Covariance structure of wavelet coefficients: theory and models in a Bayesian perspective

We present theoretical results on the random wavelet coefficients covariance structure. We use simple properties of the coefficients to derive a recursive way to compute the within- and across-scale covariances. We point out a useful link between the algorithm proposed and the two-dimensional discrete wavelet transform. We then focus on Bayesian wavelet shrinkage for estimating a function from noisy data. A prior distribution is imposed on the coefficients of the unknown function. We show how our findings on the covariance structure make it possible to specify priors that take into account the full correlation between coefficients through a parsimonious number of hyperparameters. We use Markov chain Monte Carlo methods to estimate the parameters and illustrate our method on bench-mark simulated signals.     

A nonparametric Bayesian model for inference in related longitudinal studies

Summary.  We discuss a method for combining different but related longitudinal studies to improve predictive precision. The motivation is to borrow strength across clinical studies in which the same measurements are collected at different frequencies. Key features of the data are heterogeneous populations and an unbalanced design across three studies of interest. The first two studies are phase I studies with very detailed observations on a relatively small number of patients. The third study is a large phase III study with over 1500 enrolled patients, but with relatively few measurements on each patient. Patients receive different doses of several drugs in the studies, with the phase III study containing significantly less toxic treatments. Thus, the main challenges for the analysis are to accommodate heterogeneous population distributions and to formalize borrowing strength across the studies and across the various treatment levels. We describe a hierarchical extension over suitable semiparametric longitudinal data models to achieve the inferential goal. A nonparametric random-effects model accommodates the heterogeneity of the population of patients. A hierarchical extension allows borrowing strength across different studies and different levels of treatment by introducing dependence across these nonparametric random-effects distributions. Dependence is introduced by building an analysis of variance (ANOVA) like structure over the random-effects distributions for different studies and treatment combinations. Model structure and parameter interpretation are similar to standard ANOVA models. Instead of the unknown normal means as in standard ANOVA models, however, the basic objects of inference are random distributions, namely the unknown population distributions under each study. The analysis is based on a mixture of Dirichlet processes model as the underlying semiparametric model.     

Bayesian nonparametric estimation of a copula

A copula can fully characterize the dependence of multiple variables. The purpose of this paper is to provide a Bayesian nonparametric approach to the estimation of a copula, and we do this by mixing over a class of parametric copulas. In particular, we show that any bivariate copula density can be arbitrarily accurately approximated by an infinite mixture of Gaussian copula density functions. The model can be estimated by Markov Chain Monte Carlo methods and the model is demonstrated on both simulated and real data sets.     

Numerical Bayesian inference with arbitrary prior

The purpose of the paper, is to explain how recent advances in Markov Chain Monte Carlo integration can facilitate the routine Bayesian analysis of the linear model when the prior distribution is completely user dependent. The method is based on a Metropolis-Hastings algorithm with a Student-t source distribution that can generate posterior moments as well as marginal posterior densities for model parameters. The method is illustrated with numerical examples where the combination of prior and likelihood information leads to multimodal posteriors due to prior-likelihood conflicts, and to cases where prior information can be summarized by symmetric stable Paretian distributions.     

Geometric stick-breaking processes for continuous-time Bayesian nonparametric modeling

We propose a new class of time dependent random probability measures and show how this can be used for Bayesian nonparametric inference in continuous time. By means of a nonparametric hierarchical model we define a random process with geometric stick-breaking representation and dependence structure induced via a one dimensional diffusion process of Wright-Fisher type. The sequence is shown to be a strongly stationary measure-valued process with continuous sample paths which, despite the simplicity of the weights structure, can be used for inferential purposes on the trajectory of a discretely observed continuous-time phenomenon. A simple estimation procedure is presented and illustrated with simulated and real financial data.     

Bayesian non-parametric inference for species variety with a two-parameter Poisson–Dirichlet process prior

Summary.  A Bayesian non-parametric methodology has been recently proposed to deal with the issue of prediction within species sampling problems. Such problems concern the evaluation, conditional on a sample of size n , of the species variety featured by an additional sample of size m . Genomic applications pose the additional challenge of having to deal with large values of both n and m . In such a case the computation of the Bayesian non-parametric estimators is cumbersome and prevents their implementation. We focus on the two-parameter Poisson–Dirichlet model and provide completely explicit expressions for the corresponding estimators, which can be easily evaluated for any sizes of n and m . We also study the asymptotic behaviour of the number of new species conditionally on the observed sample: such an asymptotic result, combined with a suitable simulation scheme, allows us to derive asymptotic highest posterior density intervals for the estimates of interest. Finally, we illustrate the implementation of the proposed methodology by the analysis of five expressed sequence tags data sets.     

Bayesian inference for power law processes with applications in repairable systems

Statistical models for recurrent events are of great interest in repairable systems reliability and maintenance. The adopted model under minimal repair maintenance is frequently a nonhomogeneous Poisson process with the power law process (PLP) intensity function. Although inference for the PLP is generally based on maximum likelihood theory, some advantages of the Bayesian approach have been reported in the literature. In this paper it is proposed that the PLP intensity be reparametrized in terms of (β,η), where β is the elasticity of the mean number of events with respect to time and η is the mean number of events for the period in which the system was actually observed. It is shown that β and η are orthogonal and that the likelihood becomes proportional to a product of gamma densities. Therefore, the family of natural conjugate priors is also a product of gammas. The idea is extended to the case that several realizations of the same PLP are observed along overlapping periods of time. Some Monte Carlo simulations are provided to study the frequentist behavior of the Bayesian estimates and to compare them with the maximum likelihood estimates. The results are applied to a real problem concerning the determination of the optimal periodicity of preventive maintenance for a set of power transformers. Prior distributions are elicited for β and η based on their operational interpretation and engineering expertise.     

Bayesian inference and prediction analysis of the power law process based on a natural conjugate prior

Under a natural conjugate prior with four hyperparameters, the importance sampling (IS) technique is applied to the Bayesian analysis of the power law process (PLP). Samples of the parameters of the PLP are obtained from IS. Based on these samples, not only the posterior analysis of parameters and some parameter functions in the PLP are performed conveniently, but also single-sample and two-sample prediction procedures are constructed easily. Furthermore, the sensitivity of the posterior mean of the parameter functions in the PLP is studied with respect to the hyperparameters of the natural conjugate prior and it can guide the selections of the hyperparameters directly. Coupled this sensitivity with the relations between the prior moments and the hyperparameters in the natural conjugate prior, it is possible to give directions about the selections of the prior moments to a certain degree. After some numerical experiments illustrate the rationality and feasibility of the proposed methods, an engineering example demonstrates its application.     

On nonparametric Bayesian inference for the distribution of a random sample

The nonparametric Bayesian approach for inference regarding the unknown distribution of a random sample customarily assumes that this distribution is random and arises through Dirichlet-process mixing. Previous work within this setting has focused on the mean of the posterior distribution of this random distribution, which is the predictive distribution of a future observation given the sample. Our interest here is in learning about other features of this posterior distribution as well as about posteriors associated with functionals of the distribution of the data. We indicate how to do this in the case of linear functionals. An illustration, with a sample from a Gamma distribution, utilizes Dirichlet-process mixtures of normals to recover this distribution and its features.     

Bayesian inference for circular distributions with unknown normalising constants

Very often, the likelihoods for circular data sets are of quite complicated forms, and the functional forms of the normalising constants, which depend upon the unknown parameters, are unknown. This latter problem generally precludes rigorous, exact inference (both classical and Bayesian) for circular data.Noting the paucity of literature on Bayesian circular data analysis, and also because realistic data analysis is naturally permitted by the Bayesian paradigm, we address the above problem taking a Bayesian perspective. In particular, we propose a methodology that combines importance sampling and Markov chain Monte Carlo (MCMC) in a very effective manner to sample from the posterior distribution of the parameters, given the circular data. With simulation study and real data analysis, we demonstrate the considerable reliability and flexibility of our proposed methodology in analysing circular data.     

Bayesian statistical inference of the loglogistic model with interval-censored lifetime data

Interval-censored data arise when a failure time say, T cannot be observed directly but can only be determined to lie in an interval obtained from a series of inspection times. The frequentist approach for analysing interval-censored data has been developed for some time now. It is very common due to unavailability of software in the field of biological, medical and reliability studies to simplify the interval censoring structure of the data into that of a more standard right censoring situation by imputing the midpoints of the censoring intervals. In this research paper, we apply the Bayesian approach by employing Lindley's 1980, and Tierney and Kadane 1986 numerical approximation procedures when the survival data under consideration are interval-censored. The Bayesian approach to interval-censored data has barely been discussed in literature. The essence of this study is to explore and promote the Bayesian methods when the survival data been analysed are is interval-censored. We have considered only a parametric approach by assuming that the survival data follow a loglogistic distribution model. We illustrate the proposed methods with two real data sets. A simulation study is also carried out to compare the performances of the methods.     

A new Bayesian wavelet thresholding estimator of nonparametric regression

The methods of estimation of nonparametric regression function are quite common in statistical application. In this paper, the new Bayesian wavelet thresholding estimation is considered. The new mixture prior distributions for the estimation of nonparametric regression function by applying wavelet transformation are investigated. The reversible jump algorithm to obtain the appropriate prior distributions and value of thresholding is used. The performance of the proposed estimator is assessed with simulated data from well-known test functions by comparing the convergence rate of the proposed estimator with respect to another by evaluating the average mean square error and standard deviations. Finally by applying the developed method, density function of galaxy data is estimated.     

Bayesian nonparametric density estimation under length bias

A density estimation method in a Bayesian nonparametric framework is presented when recorded data are not coming directly from the distribution of interest, but from a length biased version. From a Bayesian perspective, efforts to computationally evaluate posterior quantities conditionally on length biased data were hindered by the inability to circumvent the problem of a normalizing constant. In this article, we present a novel Bayesian nonparametric approach to the length bias sampling problem that circumvents the issue of the normalizing constant. Numerical illustrations as well as a real data example are presented and the estimator is compared against its frequentist counterpart, the kernel density estimator for indirect data of Jones.     

A method for combining inference across related nonparametric Bayesian models

Summary.  We consider the problem of combining inference in related nonparametric Bayes models. Analogous to parametric hierarchical models, the hierarchical extension formalizes borrowing strength across the related submodels. In the nonparametric context, modelling is complicated by the fact that the random quantities over which we define the hierarchy are infinite dimensional. We discuss a formal definition of such a hierarchical model. The approach includes a regression at the level of the nonparametric model. For the special case of Dirichlet process mixtures, we develop a Markov chain Monte Carlo scheme to allow efficient implementation of full posterior inference in the given model.     

Bayesian automatic polynomial wavelet regression

This paper considers the problem of Bayesian automatic polynomial wavelet regression (PWR). We propose three different Bayesian methods based on integrated likelihood, conditional empirical Bayes, and reversible jump Markov chain Monte Carlo (MCMC). From the simulation results, we find that the proposed methods are similar to or superior to the existing ones.     

A Bayesian approach to inference about a change point model with application to DNA copy number experimental data

In this paper, we study the change-point inference problem motivated by the genomic data that were collected for the purpose of monitoring DNA copy number changes. DNA copy number changes or copy number variations (CNVs) correspond to chromosomal aberrations and signify abnormality of a cell. Cancer development or other related diseases are usually relevant to DNA copy number changes on the genome. There are inherited random noises in such data, therefore, there is a need to employ an appropriate statistical model for identifying statistically significant DNA copy number changes. This type of statistical inference is evidently crucial in cancer researches, clinical diagnostic applications, and other related genomic researches. For the high-throughput genomic data resulting from DNA copy number experiments, a mean and variance change point model (MVCM) for detecting the CNVs is appropriate. We propose to use a Bayesian approach to study the MVCM for the cases of one change and propose to use a sliding window to search for all CNVs on a given chromosome. We carry out simulation studies to evaluate the estimate of the locus of the DNA copy number change using the derived posterior probability. These simulation results show that the approach is suitable for identifying copy number changes. The approach is also illustrated on several chromosomes from nine fibroblast cancer cell line data (array-based comparative genomic hybridization data). All DNA copy number aberrations that have been identified and verified by karyotyping are detected by our approach on these cell lines.     

Bayesian inference in the triangular cointegration model using a jeffreys prior

This paper presents a strategy for conducting Bayesian inference in the triangular cointegration model. A Jeffreys prior is used to circumvent an identification problem in the parameter region in which there is a near lack of cointegration. Sampling experiments are used to compare the repeated sampling performance of the approach with alternative classical cointegration methods. The Bayesian procedure is applied to testing for substitution between private and public consumption for a range of countries, with posterior estimates produced via Markov Chain Monte Carlo simulators.     

On posterior distribution of Bayesian wavelet thresholding

We investigate the posterior rate of convergence for wavelet shrinkage using a Bayesian approach in general Besov spaces. Instead of studying the Bayesian estimator related to a particular loss function, we focus on the posterior distribution itself from a nonparametric Bayesian asymptotics point of view and study its rate of convergence. We obtain the same rate as in Abramovich et al. (2004) where the authors studied the convergence of several Bayesian estimators.     

Bayesian inference for the generalized exponential distribution

The two-parameter generalized exponential (GE) distribution was introduced by Gupta and Kundu [Gupta, R.D. and Kundu, D., 1999, Generalized exponential distribution. Australian and New Zealand Journal of Statistics, 41(2), 173–188.]. It was observed that the GE can be used in situations where a skewed distribution for a nonnegative random variable is needed. In this article, the Bayesian estimation and prediction for the GE distribution, using informative priors, have been considered. Importance sampling is used to estimate the parameters, as well as the reliability function, and the Gibbs and Metropolis samplers data sets are used to predict the behavior of further observations from the distribution. Two data sets are used to illustrate the Bayesian procedure.     

Elicitation of multivariate prior distributions: A nonparametric Bayesian approach

In the context of Bayesian statistical analysis, elicitation is the process of formulating a prior density f(·)$f(·)$ about one or more uncertain quantities to represent a person's knowledge and beliefs. Several different methods of eliciting prior distributions for one unknown parameter have been proposed. However, there are relatively few methods for specifying a multivariate prior distribution and most are just applicable to specific classes of problems and/or based on restrictive conditions, such as independence of variables. Besides, many of these procedures require the elicitation of variances and correlations, and sometimes elicitation of hyperparameters which are difficult for experts to specify in practice. Garthwaite et al. (2005) discuss the different methods proposed in the literature and the difficulties of eliciting multivariate prior distributions. We describe a flexible method of eliciting multivariate prior distributions applicable to a wide class of practical problems. Our approach does not assume a parametric form for the unknown prior density f(·)$f(·)$, instead we use nonparametric Bayesian inference, modelling f(·)$f(·)$ by a Gaussian process prior distribution. The expert is then asked to specify certain summaries of his/her distribution, such as the mean, mode, marginal quantiles and a small number of joint probabilities. The analyst receives that information, treating it as a data set D   with which to update his/her prior beliefs to obtain the posterior distribution for f(·)$f(·)$. Theoretical properties of joint and marginal priors are derived and numerical illustrations to demonstrate our approach are given.