A model for markers and latent health status

We extend the bivariate Wiener process considered by Whitmore and co-workers and model the joint process of a marker and health status. The health status process is assumed to be latent or unobservable. The time to reach the primary end point or failure (death, onset of disease, etc.) is the time when the latent health status process first crosses a failure threshold level. Inferences for the model are based on two kinds of data: censored survival data and marker measurements. Covariates, such as treatment variables, risk factors and base-line conditions, are related to the model parameters through generalized linear regression functions. The model offers a much richer potential for the study of treatment efficacy than do conventional models. Treatment effects can be assessed in terms of their influence on both the failure threshold and the health status process parameters. We derive an explicit formula for the prediction of residual failure times given the current marker level. Also we discuss model validation. This model does not require the proportional hazards assumption and hence can be widely used. To demonstrate the usefulness of the model, we apply the methods in analysing data from the protocol 116a of the AIDS Clinical Trials Group.     

Joint analysis of longitudinal data comprising repeated measures and times to events

In biomedical and public health research, both repeated measures of biomarkers Y as well as times T to key clinical events are often collected for a subject. The scientific question is how the distribution of the responses [ T , Y | X ] changes with covariates X . [ T | X ] may be the focus of the estimation where Y can be used as a surrogate for T . Alternatively, T may be the time to drop-out in a study in which [ Y | X ] is the target for estimation. Also, the focus of a study might be on the effects of covariates X on both T and Y or on some underlying latent variable which is thought to be manifested in the observable outcomes. In this paper, we present a general model for the joint analysis of [ T , Y | X ] and apply the model to estimate [ T | X ] and other related functionals by using the relevant information in both T and Y . We adopt a latent variable formulation like that of Fawcett and Thomas and use it to estimate several quantities of clinical relevance to determine the efficacy of a treatment in a clinical trial setting. We use a Markov chain Monte Carlo algorithm to estimate the model's parameters. We illustrate the methodology with an analysis of data from a clinical trial comparing risperidone with a placebo for the treatment of schizophrenia.     

Block clustering with collapsed latent block models

We introduce a Bayesian extension of the latent block model for model-based block clustering of data matrices. Our approach considers a block model where block parameters may be integrated out. The result is a posterior defined over the number of clusters in rows and columns and cluster memberships. The number of row and column clusters need not be known in advance as these are sampled along with cluster memberhips using Markov chain Monte Carlo. This differs from existing work on latent block models, where the number of clusters is assumed known or is chosen using some information criteria. We analyze both simulated and real data to validate the technique.     

A poisson-gamma model for two-stage cluster sampling data

We propose a model for count data from two-stage cluster sampling, where observations within each cluster are subjected simultaneously to internal influences and external factors at the cluster level. This model can be seen as a two-stage hierarchical model with local and global predictors. This parameter-driven model causes the counts within a cluster to share a common latent factor and to be correlated. Maximum likelihood (ml) estimation based on an EM algorithm for the model is discussed. Simulation study is carried out to assess the benefit of using ml estimates compared to a standard Poisson regression analysis that ignores the within cluster correlation.     

A finite mixture model for multivariate counts under endogenous selectivity

We describe a selection model for multivariate counts, where association between the primary outcomes and the endogenous selection source is modeled through outcome-specific latent effects which are assumed to be dependent across equations. Parametric specifications of this model already exist in the literature; in this paper, we show how model parameters can be estimated in a finite mixture context. This approach helps us to consider overdispersed counts, while allowing for multivariate association and endogeneity of the selection variable. In this context, attention is focused both on bias in estimated effects when exogeneity of selection (treatment) variable is assumed, as well as on consistent estimation of the association between the random effects in the primary and in the treatment effect models, when the latter is assumed endogeneous. The model behavior is investigated through a large scale simulation experiment. An empirical example on health care utilization data is provided.     

Modeling population and subject-specific growth in a latent trait measured by multiple instruments over time using a hierarchical Bayesian framework

Psychometric growth curve modeling techniques are used to describe a person’s latent ability and how that ability changes over time based on a specific measurement instrument. However, the same instrument cannot always be used over a period of time to measure that latent ability. This is often the case when measuring traits longitudinally in children. Reasons may be that over time some measurement tools that were difficult for young children become too easy as they age resulting in floor effects or ceiling effects or both. We propose a Bayesian hierarchical model for such a scenario. Within the Bayesian model we combine information from multiple instruments used at different age ranges and having different scoring schemes to examine growth in latent ability over time. The model includes between-subject variance and within-subject variance and does not require linking item specific difficulty between the measurement tools. The model’s utility is demonstrated on a study of language ability in children from ages one to ten who are hard of hearing where measurement tool specific growth and subject-specific growth are shown in addition to a group level latent growth curve comparing the hard of hearing children to children with normal hearing.KEYWORDS: Bayesian hierarchical models, psychometric modeling, language ability, growth curve modeling, longitudinal analysis     

A continuous latent spatial model for crack initiation in bone cement

Summary.  Hip replacements rovide a means of achieving a higher quality of life for individuals who have, through aging or injury, accumulated damage to their natural joints. This is a very common operation, with over a million people a year benefiting from the procedure. The replacements themselves fail mainly as a result of the mechanical loosening of the components of the artificial joint due to damage accumulation. This damage accumulation consists of the initiation and growth of cracks in the bone cement which is used to fixate the replacement in the human body. The data come from laboratory experiments that are designed to assess the effectiveness of the bone cement in resisting damage. We examine the properties of the bone cement, with the aim being to estimate the effect that both observable and unobservable spatially varying factors have on causing crack initiation. To do this, an explicit model for the damage process is constructed taking into account the tension and compression at different locations in the specimens. A gamma random field is used to model any latent spatial factors that may be influential in crack initiation. Bayesian inference is carried out for the parameters of this field and related covariates by using Markov chain Monte Carlo techniques.     

Factor Stochastic Volatility in Mean Models: A GMM Approach

This paper provides a semiparametric framework for modeling multivariate conditional heteroskedasticity. We put forward latent stochastic volatility (SV) factors as capturing the commonality in the joint conditional variance matrix of asset returns. This approach is in line with common features as studied by Engle and Kozicki (1993), and it allows us to focus on identication of factors and factor loadings through first- and second-order conditional moments only. We assume that the time-varying part of risk premiums is based on constant prices of factor risks, and we consider a factor SV in mean model. Additional specification of both expectations and volatility of future volatility of factors provides conditional moment restrictions, through which the parameters of the model are all identied. These conditional moment restrictions pave the way for instrumental variables estimation and GMM inference.     

Latent Variable Models for Mixed Discrete and Continuous Outcomes

We propose a latent variable model for mixed discrete and continuous outcomes. The model accommodates any mixture of outcomes from an exponential family and allows for arbitrary covariate effects, as well as direct modelling of covariates on the latent variable. An EM algorithm is proposed for parameter estimation and estimates of the latent variables are produced as a by-product of the analysis. A generalized likelihood ratio test can be used to test the significance of covariates affecting the latent outcomes. This method is applied to birth defects data, where the outcomes of interest are continuous measures of size and binary indicators of minor physical anomalies. Infants who were exposed in utero to anticonvulsant medications are compared with controls.     

Generalized Linear Factor Models: A New Local EM Estimation Algorithm

In this article, a general approach to latent variable models based on an underlying generalized linear model (GLM) with factor analysis observation process is introduced. We call these models Generalized Linear Factor Models (GLFM). The observations are produced from a general model framework that involves observed and latent variables that are assumed to be distributed in the exponential family. More specifically, we concentrate on situations where the observed variables are both discretely measured (e.g., binomial, Poisson) and continuously distributed (e.g., gamma). The common latent factors are assumed to be independent with a standard multivariate normal distribution. Practical details of training such models with a new local expectation-maximization (EM) algorithm, which can be considered as a generalized EM-type algorithm, are also discussed. In conjunction with an approximated version of the Fisher score algorithm (FSA), we show how to calculate maximum likelihood estimates of the model parameters, and to yield inferences about the unobservable path of the common factors. The methodology is illustrated by an extensive Monte Carlo simulation study and the results show promising performance.     

Modeling Longitudinal Obesity Data with Intermittent Missingness Using a New Latent Variable Model

We propose a latent variable model for informative missingness in longitudinal studies which is an extension of latent dropout class model. In our model, the value of the latent variable is affected by the missingness pattern and it is also used as a covariate in modeling the longitudinal response. So the latent variable links the longitudinal response and the missingness process. In our model, the latent variable is continuous instead of categorical and we assume that it is from a normal distribution. The EM algorithm is used to obtain the estimates of the parameter we are interested in and Gauss–Hermite quadrature is used to approximate the integration of the latent variable. The standard errors of the parameter estimates can be obtained from the bootstrap method or from the inverse of the Fisher information matrix of the final marginal likelihood. Comparisons are made to the mixed model and complete-case analysis in terms of a clinical trial dataset, which is Weight Gain Prevention among Women (WGPW) study. We use the generalized Pearson residuals to assess the fit of the proposed latent variable model.     

Mixture of latent trait analyzers for model-based clustering of categorical data

Model-based clustering methods for continuous data are well established and commonly used in a wide range of applications. However, model-based clustering methods for categorical data are less standard. Latent class analysis is a commonly used method for model-based clustering of binary data and/or categorical data, but due to an assumed local independence structure there may not be a correspondence between the estimated latent classes and groups in the population of interest. The mixture of latent trait analyzers model extends latent class analysis by assuming a model for the categorical response variables that depends on both a categorical latent class and a continuous latent trait variable; the discrete latent class accommodates group structure and the continuous latent trait accommodates dependence within these groups. Fitting the mixture of latent trait analyzers model is potentially difficult because the likelihood function involves an integral that cannot be evaluated analytically. We develop a variational approach for fitting the mixture of latent trait models and this provides an efficient model fitting strategy. The mixture of latent trait analyzers model is demonstrated on the analysis of data from the National Long Term Care Survey (NLTCS) and voting in the U.S. Congress. The model is shown to yield intuitive clustering results and it gives a much better fit than either latent class analysis or latent trait analysis alone.     

Bayesian discrete latent spatial modeling of crack initiation in orthopaedic hip replacement bone cement

In this paper, we propose a spatial model for the initiation of cracks in the bone cement of hip replacement specimens. The failure of hip replacements can be attributed mainly to damage accumulation, consisting of crack initiation and growth, occurring in the cement mantle that interlocks the hip prosthesis and the femur bone. Since crack initiation is an important factor in determining the lifetime of a replacement, the understanding of the reasons for crack initiation is vital in attempting to prolong the life of the hip replacement. The data consist of crack location coordinates from five laboratory experimental models, together with stress measurements. It is known that stress plays a major role in the initiation of cracks, and it is also known that other unmeasurable factors such as air bubbles (pores) in the cement mantle are also influential. We propose an identity-link spatial Poisson regression model for the counts of cracks in discrete regions of the cement, incorporating both the measured (stress), and through a latent process, any unmeasured factors (possibly pores) that may be influential. All analysis is carried out in a Bayesian framework, allowing for the inclusion of prior information obtained from engineers, and parameter estimation for the model is done via Markov chain Monte Carlo techniques.     

Structural equation models for area health outcomes with model selection

Recent analyses seeking to explain variation in area health outcomes often consider the impact on them of latent measures (i.e. unobserved constructs) of population health risk. The latter are typically obtained by forms of multivariate analysis, with a small set of latent constructs derived from a collection of observed indicators, and a few recent area studies take such constructs to be spatially structured rather than independent over areas. A confirmatory approach is often applicable to the model linking indicators to constructs, based on substantive knowledge of relevant risks for particular diseases or outcomes. In this paper, population constructs relevant to a particular set of health outcomes are derived using an integrated model containing all the manifest variables, namely health outcome variables, as well as indicator variables underlying the latent constructs. A further feature of the approach is the use of variable selection techniques to select significant loadings and factors (especially in terms of effects of constructs on health outcomes), so ensuring parsimonious models are selected. A case study considers suicide mortality and self-harm contrasts in the East of England in relation to three latent constructs: deprivation, fragmentation and urbanicity.     

A Mixture Model for Longitudinal Partially Ranked Data

This article discusses the use of mixture models in the analysis of longitudinal partially ranked data, where respondents, for example, choose only the preferred and second preferred out of a set of items. To model such data we convert it to a set of paired comparisons. Covariates can be incorporated into the model. We use a nonparametric mixture to account for unmeasured variability in individuals over time. The resulting multi-valued mass points can be interpreted as latent classes of the items. The work is illustrated by two questions on (post)materialism in three sweeps of the British Household Panel Survey.     

Application of a predictive distribution formula to Bayesian computation for incomplete data models

We consider exact and approximate Bayesian computation in the presence of latent variables or missing data. Specifically we explore the application of a posterior predictive distribution formula derived in Sweeting And Kharroubi (2003), which is a particular form of Laplace approximation, both as an importance function and a proposal distribution. We show that this formula provides a stable importance function for use within poor man’s data augmentation schemes and that it can also be used as a proposal distribution within a Metropolis-Hastings algorithm for models that are not analytically tractable. We illustrate both uses in the case of a censored regression model and a normal hierarchical model, with both normal and Student t distributed random effects. Although the predictive distribution formula is motivated by regular asymptotic theory, it is not necessary that the likelihood has a closed form or that it possesses a local maximum.     

State-space models for multivariate longitudinal data of mixed types

We propose a class of state-space models for multivariate longitudinal data where the components of the response vector may have different distributions. The approach is based on the class of Tweedie exponential dispersion models, which accommodates a wide variety of discrete, continuous and mixed data. The latent process is assumed to be a Markov process, and the observations are conditionally independent given the latent process, over time as well as over the components of the response vector. This provides a fully parametric alternative to the quasilikelihood approach of Liang and Zeger. We estimate the regression parameters for time-varying covariates entering either via the observation model or via the latent process, based on an estimating equation derived from the Kalman smoother. We also consider analysis of residuals from both the observation model and the latent process.     

The beta distribution as a latent response model for ordinal data (I): Estimation of location and dispersion parameters

Ordinal data are often modeled using a continuous latent response distribution, which is partially observed through windows of adjacent intervals defined by cutpoints. In this paper we propose the beta distribution as a model for the latent response. The beta distribution has several advantages over the other common distributions used, e.g. , normal and logistic. In particular, it enables separate modeling of location and dispersion effects which is essential in the Taguchi method of robust design. First, we study the problem of estimating the location and dispersion parameters of a single beta distribution (representing a single treatment) from ordinal data assuming known equispaced cutpoints. Two methods of estimation are compared: the maximum likelihood method and the method of moments. Two methods of treating the data are considered: in raw discrete form and in smoothed continuousized form. A large scale simulation study is carried out to compare the different methods. The mean square errors of the estimates are obtained under a variety of parameter configurations. Comparisons are made based on the ratios of the mean square errors (called the relative efficiencies). No method is universally the best, but the maximum likelihood method using continuousized data is found to perform generally well, especially for estimating the dispersion parameter. This method is also computationally much faster than the other methods and does not experience convergence difficulties in case of sparse or empty cells. Next, the problem of estimating unknown cutpoints is addressed. Here the multiple treatments setup is considered since in an actual application, cutpoints are common to all treatments, and must be estimated from all the data. A two-step iterative algorithm is proposed for estimating the location and dispersion parameters of the treatments, and the cutpoints. The proposed beta model and McCullagh's (1980) proportional odds model are compared by fitting them to two real data sets.     

A non-iterative approach to estimating parameters in a linear structural equation model

The research described herein was motivated by a study of the relationship between the performance of students in senior high schools and at universities in China. A special linear structural equation model is established, in which some parameters are known and both the responses and the covariables are measured with errors. To explore the relationship between the true responses and latent covariables and to estimate the parameters, we suggest a non-iterative estimation approach that can account for the external dependence between the true responses and latent covariables. This approach can also deal with the collinearity problem because the use of dimension-reduction techniques can remove redundant variables. Combining further with the information that some of parameters are given, we can perform estimation for the other unknown parameters. An easily implemented algorithm is provided. A simulation is carried out to provide evidence of the performance of the approach and to compare it with existing methods. The approach is applied to the education example for illustration, and it can be readily extended to more general models.