Selection of Predictors in Distance-Based Regression

Distance-based regression is a prediction method consisting of two steps: from distances between observations we obtain latent variables which, in turn, are the regressors in an ordinary least squares linear model. Distances are computed from actually observed predictors by means of a suitable dissimilarity function. Being generally nonlinearly related with the response, their selection by the usual F tests is unavailable. In this article, we propose a solution to this predictor selection problem by defining generalized test statistics and adapting a nonparametric bootstrap method to estimate their p-values. We include a numerical example with automobile insurance data.     

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.     

A multivariate finite mixture latent trajectory model with application to dementia studies

Dementia patients exhibit considerable heterogeneity in individual trajectories of cognitive decline, with some patients showing rapid decline following diagnoses while others exhibiting slower decline or remaining stable for several years. Dementia studies often collect longitudinal measures of multiple neuropsychological tests aimed to measure patients’ decline across a number of cognitive domains. We propose a multivariate finite mixture latent trajectory model to identify distinct longitudinal patterns of cognitive decline simultaneously in multiple cognitive domains, each of which is measured by multiple neuropsychological tests. EM algorithm is used for parameter estimation and posterior probabilities are used to predict latent class membership. We present results of a simulation study demonstrating adequate performance of our proposed approach and apply our model to the Uniform Data Set from the National Alzheimer's Coordinating Center to identify cognitive decline patterns among dementia patients.     

Hidden Markov Mixture Autoregressive Models: Stability and Moments

This article introduces a parsimonious structure for mixture of autoregressive models, where the weighting coefficients are determined through latent random variables, as functions of all past observations. These latent variables follow a Markov model. We propose a dynamic programming algorithm for forecasting, which reduces the volume of calculations. We also derive limiting behavior of unconditional first moment of the process and an appropriate upper bound for the limiting value of the variance. Further more, we show convergence and stability of the second moment. Finally, we illustrate the efficacy of the proposed model by simulation.     

Augmentation schemes for particle MCMC

Particle MCMC involves using a particle filter within an MCMC algorithm. For inference of a model which involves an unobserved stochastic process, the standard implementation uses the particle filter to propose new values for the stochastic process, and MCMC moves to propose new values for the parameters. We show how particle MCMC can be generalised beyond this. Our key idea is to introduce new latent variables. We then use the MCMC moves to update the latent variables, and the particle filter to propose new values for the parameters and stochastic process given the latent variables. A generic way of defining these latent variables is to model them as pseudo-observations of the parameters or of the stochastic process. By choosing the amount of information these latent variables have about the parameters and the stochastic process we can often improve the mixing of the particle MCMC algorithm by trading off the Monte Carlo error of the particle filter and the mixing of the MCMC moves. We show that using pseudo-observations within particle MCMC can improve its efficiency in certain scenarios: dealing with initialisation problems of the particle filter; speeding up the mixing of particle Gibbs when there is strong dependence between the parameters and the stochastic process; and enabling further MCMC steps to be used within the particle filter.     

A statistical algorithm for detecting cognitive plateaus in Alzheimer’s disease

Repeated neuropsychological measurements, such as mini-mental state examination (MMSE) scores, are frequently used in Alzheimer’s disease (AD) research to study change in cognitive function of AD patients. A question of interest among dementia researchers is whether some AD patients exhibit transient “plateaus” of cognitive function in the course of the disease. We consider a statistical approach to this question, based on irregularly spaced repeated MMSE scores. We propose an algorithm that formalizes the measurement of an apparent cognitive plateau, and a procedure to evaluate the evidence of plateaus in AD using this algorithm based on applying the algorithm to the observed data and to data sets simulated from a linear mixed model. We apply these methods to repeated MMSE data from the Michigan Alzheimer’s Disease Research Center, finding a high rate of apparent plateaus and also a high rate of false discovery. Simulation studies are also conducted to assess the performance of the algorithm. In general, the false discovery rate of the algorithm is high unless the rate of decline is high compared with the measurement error of the cognitive test. It is argued that the results are not a problem of the specific algorithm chosen, but reflect a lack of information concerning the presence of plateaus in the data.     

Modelling longitudinal semicontinuous emesis volume data with serial correlation in an acupuncture clinical trial

Summary.  In longitudinal studies, we are often interested in modelling repeated assessments of volume over time. Our motivating example is an acupuncture clinical trial in which we compare the effects of active acupuncture, sham acupuncture and standard medical care on chemotherapy-induced nausea in patients being treated for advanced stage breast cancer. An important end point for this study was the daily measurement of the volume of emesis over a 14-day follow-up period. The repeated volume data contained many 0s, had apparent serial correlation and had missing observations, making analysis challenging. The paper proposes a two-part latent process model for analysing the emesis volume data which addresses these challenges. We propose a Monte Carlo EM algorithm for parameter estimation and we use this methodology to show the beneficial effects of acupuncture on reducing the volume of emesis in women being treated for breast cancer with chemotherapy. Through simulations, we demonstrate the importance of correctly modelling the serial correlation for making conditional inference. Further, we show that the correct model for the correlation structure is less important for making correct inference on marginal means.     

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 Bayesian model for estimating the malaria transition probabilities considering individuals lost to follow-up

It is known that patients may cease participating in a longitudinal study and become lost to follow-up. The objective of this article is to present a Bayesian model to estimate the malaria transition probabilities considering individuals lost to follow-up. We consider a homogeneous population, and it is assumed that the considered period of time is small enough to avoid two or more transitions from one state of health to another. The proposed model is based on a Gibbs sampling algorithm that uses information of lost to follow-up at the end of the longitudinal study. To simulate the unknown number of individuals with positive and negative states of malaria at the end of the study and lost to follow-up, two latent variables were introduced in the model. We used a real data set and a simulated data to illustrate the application of the methodology. The proposed model showed a good fit to these data sets, and the algorithm did not show problems of convergence or lack of identifiability. We conclude that the proposed model is a good alternative to estimate probabilities of transitions from one state of health to the other in studies with low adherence to follow-up.     

Distance-based approach in univariate longitudinal data analysis

In this paper, we propose a methodology to analyze longitudinal data through distances between pairs of observations (or individuals) with regard to the explanatory variables used to fit continuous response variables. Restricted maximum-likelihood and generalized least squares are used to estimate the parameters in the model. We applied this new approach to study the effect of gender and exposure on the deviant behavior variable with respect to tolerance for a group of youths studied over a period of 5 years. Were performed simulations where we compared our distance-based method with classic longitudinal analysis with both AR(1) and compound symmetry correlation structures. We compared them under Akaike and Bayesian information criterions, and the relative efficiency of the generalized variance of the errors of each model. We found small gains in the proposed model fit with regard to the classical methodology, particularly in small samples, regardless of variance, correlation, autocorrelation structure and number of time measurements.     

Maximum likelihood estimation of bivariate circular hidden Markov models from incomplete data

In this paper, we propose a hidden Markov model for the analysis of the time series of bivariate circular observations, by assuming that the data are sampled from bivariate circular densities, whose parameters are driven by the evolution of a latent Markov chain. The model segments the data by accounting for redundancies due to correlations along time and across variables. A computationally feasible expectation maximization (EM) algorithm is provided for the maximum likelihood estimation of the model from incomplete data, by treating the missing values and the states of the latent chain as two different sources of incomplete information. Importance-sampling methods facilitate the computation of bootstrap standard errors of the estimates. The methodology is illustrated on a bivariate time series of wind and wave directions and compared with popular segmentation models for bivariate circular data, which ignore correlations across variables and/or along time.     

A rare event approach to high-dimensional approximate Bayesian computation

Approximate Bayesian computation (ABC) methods permit approximate inference for intractable likelihoods when it is possible to simulate from the model. However, they perform poorly for high-dimensional data and in practice must usually be used in conjunction with dimension reduction methods, resulting in a loss of accuracy which is hard to quantify or control. We propose a new ABC method for high-dimensional data based on rare event methods which we refer to as RE-ABC. This uses a latent variable representation of the model. For a given parameter value, we estimate the probability of the rare event that the latent variables correspond to data roughly consistent with the observations. This is performed using sequential Monte Carlo and slice sampling to systematically search the space of latent variables. In contrast, standard ABC can be viewed as using a more naive Monte Carlo estimate. We use our rare event probability estimator as a likelihood estimate within the pseudo-marginal Metropolis–Hastings algorithm for parameter inference. We provide asymptotics showing that RE-ABC has a lower computational cost for high-dimensional data than standard ABC methods. We also illustrate our approach empirically, on a Gaussian distribution and an application in infectious disease modelling.     

Multivariate autoregressive extreme value process and its application for modeling the time series properties of the extreme daily asset prices

Abstract

In this article we suggest a new multivariate autoregressive process for modeling time-dependent extreme value distributed observations. The idea behind the approach is to transform the original observations to latent variables that are univariate normally distributed. Then the vector autoregressive DCC model is fitted to the multivariate latent process. The distributional properties of the suggested model are extensively studied. The process parameters are estimated by applying a two-stage estimation procedure. We derive a prediction interval for future values of the suggested process. The results are applied in an empirically study by modeling the behavior of extreme daily stock prices.     

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.     

Joint modeling and estimation for longitudinal data with informative observation and terminal event times

ABSTRACT

In many longitudinal studies, there may exist informative observation times and a dependent terminal event that stops the follow-up. In this paper, we propose a joint model for analysis of longitudinal data with informative observation times and a dependent terminal event via two latent variables. Estimation procedures are developed for parameter estimation, and asymptotic properties of the proposed estimators are derived. Simulation studies demonstrate that the proposed method performs well for practical settings. An application to a bladder cancer study is illustrated.     

Quantile regression for longitudinal data based on latent Markov subject-specific parameters

We propose a latent Markov quantile regression model for longitudinal data with non-informative drop-out. The observations, conditionally on covariates, are modeled through an asymmetric Laplace distribution. Random effects are assumed to be time-varying and to follow a first order latent Markov chain. This latter assumption is easily interpretable and allows exact inference through an ad hoc EM-type algorithm based on appropriate recursions. Finally, we illustrate the model on a benchmark data set.     

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.     

Bayesian covariance estimation and inference in latent Gaussian process models

This paper describes inference methods for functional data under the assumption that the functional data of interest are smooth latent functions, characterized by a Gaussian process, which have been observed with noise over a finite set of time points. The methods we propose are completely specified in a Bayesian environment that allows for all inferences to be performed through a simple Gibbs sampler. Our main focus is in estimating and describing uncertainty in the covariance function. However, these models also encompass functional data estimation, functional regression where the predictors are latent functions, and an automatic approach to smoothing parameter selection. Furthermore, these models require minimal assumptions on the data structure as the time points for observations do not need to be equally spaced, the number and placement of observations are allowed to vary among functions, and special treatment is not required when the number of functional observations is less than the dimensionality of those observations. We illustrate the effectiveness of these models in estimating latent functional data, capturing variation in the functional covariance estimate, and in selecting appropriate smoothing parameters in both a simulation study and a regression analysis of medfly fertility data.     

Improving estimation for beta regression models via EM-algorithm and related diagnostic tools

In this paper we propose an alternative procedure for estimating the parameters of the beta regression model. This alternative estimation procedure is based on the EM-algorithm. For this, we took advantage of the stochastic representation of the beta random variable through ratio of independent gamma random variables. We present a complete approach based on the EM-algorithm. More specifically, this approach includes point and interval estimations and diagnostic tools for detecting outlying observations. As it will be illustrated in this paper, the EM-algorithm approach provides a better estimation of the precision parameter when compared to the direct maximum likelihood (ML) approach. We present the results of Monte Carlo simulations to compare EM-algorithm and direct ML. Finally, two empirical examples illustrate the full EM-algorithm approach for the beta regression model. This paper contains a Supplementary Material.     

Bayesian estimation in the multidimensional three-parameter logistic model

The Gibbs sampler has a great potential to be an efficient and versatile estimation procedure in item response theory. In this article, based on a data augmentation scheme using the Gibbs sampler, we propose a Bayesian procedure to estimate the multidimensional three-parameter logistic model. With the introduction of the two latent variables, the full conditional distributions are tractable, and consequently the Gibbs sampling is easy to implement. Finally, the technique is illustrated by using simulated and real data, respectively.