Estimation across multiple models with application to Bayesian computing and software development

Statistical models are sometimes incorporated into computer software for making predictions about future observations. When the computer model consists of a single statistical model this corresponds to estimation of a function of the model parameters. This paper is concerned with the case that the computer model implements multiple, individually-estimated statistical sub-models. This case frequently arises, for example, in models for medical decision making that derive parameter information from multiple clinical studies. We develop a method for calculating the posterior mean of a function of the parameter vectors of multiple statistical models that is easy to implement in computer software, has high asymptotic accuracy, and has a computational cost linear in the total number of model parameters. The formula is then used to derive a general result about posterior estimation across multiple models. The utility of the results is illustrated by application to clinical software that estimates the risk of fatal coronary disease in people with diabetes.     

Bayesian calibration of computer models

We consider prediction and uncertainty analysis for systems which are approximated using complex mathematical models. Such models, implemented as computer codes, are often generic in the sense that by a suitable choice of some of the model's input parameters the code can be used to predict the behaviour of the system in a variety of specific applications. However, in any specific application the values of necessary parameters may be unknown. In this case, physical observations of the system in the specific context are used to learn about the unknown parameters. The process of fitting the model to the observed data by adjusting the parameters is known as calibration. Calibration is typically effected by ad hoc fitting, and after calibration the model is used, with the fitted input values, to predict the future behaviour of the system. We present a Bayesian calibration technique which improves on this traditional approach in two respects. First, the predictions allow for all sources of uncertainty, including the remaining uncertainty over the fitted parameters. Second, they attempt to correct for any inadequacy of the model which is revealed by a discrepancy between the observed data and the model predictions from even the best-fitting parameter values. The method is illustrated by using data from a nuclear radiation release at Tomsk, and from a more complex simulated nuclear accident exercise.     

Bayesian inference for random coefficient dynamic panel data models

We develop a hierarchical Bayesian approach for inference in random coefficient dynamic panel data models. Our approach allows for the initial values of each unit's process to be correlated with the unit-specific coefficients. We impose a stationarity assumption for each unit's process by assuming that the unit-specific autoregressive coefficient is drawn from a logitnormal distribution. Our method is shown to have favorable properties compared to the mean group estimator in a Monte Carlo study. We apply our approach to analyze energy and protein intakes among individuals from the Philippines.     

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.     

On a theorem of Stein relating Bayesian and classical inferences in group models

Let a group G act on the sample space. This paper gives another proof of a theorem of Stein relating a group invariant family of posterior Bayesian probability regions to classical confidence regions when an appropriate prior is used. The example of the central multivariate normal distribution is discussed.     

Bayesian hierarchical models for linear networks

The purpose of this study is to highlight dangerous motorways via estimating the intensity of accidents and study its pattern across the UK motorway network. Two methods have been developed to achieve this aim. First, the motorway-specific intensity is estimated by using a homogeneous Poisson process. The heterogeneity across motorways is incorporated using two-level hierarchical models. The data structure is multilevel since each motorway consists of junctions that are joined by grouped segments. In the second method, the segment-specific intensity is estimated. The homogeneous Poisson process is used to model accident data within grouped segments but heterogeneity across grouped segments is incorporated using three-level hierarchical models. A Bayesian method via Markov Chain Monte Carlo is used to estimate the unknown parameters in the models and the sensitivity to the choice of priors is assessed. The performance of the proposed models is evaluated by a simulation study and an application to traffic accidents in 2016 on the UK motorway network. The deviance information criterion (DIC) and the widely applicable information criterion (WAIC) are employed to choose between models.     

Pareto Regression: A Bayesian Analysis

Abstract

In this article, a new model is presented that is based on the Pareto distribution of the second kind, when the location parameter depends on covariates as well as unobserved heterogeneity. Bayesian analysis of the model can be performed using Markov Chain Monte Carlo techniques. The new procedures are illustrated in the context of artificial data as well as international output data.     

Inference in hybrid Bayesian networks using dynamic discretization

We consider approximate inference in hybrid Bayesian Networks (BNs) and present a new iterative algorithm that efficiently combines dynamic discretization with robust propagation algorithms on junction trees. Our approach offers a significant extension to Bayesian Network theory and practice by offering a flexible way of modeling continuous nodes in BNs conditioned on complex configurations of evidence and intermixed with discrete nodes as both parents and children of continuous nodes. Our algorithm is implemented in a commercial Bayesian Network software package, AgenaRisk, which allows model construction and testing to be carried out easily. The results from the empirical trials clearly show how our software can deal effectively with different type of hybrid models containing elements of expert judgment as well as statistical inference. In particular, we show how the rapid convergence of the algorithm towards zones of high probability density, make robust inference analysis possible even in situations where, due to the lack of information in both prior and data, robust sampling becomes unfeasible.     

Nonparametric Applications of Bayesian Inference

This article evaluates the usefulness of a nonparametric approach to Bayesian inference by presenting two applications. Our first application considers an educational choice problem. We focus on obtaining a predictive distribution for earnings corresponding to various levels of schooling. This predictive distribution incorporates the parameter uncertainty, so that it is relevant for decision making under uncertainty in the expected utility framework of microeconomics. The second application is to quantile regression. Our point here is to examine the potential of the nonparametric framework to provide inferences without relying on asymptotic approximations. Unlike in the first application, the standard asymptotic normal approximation turns out not to be a good guide.     

Hybrid Bayesian inference on HIV viral dynamic models

Modelling of HIV dynamics in AIDS research has greatly improved our understanding of the pathogenesis of HIV-1 infection and guided for the treatment of AIDS patients and evaluation of antiretroviral therapies. Some of the model parameters may have practical meanings with prior knowledge available, but others might not have prior knowledge. Incorporating priors can improve the statistical inference. Although there have been extensive Bayesian and frequentist estimation methods for the viral dynamic models, little work has been done on making simultaneous inference about the Bayesian and frequentist parameters. In this article, we propose a hybrid Bayesian inference approach for viral dynamic nonlinear mixed-effects models using the Bayesian frequentist hybrid theory developed in Yuan [Bayesian frequentist hybrid inference, Ann. Statist. 37 (2009), pp. 2458–2501]. Compared with frequentist inference in a real example and two simulation examples, the hybrid Bayesian approach is able to improve the inference accuracy without compromising the computational load.     

Bayesian two-stage optimal design for mixture models

In this paper, a Bayesian two-stage D–D optimal design for mixture experimental models under model uncertainty is developed. A Bayesian D-optimality criterion is used in the first stage to minimize the determinant of the posterior variances of the parameters. The second stage design is then generated according to an optimalityprocedure that collaborates with the improved model from the first stage data. The results show that a Bayesian two-stage D–D-optimal design for mixture experiments under model uncertainty is more efficient than both the Bayesian one-stage D-optimal design and the non-Bayesian one-stage D-optimal design in most situations. Furthermore, simulations are used to obtain a reasonable ratio of the sample sizes between the two stages.     

Testing a linear ARMA model against threshold-ARMA models: A Bayesian approach

We introduce a Bayesian approach to test linear autoregressive moving-average (ARMA) models against threshold autoregressive moving-average (TARMA) models. First, the marginal posterior densities of all parameters, including the threshold and delay, of a TARMA model are obtained by using Gibbs sampler with Metropolis–Hastings algorithm. Second, reversible-jump Markov chain Monte Carlo (RJMCMC) method is adopted to calculate the posterior probabilities for ARMA and TARMA models: Posterior evidence in favor of TARMA models indicates threshold nonlinearity. Finally, based on RJMCMC scheme and Akaike information criterion (AIC) or Bayesian information criterion (BIC), the procedure for modeling TARMA models is exploited. Simulation experiments and a real data example show that our method works well for distinguishing an ARMA from a TARMA model and for building TARMA models.     

Bayesian Approach to Multicentre Sparse Data

In a 2 × 2 contingency table, when the sample size is small, there may be a number of cells that contain few or no observations, usually referred to as sparse data. In such cases, a common recommendation in the conventional frequentist methods is adding a small constant to every cell of the observed table to find the estimates of the unknown parameters. However, this approach is based on asymptotic properties of the estimates and may work poorly for small samples. An alternative approach would be to use Bayesian methods in order to provide better insight into the problem of sparse data coupled with fewer centers, which would otherwise be difficult to carry out the analysis. In this article, an attempt has been made to use hierarchical Bayesian model to a multicenter data on the effect of a surgical treatment with standard foot care among leprosy patients with posterior tibial nerve damage which is summarized as seven 2 × 2 tables. Monte Carlo Markov Chain (MCMC) techniques are applied in estimating the parameters of interest under sparse data setup.     

A comparison of Bayesian model selection based on MCMC with an application to GARCH-type models

This paper presents a comprehensive review and comparison of five computational methods for Bayesian model selection, based on MCMC simulations from posterior model parameter distributions. We apply these methods to a well-known and important class of models in financial time series analysis, namely GARCH and GARCH-t models for conditional return distributions (assuming normal and t-distributions). We compare their performance with the more common maximum likelihood-based model selection for simulated and real market data. All five MCMC methods proved reliable in the simulation study, although differing in their computational demands. Results on simulated data also show that for large degrees of freedom (where the t-distribution becomes more similar to a normal one), Bayesian model selection results in better decisions in favor of the true model than maximum likelihood. Results on market data show the instability of the harmonic mean estimator and reliability of the advanced model selection methods.     

Multivariate stochastic volatility with Bayesian dynamic linear models

This paper develops a Bayesian procedure for estimation and forecasting of the volatility of multivariate time series. The foundation of this work is the matrix-variate dynamic linear model, for the volatility of which we adopt a multiplicative stochastic evolution, using Wishart and singular multivariate beta distributions. A diagonal matrix of discount factors is employed in order to discount the variances element by element and therefore allowing a flexible and pragmatic variance modelling approach. Diagnostic tests and sequential model monitoring are discussed in some detail. The proposed estimation theory is applied to a four-dimensional time series, comprising spot prices of aluminium, copper, lead and zinc of the London metal exchange. The empirical findings suggest that the proposed Bayesian procedure can be effectively applied to financial data, overcoming many of the disadvantages of existing volatility models.     

Following a moving target—Monte Carlo inference for dynamic Bayesian models

Markov chain Monte Carlo (MCMC) sampling is a numerically intensive simulation technique which has greatly improved the practicality of Bayesian inference and prediction. However, MCMC sampling is too slow to be of practical use in problems involving a large number of posterior (target) distributions, as in dynamic modelling and predictive model selection. Alternative simulation techniques for tracking moving target distributions, known as particle filters, which combine importance sampling, importance resampling and MCMC sampling, tend to suffer from a progressive degeneration as the target sequence evolves. We propose a new technique, based on these same simulation methodologies, which does not suffer from this progressive degeneration.     

Bayesian analysis of reliability in multicomponent stress-strength models

This paper provides a Bayesian treatment of the problem of inference about the reliability of a multicomponent stress-strength system which functions if s or more of k identical components simultaneously operate. All stresses and strengths are assumed to be independent, exponentially distributed random variables. Exact and approximate asymptotic posterior distributions for the reliability are derived, and the results are illustrated by a numerical example.     

Bayesian monitoring of local residual autocorrelations taking into account the run-length

This paper proposes new two-sided monitoring algorithms for detecting the presence of first order residual autocorrelations in Dynamic Normal Models. The methodology uses a Bayesian decision approach with loss function which takes into account the run-length of the process. The power and mean run-length of the proposed algorithms are analysed by Monte Carlo methods. The results obtained improve those corresponding to the monitoring algorithm for residual autocorrelations proposed in Gargallo and Salvador [2003. Monitoring residual autocorrelations in dynamic linear models. Comm. Statist. Simulation Comput. 32(4), 1079–1104.] with respect to the run-length, and also exhibit more homogeneous behaviour.     

A Bayesian approach for estimating antiviral efficacy in HIV dynamic models

The study of HIV dynamics is one of the most important developments in recent AIDS research. It has led to a new understanding of the pathogenesis of HIV infection. Although important findings in HIV dynamics have been published in prestigious scientific journals, the statistical methods for parameter estimation and model-fitting used in those papers appear surprisingly crude and have not been studied in more detail. For example, the unidentifiable parameters were simply imputed by mean estimates from previous studies, and important pharmacological/clinical factors were not considered in the modelling. In this paper, a viral dynamic model is developed to evaluate the effect of pharmacokinetic variation, drug resistance and adherence on antiviral responses. In the context of this model, we investigate a Bayesian modelling approach under a non-linear mixed-effects (NLME) model framework. In particular, our modelling strategy allows us to estimate time-varying antiviral efficacy of a regimen during the whole course of a treatment period by incorporating the information of drug exposure and drug susceptibility. Both simulated and real clinical data examples are given to illustrate the proposed approach. The Bayesian approach has great potential to be used in many aspects of viral dynamics modelling since it allow us to fit complex dynamic models and identify all the model parameters. Our results suggest that Bayesian approach for estimating parameters in HIV dynamic models is flexible and powerful.