Membranes,mitochondria and amoebae: shape models

Most real-world shapes and images are characterized by high variability- they are not rigid, like crystals, for example—but they are strongly structured. Therefore, a fundamental task in the understanding and analysis of such image ensembles is the construction of models that incorporate both variability and structure in a mathematically precise way. The global shape models introduced in Grenander's general pattern theory are intended to do this. In this paper, we describe the representation of two-dimensional mitochondria and membranes in electron microscope photographs, and three-dimensional amoebae in optical sectioning microscopy. There are three kinds of variability to all of these patterns, which these representations accommodate. The first is the variability in shape and viewing orientation. For this, the typical structure is represented via linear, circular and spherical templates, with the variability accomodated via the application of transformations applied to the templates. The transformations form groups: scale, rotation and translation. They are locally applied throughout the continuum and of high dimension. The second is the textural variability; the inside and outside of these basic shapes are subject to random variation, as well as sensor noise. For this, statistical sensor models and Markov random field texture models are used to connect the constituent structures of the shapes to the measured data. The third variability type is associated with the fact that each scene is made up of a variable number of shapes; this number is not assumed to be known a priori. Each scene has a variable number of parameters encoding the transformations of the templates appropriate for that scene. For this, a single posterior distribution is defined over the countable union of spaces representing models of varying numbers of shapes. Bayesian inference is performed via computation of the conditional expectation of the parametrically defined shapes under the posterior. These conditional mean estimates are generated using jump-diffusion processes. Results for membranes, mitochondria and amoebae are shown.     

ALLOCATION OF REMOTELY SENSED DATA USING MARKOV MODELS FOR IMAGE DATA AND PIXEL LABELS

For remotely sensed data, this paper reviews the Bayesian approach to the allocation of picture elements (pixels) to groups. Group labels are assumed a priori to be spatially correlated and, conditional on the labels, the image data are also assumed to be spatially correlated. The models considered have the property that the posterior distribution of the pixel labels given the image data inherits conditional independence constraints. Two allocation algorithms which exploit this fad are discussed. These algorithms are based on maximising the posterior distribution, and involve the use of neighbouring image and label data to update the label of any given pixel. The effect of spatial correlation in the image data on allocation performance is examined.     

Markov chain Monte Carlo with the Integrated Nested Laplace Approximation

The Integrated Nested Laplace Approximation (INLA) has established itself as a widely used method for approximate inference on Bayesian hierarchical models which can be represented as a latent Gaussian model (LGM). INLA is based on producing an accurate approximation to the posterior marginal distributions of the parameters in the model and some other quantities of interest by using repeated approximations to intermediate distributions and integrals that appear in the computation of the posterior marginals. INLA focuses on models whose latent effects are a Gaussian Markov random field. For this reason, we have explored alternative ways of expanding the number of possible models that can be fitted using the INLA methodology. In this paper, we present a novel approach that combines INLA and Markov chain Monte Carlo (MCMC). The aim is to consider a wider range of models that can be fitted with INLA only when some of the parameters of the model have been fixed. We show how new values of these parameters can be drawn from their posterior by using conditional models fitted with INLA and standard MCMC algorithms, such as Metropolis–Hastings. Hence, this will extend the use of INLA to fit models that can be expressed as a conditional LGM. Also, this new approach can be used to build simpler MCMC samplers for complex models as it allows sampling only on a limited number of parameters in the model. We will demonstrate how our approach can extend the class of models that could benefit from INLA, and how the R-INLA package will ease its implementation. We will go through simple examples of this new approach before we discuss more advanced applications with datasets taken from the relevant literature. In particular, INLA within MCMC will be used to fit models with Laplace priors in a Bayesian Lasso model, imputation of missing covariates in linear models, fitting spatial econometrics models with complex nonlinear terms in the linear predictor and classification of data with mixture models. Furthermore, in some of the examples we could exploit INLA within MCMC to make joint inference on an ensemble of model parameters.     

Bayesian analysis of elapsed times in continuous‐time Markov chains

The authors consider Bayesian analysis for continuous‐time Markov chain models based on a conditional reference prior. For such models, inference of the elapsed time between chain observations depends heavily on the rate of decay of the prior as the elapsed time increases. Moreover, improper priors on the elapsed time may lead to improper posterior distributions. In addition, an infinitesimal rate matrix also characterizes this class of models. Experts often have good prior knowledge about the parameters of this matrix. The authors show that the use of a proper prior for the rate matrix parameters together with the conditional reference prior for the elapsed time yields a proper posterior distribution. The authors also demonstrate that, when compared to analyses based on priors previously proposed in the literature, a Bayesian analysis on the elapsed time based on the conditional reference prior possesses better frequentist properties. The type of prior thus represents a better default prior choice for estimation software.     

Bayesian multiple comparison of models for binary data with inequality constraints

In this paper we consider generalized linear models for binary data subject to inequality constraints on the regression coefficients, and propose a simple and efficient Bayesian method for parameter estimation and model selection by using Markov chain Monte Carlo (MCMC). In implementing MCMC, we introduce appropriate latent variables and use a simple approximation of a link function, to resolve computational difficulties and obtain convenient forms for full conditional posterior densities of elements of parameters. Bayes factors are computed via the Savage-Dickey density ratios and the method of Oh (Comput. Stat. Data Anal. 29:411–427, 1999), for which posterior samples from the full model with no degenerate parameter and the full conditional posterior densities of elements are needed. Since it uses one set of posterior samples from the full model for any model in consideration, it performs simultaneous comparison of all possible models and is very efficient compared with other model selection methods which require one to fit all candidate models. A simulation study shows that significant improvements can be made by taking the constraints into account. Real data on purchase intention of a product subject to order constraints is analyzed by using the proposed method. The analysis results show that there exist some price changes which significantly affect the consumer behavior. The results also show the importance of simultaneous comparison of models rather than separate pairwise comparisons of models since the latter may yield misleading results from ignoring possible correlations between parameters.     

On double hysteretic heteroskedastic model

ABSTRACT

This paper proposes a hysteretic autoregressive model with GARCH specification and a skew Student's t-error distribution for financial time series. With an integrated hysteresis zone, this model allows both the conditional mean and conditional volatility switching in a regime to be delayed when the hysteresis variable lies in a hysteresis zone. We perform Bayesian estimation via an adaptive Markov Chain Monte Carlo sampling scheme. The proposed Bayesian method allows simultaneous inferences for all unknown parameters, including threshold values and a delay parameter. To implement model selection, we propose a numerical approximation of the marginal likelihoods to posterior odds. The proposed methodology is illustrated using simulation studies and two major Asia stock basis series. We conduct a model comparison for variant hysteresis and threshold GARCH models based on the posterior odds ratios, finding strong evidence of the hysteretic effect and some asymmetric heavy-tailness. Versus multi-regime threshold GARCH models, this new collection of models is more suitable to describe real data sets. Finally, we employ Bayesian forecasting methods in a Value-at-Risk study of the return series.     

Bootstrapping the conditional copula

This paper is concerned with inference about the dependence or association between two random variables conditionally upon the given value of a covariate. A way to describe such a conditional dependence is via a conditional copula function. Nonparametric estimators for a conditional copula then lead to nonparametric estimates of conditional association measures such as a conditional Kendall's tau. The limiting distributions of nonparametric conditional copula estimators are rather involved. In this paper we propose a bootstrap procedure for approximating these distributions and their characteristics, and establish its consistency. We apply the proposed bootstrap procedure for constructing confidence intervals for conditional association measures, such as a conditional Blomqvist beta and a conditional Kendall's tau. The performances of the proposed methods are investigated via a simulation study involving a variety of models, ranging from models in which the dependence (weak or strong) on the covariate is only through the copula and not through the marginals, to models in which this dependence appears in both the copula and the marginal distributions. As a conclusion we provide practical recommendations for constructing bootstrap-based confidence intervals for the discussed conditional association measures.     

Logarithmic and power transformations in the context of fractionally integrated processes

In this article we examine the effect that logarithmic and power transformations have on the order of integration in raw time series. For this purpose, we use a version of the tests of Robinson (1994) that permits us to test I ( d ) statistical models. The results, obtained via Monte Carlo, show that there is no effect in the degree of dependence of the series when this type of transformations are employed, resulting thus in useful mechanisms to be applied when a more plausible economic interpretation of the data is required.     

Bayesian Analysis of Stochastic Volatility Models

New techniques for the analysis of stochastic volatility models in which the logarithm of conditional variance follows an autoregressive model are developed. A cyclic Metropolis algorithm is used to construct a Markov-chain simulation tool. Simulations from this Markov chain converge in distribution to draws from the posterior distribution enabling exact finite-sample inference. The exact solution to the filtering/smoothing problem of inferring about the unobserved variance states is a by-product of our Markov-chain method. In addition, multistep-ahead predictive densities can be constructed that reflect both inherent model variability and parameter uncertainty. We illustrate our method by analyzing both daily and weekly data on stock returns and exchange rates. Sampling experiments are conducted to compare the performance of Bayes estimators to method of moments and quasi-maximum likelihood estimators proposed in the literature. In both parameter estimation and filtering, the Bayes estimators outperform these other approaches.     

Joint response graphs and separation induced by triangular systems

Summary.  We consider joint probability distributions generated recursively in terms of univariate conditional distributions satisfying conditional independence restrictions. The independences are captured by missing edges in a directed graph. A matrix form of such a graph, called the generating edge matrix, is triangular so the distributions that are generated over such graphs are called triangular systems. We study consequences of triangular systems after grouping or reordering of the variables for analyses as chain graph models, i.e. for alternative recursive factorizations of the given density using joint conditional distributions. For this we introduce families of linear triangular equations which do not require assumptions of distributional form. The strength of the associations that are implied by such linear families for chain graph models is derived. The edge matrices of chain graphs that are implied by any triangular system are obtained by appropriately transforming the generating edge matrix. It is shown how induced independences and dependences can be studied by graphs, by edge matrix calculations and via the properties of densities. Some ways of using the results are illustrated.     

Estimation and inference of the joint conditional distribution for multivariate longitudinal data using nonparametric copulas

In this paper we study estimating the joint conditional distributions of multivariate longitudinal outcomes using regression models and copulas. For the estimation of marginal models, we consider a class of time-varying transformation models and combine the two marginal models using nonparametric empirical copulas. Our models and estimation method can be applied in many situations where the conditional mean-based models are not good enough. Empirical copulas combined with time-varying transformation models may allow quite flexible modelling for the joint conditional distributions for multivariate longitudinal data. We derive the asymptotic properties for the copula-based estimators of the joint conditional distribution functions. For illustration we apply our estimation method to an epidemiological study of childhood growth and blood pressure.     

A Simple Analysis of the Exact Probability Matching Prior in the Location-Scale Model

It has long been asserted that in univariate location-scale models, when concerned with inference for either the location or scale parameter, the use of the inverse of the scale parameter as a Bayesian prior yields posterior credible sets that have exactly the correct frequentist confidence set interpretation. This claim dates to at least Peers, and has subsequently been noted by various authors, with varying degrees of justification. We present a simple, direct demonstration of the exact matching property of the posterior credible sets derived under use of this prior in the univariate location-scale model. This is done by establishing an equivalence between the conditional frequentist and posterior densities of the pivotal quantities on which conditional frequentist inferences are based.     

Bayesian Conditional Mean Estimation in Log‐Normal Linear Regression Models with Finite Quadratic Expected Loss

Log‐normal linear regression models are popular in many fields of research. Bayesian estimation of the conditional mean of the dependent variable is problematic as many choices of the prior for the variance (on the log‐scale) lead to posterior distributions with no finite moments. We propose a generalized inverse Gaussian prior for this variance and derive the conditions on the prior parameters that yield posterior distributions of the conditional mean of the dependent variable with finite moments up to a pre‐specified order. The conditions depend on one of the three parameters of the suggested prior; the other two have an influence on inferences for small and medium sample sizes. A second goal of this paper is to discuss how to choose these parameters according to different criteria including the optimization of frequentist properties of posterior means.     

Bayesian inference for smooth transition autoregressive (STAR) model: A prior sensitivity analysis

The main aim of this paper is to perform sensitivity analysis to the specification of prior distributions in a Bayesian analysis setting of STAR models. To achieve this aim, the joint posterior distribution of model order, coefficient, and implicit parameters in the logistic STAR model is first being presented. The conditional posterior distributions are then shown, followed by the design of a posterior simulator using a combination of Metropolis-Hastings, Gibbs Sampler, RJMCMC, and Multiple Try Metropolis algorithms, respectively. Following this, simulation studies and a case study on the prior sensitivity for the implicit parameters are being detailed at the end.     

Bayesian inference of the fully specified subdistribution model for survival data with competing risks

Competing risks data are routinely encountered in various medical applications due to the fact that patients may die from different causes. Recently, several models have been proposed for fitting such survival data. In this paper, we develop a fully specified subdistribution model for survival data in the presence of competing risks via a subdistribution model for the primary cause of death and conditional distributions for other causes of death. Various properties of this fully specified subdistribution model have been examined. An efficient Gibbs sampling algorithm via latent variables is developed to carry out posterior computations. Deviance information criterion (DIC) and logarithm of the pseudomarginal likelihood (LPML) are used for model comparison. An extensive simulation study is carried out to examine the performance of DIC and LPML in comparing the cause-specific hazards model, the mixture model, and the fully specified subdistribution model. The proposed methodology is applied to analyze a real dataset from a prostate cancer study in detail.     

Quantile Regression for Location‐Scale Time Series Models with Conditional Heteroscedasticity

This paper considers quantile regression for a wide class of time series models including autoregressive and moving average (ARMA) models with asymmetric generalized autoregressive conditional heteroscedasticity errors. The classical mean‐variance models are reinterpreted as conditional location‐scale models so that the quantile regression method can be naturally geared into the considered models. The consistency and asymptotic normality of the quantile regression estimator is established in location‐scale time series models under mild conditions. In the application of this result to ARMA‐generalized autoregressive conditional heteroscedasticity models, more primitive conditions are deduced to obtain the asymptotic properties. For illustration, a simulation study and a real data analysis are provided.     

A Graphical Diagnostic for Identifying Influential Model Choices in Bayesian Hierarchical Models

Abstract. Real‐world phenomena are frequently modelled by Bayesian hierarchical models. The building‐blocks in such models are the distribution of each variable conditional on parent and/or neighbour variables in the graph. The specifications of centre and spread of these conditional distributions may be well motivated, whereas the tail specifications are often left to convenience. However, the posterior distribution of a parameter may depend strongly on such arbitrary tail specifications. This is not easily detected in complex models. In this article, we propose a graphical diagnostic, the Local critique plot, which detects such influential statistical modelling choices at the node level. It identifies the properties of the information coming from the parents and neighbours (the local prior) and from the children and co‐parents (the lifted likelihood) that are influential on the posterior distribution, and examines local conflict between these distinct information sources. The Local critique plot can be derived for all parameters in a chain graph model.     

Quasi Bayesian likelihood

If the form of the distribution of data is unknown, the Bayesian method fails in the parametric inference because there is no posterior distribution of the parameter. In this paper, a theoretical framework of Bayesian likelihood is introduced via the Hilbert space method, which is free of the distributions of data and the parameter. The posterior distribution and posterior score function based on given inner products are defined and, consequently, the quasi posterior distribution and quasi posterior score function are derived, respectively, as the projections of the posterior distribution and posterior score function onto the space spanned by given estimating functions. In the space spanned by data, particularly, an explicit representation for the quasi posterior score function is obtained, which can be derived as a projection of the true posterior score function onto this space. The methods of constructing conservative quasi posterior score and quasi posterior log-likelihood are proposed. Some examples are given to illustrate the theoretical results. As an application, the quasi posterior distribution functions are used to select variables for generalized linear models. It is proved that, for linear models, the variable selections via quasi posterior distribution functions are equivalent to the variable selections via the penalized residual sum of squares or regression sum of squares.     

Modelling Poisson marked point processes using bivariate mixture transition distributions

A class of bivariate continuous-discrete distributions is proposed to fit Poisson dynamic models in a single unified framework via bivariate mixture transition distributions (BMTDs). Potential advantages of this class over the current models include its ability to capture stretches, bursts and nonlinear patterns characterized by Internet network traffic, high-frequency financial data and many others. It models the inter-arrival times and the number of arrivals (marks) in a single unified model which benefits from the dependence structure of the data. The continuous marginal distributions of this class include as special cases the exponential, gamma, Weibull and Rayleigh distributions (for the inter-arrival times), whereas the discrete marginal distributions are geometric and negative binomial. The conditional distributions are Poisson and Erlang. Maximum-likelihood estimation is discussed and parameter estimates are obtained using an expectation–maximization algorithm, while the standard errors are estimated using the missing information principle. It is shown via real data examples that the proposed BMTD models appear to capture data features better than other competing models.     

Missing covariates in generalized linear models when the missing data mechanism is non-ignorable

We propose a method for estimating parameters in generalized linear models with missing covariates and a non-ignorable missing data mechanism. We use a multinomial model for the missing data indicators and propose a joint distribution for them which can be written as a sequence of one-dimensional conditional distributions, with each one-dimensional conditional distribution consisting of a logistic regression. We allow the covariates to be either categorical or continuous. The joint covariate distribution is also modelled via a sequence of one-dimensional conditional distributions, and the response variable is assumed to be completely observed. We derive the E- and M-steps of the EM algorithm with non-ignorable missing covariate data. For categorical covariates, we derive a closed form expression for the E- and M-steps of the EM algorithm for obtaining the maximum likelihood estimates (MLEs). For continuous covariates, we use a Monte Carlo version of the EM algorithm to obtain the MLEs via the Gibbs sampler. Computational techniques for Gibbs sampling are proposed and implemented. The parametric form of the assumed missing data mechanism itself is not `testable' from the data, and thus the non-ignorable modelling considered here can be viewed as a sensitivity analysis concerning a more complicated model. Therefore, although a model may have `passed' the tests for a certain missing data mechanism, this does not mean that we have captured, even approximately, the correct missing data mechanism. Hence, model checking for the missing data mechanism and sensitivity analyses play an important role in this problem and are discussed in detail. Several simulations are given to demonstrate the methodology. In addition, a real data set from a melanoma cancer clinical trial is presented to illustrate the methods proposed.