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.     

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.     

A simple method for finding a legal configuration in complex Bayesian networks

This paper deals with an important problem with large and complex Bayesian networks. Exact inference in these networks is simply not feasible owing to the huge storage requirements of exact methods. Markov chain Monte Carlo methods, however, are able to deal with these large networks but to do this they require an initial legal configuration to set off the sampler. So far nondeterministic methods such as forward sampling have often been used for this, even though the forward sampler may take an eternity to come up with a legal configuration. In this paper a novel algorithm will be presented that allows a legal configuration in a general Bayesian network to be found in polynomial time in almost all cases. The algorithm will not be proved deterministic but empirical results will demonstrate that this holds in most cases. Also, the algorithm will be justified by its simplicity and ease of implementation.     

Bayesian inference for a discretely observed stochastic kinetic model

The ability to infer parameters of gene regulatory networks is emerging as a key problem in systems biology. The biochemical data are intrinsically stochastic and tend to be observed by means of discrete-time sampling systems, which are often limited in their completeness. In this paper we explore how to make Bayesian inference for the kinetic rate constants of regulatory networks, using the stochastic kinetic Lotka-Volterra system as a model. This simple model describes behaviour typical of many biochemical networks which exhibit auto-regulatory behaviour. Various MCMC algorithms are described and their performance evaluated in several data-poor scenarios. An algorithm based on an approximating process is shown to be particularly efficient.     

Bayesian analysis of the scatterometer wind retrieval inverse problem: some new approaches

Summary.  The retrieval of wind vectors from satellite scatterometer observations is a non-linear inverse problem. A common approach to solving inverse problems is to adopt a Bayesian framework and to infer the posterior distribution of the parameters of interest given the observations by using a likelihood model relating the observations to the parameters, and a prior distribution over the parameters. We show how Gaussian process priors can be used efficiently with a variety of likelihood models, using local forward (observation) models and direct inverse models for the scatterometer. We present an enhanced Markov chain Monte Carlo method to sample from the resulting multimodal posterior distribution. We go on to show how the computational complexity of the inference can be controlled by using a sparse, sequential Bayes algorithm for estimation with Gaussian processes. This helps to overcome the most serious barrier to the use of probabilistic, Gaussian process methods in remote sensing inverse problems, which is the prohibitively large size of the data sets. We contrast the sampling results with the approximations that are found by using the sparse, sequential Bayes algorithm.     

大数据背景下非概率抽样的统计推断问题

利用大数据进行抽样,很多情况下抽样框的构造比较困难,使得抽取的样本属于非概率样本,难以将传统的抽样推断理论应用到非概率样本中,如何解决非概率抽样的统计推断问题,是大数据背景下抽样调查面临的严重挑战。本文提出了解决非概率抽样统计推断问题的基本思路：一是抽样方法,可以考虑基于样本匹配的样本选择、链接跟踪抽样方法等,使得到的非概率样本近似于概率样本,从而可采用概率样本的统计推断理论;二是权数的构造与调整,可以考虑基于伪设计、模型和倾向得分等方法得到类似于概率样本的基础权数;三是估计,可以考虑基于伪设计、模型和贝叶斯的混合概率估计。最后,以基于样本匹配的样本选择为例探讨了具体解决方法。     

Bayesian neural tree models for nonparametric regression

Frequentist and Bayesian methods differ in many aspects but share some basic optimal properties. In real-life prediction problems, situations exist in which a model based on one of the above paradigms is preferable depending on some subjective criteria. Nonparametric classification and regression techniques, such as decision trees and neural networks, have both frequentist (classification and regression trees (CARTs) and artificial neural networks) as well as Bayesian counterparts (Bayesian CART and Bayesian neural networks) to learning from data. In this paper, we present two hybrid models combining the Bayesian and frequentist versions of CART and neural networks, which we call the Bayesian neural tree (BNT) models. BNT models can simultaneously perform feature selection and prediction, are highly flexible, and generalise well in settings with limited training observations. We study the statistical consistency of the proposed approaches and derive the optimal value of a vital model parameter. The excellent performance of the newly proposed BNT models is shown using simulation studies. We also provide some illustrative examples using a wide variety of standard regression datasets from a public available machine learning repository to show the superiority of the proposed models in comparison to popularly used Bayesian CART and Bayesian neural network models.     

A new multivariate imputation method based on Bayesian networks

Dealing with incomplete data is a pervasive problem in statistical surveys. Bayesian networks have been recently used in missing data imputation. In this research, we propose a new methodology for the multivariate imputation of missing data using discrete Bayesian networks and conditional Gaussian Bayesian networks. Results from imputing missing values in coronary artery disease data set and milk composition data set as well as a simulation study from cancer-neapolitan network are presented to demonstrate and compare the performance of three Bayesian network-based imputation methods with those of multivariate imputation by chained equations (MICE) and the classical hot-deck imputation method. To assess the effect of the structure learning algorithm on the performance of the Bayesian network-based methods, two methods called Peter-Clark algorithm and greedy search-and-score have been applied. Bayesian network-based methods are: first, the method introduced by Di Zio et al. [Bayesian networks for imputation, J. R. Stat. Soc. Ser. A 167 (2004), 309–322] in which, each missing item of a variable is imputed using the information given in the parents of that variable; second, the method of Di Zio et al. [Multivariate techniques for imputation based on Bayesian networks, Neural Netw. World 15 (2005), 303–310] which uses the information in the Markov blanket set of the variable to be imputed and finally, our new proposed method which applies the whole available knowledge of all variables of interest, consisting the Markov blanket and so the parent set, to impute a missing item. Results indicate the high quality of our new proposed method especially in the presence of high missingness percentages and more connected networks. Also the new method have shown to be more efficient than the MICE method for small sample sizes with high missing rates.     

Inference for Lévy‐Driven Stochastic Volatility Models via Adaptive Sequential Monte Carlo

Abstract. We investigate simulation methodology for Bayesian inference in Lévy‐driven stochastic volatility (SV) models. Typically, Bayesian inference from such models is performed using Markov chain Monte Carlo (MCMC); this is often a challenging task. Sequential Monte Carlo (SMC) samplers are methods that can improve over MCMC; however, there are many user‐set parameters to specify. We develop a fully automated SMC algorithm, which substantially improves over the standard MCMC methods in the literature. To illustrate our methodology, we look at a model comprised of a Heston model with an independent, additive, variance gamma process in the returns equation. The driving gamma process can capture the stylized behaviour of many financial time series and a discretized version, fit in a Bayesian manner, has been found to be very useful for modelling equity data. We demonstrate that it is possible to draw exact inference, in the sense of no time‐discretization error, from the Bayesian SV model.     

Bayesian inference over ICA models: application to multibiometric score fusion with quality estimates

Bayesian networks are not well-formulated for continuous variables. The majority of recent works dealing with Bayesian inference are restricted only to special types of continuous variables such as the conditional linear Gaussian model for Gaussian variables. In this context, an exact Bayesian inference algorithm for clusters of continuous variables which may be approximated by independent component analysis models is proposed. The complexity in memory space is linear and the overfitting problem is attenuated, while the inference time is still exponential. Experiments for multibiometric score fusion with quality estimates are conducted, and it is observed that the performances are satisfactory compared to some known fusion techniques.     

Importance sampling for signal extraction model in time series analysis

In time series analysis, signal extraction model (SEM) is used to estimate unobserved signal component from observed time series data. Since parameters of the components in SEM are often unknown in practice, a commonly used method is to estimate unobserved signal component using the maximum likelihood estimates (MLEs) of parameters of the components. This paper explores an alternative way to estimate unobserved signal component when parameters of the components are unknown. The suggested method makes use of importance sampling (IS) with Bayesian inference. The basic idea is to treat parameters of the components in SEM as a random vector and compute a posterior probability density function of the parameters using Bayesian inference. Then IS method is applied to integrate out the parameters and thus estimates of unobserved signal component, unconditional to the parameters, can be obtained. This method is illustrated with a real time series data. Then a Monte Carlo study with four different types of time series models is carried out to compare a performance of this method with that of a commonly used method. The study shows that IS method with Bayesian inference is computationally feasible and robust, and more efficient in terms of mean square errors (MSEs) than a commonly used method.     

Bayesian inference in two‐arm trials using relative belief ratios

Various methodologies proposed for some inference problems associated with two‐arm trails are known to suffer from difficulties, as documented in Senn (2001). We propose an alternative Bayesian approach to these problems that deals with these difficulties through providing an explicit measure of statistical evidence and the strength of this evidence. Bayesian methods are often criticized for their intrinsic subjectivity. We show how these concerns can be dealt with through assessing the bias induced by a prior model checking and checking for prior‐data conflict. Copyright © 2015 John Wiley & Sons, Ltd.     

Information analysis of local suppression scheme based on a spatial-temporal model

In a wireless sensor network, data collection is relatively cheap whereas data transmission is relatively expensive. Thus, preserving battery life is critical. If the process of interest is sufficiently predictable, the suppression in transmission can be adopted to improve efficiency of sensor networks because the loss of information is not great. The prime interest lies in finding an inference-efficient way to support suppressed data collection application. In this paper, we present a suppression scheme for a multiple nodes setting with spatio-temporal processes, especially when process knowledge is insufficient. We also explore the impact of suppression schemes on the inference of the regional processes under various suppression levels. Finally, we formalize the hierarchical Bayesian model for these schemes.     

An intuitive risk factors search algorithm: usage of the Bayesian network technique in personalized medicine

The article focuses on the application of the Bayesian networks (BN) technique to problems of personalized medicine. The simple (intuitive) algorithm of BN optimization with respect to the number of nodes using naive network topology is developed. This algorithm allows to increase the BN prediction quality and to identify the most important variables of the network. The parallel program implementing the algorithm has demonstrated good scalability with an increase in the computational cores number, and it can be applied to the large patients database containing thousands of variables. This program is applied for the prediction for the unfavorable outcome of coronary artery disease (CAD) for patients who survived the acute coronary syndrome (ACS). As a result, the quality of the predictions of the investigated networks was significantly improved and the most important risk factors were detected. The significance of the tumor necrosis factor-alpha gene polymorphism for the prediction of the unfavorable outcome of CAD for patients survived after ACS was revealed for the first time.     

Automatic Bayesian quantile regression curve fitting

Quantile regression, including median regression, as a more completed statistical model than mean regression, is now well known with its wide spread applications. Bayesian inference on quantile regression or Bayesian quantile regression has attracted much interest recently. Most of the existing researches in Bayesian quantile regression focus on parametric quantile regression, though there are discussions on different ways of modeling the model error by a parametric distribution named asymmetric Laplace distribution or by a nonparametric alternative named scale mixture asymmetric Laplace distribution. This paper discusses Bayesian inference for nonparametric quantile regression. This general approach fits quantile regression curves using piecewise polynomial functions with an unknown number of knots at unknown locations, all treated as parameters to be inferred through reversible jump Markov chain Monte Carlo (RJMCMC) of Green (Biometrika 82:711–732, 1995). Instead of drawing samples from the posterior, we use regression quantiles to create Markov chains for the estimation of the quantile curves. We also use approximate Bayesian factor in the inference. This method extends the work in automatic Bayesian mean curve fitting to quantile regression. Numerical results show that this Bayesian quantile smoothing technique is competitive with quantile regression/smoothing splines of He and Ng (Comput. Stat. 14:315–337, 1999) and P-splines (penalized splines) of Eilers and de Menezes (Bioinformatics 21(7):1146–1153, 2005).     

EXACT INFERENCE IN FOUR-PARAMETER GENERALIZED GAMMA DISTRIBUTIONS

The paper considers Bayesian analysis of the generalized four-parameter gamma distribution. Estimation of parameters using classical techniques is associated with important technical problems while Bayesian methods are not currently available for such distributions. Posterior inference is performed using numerical methods organized around Gibbs sampling. Predictive distributions and reliability can be estimated routinely using the proposed methods.     

Bayesian modeling using a class of bimodal skew-elliptical distributions

We consider Bayesian inference using an extension of the family of skew-elliptical distributions studied by Azzalini [1985. A class of distributions which includes the normal ones. Scand. J. Statist. Theory and Applications 12 (2), 171–178]. This new class is referred to as bimodal skew-elliptical (BSE) distributions. The elements of the BSE class can take quite different forms. In particular, they can adopt both uni- and bimodal shapes. The bimodal case behaves similarly to mixtures of two symmetric distributions and we compare inference under the BSE family with the specific case of mixtures of two normal distributions. We study the main properties of the general class and illustrate its applications to two problems involving density estimation and linear regression.     

A re-evaluation of random-effects meta-analysis

Summary.  Meta-analysis in the presence of unexplained heterogeneity is frequently undertaken by using a random-effects model, in which the effects underlying different studies are assumed to be drawn from a normal distribution. Here we discuss the justification and interpretation of such models, by addressing in turn the aims of estimation, prediction and hypothesis testing. A particular issue that we consider is the distinction between inference on the mean of the random-effects distribution and inference on the whole distribution. We suggest that random-effects meta-analyses as currently conducted often fail to provide the key results, and we investigate the extent to which distribution-free, classical and Bayesian approaches can provide satisfactory methods. We conclude that the Bayesian approach has the advantage of naturally allowing for full uncertainty, especially for prediction. However, it is not without problems, including computational intensity and sensitivity to a priori judgements. We propose a simple prediction interval for classical meta-analysis and offer extensions to standard practice of Bayesian meta-analysis, making use of an example of studies of 'set shifting' ability in people with eating disorders.     

Objective Bayesian Inference for the Half-Normal and Half-t Distributions

In this article, Bayesian inference for the half-normal and half-t distributions using uninformative priors is considered. It is shown that exact Bayesian inference can be undertaken for the half-normal distribution without the need for Gibbs sampling. Simulation is then used to compare the sampling properties of Bayesian point and interval estimators with those of their maximum likelihood based counterparts. Inference for the half-t distribution based on the use of Gibbs sampling is outlined, and an approach to model comparison based on the use of Bayes factors is discussed. The fitting of the half-normal and half-t models is illustrated using real data on the body fat measurements of elite athletes.