Approximate Bayesian computational methods

Approximate Bayesian Computation (ABC) methods, also known as likelihood-free techniques, have appeared in the past ten years as the most satisfactory approach to intractable likelihood problems, first in genetics then in a broader spectrum of applications. However, these methods suffer to some degree from calibration difficulties that make them rather volatile in their implementation and thus render them suspicious to the users of more traditional Monte Carlo methods. In this survey, we study the various improvements and extensions brought on the original ABC algorithm in recent years.     

贝叶斯统计推断及其主要进展

贝叶斯统计推断作为现代统计分析方法的重要内容,对于统计学理论的发展具有里程碑的作用。深入总结其研究的主要进展,具有重要的现实意义。在查阅国内外重要学术研究资料的基础上,从贝叶斯统计推断的思想、与古典统计的研究思路比较和贝叶斯统计推断研究的主要进展三个方面作了综述与介绍,力图达到认识贝叶斯统计推断及其研究现状的目的。     

A Bayesian approach to sequential analysis in post‐licensure vaccine safety surveillance

With rapid development of computing technology, Bayesian statistics have increasingly gained more attention in various areas of public health. However, the full potential of Bayesian sequential methods applied to vaccine safety surveillance has not yet been realized, despite acknowledged practical benefits and philosophical advantages of Bayesian statistics. In this paper, we describe how sequential analysis can be performed in a Bayesian paradigm in the field of vaccine safety. We compared the performance of the frequentist sequential method, specifically, Maximized Sequential Probability Ratio Test (MaxSPRT), and a Bayesian sequential method using simulations and a real world vaccine safety example. The performance is evaluated using three metrics: false positive rate, false negative rate, and average earliest time to signal. Depending on the background rate of adverse events, the Bayesian sequential method could significantly improve the false negative rate and decrease the earliest time to signal. We consider the proposed Bayesian sequential approach to be a promising alternative for vaccine safety surveillance.     

Markov models and Bayesian methods in image analysis

Markov random field models and Bayesian methods have provided answers to various contemporary problems in image analysis. We give a very brief introduction to the topic. In particular, we highlight the use of Bayesian methods in classifying the image into different classes. Some other current developments are also described and their relationship with other chapters in this volume is indicated. Some future directions are also outlined.     

Bayesian Statistical Inference for Weighted Exponential Distribution

Exponential distribution has an extensive application in reliability. Introducing shape parameter to this distribution have produced various distribution functions. In their study in 2009, Gupta and Kundu brought another distribution function using Azzalini's method, which is applicable in reliability and named as weighted exponential (WE) distribution. The parameters of this distribution function have been recently estimated by the above two authors in classical statistics. In this paper, Bayesian estimates of the parameters are derived. To achieve this purpose we use Lindley's approximation method for the integrals that cannot be solved in closed form. Furthermore, a Gibbs sampling procedure is used to draw Markov chain Monte Carlo samples from the posterior distribution indirectly and then the Bayes estimates of parameters are derived. The estimation of reliability and hazard functions are also discussed. At the end of the paper, some comparisons between classical and Bayesian estimation methods are studied by using Monte Carlo simulation study. The simulation study incorporates complete and Type-II censored samples.     

Bayesian model selection using test statistics

Summary.  Existing Bayesian model selection procedures require the specification of prior distributions on the parameters appearing in every model in the selection set. In practice, this requirement limits the application of Bayesian model selection methodology. To overcome this limitation, we propose a new approach towards Bayesian model selection that uses classical test statistics to compute Bayes factors between possible models. In several test cases, our approach produces results that are similar to previously proposed Bayesian model selection and model averaging techniques in which prior distributions were carefully chosen. In addition to eliminating the requirement to specify complicated prior distributions, this method offers important computational and algorithmic advantages over existing simulation-based methods. Because it is easy to evaluate the operating characteristics of this procedure for a given sample size and specified number of covariates, our method facilitates the selection of hyperparameter values through prior-predictive simulation.     

Bayesian methods for analysing ringing data

A major recent development in statistics has been the use of fast computational methods of Markov chain Monte Carlo. These procedures allow Bayesian methods to be used in quite complex modelling situations. In this paper, we shall use a range of real data examples involving lapwings, shags, teal, dippers, and herring gulls, to illustrate the power and range of Bayesian techniques. The topics include: prior sensitivity; the use of reversible-jump MCMC for constructing model probabilities and comparing models, with particular reference to models with random effects; model-averaging; and the construction of Bayesian measures of goodness-of-fit. Throughout, there will be discussion of the practical aspects of the work - for instance explaining when and when not to use the BUGS package.     

Bayesian methods for analysing ringing data

A major recent development in statistics has been the use of fast computational methods of Markov chain Monte Carlo. These procedures allow Bayesian methods to be used in quite complex modelling situations. In this paper, we shall use a range of real data examples involving lapwings, shags, teal, dippers, and herring gulls, to illustrate the power and range of Bayesian techniques. The topics include: prior sensitivity; the use of reversible-jump MCMC for constructing model probabilities and comparing models, with particular reference to models with random effects; model-averaging; and the construction of Bayesian measures of goodness-of-fit. Throughout, there will be discussion of the practical aspects of the work - for instance explaining when and when not to use the BUGS package.     

Bayesian structural equation modeling for the health index

There are many factors which could influence the level of health of an individual. These factors are interactive and their overall effects on health are usually measured by an index which is called as health index. The health index could also be used as an indicator to describe the health level of a community. Since the health index is important, many research have been done to study its determinant. The main purpose of this study is to model the health index of an individual based on classical structural equation modeling (SEM) and Bayesian SEM. For estimation of the parameters in the measurement and structural equation models, the classical SEM applies the robust-weighted least-square approach, while the Bayesian SEM implements the Gibbs sampler algorithm. The Bayesian SEM approach allows the user to use the prior information for updating the current information on the parameter. Both methods are applied to the data gathered from a survey conducted in Hulu Langat, a district in Malaysia. Based on the classical and the Bayesian SEM, it is found that demographic status and lifestyle are significantly related to the health index. However, mental health has no significant relation to the health index.     

Teaching Elementary Bayesian Statistics with Real Applications in Science

University courses in elementary statistics are usually taught from a frequentist perspective. In this paper I suggest how such courses can be taught using a Bayesian approach, and I indicate why beginning students are well served by a Bayesian course. A principal focus of any good elementary course is the application of statistics to real and important scientific problems. The Bayesian approach fits neatly with a scientific focus. Bayesians take a larger view, and one not limited to data analysis. In particular, the Bayesian approach is subjective, and requires assessing prior probabilities. This requirement forces users to relate current experimental evidence to other available information–-including previous experiments of a related nature, where “related” is judged subjectively. I discuss difficulties faced by instructors and students in elementary Bayesian courses, and provide a sample syllabus for an elementary Bayesian course.     

Credit risk assessment with Bayesian model averaging

Many credit risk models are based on the selection of a single logistic regression model, on which to base parameter estimation. When many competing models are available, and without enough guidance from economical theory, model averaging represents an appealing alternative to the selection of single models. Despite model averaging approaches have been present in statistics for many years, only recently they are starting to receive attention in economics and finance applications. This contribution shows how Bayesian model averaging can be applied to credit risk estimation, a research area that has received a great deal of attention recently, especially in the light of the global financial crisis of the last few years and the correlated attempts to regulate international finance. The paper considers the use of logistic regression models under the Bayesian Model Averaging paradigm. We argue that Bayesian model averaging is not only more correct from a theoretical viewpoint, but also slightly superior, in terms of predictive performance, with respect to single selected models.     

25 years of Bayesian methods in the pharmaceutical industry: a personal, statistical bummel

Twenty-five years ago the use of Bayesian methods in Pharmaceutical R&D was non-existent. Today that is no longer true. In this paper I describe my own personal journey along the road of discovery of Bayesian methods to routine use in the pharmaceutical industry.     

A Bayesian approach of joint models for clustered zero-inflated count data with skewness and measurement errors

Count data with excess zeros are widely encountered in the fields of biomedical, medical, public health and social survey, etc. Zero-inflated Poisson (ZIP) regression models with mixed effects are useful tools for analyzing such data, in which covariates are usually incorporated in the model to explain inter-subject variation and normal distribution is assumed for both random effects and random errors. However, in many practical applications, such assumptions may be violated as the data often exhibit skewness and some covariates may be measured with measurement errors. In this paper, we deal with these issues simultaneously by developing a Bayesian joint hierarchical modeling approach. Specifically, by treating intercepts and slopes in logistic and Poisson regression as random, a flexible two-level ZIP regression model is proposed, where a covariate process with measurement errors is established and a skew-t-distribution is considered for both random errors and random effects. Under the Bayesian framework, model selection is carried out using deviance information criterion (DIC) and a goodness-of-fit statistics is also developed for assessing the plausibility of the posited model. The main advantage of our method is that it allows for more robustness and correctness for investigating heterogeneity from different levels, while accommodating the skewness and measurement errors simultaneously. An application to Shanghai Youth Fitness Survey is used as an illustrate example. Through this real example, it is showed that our approach is of interest and usefulness for applications.     

Bayesian variable window scan statistics

In this article two-stage hierarchical Bayesian models are used for the observed occurrences of events in a rectangular region. Two Bayesian variable window scan statistics are introduced to test the null hypothesis that the observed events follow a specified two-stage hierarchical model vs an alternative that indicates a local increase in the average number of observed events in a subregion (clustering). Both procedures are based on a sequence of Bayes factors and their p$p$-values that have been generated via simulation of posterior samples of the parameters, under the null and alternative hypotheses. The posterior samples of the parameters have been generated by employing Gibbs sampling via introduction of auxiliary variables. Numerical results are presented to evaluate the performance of these variable window scan statistics.     

A Bayesian approach to the statistical analysis of device preference studies

Drug delivery devices are required to have excellent technical specifications to deliver drugs accurately, and in addition, the devices should provide a satisfactory experience to patients because this can have a direct effect on drug compliance. To compare patients' experience with two devices, cross-over studies with patient-reported outcomes (PRO) as response variables are often used. Because of the strength of cross-over designs, each subject can directly compare the two devices by using the PRO variables, and variables indicating preference (preferring A, preferring B, or no preference) can be easily derived. Traditionally, methods based on frequentist statistics can be used to analyze such preference data, but there are some limitations for the frequentist methods. Recently, Bayesian methods are considered an acceptable method by the US Food and Drug Administration to design and analyze device studies. In this paper, we propose a Bayesian statistical method to analyze the data from preference trials. We demonstrate that the new Bayesian estimator enjoys some optimal properties versus the frequentist estimator.     

Dynamic Bayesian analysis for irregularly and incompletely observed contingency tables

Pre-election surveys are usually conducted several times to forecast election results before the actual voting. It is common that each survey includes a substantial number of non-responses and that the successive survey results are seen as a stochastic multinomial time series evolving over time. We propose a dynamic Bayesian model to examine how multinomial time series evolve over time for the irregularly observed contingency tables and to determine how sensitively the dynamic structure reacts to an unexpected event, such as a candidate scandal. Further, we test whether non-responses are non-ignorable to determine if non-responses need to be imputed for better forecast. We also suggest a Bayesian method that overcomes the boundary solution problem and show that the proposed method outperforms the previous Bayesian methods. Our dynamic Bayesian model is applied to the two pre-election surveys for the 2007 Korea presidential candidate election and for the 1998 Ohio general election.     

Bayesian single-arm phase II trial designs with time-to-event endpoints

For the cancer clinical trials with immunotherapy and molecularly targeted therapy, time-to-event endpoint is often a desired endpoint. In this paper, we present an event-driven approach for Bayesian one-stage and two-stage single-arm phase II trial designs. Two versions of Bayesian one-stage designs were proposed with executable algorithms and meanwhile, we also develop theoretical relationships between the frequentist and Bayesian designs. These findings help investigators who want to design a trial using Bayesian approach have an explicit understanding of how the frequentist properties can be achieved. Moreover, the proposed Bayesian designs using the exact posterior distributions accommodate the single-arm phase II trials with small sample sizes. We also proposed an optimal two-stage approach, which can be regarded as an extension of Simon's two-stage design with the time-to-event endpoint. Comprehensive simulations were conducted to explore the frequentist properties of the proposed Bayesian designs and an R package BayesDesign can be assessed via R CRAN for convenient use of the proposed methods.     

Bayesian composite quantile regression for linear mixed-effects models

Longitudinal data are commonly modeled with the normal mixed-effects models. Most modeling methods are based on traditional mean regression, which results in non robust estimation when suffering extreme values or outliers. Median regression is also not a best choice to estimation especially for non normal errors. Compared to conventional modeling methods, composite quantile regression can provide robust estimation results even for non normal errors. In this paper, based on a so-called pseudo composite asymmetric Laplace distribution (PCALD), we develop a Bayesian treatment to composite quantile regression for mixed-effects models. Furthermore, with the location-scale mixture representation of the PCALD, we establish a Bayesian hierarchical model and achieve the posterior inference of all unknown parameters and latent variables using Markov Chain Monte Carlo (MCMC) method. Finally, this newly developed procedure is illustrated by some Monte Carlo simulations and a case analysis of HIV/AIDS clinical data set.     

A hierarchical Bayesian model for binary data incorporating selection bias

We consider a Bayesian nonignorable model to accommodate a nonignorable selection mechanism for predicting small area proportions. Our main objective is to extend a model on selection bias in a previously published paper, coauthored by four authors, to accommodate small areas. These authors assume that the survey weights (or their reciprocals that we also call selection probabilities) are available, but there is no simple relation between the binary responses and the selection probabilities. To capture the nonignorable selection bias within each area, they assume that the binary responses and the selection probabilities are correlated. To accommodate the small areas, we extend their model to a hierarchical Bayesian nonignorable model and we use Markov chain Monte Carlo methods to fit it. We illustrate our methodology using a numerical example obtained from data on activity limitation in the U.S. National Health Interview Survey. We also perform a simulation study to assess the effect of the correlation between the binary responses and the selection probabilities.