Statistical inference for a semiparametric measurement error regression model with heteroscedastic errors

Efficient inference for regression models requires that the heteroscedasticity be taken into account. We consider statistical inference under heteroscedasticity in a semiparametric measurement error regression model, in which some covariates are measured with errors. This paper has multiple components. First, we propose a new method for testing the heteroscedasticity. The advantages of the proposed method over the existing ones are that it does not need any nonparametric estimation and does not involve any mismeasured variables. Second, we propose a new two-step estimator for the error variances if there is heteroscedasticity. Finally, we propose a weighted estimating equation-based estimator (WEEBE) for the regression coefficients and establish its asymptotic properties. Compared with existing estimators, the proposed WEEBE is asymptotically more efficient, avoids undersmoothing the regressor functions and requires less restrictions on the observed regressors. Simulation studies show that the proposed test procedure and estimators have nice finite sample performance. A real data set is used to illustrate the utility of our proposed methods.     

A corrected likelihood method for the proportional hazards model with covariates subject to measurement error

There has been extensive interest in discussing inference methods for survival data when some covariates are subject to measurement error. It is known that standard inferential procedures produce biased estimation if measurement error is not taken into account. With the Cox proportional hazards model a number of methods have been proposed to correct bias induced by measurement error, where the attention centers on utilizing the partial likelihood function. It is also of interest to understand the impact on estimation of the baseline hazard function in settings with mismeasured covariates. In this paper we employ a weakly parametric form for the baseline hazard function and propose simple unbiased estimating functions for estimation of parameters. The proposed method is easy to implement and it reveals the connection between the naive method ignoring measurement error and the corrected method with measurement error accounted for. Simulation studies are carried out to evaluate the performance of the estimators as well as the impact of ignoring measurement error in covariates. As an illustration we apply the proposed methods to analyze a data set arising from the Busselton Health Study [Knuiman, M.W., Cullent, K.J., Bulsara, M.K., Welborn, T.A., Hobbs, M.S.T., 1994. Mortality trends, 1965 to 1989, in Busselton, the site of repeated health surveys and interventions. Austral. J. Public Health 18, 129–135].     

Linear mode regression with covariate measurement error

We consider estimating the mode of a response given an error‐prone covariate. It is shown that ignoring measurement error typically leads to inconsistent inference for the conditional mode of the response given the true covariate, as well as misleading inference for regression coefficients in the conditional mode model. To account for measurement error, we first employ the Monte Carlo corrected score method (Novick & Stefanski, 2002) to obtain an unbiased score function based on which the regression coefficients can be estimated consistently. To relax the normality assumption on measurement error this method requires, we propose another method where deconvoluting kernels are used to construct an objective function that is maximized to obtain consistent estimators of the regression coefficients. Besides rigorous investigation on asymptotic properties of the new estimators, we study their finite sample performance via extensive simulation experiments, and find that the proposed methods substantially outperform a naive inference method that ignores measurement error. The Canadian Journal of Statistics 47: 262–280; 2019 © 2019 Statistical Society of Canada     

Model selection in high-dimensional noisy data: a simulation study

In many practical applications, high-dimensional regression analyses have to take into account measurement error in the covariates. It is thus necessary to extend regularization methods, that can handle the situation where the number of covariates p largely exceed the sample size n, to the case in which covariates are also mismeasured. A variety of methods are available in this context, but many of them rely on knowledge about the measurement error and the structure of its covariance matrix. In this paper, we set the goal to compare some of these methods, focusing on situations relevant for practical applications. In particular, we will evaluate these methods in setups in which the measurement error distribution and dependence structure are not known and have to be estimated from data. Our focus is on variable selection, and the evaluation is based on extensive simulations.     

Nonparametric covariate adjustment for receiver operating characteristic curves

The accuracy of a diagnostic test is typically characterized using the receiver operating characteristic (ROC) curve. Summarizing indexes such as the area under the ROC curve (AUC) are used to compare different tests as well as to measure the difference between two populations. Often additional information is available on some of the covariates which are known to influence the accuracy of such measures. The authors propose nonparametric methods for covariate adjustment of the AUC. Models with normal errors and possibly non‐normal errors are discussed and analyzed separately. Nonparametric regression is used for estimating mean and variance functions in both scenarios. In the model that relaxes the assumption of normality, the authors propose a covariate‐adjusted Mann–Whitney estimator for AUC estimation which effectively uses available data to construct working samples at any covariate value of interest and is computationally efficient for implementation. This provides a generalization of the Mann–Whitney approach for comparing two populations by taking covariate effects into account. The authors derive asymptotic properties for the AUC estimators in both settings, including asymptotic normality, optimal strong uniform convergence rates and mean squared error (MSE) consistency. The MSE of the AUC estimators was also assessed in smaller samples by simulation. Data from an agricultural study were used to illustrate the methods of analysis. The Canadian Journal of Statistics 38:27–46; 2010 © 2009 Statistical Society of Canada     

Nonparametric hierarchical Bayes analysis of binomial data via Bernstein polynomial priors

For binomial data analysis, many methods based on empirical Bayes interpretations have been developed, in which a variance‐stabilizing transformation and a normality assumption are usually required. To achieve the greatest model flexibility, we conduct nonparametric Bayesian inference for binomial data and employ a special nonparametric Bayesian prior—the Bernstein–Dirichlet process (BDP)—in the hierarchical Bayes model for the data. The BDP is a special Dirichlet process (DP) mixture based on beta distributions, and the posterior distribution resulting from it has a smooth density defined on [0, 1]. We examine two Markov chain Monte Carlo procedures for simulating from the resulting posterior distribution, and compare their convergence rates and computational efficiency. In contrast to existing results for posterior consistency based on direct observations, the posterior consistency of the BDP, given indirect binomial data, is established. We study shrinkage effects and the robustness of the BDP‐based posterior estimators in comparison with several other empirical and hierarchical Bayes estimators, and we illustrate through examples that the BDP‐based nonparametric Bayesian estimate is more robust to the sample variation and tends to have a smaller estimation error than those based on the DP prior. In certain settings, the new estimator can also beat Stein's estimator, Efron and Morris's limited‐translation estimator, and many other existing empirical Bayes estimators. The Canadian Journal of Statistics 40: 328–344; 2012 © 2012 Statistical Society of Canada     

Constrained penalized splines

The penalized spline is a popular method for function estimation when the assumption of “smoothness” is valid. In this paper, methods for estimation and inference are proposed using penalized splines under additional constraints of shape, such as monotonicity or convexity. The constrained penalized spline estimator is shown to have the same convergence rates as the corresponding unconstrained penalized spline, although in practice the squared error loss is typically smaller for the constrained versions. The penalty parameter may be chosen with generalized cross‐validation, which also provides a method for determining if the shape restrictions hold. The method is not a formal hypothesis test, but is shown to have nice large‐sample properties, and simulations show that it compares well with existing tests for monotonicity. Extensions to the partial linear model, the generalized regression model, and the varying coefficient model are given, and examples demonstrate the utility of the methods. The Canadian Journal of Statistics 40: 190–206; 2012 © 2012 Statistical Society of Canada     

Approximate estimations in capture–recapture model with heteroscedastic measurement errors

In a capture–recapture experiment, the number of measurements for individual covariates usually equals the number of captures. This creates a heteroscedastic measurement error problem and the usual surrogate condition does not hold in the context of a measurement error model. This study adopts a small measurement error assumption to approximate the conventional estimating functions and the population size estimator. This study also investigates the biases of the resulting estimators. In addition, modifications for two common approximation methods, regression calibration and simulation extrapolation, to accommodate heteroscedastic measurement error are also discussed. These estimation methods are examined through simulations and illustrated by analysing a capture–recapture data set.     

R package for analysis of data with mixed measurement error and misclassification in covariates: augSIMEX

Measurement error and misclassification arise commonly in various data collection processes. It is well-known that ignoring these features in the data analysis usually leads to biased inference. With the generalized linear model setting, Yi et al. [Functional and structural methods with mixed measurement error and misclassification in covariates. J Am Stat Assoc. 2015;110:681–696] developed inference methods to adjust for the effects of measurement error in continuous covariates and misclassification in discrete covariates simultaneously for the scenario where validation data are available. The augmented simulation-extrapolation (SIMEX) approach they developed generalizes the usual SIMEX method which is only applicable to handle continuous error-prone covariates. To implement this method, we develop an R package, augSIMEX, for public use. Simulation studies are conducted to illustrate the use of the algorithm. This package is available at CRAN.     

Estimation methods for time‐dependent AUC models with survival data

The performance of clinical tests for disease screening is often evaluated using the area under the receiver‐operating characteristic (ROC) curve (AUC). Recent developments have extended the traditional setting to the AUC with binary time‐varying failure status. Without considering covariates, our first theme is to propose a simple and easily computed nonparametric estimator for the time‐dependent AUC. Moreover, we use generalized linear models with time‐varying coefficients to characterize the time‐dependent AUC as a function of covariate values. The corresponding estimation procedures are proposed to estimate the parameter functions of interest. The derived limiting Gaussian processes and the estimated asymptotic variances enable us to construct the approximated confidence regions for the AUCs. The finite sample properties of our proposed estimators and inference procedures are examined through extensive simulations. An analysis of the AIDS Clinical Trials Group (ACTG) 175 data is further presented to show the applicability of the proposed methods. The Canadian Journal of Statistics 38:8–26; 2010 © 2009 Statistical Society of Canada     

Inference after variable selection using restricted permutation methods

When confronted with multiple covariates and a response variable, analysts sometimes apply a variable‐selection algorithm to the covariate‐response data to identify a subset of covariates potentially associated with the response, and then wish to make inferences about parameters in a model for the marginal association between the selected covariates and the response. If an independent data set were available, the parameters of interest could be estimated by using standard inference methods to fit the postulated marginal model to the independent data set. However, when applied to the same data set used by the variable selector, standard (“naive”) methods can lead to distorted inferences. The authors develop testing and interval estimation methods for parameters reflecting the marginal association between the selected covariates and response variable, based on the same data set used for variable selection. They provide theoretical justification for the proposed methods, present results to guide their implementation, and use simulations to assess and compare their performance to a sample‐splitting approach. The methods are illustrated with data from a recent AIDS study. The Canadian Journal of Statistics 37: 625–644; 2009 © 2009 Statistical Society of Canada     

Generalized partially linear varying-coefficient models

Generalized varying-coefficient models are useful extensions of generalized linear models. They arise naturally when investigating how regression coefficients change over different groups characterized by certain covariates such as age. In this paper, we extend these models to generalized partially linear varying-coefficient models, in which some coefficients are constants and the others are functions of certain covariates. Procedures for estimating the linear and non-parametric parts are developed and their associated statistical properties are studied. The methods proposed are illustrated using some simulations and real data analysis.     

Bayesian Semiparametric Modelling in Quantile Regression

Abstract. We propose a Bayesian semiparametric methodology for quantile regression modelling. In particular, working with parametric quantile regression functions, we develop Dirichlet process mixture models for the error distribution in an additive quantile regression formulation. The proposed non‐parametric prior probability models allow the shape of the error density to adapt to the data and thus provide more reliable predictive inference than models based on parametric error distributions. We consider extensions to quantile regression for data sets that include censored observations. Moreover, we employ dependent Dirichlet processes to develop quantile regression models that allow the error distribution to change non‐parametrically with the covariates. Posterior inference is implemented using Markov chain Monte Carlo methods. We assess and compare the performance of our models using both simulated and real data sets.     

Sequential design for nonparametric inference

The performance of nonparametric function estimates often depends on the choice of design points. Based on the mean integrated squared error criterion, we propose a sequential design procedure that updates the model knowledge and optimal design density sequentially. The methodology is developed under a general framework covering a wide range of nonparametric inference problems, such as conditional mean and variance functions, the conditional distribution function, the conditional quantile function in quantile regression, functional coefficients in varying coefficient models and semiparametric inferences. Based on our empirical studies, nonparametric inference based on the proposed sequential design is more efficient than the uniform design and its performance is close to the true but unknown optimal design. The Canadian Journal of Statistics 40: 362–377; 2012 © 2012 Statistical Society of Canada     

Estimation in capture–recapture models when covariates are subject to measurement errors and missing data

For capture–recapture models when covariates are subject to measurement errors and missing data, a set of estimating equations is constructed to estimate population size and relevant parameters. These estimating equations can be solved by an algorithm similar to the EM algorithm. The proposed method is also applicable to the situation when covariates with no measurement errors have missing data. Simulation studies are used to assess the performance of the proposed estimator. The estimator is also applied to a capture–recapture experiment on the bird species Prinia flaviventris in Hong Kong. The Canadian Journal of Statistics 37: 645–658; 2009 © 2009 Statistical Society of Canada     

SAVE: Robust or not?

Abstract

Sliced average variance estimation (SAVE) is one of the best methods for estimating central dimension-reduction subspace in semi parametric regression models when covariates are normal. In recent days SAVE is being used to analyze DNA microarray data especially in tumor classification but most important drawback is normality of covariates. In this article, the asymptotic behavior of estimates of CDR space under varying slice size is studied through simulation studies when covariates are non normal but follows linearity condition as well as when covariates slightly perturbed from normal distribution and we observed that serious error may occur under violation normality assumption.     

Wavelet estimation in time-varying coefficient time series models with measurement errors

The article studies a time-varying coefficient time series model in which some of the covariates are measured with additive errors. In order to overcome the bias of estimator of the coefficient functions when measurement errors are ignored, we propose a modified least squares estimator based on wavelet procedures. The advantage of the wavelet method is to avoid the restrictive smoothness requirement for varying-coefficient functions of the traditional smoothing approaches, such as kernel and local polynomial methods. The asymptotic properties of the proposed wavelet estimators are established under the α-mixing conditions and without specifying the error distribution. These results can be used to make asymptotically valid statistical inference.     

Fast accelerated failure time modeling for case-cohort data

Semiparametric accelerated failure time (AFT) models directly relate the expected failure times to covariates and are a useful alternative to models that work on the hazard function or the survival function. For case-cohort data, much less development has been done with AFT models. In addition to the missing covariates outside of the sub-cohort in controls, challenges from AFT model inferences with full cohort are retained. The regression parameter estimator is hard to compute because the most widely used rank-based estimating equations are not smooth. Further, its variance depends on the unspecified error distribution, and most methods rely on computationally intensive bootstrap to estimate it. We propose fast rank-based inference procedures for AFT models, applying recent methodological advances to the context of case-cohort data. Parameters are estimated with an induced smoothing approach that smooths the estimating functions and facilitates the numerical solution. Variance estimators are obtained through efficient resampling methods for nonsmooth estimating functions that avoids full blown bootstrap. Simulation studies suggest that the recommended procedure provides fast and valid inferences among several competing procedures. Application to a tumor study demonstrates the utility of the proposed method in routine data analysis.     

Locally Efficient Semiparametric Estimators for Proportional Hazards Models with Measurement Error

We propose a new class of semiparametric estimators for proportional hazards models in the presence of measurement error in the covariates, where the baseline hazard function, the hazard function for the censoring time, and the distribution of the true covariates are considered as unknown infinite dimensional parameters. We estimate the model components by solving estimating equations based on the semiparametric efficient scores under a sequence of restricted models where the logarithm of the hazard functions are approximated by reduced rank regression splines. The proposed estimators are locally efficient in the sense that the estimators are semiparametrically efficient if the distribution of the error‐prone covariates is specified correctly and are still consistent and asymptotically normal if the distribution is misspecified. Our simulation studies show that the proposed estimators have smaller biases and variances than competing methods. We further illustrate the new method with a real application in an HIV clinical trial.     

Analyzing panel count data with a dependent observation process and a terminal event

Panel count data occur in many fields and a number of approaches have been developed. However, most of these approaches are for situations where there is no terminal event and the observation process is independent of the underlying recurrent event process unconditionally or conditional on the covariates. In this paper, we discuss a more general situation where the observation process is informative and there exists a terminal event which precludes further occurrence of the recurrent events of interest. For the analysis, a semiparametric transformation model is presented for the mean function of the underlying recurrent event process among survivors. To estimate the regression parameters, an estimating equation approach is proposed in which an inverse survival probability weighting technique is used. The asymptotic distribution of the proposed estimates is provided. Simulation studies are conducted and suggest that the proposed approach works well for practical situations. An illustrative example is provided. The Canadian Journal of Statistics 41: 174–191; 2013 © 2012 Statistical Society of Canada