regression based dynamical models are called differential equation models. Parameter inference from differential equation models poses computational challenges mainly due to the fact that analytic solutions to most differential equations are not available. In this paper, we propose an approximation method for obtaining the posterior distribution of parameters in differential equation models. The approximation is done in two steps. In the first step, the solution of a differential equation is approximated by the general one-step method which is a class of numerical numerical methods for ordinary differential equations including the Euler and the Runge-Kutta procedures; in the second step, nuisance parameters are marginalized using Laplace approximation. The proposed Laplace approximated posterior gives a computationally fast alternative to the full Bayesian computational scheme (such as Makov Chain Monte Carlo) and produces more accurate and stable estimators than the popular smoothing methods (called collocation methods) based on frequentist procedures. For a theoretical support of the proposed method, we prove that the Laplace approximated posterior converges to the actual posterior under certain conditions and analyze the relation between the order of numerical error and its Laplace approximation. The proposed method is tested on simulated data sets and compared with the other existing methods.     

Parametric simultaneous robust inferences for regression coefficient under generalized linear models

In this article, the parametric robust regression approaches are proposed for making inferences about regression parameters in the setting of generalized linear models (GLMs). The proposed methods are able to test hypotheses on the regression coefficients in the misspecified GLMs. More specifically, it is demonstrated that with large samples, the normal and gamma regression models can be properly adjusted to become asymptotically valid for inferences about regression parameters under model misspecification. These adjusted regression models can provide the correct type I and II error probabilities and the correct coverage probability for continuous data, as long as the true underlying distributions have finite second moments.     

Bayesian LASSO-Regularized quantile regression for linear regression models with autoregressive errors

Quantile regression (QR) is a natural alternative for depicting the impact of covariates on the conditional distributions of a outcome variable instead of the mean. In this paper, we investigate Bayesian regularized QR for the linear models with autoregressive errors. LASSO-penalized type priors are forced on regression coefficients and autoregressive parameters of the model. Gibbs sampler algorithm is employed to draw the full posterior distributions of unknown parameters. Finally, the proposed procedures are illustrated by some simulation studies and applied to a real data analysis of the electricity consumption.     

Extending conditional likelihood in models for stratified binary data

The conditional likelihood is widely used in logistic regression models with stratified binary data. In particular, it leads to accurate inference for the parameters of interest, which are common to all strata, eliminating stratum-specific nuisance parameters. The modified profile likelihood is an accurate approximation to the conditional likelihood, but has the advantage of being available for general parametric models. Here, we propose the modified profile likelihood as an ideal extension of the conditional likelihood in generalized linear models for binary data, with generic link function. An important feature is that for the implementation we only need standard outputs of routines for generalized linear models. The accuracy of the method is supported by theoretical properties and is confirmed by simulation results.This research was supported by MIUR COFIN 2001-2003.     

On detecting influential data and selecting regression variables

The analysis of residuals may reveal various functional forms suitable for the regression model. In this paper, we investigate some selection criteria for selecting important regression variables. In doing so, we use statistical selection and ranking procedures. Thus, we derive an appropriate criterion to measure the influence and bias for the reduced models. We show that the reduced models are based on some noncentrality parameters which provide a measure of goodness of fit for the fitted models. In this paper, we also discuss the relationships of influence diagnostics and the statistic proposed earlier by Gupta and Huang (J. Statist. Plann. Inference 20 (1988) 155–167). We introduce a new measure for detecting influential data as an alternative to Cook's measure.     

The analysis of multivariate recurrent events with partially missing event types

In many clinical studies, subjects are at risk of experiencing more than one type of potentially recurrent event. In some situations, however, the occurrence of an event is observed, but the specific type is not determined. We consider the analysis of this type of incomplete data when the objectives are to summarize features of conditional intensity functions and associated treatment effects, and to study the association between different types of event. Here we describe a likelihood approach based on joint models for the multi-type recurrent events where parameter estimation is obtained from a Monte-Carlo EM algorithm. Simulation studies show that the proposed method gives unbiased estimators for regression coefficients and variance–covariance parameters, and the coverage probabilities of confidence intervals for regression coefficients are close to the nominal level. When the distribution of the frailty variable is misspecified, the method still provides estimators of the regression coefficients with good properties. The proposed method is applied to a motivating data set from an asthma study in which exacerbations were to be sub-typed by cellular analysis of sputum samples as eosinophilic or non-eosinophilic.     

Sampling from the posterior distribution in generalized linear mixed models

Generalized linear mixed models provide a unified framework for treatment of exponential family regression models, overdispersed data and longitudinal studies. These problems typically involve the presence of random effects and this paper presents a new methodology for making Bayesian inference about them. The approach is simulation-based and involves the use of Markov chain Monte Carlo techniques. The usual iterative weighted least squares algorithm is extended to include a sampling step based on the Metropolis–Hastings algorithm thus providing a unified iterative scheme. Non-normal prior distributions for the regression coefficients and for the random effects distribution are considered. Random effect structures with nesting required by longitudinal studies are also considered. Particular interests concern the significance of regression coefficients and assessment of the form of the random effects. Extensions to unknown scale parameters, unknown link functions, survival and frailty models are outlined.     

Variable selection in partially linear additive models for modal regression

Based on B-spline basis functions and smoothly clipped absolute deviation (SCAD) penalty, we present a new estimation and variable selection procedure based on modal regression for partially linear additive models. The outstanding merit of the new method is that it is robust against outliers or heavy-tail error distributions and performs no worse than the least-square-based estimation for normal error case. The main difference is that the standard quadratic loss is replaced by a kernel function depending on a bandwidth that can be automatically selected based on the observed data. With appropriate selection of the regularization parameters, the new method possesses the consistency in variable selection and oracle property in estimation. Finally, both simulation study and real data analysis are performed to examine the performance of our approach.     

Empirical Likelihood Inference for the Cox Model with Time-dependent Coefficients via Local Partial Likelihood

Abstract.  The Cox model with time-dependent coefficients has been studied by a number of authors recently. In this paper, we develop empirical likelihood (EL) pointwise confidence regions for the time-dependent regression coefficients via local partial likelihood smoothing. The EL simultaneous confidence bands for a linear combination of the coefficients are also derived based on the strong approximation methods. The EL ratio is formulated through the local partial log-likelihood for the regression coefficient functions. Our numerical studies indicate that the EL pointwise/simultaneous confidence regions/bands have satisfactory finite sample performances. Compared with the confidence regions derived directly based on the asymptotic normal distribution of the local constant estimator, the EL confidence regions are overall tighter and can better capture the curvature of the underlying regression coefficient functions. Two data sets, the gastric cancer data and the Mayo Clinic primary biliary cirrhosis data, are analysed using the proposed method.     

Robust variable selection and parametric component identification in varying coefficient models

ABSTRACT

In this paper, we study a novelly robust variable selection and parametric component identification simultaneously in varying coefficient models. The proposed estimator is based on spline approximation and two smoothly clipped absolute deviation (SCAD) penalties through rank regression, which is robust with respect to heavy-tailed errors or outliers in the response. Furthermore, when the tuning parameter is chosen by modified BIC criterion, we show that the proposed procedure is consistent both in variable selection and the separation of varying and constant coefficients. In addition, the estimators of varying coefficients possess the optimal convergence rate under some assumptions, and the estimators of constant coefficients have the same asymptotic distribution as their counterparts obtained when the true model is known. Simulation studies and a real data example are undertaken to assess the finite sample performance of the proposed variable selection procedure.