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.     

A mixture latent variable model for modeling mixed data in heterogeneous populations and its applications

Latent variable models are widely used for jointly modeling of mixed data including nominal, ordinal, count and continuous data. In this paper, we consider a latent variable model for jointly modeling relationships between mixed binary, count and continuous variables with some observed covariates. We assume that, given a latent variable, mixed variables of interest are independent and count and continuous variables have Poisson distribution and normal distribution, respectively. As such data may be extracted from different subpopulations, consideration of an unobserved heterogeneity has to be taken into account. A mixture distribution is considered (for the distribution of the latent variable) which accounts the heterogeneity. The generalized EM algorithm which uses the Newton–Raphson algorithm inside the EM algorithm is used to compute the maximum likelihood estimates of parameters. The standard errors of the maximum likelihood estimates are computed by using the supplemented EM algorithm. Analysis of the primary biliary cirrhosis data is presented as an application of the proposed model.     

Gaussian Scale Mixture Models for Robust Linear Multivariate Regression with Missing Data

We present an algorithm for multivariate robust Bayesian linear regression with missing data. The iterative algorithm computes an approximative posterior for the model parameters based on the variational Bayes (VB) method. Compared to the EM algorithm, the VB method has the advantage that the variance for the model parameters is also computed directly by the algorithm. We consider three families of Gaussian scale mixture models for the measurements, which include as special cases the multivariate t distribution, the multivariate Laplace distribution, and the contaminated normal model. The observations can contain missing values, assuming that the missing data mechanism can be ignored. A Matlab/Octave implementation of the algorithm is presented and applied to solve three reference examples from the literature.     

Case-deletion Influence Measures for the Data from Multivariate t Distributions

For the data from multivariate t distributions, it is very hard to make an influence analysis based on the probability density function since its expression is intractable. In this paper, we present a technique for influence analysis based on the mixture distribution and EM algorithm. In fact, the multivariate t distribution can be considered as a particular Gaussian mixture by introducing the weights from the Gamma distribution. We treat the weights as the missing data and develop the influence analysis for the data from multivariate t distributions based on the conditional expectation of the complete-data log-likelihood function in the EM algorithm. Several case-deletion measures are proposed for detecting influential observations from multivariate t distributions. Two numerical examples are given to illustrate our methodology.     

NONLINEAR TUBE-FITTING FOR THE ANALYSIS OF ANATOMICAL AND FUNCTIONAL STRUCTURES

We are concerned with the estimation of the exterior surface and interior summaries of tube-shaped anatomical structures. This interest is motivated by two distinct scientific goals, one dealing with the distribution of HIV microbicide in the colon and the other with measuring degradation in white-matter tracts in the brain. Our problem is posed as the estimation of the support of a distribution in three dimensions from a sample from that distribution, possibly measured with error. We propose a novel tube-fitting algorithm to construct such estimators. Further, we conduct a simulation study to aid in the choice of a key parameter of the algorithm, and we test our algorithm with validation study tailored to the motivating data sets. Finally, we apply the tube-fitting algorithm to a colon image produced by single photon emission computed tomography (SPECT) and to a white-matter tract image produced using diffusion tensor imaging (DTI).     

Bayesian quantile regression for longitudinal data models

In this paper, we discuss a fully Bayesian quantile inference using Markov Chain Monte Carlo (MCMC) method for longitudinal data models with random effects. Under the assumption of error term subject to asymmetric Laplace distribution, we establish a hierarchical Bayesian model and obtain the posterior distribution of unknown parameters at τ-th level. We overcome the current computational limitations using two approaches. One is the general MCMC technique with Metropolis–Hastings algorithm and another is the Gibbs sampling from the full conditional distribution. These two methods outperform the traditional frequentist methods under a wide array of simulated data models and are flexible enough to easily accommodate changes in the number of random effects and in their assumed distribution. We apply the Gibbs sampling method to analyse a mouse growth data and some different conclusions from those in the literatures are obtained.     

The generalized Poisson-binomial distribution and the computation of its distribution function

The Poisson-binomial distribution is useful in many applied problems in engineering, actuarial science and data mining. The Poisson-binomial distribution models the distribution of the sum of independent but non-identically distributed random indicators whose success probabilities vary. In this paper, we extend the Poisson-binomial distribution to a generalized Poisson-binomial (GPB) distribution. The GPB distribution corresponds to the case where the random indicators are replaced by two-point random variables, which can take two arbitrary values instead of 0 and 1 as in the case of random indicators. The GPB distribution has found applications in many areas such as voting theory, actuarial science, warranty prediction and probability theory. As the GPB distribution has not been studied in detail so far, we introduce this distribution first and then derive its theoretical properties. We develop an efficient algorithm for the computation of its distribution function, using the fast Fourier transform. We test the accuracy of the developed algorithm by comparing it with enumeration-based exact method and the results from the binomial distribution. We also study the computational time of the algorithm under various parameter settings. Finally, we discuss the factors affecting the computational efficiency of the proposed algorithm and illustrate the use of the software package.     

Model-based clustering of multivariate ordinal data relying on a stochastic binary search algorithm

We design a probability distribution for ordinal data by modeling the process generating data, which is assumed to rely only on order comparisons between categories. Contrariwise, most competitors often either forget the order information or add a non-existent distance information. The data generating process is assumed, from optimality arguments, to be a stochastic binary search algorithm in a sorted table. The resulting distribution is natively governed by two meaningful parameters (position and precision) and has very appealing properties: decrease around the mode, shape tuning from uniformity to a Dirac, identifiability. Moreover, it is easily estimated by an EM algorithm since the path in the stochastic binary search algorithm can be considered as missing values. Using then the classical latent class assumption, the previous univariate ordinal model is straightforwardly extended to model-based clustering for multivariate ordinal data. Parameters of this mixture model are estimated by an AECM algorithm. Both simulated and real data sets illustrate the great potential of this model by its ability to parsimoniously identify particularly relevant clusters which were unsuspected by some traditional competitors.     

Likelihood inference for exchangeable continuous data with covariates and varying cluster sizes; use of the Farlie–Gumbel–Morgenstern model

This article investigates the Farlie–Gumbel–Morgenstern class of models for exchangeable continuous data. We show how the model specification can account for both individual and cluster level covariates, we derive insights from comparisons with the multivariate normal distribution, and we discuss maximum likelihood inference when a sample of independent clusters of varying sizes is available. We propose a method for maximum likelihood estimation which is an alternative to direct numerical maximization of the likelihood that sometimes exhibits non-convergence problems. We describe an algorithm for generating samples from the exchangeable multivariate Farlie–Gumbel–Morgenstern distribution with any marginals, using the structural properties of the distribution. Finally, we present the results of a simulation study designed to assess the properties of the maximum likelihood estimators, and we illustrate the use of the FGM distributions with the analysis of a small data set from a developmental toxicity study.     

Bivariate Kumaraswamy distribution: properties and a new method to generate bivariate classes

In this paper, we introduce a bivariate Kumaraswamy (BVK) distribution whose marginals are Kumaraswamy distributions. The cumulative distribution function of this bivariate model has absolutely continuous and singular parts. Representations for the cumulative and density functions are presented and properties such as marginal and conditional distributions, product moments and conditional moments are obtained. We show that the BVK model can be obtained from the Marshall and Olkin survival copula and obtain a tail dependence measure. The estimation of the parameters by maximum likelihood is discussed and the Fisher information matrix is determined. We propose an EM algorithm to estimate the parameters. Some simulations are presented to verify the performance of the direct maximum-likelihood estimation and the proposed EM algorithm. We also present a method to generate bivariate distributions from our proposed BVK distribution. Furthermore, we introduce a BVK distribution which has only an absolutely continuous part and discuss some of its properties. Finally, a real data set is analysed for illustrative purposes.     

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.     

Prior specification of neighbourhood and interaction structure in binary Markov random fields

We formulate a prior distribution for the energy function of stationary binary Markov random fields (MRFs) defined on a rectangular lattice. In the prior we assign distributions to all parts of the energy function. In particular we define priors for the neighbourhood structure of the MRF, what interactions to include in the model, and for potential values. We define a reversible jump Markov chain Monte Carlo (RJMCMC) procedure to simulate from the corresponding posterior distribution when conditioned to an observed scene. Thereby we are able to learn both the neighbourhood structure and the parametric form of the MRF from the observed scene. We circumvent evaluations of the intractable normalising constant of the MRF when running the RJMCMC algorithm by adopting a previously defined approximate auxiliary variable algorithm. We demonstrate the usefulness of our prior in two simulation examples and one real data example.     

Estimating the point of intersection of two lines under correlation

This paper introduces a new biostatistical approach to the problems of estimating true values and approximating the distribution of true values from unreliable data.We present the basic rationale for the unmixing method and report on a simulation study of its properties in estimating the centiles of a skewed, outlier-prone class of distributions.We also present an application to highly skewed USDA vitamin A intake data, and a pseudo-code version of the unmixing algorithm that we hope will allow other researchers to experiment with it     

A robust multivariate Birnbaum–Saunders distribution: EM estimation

We propose here a robust multivariate extension of the bivariate Birnbaum–Saunders (BS) distribution derived by Kundu et al. [Bivariate Birnbaum–Saunders distribution and associated inference. J Multivariate Anal. 2010;101:113–125], based on scale mixtures of normal (SMN) distributions that are used for modelling symmetric data. This resulting multivariate BS-type distribution is an absolutely continuous distribution whose marginal and conditional distributions are of BS-type distribution of Balakrishnan et al. [Estimation in the Birnbaum–Saunders distribution based on scalemixture of normals and the EM algorithm. Stat Oper Res Trans. 2009;33:171–192]. Due to the complexity of the likelihood function, parameter estimation by direct maximization is very difficult to achieve. For this reason, we exploit the nice hierarchical representation of the proposed distribution to propose a fast and accurate EM algorithm for computing the maximum likelihood (ML) estimates of the model parameters. We then evaluate the finite-sample performance of the developed EM algorithm and the asymptotic properties of the ML estimates through empirical experiments. Finally, we illustrate the obtained results with a real data and display the robustness feature of the estimation procedure developed here.     

Estimation and prediction for Chen distribution with bathtub shape under progressive censoring

We consider estimation of the unknown parameters of Chen distribution [Chen Z. A new two-parameter lifetime distribution with bathtub shape or increasing failure rate function. Statist Probab Lett. 2000;49:155–161] with bathtub shape using progressive-censored samples. We obtain maximum likelihood estimates by making use of an expectation–maximization algorithm. Different Bayes estimates are derived under squared error and balanced squared error loss functions. It is observed that the associated posterior distribution appears in an intractable form. So we have used an approximation method to compute these estimates. A Metropolis–Hasting algorithm is also proposed and some more approximate Bayes estimates are obtained. Asymptotic confidence interval is constructed using observed Fisher information matrix. Bootstrap intervals are proposed as well. Sample generated from MH algorithm are further used in the construction of HPD intervals. Finally, we have obtained prediction intervals and estimates for future observations in one- and two-sample situations. A numerical study is conducted to compare the performance of proposed methods using simulations. Finally, we analyse real data sets for illustration purposes.     

AN ALTERNATIVE PARAMETRIC APPROACH FOR DISCRETE MISSING DATA PROBLEMS

We propose an iterative method of estimation for discrete missing data problems that is conceptually different from the Expectation–Maximization (EM) algorithm and that does not in general yield the observed data maximum likelihood estimate (MLE). The proposed approach is based conceptually upon weighting the set of possible complete-data MLEs. Its implementation avoids the expectation step of EM, which can sometimes be problematic. In the simple case of Bernoulli trials missing completely at random, the iterations of the proposed algorithm are equivalent to the EM iterations. For a familiar genetics-oriented multinomial problem with missing count data and for the motivating example with epidemiologic applications that involves a mixture of a left censored normal distribution with a point mass at zero, we investigate the finite sample performance of the proposed estimator and find it to be competitive with that of the MLE. We give some intuitive justification for the method, and we explore an interesting connection between our algorithm and multiple imputation in order to suggest an approach for estimating standard errors.     

Sequential Monte Carlo on large binary sampling spaces

A Monte Carlo algorithm is said to be adaptive if it automatically calibrates its current proposal distribution using past simulations. The choice of the parametric family that defines the set of proposal distributions is critical for good performance. In this paper, we present such a parametric family for adaptive sampling on high dimensional binary spaces. A practical motivation for this problem is variable selection in a linear regression context. We want to sample from a Bayesian posterior distribution on the model space using an appropriate version of Sequential Monte Carlo. Raw versions of Sequential Monte Carlo are easily implemented using binary vectors with independent components. For high dimensional problems, however, these simple proposals do not yield satisfactory results. The key to an efficient adaptive algorithm are binary parametric families which take correlations into account, analogously to the multivariate normal distribution on continuous spaces. We provide a review of models for binary data and make one of them work in the context of Sequential Monte Carlo sampling. Computational studies on real life data with about a hundred covariates suggest that, on difficult instances, our Sequential Monte Carlo approach clearly outperforms standard techniques based on Markov chain exploration.     

An Application of EM Algorithm to a Change-Point Problem

We consider the problem of change-point in a classical framework while assuming a probability distribution for the change-point. An EM algorithm is proposed to estimate the distribution of the change-point. A change-point model for multiple profiles is also proposed, and EM algorithm is presented to estimate the model. Two examples of Illinois traffic data and Dow Jones Industrial Averages are used to demonstrate the proposed methods.     

Exact and efficient Bayesian inference for multiple changepoint problems

We demonstrate how to perform direct simulation from the posterior distribution of a class of multiple changepoint models where the number of changepoints is unknown. The class of models assumes independence between the posterior distribution of the parameters associated with segments of data between successive changepoints. This approach is based on the use of recursions, and is related to work on product partition models. The computational complexity of the approach is quadratic in the number of observations, but an approximate version, which introduces negligible error, and whose computational cost is roughly linear in the number of observations, is also possible. Our approach can be useful, for example within an MCMC algorithm, even when the independence assumptions do not hold. We demonstrate our approach on coal-mining disaster data and on well-log data. Our method can cope with a range of models, and exact simulation from the posterior distribution is possible in a matter of minutes.     

Robust parameter estimation of regression model with AR(p) error terms

In this article, we consider a linear regression model with AR(p) error terms with the assumption that the error terms have a t distribution as a heavy-tailed alternative to the normal distribution. We obtain the estimators for the model parameters by using the conditional maximum likelihood (CML) method. We conduct an iteratively reweighting algorithm (IRA) to find the estimates for the parameters of interest. We provide a simulation study and three real data examples to illustrate the performance of the proposed robust estimators based on t distribution.