A Bayesian semiparametric accelerated failure time model for arbitrarily censored data with covariates subject to measurement error

A flexible Bayesian semiparametric accelerated failure time (AFT) model is proposed for analyzing arbitrarily censored survival data with covariates subject to measurement error. Specifically, the baseline error distribution in the AFT model is nonparametrically modeled as a Dirichlet process mixture of normals. Classical measurement error models are imposed for covariates subject to measurement error. An efficient and easy-to-implement Gibbs sampler, based on the stick-breaking formulation of the Dirichlet process combined with the techniques of retrospective and slice sampling, is developed for the posterior calculation. An extensive simulation study is conducted to illustrate the advantages of our approach.     

Adaptive sampling for Bayesian geospatial models

Bayesian hierarchical modeling with Gaussian process random effects provides a popular approach for analyzing point-referenced spatial data. For large spatial data sets, however, generic posterior sampling is infeasible due to the extremely high computational burden in decomposing the spatial correlation matrix. In this paper, we propose an efficient algorithm—the adaptive griddy Gibbs (AGG) algorithm—to address the computational issues with large spatial data sets. The proposed algorithm dramatically reduces the computational complexity. We show theoretically that the proposed method can approximate the real posterior distribution accurately. The sufficient number of grid points for a required accuracy has also been derived. We compare the performance of AGG with that of the state-of-the-art methods in simulation studies. Finally, we apply AGG to spatially indexed data concerning building energy consumption.     

Doubly robust estimation of partially linear models for longitudinal data with dropouts and measurement error in covariates

In longitudinal studies, missing responses and mismeasured covariates are commonly seen due to the data collection process. Without cautiousness in data analysis, inferences from the standard statistical approaches may lead to wrong conclusions. In order to improve the estimation for longitudinal data analysis, a doubly robust estimation method for partially linear models, which can simultaneously account for the missing responses and mismeasured covariates, is proposed. Imprecisions of covariates are corrected by taking advantage of the independence between replicate measurement errors, and missing responses are handled by the doubly robust estimation under the mechanism of missing at random. The asymptotic properties of the proposed estimators are established under regularity conditions, and simulation studies demonstrate desired properties. Finally, the proposed method is applied to data from the Lifestyle Education for Activity and Nutrition study.     

Empirical Bayes estimation in finite population sampling under functional measurement error models

The paper considers simultaneous estimation of finite population means for several strata. A model-based approach is taken, where the covariates in the super-population model are subject to measurement errors. Empirical Bayes (EB) estimators of the strata means are developed and an asymptotic expression for the MSE of the EB estimators is provided. It is shown that the proposed EB estimators are “first order optimal” in the sense of Robbins [1956. An empirical Bayes approach to statistics. In: Proceedings of the Third Berkeley Symposium on Mathematical Statistics and Probability, vol. 1, University of California Press, Berkeley, pp. 157–164], while the regular EB estimators which ignore the measurement error are not.     

Bayesian analysis of bivariate competing risks models with covariates

Bivariate exponential models have often been used for the analysis of competing risks data involving two correlated risk components. Competing risks data consist only of the time to failure and cause of failure. In situations where there is positive probability of simultaneous failure, possibly the most widely used model is the Marshall–Olkin (J. Amer. Statist. Assoc. 62 (1967) 30) bivariate lifetime model. This distribution is not absolutely continuous as it involves a singularity component. However, the likelihood function based on the competing risks data is then identifiable, and any inference, Bayesian or frequentist, can be carried out in a straightforward manner. For the analysis of absolutely continuous bivariate exponential models, standard approaches often run into difficulty due to the lack of a fully identifiable likelihood (Basu and Ghosh; Commun. Statist. Theory Methods 9 (1980) 1515). To overcome the nonidentifiability, the usual frequentist approach is based on an integrated likelihood. Such an approach is implicit in Wada et al. (Calcutta Statist. Assoc. Bull. 46 (1996) 197) who proved some related asymptotic results. We offer in this paper an alternative Bayesian approach. Since systematic prior elicitation is often difficult, the present study focuses on Bayesian analysis with noninformative priors. It turns out that with an appropriate reparameterization, standard noninformative priors such as Jeffreys’ prior and its variants can be applied directly even though the likelihood is not fully identifiable. Two noninformative priors are developed that consist of Laplace's prior for nonidentifiable parameters and Laplace's and Jeffreys's priors for identifiable parameters. The resulting Bayesian procedures possess some frequentist optimality properties as well. Finally, these Bayesian methods are illustrated with analyses of a data set originating out of a lung cancer clinical trial conducted by the Eastern Cooperative Oncology Group.     

Ultrahigh-dimensional sufficient dimension reduction for censored data with measurement error in covariates

In this paper, we consider the ultrahigh-dimensional sufficient dimension reduction (SDR) for censored data and measurement error in covariates. We first propose the feature screening procedure based on censored data and the covariates subject to measurement error. With the suitable correction of mismeasurement, the error-contaminated variables detected by the proposed feature screening procedure are the same as the truly important variables. Based on the selected active variables, we develop the SDR method to estimate the central subspace and the structural dimension with both censored data and measurement error incorporated. The theoretical results of the proposed method are established. Simulation studies are reported to assess the performance of the proposed method. The proposed method is implemented to NKI breast cancer data.     

Bayesian methods for generalized linear models with covariates missing at random

The authors propose methods for Bayesian inference for generalized linear models with missing covariate data. They specify a parametric distribution for the covariates that is written as a sequence of one‐dimensional conditional distributions. They propose an informative class of joint prior distributions for the regression coefficients and the parameters arising from the covariate distributions. They examine the properties of the proposed prior and resulting posterior distributions. They also present a Bayesian criterion for comparing various models, and a calibration is derived for it. A detailed simulation is conducted and two real data sets are examined to demonstrate the methodology.     

A Bayesian predictive inference for small area means incorporating covariates and sampling weights

The main goal in small area estimation is to use models to ‘borrow strength’ from the ensemble because the direct estimates of small area parameters are generally unreliable. However, model-based estimates from the small areas do not usually match the value of the single estimate for the large area. Benchmarking is done by applying a constraint, internally or externally, to ensure that the ‘total’ of the small areas matches the ‘grand total’. This is particularly useful because it is difficult to check model assumptions owing to the sparseness of the data. We use a Bayesian nested error regression model, which incorporates unit-level covariates and sampling weights, to develop a method to internally benchmark the finite population means of small areas. We use two examples to illustrate our method. We also perform a simulation study to further assess the properties of our method.     

Exact and efficient Bayesian inference for multiple changepoint problems

We demonstrate how to perform direct simulation from the posterior distribution of a class of multiple changepoint models where the number of changepoints is unknown. The class of models assumes independence between the posterior distribution of the parameters associated with segments of data between successive changepoints. This approach is based on the use of recursions, and is related to work on product partition models. The computational complexity of the approach is quadratic in the number of observations, but an approximate version, which introduces negligible error, and whose computational cost is roughly linear in the number of observations, is also possible. Our approach can be useful, for example within an MCMC algorithm, even when the independence assumptions do not hold. We demonstrate our approach on coal-mining disaster data and on well-log data. Our method can cope with a range of models, and exact simulation from the posterior distribution is possible in a matter of minutes.     

Bayesian testing for independence of two categorical variables under two-stage cluster sampling with covariates

We consider Bayesian testing for independence of two categorical variables with covariates for a two-stage cluster sample. This is a difficult problem because we have a complex sample (i.e. cluster sample), not a simple random sample. Our approach is to convert the cluster sample with covariates into an equivalent simple random sample without covariates, which provides a surrogate of the original sample. Then, this surrogate sample is used to compute the Bayes factor to make an inference about independence. We apply our methodology to the data from the Trend in International Mathematics and Science Study [30] for fourth grade US students to assess the association between the mathematics and science scores represented as categorical variables. We show that if there is strong association between two categorical variables, there is no significant difference between the tests with and without the covariates. We also performed a simulation study to further understand the effect of covariates in various situations. We found that for borderline cases (moderate association between the two categorical variables), there are noticeable differences in the test with and without covariates.     

Mixture models in measurement error problems, with reference to epidemiological studies

Summary. The paper focuses on a Bayesian treatment of measurement error problems and on the question of the specification of the prior distribution of the unknown covariates. It presents a flexible semiparametric model for this distribution based on a mixture of normal distributions with an unknown number of components. Implementation of this prior model as part of a full Bayesian analysis of measurement error problems is described in classical set-ups that are encountered in epidemiological studies: logistic regression between unknown covariates and outcome, with a normal or log-normal error model and a validation group. The feasibility of this combined model is tested and its performance is demonstrated in a simulation study that includes an assessment of the influence of misspecification of the prior distribution of the unknown covariates and a comparison with the semiparametric maximum likelihood method of Roeder, Carroll and Lindsay. Finally, the methodology is illustrated on a data set on coronary heart disease and cholesterol levels in blood.     

Bayes and minimax estimators for two-stage sampling from a finite population under measurement error models

We consider Bayes and Minimax estimates of population mean in sampling from a finite population in two-stages using simple random sampling without replacement at each stage, when the true values of the characteristic cannot be observed but only the values mixed with some measurement errors are observed. Minimax values of sample sizes have been found in case of equal-sized clusters and equal-sized second stage samples.     

Exact Bayesian variable sampling plans for the exponential distribution with progressive hybrid censoring

From the exact distribution of the maximum likelihood estimator of the average lifetime based on progressive hybrid exponential censored sample, we derive an explicit expression for the Bayes risk of a sampling plan when a quadratic loss function is used. The simulated annealing algorithm is then used to determine the optimal sampling plan. Some optimal Bayes solutions under progressive hybrid and ordinary hybrid censoring schemes are presented to illustrate the effectiveness of the proposed method.     

Using the EM algorithm for Bayesian variable selection in logistic regression models with related covariates

We develop a Bayesian variable selection method for logistic regression models that can simultaneously accommodate qualitative covariates and interaction terms under various heredity constraints. We use expectation-maximization variable selection (EMVS) with a deterministic annealing variant as the platform for our method, due to its proven flexibility and efficiency. We propose a variance adjustment of the priors for the coefficients of qualitative covariates, which controls false-positive rates, and a flexible parameterization for interaction terms, which accommodates user-specified heredity constraints. This method can handle all pairwise interaction terms as well as a subset of specific interactions. Using simulation, we show that this method selects associated covariates better than the grouped LASSO and the LASSO with heredity constraints in various exploratory research scenarios encountered in epidemiological studies. We apply our method to identify genetic and non-genetic risk factors associated with smoking experimentation in a cohort of Mexican-heritage adolescents.     

Exact Bayesian inference for off-line change-point detection in tree-structured graphical models

We consider the problem of change-point detection in multivariate time-series. The multivariate distribution of the observations is supposed to follow a graphical model, whose graph and parameters are affected by abrupt changes throughout time. We demonstrate that it is possible to perform exact Bayesian inference whenever one considers a simple class of undirected graphs called spanning trees as possible structures. We are then able to integrate on the graph and segmentation spaces at the same time by combining classical dynamic programming with algebraic results pertaining to spanning trees. In particular, we show that quantities such as posterior distributions for change-points or posterior edge probabilities over time can efficiently be obtained. We illustrate our results on both synthetic and experimental data arising from biology and neuroscience.     

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].     

Correcting data for measurement error in generalized linear models

This paper discusses a general strategy for reducing measurement-error-induced bias in statistical models. It is assumed that the measurement error is unbiased with a known variance although no other distributional assumptions on the measurement-error are employed,

Using a preliminary fit of the model to the observed data, a transformation of the variable measured with error is estimated. The transformation is constructed so that the estimates obtained by refitting the model to the ‘corrected’ data have smaller bias,

Whereas the general strategy can be applied in a number of settings, this paper focuses on the problem of covariate measurement error in generalized linear models, Two estimators are derived and their effectiveness at reducing bias is demonstrated in a Monte Carlo study.