Assessing Placebo Response Using Bayesian Hierarchical Survival Models

The National Institute of Mental Health (NIMH) Collaborative Study of Long-Term Maintenance Drug Therapy in Recurrent Affective Illness was a multicenter randomized controlled clinical trial designed to determine the efficacy of a pharmacotherapy for the prevention of the recurrence of unipolar affective disorders. The outcome of interest in this study was the time until the recurrence of a depressive episode. The data show much heterogeneity between centers for the placebo group. The aim of this paper is to use Bayesian hierarchical survival models to investigate the heterogeneity of placebo effects among centers in the NIMH study. This heterogeneity is explored in terms of the marginal posterior distributions of parameters of interest and predictive distributions of future observations. The Gibbs sampling algorithm is used to approximate posterior and predictive distributions. Sensitivity of results to the assumption of a constant hazard survival distribution at the first stage of the hierarchy is examined by comparing results derived from a two component exponential mixture and a two component exponential changepoint model to the results derived from an exponential model. The second component of the mixture and changepoint models is assumed to be a surviving fraction. For each of these first stage parametric models sensitivity of results to second stage prior distributions is also examined. This revised version was published online in July 2006 with corrections to the Cover Date.     

Evaluating the ROC performance of markers for future events

Receiver operating characteristic (ROC) curves play a central role in the evaluation of biomarkers and tests for disease diagnosis. Predictors for event time outcomes can also be evaluated with ROC curves, but the time lag between marker measurement and event time must be acknowledged. We discuss different definitions of time-dependent ROC curves in the context of real applications. Several approaches have been proposed for estimation. We contrast retrospective versus prospective methods in regards to assumptions and flexibility, including their capacities to incorporate censored data, competing risks and different sampling schemes. Applications to two datasets are presented.     

A Bayesian method for estimating the accuracy of recalled depression

Summary.  We develop a Bayesian method that allows us to compare weekly depression states recalled for a 3-month period to cross-sectionally assessed measurements of current depression assessed during randomly timed phone interviews. Using these data, we examine the accuracy of recalled depression by linking a spline model for recalled depression and a logistic model for current depression. The logistic model includes the model-based probability of depression based on recall as a covariate and covariates potentially related to the accuracy of recall. The model that we propose allows variability in both measures and can be modified to examine general relationships between longitudinal and cross-sectional measurements.     

A Note on Bayesian Prediction from the Regression Model with Informative Priors

This paper considers the problem of undertaking a predictive analysis from a regression model when proper conjugate priors are used. It shows how the prior information can be incorporated as a virtual experiment by augmenting the data, and it derives expressions for both the prior and the posterior predictive densities. The results obtained are of considerable practical importance to practitioners of Bayesian regression methods.     

On selection of a suitable prior for the posterior analysis of censored mixture of Topp Leone distribution

The paper aims to select a suitable prior for the Bayesian analysis of the two-component mixture of the Topp Leone model under doubly censored samples and left censored samples for the first component and right censored samples for the second component. The posterior analysis has been carried out under the assumption of a class of informative and noninformative priors using a couple of loss functions. The comparison among the different Bayes estimators has been made under a simulation study and a real life example. The model comparison criterion has been used to select a suitable prior for the Bayesian analysis. The hazard rate of the Topp Leone mixture model has been compared for a range of parametric values.     

Approximate Bayesian analysis of doubly censored samples from mixture of two Weibull distributions

The purpose of the paper is to estimate the parameters of the two-component mixture of Weibull distribution under doubly censored samples using Bayesian approach. The choice of Weibull distribution is made due to its (i) capability to model failure time data from engineering, medical and biological sciences (ii) added advantages over the well-known lifetime distributions such as exponential, Raleigh, lognormal and gamma distribution in terms of flexibility, increasing and decreasing hazard rate and closed-form distribution function and hazard rate. The proposed two-component mixture of Weibull distribution is even more flexible than its conventional form. However, the estimation of the parameters from the proposed mixture is more complex. Further, we have assumed couple of loss functions under non informative prior for the Bayesian analysis of the parameters from the mixture model. As the resultant Bayes estimators and associated posterior risks cannot be derived in the closed form, we have used the importance sampling and Lindley’s approximation to obtain the approximate estimates for the parameters of the mixture model. The comparison between the performances of approximation techniques has been made on the basis of simulation study and real-life data analysis. The importance sampling is found to be better than Lindley’s approximation as it gives better estimation for shape and mixing parameters of the mixture model and computations under this technique are much easier/shorter than those under Lindley’s approximation.     

Augmented mixed beta regression models with skew-normal independent distributions: Bayesian analysis of labor force data

Abstract

Augmented mixed beta regression models are suitable choices for modeling continuous response variables on the closed interval [0, 1]. The random eeceeects in these models are typically assumed to be normally distributed, but this assumption is frequently violated in some applied studies. In this paper, an augmented mixed beta regression model with skew-normal independent distribution for random effects are used. Next, we adopt a Bayesian approach for parameter estimation using the MCMC algorithm. The methods are then evaluated using some intensive simulation studies. Finally, the proposed models have applied to analyze a dataset from an Iranian Labor Force Survey.     

A Comparative Study of Approaches for Predicting Prostate Cancer from Longitudinal Data

Disease prediction based on longitudinal data can be done using various modeling approaches. Alternative approaches are compared using data from a longitudinal study to predict the onset of disease. The data are modeled using linear mixed-effects models. Posterior probabilities of group membership are computed starting with the first observation and sequentially adding observations until the subject is classified as developing the disease or until the last measurement is used. Individuals are classified by computing posterior probabilities using the marginal distributions of the mixed-effects models, the conditional distributions (conditional on the group-specific random effects), and the distributions of the random effects.     

A Bayesian cluster analysis of election results

A Bayesian cluster analysis for the results of an election based on multinomial mixture models is proposed. The number of clusters is chosen based on the careful comparison of the results with predictive simulations from the models, and by checking whether models capture most of the spatial dependence in the results. By implementing the analysis on five recent elections in Barcelona, the reader is walked through the choice of the best statistics and graphical displays to help chose a model and present the results. Even though the models do not use any information about the location of the areas in which the results are broken into, in the example they uncover a four-cluster structure with a strong spatial dependence, that is very stable over time and relates to the demographic composition.     

Bayesian projection of the acquired immune deficiency syndrome epidemic

Short-term projections of the acquired immune deficiency syndrome (AIDS) epidemic in England and Wales have been regularly updated since the publication of the Cox report in 1988. The key approach for those updates has been the back-calculation method, which has been informally adapted to acknowledge various sources of uncertainty as well as to incorporate increasingly available information on the spread of the human immunodeficiency virus (HIV) in the population. We propose a Bayesian formulation of the back-calculation method which allows a formal treatment of uncertainty and the inclusion of extra information, within a single coherent composite model. Estimation of the variably dimensioned model is carried out by using reversible-jump Markov chain Monte Carlo methods. Application of the model to data for homosexual and bisexual males in England and Wales is presented, and the role of the various sources of information and model assumptions is appraised. Our results show a massive peak in HIV infections around 1983 and suggest that the incidence of AIDS has now reached a plateau, although there is still substantial uncertainty about the future.     

Nonparametric Estimation and Hypothesis Testing on the Partial Area Under Receiver Operating Characteristic Curves

ABSTRACT

The area under a receiver operating characteristic curve is a useful index of the accuracy of a diagnostic test. When the diagnostic ability of a new biomarker is of interest only in a certain range of specificity, the partial area under the curve becomes desirable. In this article, we extend Bamber's (1975 Bamber , D. ( 1975 ). The area above the ordinal dominance graph and the area below the receiver operating characteristics graph. J. Math. Psychol. 12 : 387 – 415 . [CSA] [Crossref], [Web of Science ®] , [Google Scholar]) results and show that the partial area under a receiver operating characteristic curve is the probability of a constrained stochastic ordering. We then construct a ‘weighted’ Mann-Whitney statistic as an estimator of the partial area and investigate its statistical properties. A testing procedure is also developed to compare partial area under two receiver operating characteristic curves. The methods are exemplified with data from biomarkers associated with coronary heart disease.     

Bayesian analysis of screening data: Application to AIDS in blood donors

The rapid increase in the number of AIDS cases during the 1980s and the spread of the disease from the high-risk groups into the general population has created widespread concern. In particular, assessing the accuracy of the screening tests used to detect antibodies to the HIV (AIDS) virus in donated blood and determining the prevalance of the disease in the population are fundamental statistical problems. Because the prevalence of AIDS varies widely by geographic region and data on the number of infected blood donors are published regularly, Bayesian methods, which utilize prior results and update them as new data become available, are quite useful. In this paper we develop a Bayesian procedure for estimating the prevalence of a rare disease, the sensitivity and specificity of the screening tests, and the predictive value of a positive or negative screening test. We apply the procedure to data on blood donors in the United States and in Canada. Our results augment those described in Gastwirth (1987) using classical methods. Indeed, we show that the inclusion of sound prior knowledge into the statistical analysis does not yield sufficiently precise estimates of the predictive value of a positive test. Hence confirmatory testing is needed to obtain reliable estimates. The emphasis of the Bayesian predictive paradigm on prediction intervals for future data yields a valuable insight. We demonstrate that using them might have detected a decline in the specificity of the most frequently used screening test earlier than it apparently was.     

Practical Bayesian estimation of a finite beta mixture through gibbs sampling and its applications

This paper deals with a Bayesian analysis of a finite Beta mixture model. We present approximation method to evaluate the posterior distribution and Bayes estimators by Gibbs sampling, relying on the missing data structure of the mixture model. Experimental results concern contextual and non-contextual evaluations. The non-contextual evaluation is based on synthetic histograms, while the contextual one model the class-conditional densities of pattern-recognition data sets. The Beta mixture is also applied to estimate the parameters of SAR images histograms.     

Probabilistic sensitivity analysis of complex models: a Bayesian approach

Summary.  In many areas of science and technology, mathematical models are built to simulate complex real world phenomena. Such models are typically implemented in large computer programs and are also very complex, such that the way that the model responds to changes in its inputs is not transparent. Sensitivity analysis is concerned with understanding how changes in the model inputs influence the outputs. This may be motivated simply by a wish to understand the implications of a complex model but often arises because there is uncertainty about the true values of the inputs that should be used for a particular application. A broad range of measures have been advocated in the literature to quantify and describe the sensitivity of a model's output to variation in its inputs. In practice the most commonly used measures are those that are based on formulating uncertainty in the model inputs by a joint probability distribution and then analysing the induced uncertainty in outputs, an approach which is known as probabilistic sensitivity analysis. We present a Bayesian framework which unifies the various tools of prob- abilistic sensitivity analysis. The Bayesian approach is computationally highly efficient. It allows effective sensitivity analysis to be achieved by using far smaller numbers of model runs than standard Monte Carlo methods. Furthermore, all measures of interest may be computed from a single set of runs.     

Adjusting ROC curves for covariates in the presence of verification bias

The ROC (receiver operating characteristic) curve is frequently used for describing effectiveness of a diagnostic marker or test. Classical estimation of the ROC curve uses independent identically distributed samples taken randomly from the healthy and diseased populations. Frequently not all subjects undergo a definitive gold standard assessment of disease status (verification). Estimation of the ROC curve based on data only from subjects with verified disease status may be badly biased (verification bias). In this work we investigate the properties of the doubly robust (DR) method for estimating the ROC curve adjusted for covariates (ROC regression) under verification bias. We develop the estimator's asymptotic distribution and examine its finite sample size properties via a simulation study. We apply this procedure to fingerstick postprandial blood glucose measurement data adjusting for age.     

Assessing accuracy of a continuous screening test in the presence of verification bias

Summary.  In studies to assess the accuracy of a screening test, often definitive disease assessment is too invasive or expensive to be ascertained on all the study subjects. Although it may be more ethical or cost effective to ascertain the true disease status with a higher rate in study subjects where the screening test or additional information is suggestive of disease, estimates of accuracy can be biased in a study with such a design. This bias is known as verification bias. Verification bias correction methods that accommodate screening tests with binary or ordinal responses have been developed; however, no verification bias correction methods exist for tests with continuous results. We propose and compare imputation and reweighting bias-corrected estimators of true and false positive rates, receiver operating characteristic curves and area under the receiver operating characteristic curve for continuous tests. Distribution theory and simulation studies are used to compare the proposed estimators with respect to bias, relative efficiency and robustness to model misspecification. The bias correction estimators proposed are applied to data from a study of screening tests for neonatal hearing loss.     

A gamma-mixture class of distributions with Bayesian application

In this article, a subjective Bayesian approach is followed to derive estimators for the parameters of the normal model by assuming a gamma-mixture class of prior distributions, which includes the gamma and the noncentral gamma as special cases. An innovative approach is proposed to find the analytical expression of the posterior density function when a complicated prior structure is ensued. The simulation studies and a real dataset illustrate the modeling advantages of this proposed prior and support some of the findings.     

Gibbs sampling method for the Bayesian adaptive elastic net

This article considers the adaptive elastic net estimator for regularized mean regression from a Bayesian perspective. Representing the Laplace distribution as a mixture of Bartlett–Fejer kernels with a Gamma mixing density, a Gibbs sampling algorithm for the adaptive elastic net is developed. By introducing slice variables, it is shown that the mixture representation provides a Gibbs sampler that can be accomplished by sampling from either truncated normal or truncated Gamma distribution. The proposed method is illustrated using several simulation studies and analyzing a real dataset. Both simulation studies and real data analysis indicate that the proposed approach performs well.     

New improvements in the use of dependence measures for sensitivity analysis and screening

ABSTRACT

Physical phenomena are commonly modelled by time consuming numerical simulators, function of many uncertain parameters whose influences can be measured via a global sensitivity analysis. The usual variance-based indices require too many simulations, especially as the inputs are numerous. To address this limitation, we consider recent advances in dependence measures, focusing on the distance correlation and the Hilbert–Schmidt independence criterion. We study and use these indices for a screening purpose. Numerical tests reveal differences between variance-based indices and dependence measures. Then, two approaches are proposed to use the latter for a screening purpose. The first approach uses independence tests, with existing asymptotic versions and spectral extensions; bootstrap versions are also proposed. The second considers a linear model with dependence measures, coupled to a bootstrap selection method or a Lasso penalization. Numerical experiments show their potential in the presence of many non-influential inputs and give successful results for a nuclear reliability application.