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1.  A joint model of longitudinal and competing risks survival data with heterogeneous random effects and outlying longitudinal measurements 
Statistics and its interface  2010;3(2):185-195.
This article proposes a joint model for longitudinal measurements and competing risks survival data. The model consists of a linear mixed effects sub-model with t-distributed measurement errors for the longitudinal outcome, a proportional cause-specific hazards frailty sub-model for the survival outcome, and a regression sub-model for the variance-covariance matrix of the multivariate latent random effects based on a modified Cholesky decomposition. A Bayesian MCMC procedure is developed for parameter estimation and inference. Our method is insensitive to outlying longitudinal measurements in the presence of non-ignorable missing data due to dropout. Moreover, by modeling the variance-covariance matrix of the latent random effects, our model provides a useful framework for handling high-dimensional heterogeneous random effects and testing the homogeneous random effects assumption which is otherwise untestable in commonly used joint models. Finally, our model enables analysis of a survival outcome with intermittently measured time-dependent covariates and possibly correlated competing risks and dependent censoring, as well as joint analysis of the longitudinal and survival outcomes. Illustrations are given using a real data set from a lung study and simulation.
PMCID: PMC3166346  PMID: 21892381
Joint model; Competing risks; Bayesian analysis; Cholesky decomposition; Mixed effects model; MCMC; Modeling random effects covariance matrix; Outlier
2.  A Nonparametric Prior for Simultaneous Covariance Estimation 
Biometrika  2012;100(1):10.1093/biomet/ass060.
Summary
In the modeling of longitudinal data from several groups, appropriate handling of the dependence structure is of central importance. Standard methods include specifying a single covariance matrix for all groups or independently estimating the covariance matrix for each group without regard to the others, but when these model assumptions are incorrect, these techniques can lead to biased mean effects or loss of efficiency, respectively. Thus, it is desirable to develop methods to simultaneously estimate the covariance matrix for each group that will borrow strength across groups in a way that is ultimately informed by the data. In addition, for several groups with covariance matrices of even medium dimension, it is difficult to manually select a single best parametric model among the huge number of possibilities given by incorporating structural zeros and/or commonality of individual parameters across groups. In this paper we develop a family of nonparametric priors using the matrix stick-breaking process of Dunson et al. (2008) that seeks to accomplish this task by parameterizing the covariance matrices in terms of the parameters of their modified Cholesky decomposition (Pourahmadi, 1999). We establish some theoretic properties of these priors, examine their effectiveness via a simulation study, and illustrate the priors using data from a longitudinal clinical trial.
doi:10.1093/biomet/ass060
PMCID: PMC3852937  PMID: 24324281
Bayesian nonparametric inference; Cholesky decomposition; matrix stick-breaking process; simultaneous covariance estimation; sparsity
3.  Dynamic Conditionally Linear Mixed Models for Longitudinal Data 
Biometrics  2002;58(1):225-231.
Summary
We develop a new class of models, dynamic conditionally linear mixed models, for longitudinal data by decomposing the within-subject covariance matrix using a special Cholesky decomposition. Here ‘dynamic’ means using past responses as covariates and ‘conditional linearity’ means that parameters entering the model linearly may be random, but nonlinear parameters are nonrandom. This setup offers several advantages and is surprisingly similar to models obtained from the first-order linearization method applied to nonlinear mixed models. First, it allows for flexible and computationally tractable models that include a wide array of covariance structures; these structures may depend on covariates and hence may differ across subjects. This class of models includes, e.g., all standard linear mixed models, antedependence models, and Vonesh–Carter models. Second, it guarantees the fitted marginal covariance matrix of the data is positive definite. We develop methods for Bayesian inference and motivate the usefulness of these models using a series of longitudinal depression studies for which the features of these new models are well suited.
PMCID: PMC2755537  PMID: 11890319
Covariance matrix; Heterogeneity; Hierarchical models; Markov chain Monte Carlo; Missing data; Unconstrained parameterization
4.  A general joint model for longitudinal measurements and competing risks survival data with heterogeneous random effects 
Lifetime data analysis  2010;17(1):80-100.
This article studies a general joint model for longitudinal measurements and competing risks survival data. The model consists of a linear mixed effects sub-model for the longitudinal outcome, a proportional cause-specific hazards frailty sub-model for the competing risks survival data, and a regression sub-model for the variance–covariance matrix of the multivariate latent random effects based on a modified Cholesky decomposition. The model provides a useful approach to adjust for non-ignorable missing data due to dropout for the longitudinal outcome, enables analysis of the survival outcome with informative censoring and intermittently measured time-dependent covariates, as well as joint analysis of the longitudinal and survival outcomes. Unlike previously studied joint models, our model allows for heterogeneous random covariance matrices. It also offers a framework to assess the homogeneous covariance assumption of existing joint models. A Bayesian MCMC procedure is developed for parameter estimation and inference. Its performances and frequentist properties are investigated using simulations. A real data example is used to illustrate the usefulness of the approach.
doi:10.1007/s10985-010-9169-6
PMCID: PMC3162577  PMID: 20549344
Cause-specific hazard; Bayesian analysis; Cholesky decomposition; Mixed effects model; MCMC; Modeling covariance matrices
5.  Influence of priors in Bayesian estimation of genetic parameters for multivariate threshold models using Gibbs sampling 
Simulated data were used to investigate the influence of the choice of priors on estimation of genetic parameters in multivariate threshold models using Gibbs sampling. We simulated additive values, residuals and fixed effects for one continuous trait and liabilities of four binary traits, and QTL effects for one of the liabilities. Within each of four replicates six different datasets were generated which resembled different practical scenarios in horses with respect to number and distribution of animals with trait records and availability of QTL information. (Co)Variance components were estimated using a Bayesian threshold animal model via Gibbs sampling. The Gibbs sampler was implemented with both a flat and a proper prior for the genetic covariance matrix. Convergence problems were encountered in > 50% of flat prior analyses, with indications of potential or near posterior impropriety between about round 10 000 and 100 000. Terminations due to non-positive definite genetic covariance matrix occurred in flat prior analyses of the smallest datasets. Use of a proper prior resulted in improved mixing and convergence of the Gibbs chain. In order to avoid (near) impropriety of posteriors and extremely poorly mixing Gibbs chains, a proper prior should be used for the genetic covariance matrix when implementing the Gibbs sampler.
doi:10.1186/1297-9686-39-2-123
PMCID: PMC2682833  PMID: 17306197
Gibbs sampling; multivariate threshold model; covariance estimates; flat prior; proper prior
6.  Bayesian estimation in animal breeding using the Dirichlet process prior for correlated random effects 
In the case of the mixed linear model the random effects are usually assumed to be normally distributed in both the Bayesian and classical frameworks. In this paper, the Dirichlet process prior was used to provide nonparametric Bayesian estimates for correlated random effects. This goal was achieved by providing a Gibbs sampler algorithm that allows these correlated random effects to have a nonparametric prior distribution. A sampling based method is illustrated. This method which is employed by transforming the genetic covariance matrix to an identity matrix so that the random effects are uncorrelated, is an extension of the theory and the results of previous researchers. Also by using Gibbs sampling and data augmentation a simulation procedure was derived for estimating the precision parameter M associated with the Dirichlet process prior. All needed conditional posterior distributions are given. To illustrate the application, data from the Elsenburg Dormer sheep stud were analysed. A total of 3325 weaning weight records from the progeny of 101 sires were used.
doi:10.1186/1297-9686-35-2-137
PMCID: PMC2732692  PMID: 12633530
Bayesian methods; mixed linear model; Dirichlet process prior; correlated random effects; Gibbs sampler
7.  Modeling Covariance Matrices via Partial Autocorrelations 
Journal of multivariate analysis  2009;100(10):2352-2363.
Summary
We study the role of partial autocorrelations in the reparameterization and parsimonious modeling of a covariance matrix. The work is motivated by and tries to mimic the phenomenal success of the partial autocorrelations function (PACF) in model formulation, removing the positive-definiteness constraint on the autocorrelation function of a stationary time series and in reparameterizing the stationarity-invertibility domain of ARMA models. It turns out that once an order is fixed among the variables of a general random vector, then the above properties continue to hold and follows from establishing a one-to-one correspondence between a correlation matrix and its associated matrix of partial autocorrelations. Connections between the latter and the parameters of the modified Cholesky decomposition of a covariance matrix are discussed. Graphical tools similar to partial correlograms for model formulation and various priors based on the partial autocorrelations are proposed. We develop frequentist/Bayesian procedures for modelling correlation matrices, illustrate them using a real dataset, and explore their properties via simulations.
doi:10.1016/j.jmva.2009.04.015
PMCID: PMC2748961  PMID: 20161018
Autoregressive parameters; Cholesky decomposition; Positive-definiteness constraint; Levinson-Durbin algorithm; Prediction variances; Uniform and Reference Priors; Markov Chain Monte Carlo
8.  Equivalence of multibreed animal models and hierarchical Bayes analysis for maternally influenced traits 
Background
It has been argued that multibreed animal models should include a heterogeneous covariance structure. However, the estimation of the (co)variance components is not an easy task, because these parameters can not be factored out from the inverse of the additive genetic covariance matrix. An alternative model, based on the decomposition of the genetic covariance matrix by source of variability, provides a much simpler formulation. In this study, we formalize the equivalence between this alternative model and the one derived from the quantitative genetic theory. Further, we extend the model to include maternal effects and, in order to estimate the (co)variance components, we describe a hierarchical Bayes implementation. Finally, we implement the model to weaning weight data from an Angus × Hereford crossbred experiment.
Methods
Our argument is based on redefining the vectors of breeding values by breed origin such that they do not include individuals with null contributions. Next, we define matrices that retrieve the null-row and the null-column pattern and, by means of appropriate algebraic operations, we demonstrate the equivalence. The extension to include maternal effects and the estimation of the (co)variance components through the hierarchical Bayes analysis are then straightforward. A FORTRAN 90 Gibbs sampler was specifically programmed and executed to estimate the (co)variance components of the Angus × Hereford population.
Results
In general, genetic (co)variance components showed marginal posterior densities with a high degree of symmetry, except for the segregation components. Angus and Hereford breeds contributed with 50.26% and 41.73% of the total direct additive variance, and with 23.59% and 59.65% of the total maternal additive variance. In turn, the contribution of the segregation variance was not significant in either case, which suggests that the allelic frequencies in the two parental breeds were similar.
Conclusion
The multibreed maternal animal model introduced in this study simplifies the problem of estimating (co)variance components in the framework of a hierarchical Bayes analysis. Using this approach, we obtained for the first time estimates of the full set of genetic (co)variance components. It would be interesting to assess the performance of the procedure with field data, especially when interbreed information is limited.
doi:10.1186/1297-9686-42-20
PMCID: PMC2909157  PMID: 20540758
9.  An efficient technique for Bayesian modeling of family data using the BUGS software 
Frontiers in Genetics  2014;5:390.
Linear mixed models have become a popular tool to analyze continuous data from family-based designs by using random effects that model the correlation of subjects from the same family. However, mixed models for family data are challenging to implement with the BUGS (Bayesian inference Using Gibbs Sampling) software because of the high-dimensional covariance matrix of the random effects. This paper describes an efficient parameterization that utilizes the singular value decomposition of the covariance matrix of random effects, includes the BUGS code for such implementation, and extends the parameterization to generalized linear mixed models. The implementation is evaluated using simulated data and an example from a large family-based study is presented with a comparison to other existing methods.
doi:10.3389/fgene.2014.00390
PMCID: PMC4235415  PMID: 25477899
BUGS; parameterization; family-based study; covariance matrix; linear mixed models
10.  Flexible estimation of covariance function by penalized spline with application to longitudinal family data 
Statistics in medicine  2011;30(15):1883-1897.
Longitudinal data are routinely collected in biomedical research studies. A natural model describing longitudinal data decomposes an individual’s outcome as the sum of a population mean function and random subject-specific deviations. When parametric assumptions are too restrictive, methods modeling the population mean function and the random subject-specific functions nonparametrically are in demand. In some applications, it is desirable to estimate a covariance function of random subject-specific deviations. In this work, flexible yet computationally efficient methods are developed for a general class of semiparametric mixed effects models, where the functional forms of the population mean and the subject-specific curves are unspecified. We estimate nonparametric components of the model by penalized spline (P-spline, [1]), and reparametrize the random curve covariance function by a modified Cholesky decomposition [2] which allows for unconstrained estimation of a positive semidefinite matrix. To provide smooth estimates, we penalize roughness of fitted curves and derive closed form solutions in the maximization step of an EM algorithm. In addition, we present models and methods for longitudinal family data where subjects in a family are correlated and we decompose the covariance function into a subject-level source and observation-level source. We apply these methods to the multi-level Framingham Heart Study data to estimate age-specific heritability of systolic blood pressure (SBP) nonparametrically.
doi:10.1002/sim.4236
PMCID: PMC3115522  PMID: 21491474
Multi-level functional data; Cholesky decomposition; Age-specific heritability; Framingham Heart Study
11.  A Penalized spline approach to functional mixed effects model analysis 
Biometrics  2007;64(3):751-761.
Summary
In this work, we propose penalized spline based methods for functional mixed effects models with varying coefficients. We decompose longitudinal outcomes as a sum of several terms: a population mean function, covariates with time-varying coefficients, functional subject-specific random effects and residual measurement error processes. Using penalized splines, we propose nonparametric estimation of the population mean function, varying-coefficient, random subject-specific curves and the associated covariance function which represents between-subject variation and the variance function of the residual measurement errors which represents within-subject variation. Proposed methods offer flexible estimation of both the population-level and subject-level curves. In addition, decomposing variability of the outcomes as a between-subject and a within-subject source is useful in identifying the dominant variance component therefore optimally model a covariance function. We use a likelihood based method to select multiple smoothing parameters. Furthermore, we study the asymptotics of the baseline P-spline estimator with longitudinal data. We conduct simulation studies to investigate performance of the proposed methods. The benefit of the between- and within-subject covariance decomposition is illustrated through an analysis of Berkeley growth data where we identified clearly distinct patterns of the between- and within-subject covariance functions of children's heights. We also apply the proposed methods to estimate the effect of anti-hypertensive treatment from the Framingham Heart Study data.
doi:10.1111/j.1541-0420.2007.00940.x
PMCID: PMC2996855  PMID: 18047528
Multi-level functional data; Functional random effects; Semiparametric longitudinal data analysis
12.  A heteroskedastic error covariance matrix estimator using a first-order conditional autoregressive Markov simulation for deriving asympotical efficient estimates from ecological sampled Anopheles arabiensis aquatic habitat covariates 
Malaria Journal  2009;8:216.
Background
Autoregressive regression coefficients for Anopheles arabiensis aquatic habitat models are usually assessed using global error techniques and are reported as error covariance matrices. A global statistic, however, will summarize error estimates from multiple habitat locations. This makes it difficult to identify where there are clusters of An. arabiensis aquatic habitats of acceptable prediction. It is therefore useful to conduct some form of spatial error analysis to detect clusters of An. arabiensis aquatic habitats based on uncertainty residuals from individual sampled habitats. In this research, a method of error estimation for spatial simulation models was demonstrated using autocorrelation indices and eigenfunction spatial filters to distinguish among the effects of parameter uncertainty on a stochastic simulation of ecological sampled Anopheles aquatic habitat covariates. A test for diagnostic checking error residuals in an An. arabiensis aquatic habitat model may enable intervention efforts targeting productive habitats clusters, based on larval/pupal productivity, by using the asymptotic distribution of parameter estimates from a residual autocovariance matrix. The models considered in this research extends a normal regression analysis previously considered in the literature.
Methods
Field and remote-sampled data were collected during July 2006 to December 2007 in Karima rice-village complex in Mwea, Kenya. SAS 9.1.4® was used to explore univariate statistics, correlations, distributions, and to generate global autocorrelation statistics from the ecological sampled datasets. A local autocorrelation index was also generated using spatial covariance parameters (i.e., Moran's Indices) in a SAS/GIS® database. The Moran's statistic was decomposed into orthogonal and uncorrelated synthetic map pattern components using a Poisson model with a gamma-distributed mean (i.e. negative binomial regression). The eigenfunction values from the spatial configuration matrices were then used to define expectations for prior distributions using a Markov chain Monte Carlo (MCMC) algorithm. A set of posterior means were defined in WinBUGS 1.4.3®. After the model had converged, samples from the conditional distributions were used to summarize the posterior distribution of the parameters. Thereafter, a spatial residual trend analyses was used to evaluate variance uncertainty propagation in the model using an autocovariance error matrix.
Results
By specifying coefficient estimates in a Bayesian framework, the covariate number of tillers was found to be a significant predictor, positively associated with An. arabiensis aquatic habitats. The spatial filter models accounted for approximately 19% redundant locational information in the ecological sampled An. arabiensis aquatic habitat data. In the residual error estimation model there was significant positive autocorrelation (i.e., clustering of habitats in geographic space) based on log-transformed larval/pupal data and the sampled covariate depth of habitat.
Conclusion
An autocorrelation error covariance matrix and a spatial filter analyses can prioritize mosquito control strategies by providing a computationally attractive and feasible description of variance uncertainty estimates for correctly identifying clusters of prolific An. arabiensis aquatic habitats based on larval/pupal productivity.
doi:10.1186/1475-2875-8-216
PMCID: PMC2760564  PMID: 19772590
13.  Unsupervised Bayesian linear unmixing of gene expression microarrays 
BMC Bioinformatics  2013;14:99.
Background
This paper introduces a new constrained model and the corresponding algorithm, called unsupervised Bayesian linear unmixing (uBLU), to identify biological signatures from high dimensional assays like gene expression microarrays. The basis for uBLU is a Bayesian model for the data samples which are represented as an additive mixture of random positive gene signatures, called factors, with random positive mixing coefficients, called factor scores, that specify the relative contribution of each signature to a specific sample. The particularity of the proposed method is that uBLU constrains the factor loadings to be non-negative and the factor scores to be probability distributions over the factors. Furthermore, it also provides estimates of the number of factors. A Gibbs sampling strategy is adopted here to generate random samples according to the posterior distribution of the factors, factor scores, and number of factors. These samples are then used to estimate all the unknown parameters.
Results
Firstly, the proposed uBLU method is applied to several simulated datasets with known ground truth and compared with previous factor decomposition methods, such as principal component analysis (PCA), non negative matrix factorization (NMF), Bayesian factor regression modeling (BFRM), and the gradient-based algorithm for general matrix factorization (GB-GMF). Secondly, we illustrate the application of uBLU on a real time-evolving gene expression dataset from a recent viral challenge study in which individuals have been inoculated with influenza A/H3N2/Wisconsin. We show that the uBLU method significantly outperforms the other methods on the simulated and real data sets considered here.
Conclusions
The results obtained on synthetic and real data illustrate the accuracy of the proposed uBLU method when compared to other factor decomposition methods from the literature (PCA, NMF, BFRM, and GB-GMF). The uBLU method identifies an inflammatory component closely associated with clinical symptom scores collected during the study. Using a constrained model allows recovery of all the inflammatory genes in a single factor.
doi:10.1186/1471-2105-14-99
PMCID: PMC3681645  PMID: 23506672
14.  Bayesian Inference in Semiparametric Mixed Models for Longitudinal Data 
Biometrics  2009;66(1):70-78.
SUMMARY
We consider Bayesian inference in semiparametric mixed models (SPMMs) for longitudinal data. SPMMs are a class of models that use a nonparametric function to model a time effect, a parametric function to model other covariate effects, and parametric or nonparametric random effects to account for the within-subject correlation. We model the nonparametric function using a Bayesian formulation of a cubic smoothing spline, and the random effect distribution using a normal distribution and alternatively a nonparametric Dirichlet process (DP) prior. When the random effect distribution is assumed to be normal, we propose a uniform shrinkage prior (USP) for the variance components and the smoothing parameter. When the random effect distribution is modeled nonparametrically, we use a DP prior with a normal base measure and propose a USP for the hyperparameters of the DP base measure. We argue that the commonly assumed DP prior implies a nonzero mean of the random effect distribution, even when a base measure with mean zero is specified. This implies weak identifiability for the fixed effects, and can therefore lead to biased estimators and poor inference for the regression coefficients and the spline estimator of the nonparametric function. We propose an adjustment using a postprocessing technique. We show that under mild conditions the posterior is proper under the proposed USP, a flat prior for the fixed effect parameters, and an improper prior for the residual variance. We illustrate the proposed approach using a longitudinal hormone dataset, and carry out extensive simulation studies to compare its finite sample performance with existing methods.
doi:10.1111/j.1541-0420.2009.01227.x
PMCID: PMC3081790  PMID: 19432777
Dirichlet process prior; Identifiability; Postprocessing; Random effects; Smoothing spline; Uniform shrinkage prior; Variance components
15.  Linear mixed-effects modeling approach to FMRI group analysis 
NeuroImage  2013;73:176-190.
Conventional group analysis is usually performed with Student-type t-test, regression, or standard AN(C)OVA in which the variance–covariance matrix is presumed to have a simple structure. Some correction approaches are adopted when assumptions about the covariance structure is violated. However, as experiments are designed with different degrees of sophistication, these traditional methods can become cumbersome, or even be unable to handle the situation at hand. For example, most current FMRI software packages have difficulty analyzing the following scenarios at group level: (1) taking within-subject variability into account when there are effect estimates from multiple runs or sessions; (2) continuous explanatory variables (covariates) modeling in the presence of a within-subject (repeated measures) factor, multiple subject-grouping (between-subjects) factors, or the mixture of both; (3) subject-specific adjustments in covariate modeling; (4) group analysis with estimation of hemodynamic response (HDR) function by multiple basis functions; (5) various cases of missing data in longitudinal studies; and (6) group studies involving family members or twins.
Here we present a linear mixed-effects modeling (LME) methodology that extends the conventional group analysis approach to analyze many complicated cases, including the six prototypes delineated above, whose analyses would be otherwise either difficult or unfeasible under traditional frameworks such as AN(C)OVA and general linear model (GLM). In addition, the strength of the LME framework lies in its flexibility to model and estimate the variance–covariance structures for both random effects and residuals. The intraclass correlation (ICC) values can be easily obtained with an LME model with crossed random effects, even at the presence of confounding fixed effects. The simulations of one prototypical scenario indicate that the LME modeling keeps a balance between the control for false positives and the sensitivity for activation detection. The importance of hypothesis formulation is also illustrated in the simulations. Comparisons with alternative group analysis approaches and the limitations of LME are discussed in details.
doi:10.1016/j.neuroimage.2013.01.047
PMCID: PMC3638840  PMID: 23376789
FMRI group analysis; GLM; AN(C)OVA; LME; ICC; AFNI; R
16.  MOMENT-BASED METHOD FOR RANDOM EFFECTS SELECTION IN LINEAR MIXED MODELS 
Statistica Sinica  2012;22(4):1539-1562.
The selection of random effects in linear mixed models is an important yet challenging problem in practice. We propose a robust and unified framework for automatically selecting random effects and estimating covariance components in linear mixed models. A moment-based loss function is first constructed for estimating the covariance matrix of random effects. Two types of shrinkage penalties, a hard thresholding operator and a new sandwich-type soft-thresholding penalty, are then imposed for sparse estimation and random effects selection. Compared with existing approaches, the new procedure does not require any distributional assumption on the random effects and error terms. We establish the asymptotic properties of the resulting estimator in terms of its consistency in both random effects selection and variance component estimation. Optimization strategies are suggested to tackle the computational challenges involved in estimating the sparse variance-covariance matrix. Furthermore, we extend the procedure to incorporate the selection of fixed effects as well. Numerical results show promising performance of the new approach in selecting both random and fixed effects and, consequently, improving the efficiency of estimating model parameters. Finally, we apply the approach to a data set from the Amsterdam Growth and Health study.
doi:10.5705/ss.2011.054
PMCID: PMC3480741  PMID: 23105913
Hard thresholding; Linear mixed model; Shrinkage estimation; Variance component selection
17.  Bayesian sparse graphical models and their mixtures 
Stat  2014;3(1):109-125.
We propose Bayesian methods for Gaussian graphical models that lead to sparse and adaptively shrunk estimators of the precision (inverse covariance) matrix. Our methods are based on lasso-type regularization priors leading to parsimonious parameterization of the precision matrix, which is essential in several applications involving learning relationships among the variables. In this context, we introduce a novel type of selection prior that develops a sparse structure on the precision matrix by making most of the elements exactly zero, in addition to ensuring positive definiteness – thus conducting model selection and estimation simultaneously. More importantly, we extend these methods to analyze clustered data using finite mixtures of Gaussian graphical model and infinite mixtures of Gaussian graphical models. We discuss appropriate posterior simulation schemes to implement posterior inference in the proposed models, including the evaluation of normalizing constants that are functions of parameters of interest, which result from the restriction of positive definiteness on the correlation matrix. We evaluate the operating characteristics of our method via several simulations and demonstrate the application to real data examples in genomics.
doi:10.1002/sta4.49
PMCID: PMC4059614  PMID: 24948842
bayesian; covariance selection; finite mixtures; gaussian graphical models; infinite mixtures; sparse modeling
18.  Simultaneous Bayesian Inference for Linear, Nonlinear and Semiparametric Mixed-Effects Models with Skew-Normality and Measurement Errors in Covariates 
In recent years, various mixed-effects models have been suggested for estimating viral decay rates in HIV dynamic models for complex longitudinal data. Among those models are linear mixed-effects (LME), nonlinear mixed-effects (NLME), and semiparametric nonlinear mixed-effects (SNLME) models. However, a critical question is whether these models produce coherent estimates of viral decay rates, and if not, which model is appropriate and should be used in practice. In addition, one often assumes that a model random error is normally distributed, but the normality assumption may be unrealistic, particularly if the data exhibit skewness. Moreover, some covariates such as CD4 cell count may be often measured with substantial errors. This paper addresses these issues simultaneously by jointly modeling the response variable with skewness and a covariate process with measurement errors using a Bayesian approach to investigate how estimated parameters are changed or different under these three models. A real data set from an AIDS clinical trial study was used to illustrate the proposed models and methods. It was found that there was a significant incongruity in the estimated decay rates in viral loads based on the three mixed-effects models, suggesting that the decay rates estimated by using Bayesian LME or NLME joint models should be interpreted differently from those estimated by using Bayesian SNLME joint models. The findings also suggest that the Bayesian SNLME joint model is preferred to other models because an arbitrary data truncation is not necessary; and it is also shown that the models with a skew-normal distribution and/or measurement errors in covariate may achieve reliable results when the data exhibit skewness.
doi:10.2202/1557-4679.1292
PMCID: PMC3404555  PMID: 22848189
Bayesian analysis; covariate measurement errors; HIV dynamics; mixed-effects joint models; skew-normal distribution
19.  Dynamic semiparametric Bayesian models for genetic mapping of complex trait with irregular longitudinal data 
Statistics in medicine  2012;32(3):509-523.
Many phenomena of fundamental importance to biology and biomedicine arise as a dynamic curve, such as organ growth and HIV dynamics. The genetic mapping of these traits is challenged by longitudinal variables measured at irregular and possibly subject-specific time points, in which case nonnegative definiteness of the estimated covariance matrix needs to be guaranteed. We present a semiparametric approach for genetic mapping within the mixture-model setting by jointly modeling mean and covariance structures for irregular longitudinal data. Penalized spline is used to model the mean functions of individual QTL genotypes as latent variables while an extended generalized linear model is used to approximate the covariance matrix. The parameters for modeling the mean-covariances are estimated by MCMC, using Gibbs sampler and Metropolis Hastings algorithm. We derive the full conditional distributions for the mean and covariance parameters and compute Bayes factors to test the hypothesis about the existence of significant QTLs. The model was used to screen the existence of specific QTLs for age-specific change of body mass index with a sparse longitudinal dataset. The new model provides powerful means for broadening the application of genetic mapping to reveal the genetic control of dynamic traits.
doi:10.1002/sim.5535
PMCID: PMC3770845  PMID: 22903809
Cholesky decomposition; genetic mapping; MCMC; penalized spline; quantitative trait loci
20.  A Semiparametric Approach to Simultaneous Covariance Estimation for Bivariate Sparse Longitudinal Data 
Biometrics  2014;70(1):33-43.
Summary
Estimation of the covariance structure for irregular sparse longitudinal data has been studied by many authors in recent years but typically using fully parametric specifications. In addition, when data are collected from several groups over time, it is known that assuming the same or completely different covariance matrices over groups can lead to loss of efficiency and/or bias. Nonparametric approaches have been proposed for estimating the covariance matrix for regular univariate longitudinal data by sharing information across the groups under study. For the irregular case, with longitudinal measurements that are bivariate or multivariate, modeling becomes more difficult. In this article, to model bivariate sparse longitudinal data from several groups, we propose a flexible covariance structure via a novel matrix stick-breaking process for the residual covariance structure and a Dirichlet process mixture of normals for the random effects. Simulation studies are performed to investigate the effectiveness of the proposed approach over more traditional approaches. We also analyze a subset of Framingham Heart Study data to examine how the blood pressure trajectories and covariance structures differ for the patients from different BMI groups (high, medium and low) at baseline.
doi:10.1111/biom.12133
PMCID: PMC3954444  PMID: 24400941
Covariance matrix; DIC; Dirichlet process mixture of normals; MCMC
21.  Bayesian modeling of the dependence in longitudinal data via partial autocorrelations and marginal variances 
Summary
Many parameters and positive-definiteness are two major obstacles in estimating and modelling a correlation matrix for longitudinal data. In addition, when longitudinal data is incomplete, incorrectly modelling the correlation matrix often results in bias in estimating mean regression parameters. In this paper, we introduce a flexible and parsimonious class of regression models for a covariance matrix parameterized using marginal variances and partial autocorrelations. The partial autocorrelations can freely vary in the interval (–1, 1) while maintaining positive definiteness of the correlation matrix so the regression parameters in these models will have no constraints. We propose a class of priors for the regression coefficients and examine the importance of correctly modeling the correlation structure on estimation of longitudinal (mean) trajectories and the performance of the DIC in choosing the correct correlation model via simulations. The regression approach is illustrated on data from a longitudinal clinical trial.
doi:10.1016/j.jmva.2012.11.010
PMCID: PMC3640593  PMID: 23645941
Markov Chain Monte Carlo; Generalized linear model; Uniform prior
22.  Bayesian adaptive Markov chain Monte Carlo estimation of genetic parameters 
Heredity  2012;109(4):235-245.
Accurate and fast estimation of genetic parameters that underlie quantitative traits using mixed linear models with additive and dominance effects is of great importance in both natural and breeding populations. Here, we propose a new fast adaptive Markov chain Monte Carlo (MCMC) sampling algorithm for the estimation of genetic parameters in the linear mixed model with several random effects. In the learning phase of our algorithm, we use the hybrid Gibbs sampler to learn the covariance structure of the variance components. In the second phase of the algorithm, we use this covariance structure to formulate an effective proposal distribution for a Metropolis-Hastings algorithm, which uses a likelihood function in which the random effects have been integrated out. Compared with the hybrid Gibbs sampler, the new algorithm had better mixing properties and was approximately twice as fast to run. Our new algorithm was able to detect different modes in the posterior distribution. In addition, the posterior mode estimates from the adaptive MCMC method were close to the REML (residual maximum likelihood) estimates. Moreover, our exponential prior for inverse variance components was vague and enabled the estimated mode of the posterior variance to be practically zero, which was in agreement with the support from the likelihood (in the case of no dominance). The method performance is illustrated using simulated data sets with replicates and field data in barley.
doi:10.1038/hdy.2012.35
PMCID: PMC3464018  PMID: 22805656
adaptive MCMC; identifiability problem; Bayesian analysis; Gibbs sampling; estimation of genetic parameters
23.  Sparse Bayesian infinite factor models 
Biometrika  2011;98(2):291-306.
We focus on sparse modelling of high-dimensional covariance matrices using Bayesian latent factor models. We propose a multiplicative gamma process shrinkage prior on the factor loadings which allows introduction of infinitely many factors, with the loadings increasingly shrunk towards zero as the column index increases. We use our prior on a parameter-expanded loading matrix to avoid the order dependence typical in factor analysis models and develop an efficient Gibbs sampler that scales well as data dimensionality increases. The gain in efficiency is achieved by the joint conjugacy property of the proposed prior, which allows block updating of the loadings matrix. We propose an adaptive Gibbs sampler for automatically truncating the infinite loading matrix through selection of the number of important factors. Theoretical results are provided on the support of the prior and truncation approximation bounds. A fast algorithm is proposed to produce approximate Bayes estimates. Latent factor regression methods are developed for prediction and variable selection in applications with high-dimensional correlated predictors. Operating characteristics are assessed through simulation studies, and the approach is applied to predict survival times from gene expression data.
doi:10.1093/biomet/asr013
PMCID: PMC3419391  PMID: 23049129
Adaptive Gibbs sampling; Factor analysis; High-dimensional data; Multiplicative gamma process; Parameter expansion; Regularization; Shrinkage
24.  Flexible marginalized models for bivariate longitudinal ordinal data 
Biostatistics (Oxford, England)  2013;14(3):462-476.
Random effects models are commonly used to analyze longitudinal categorical data. Marginalized random effects models are a class of models that permit direct estimation of marginal mean parameters and characterize serial correlation for longitudinal categorical data via random effects (Heagerty, 1999). Marginally specified logistic-normal models for longitudinal binary data. Biometrics 55, 688–698; Lee and Daniels, 2008. Marginalized models for longitudinal ordinal data with application to quality of life studies. Statistics in Medicine 27, 4359–4380). In this paper, we propose a Kronecker product (KP) covariance structure to capture the correlation between processes at a given time and the correlation within a process over time (serial correlation) for bivariate longitudinal ordinal data. For the latter, we consider a more general class of models than standard (first-order) autoregressive correlation models, by re-parameterizing the correlation matrix using partial autocorrelations (Daniels and Pourahmadi, 2009). Modeling covariance matrices via partial autocorrelations. Journal of Multivariate Analysis 100, 2352–2363). We assess the reasonableness of the KP structure with a score test. A maximum marginal likelihood estimation method is proposed utilizing a quasi-Newton algorithm with quasi-Monte Carlo integration of the random effects. We examine the effects of demographic factors on metabolic syndrome and C-reactive protein using the proposed models.
doi:10.1093/biostatistics/kxs058
PMCID: PMC3677737  PMID: 23365416
Kronecker product; Metabolic syndrome; Partial autocorrelation
25.  Bayesian estimation of genetic parameters for multivariate threshold and continuous phenotypes and molecular genetic data in simulated horse populations using Gibbs sampling 
BMC Genetics  2007;8:19.
Background
Requirements for successful implementation of multivariate animal threshold models including phenotypic and genotypic information are not known yet. Here simulated horse data were used to investigate the properties of multivariate estimators of genetic parameters for categorical, continuous and molecular genetic data in the context of important radiological health traits using mixed linear-threshold animal models via Gibbs sampling. The simulated pedigree comprised 7 generations and 40000 animals per generation. Additive genetic values, residuals and fixed effects for one continuous trait and liabilities of four binary traits were simulated, resembling situations encountered in the Warmblood horse. Quantitative trait locus (QTL) effects and genetic marker information were simulated for one of the liabilities. Different scenarios with respect to recombination rate between genetic markers and QTL and polymorphism information content of genetic markers were studied. For each scenario ten replicates were sampled from the simulated population, and within each replicate six different datasets differing in number and distribution of animals with trait records and availability of genetic marker information were generated. (Co)Variance components were estimated using a Bayesian mixed linear-threshold animal model via Gibbs sampling. Residual variances were fixed to zero and a proper prior was used for the genetic covariance matrix.
Results
Effective sample sizes (ESS) and biases of genetic parameters differed significantly between datasets. Bias of heritability estimates was -6% to +6% for the continuous trait, -6% to +10% for the binary traits of moderate heritability, and -21% to +25% for the binary traits of low heritability. Additive genetic correlations were mostly underestimated between the continuous trait and binary traits of low heritability, under- or overestimated between the continuous trait and binary traits of moderate heritability, and overestimated between two binary traits. Use of trait information on two subsequent generations of animals increased ESS and reduced bias of parameter estimates more than mere increase of the number of informative animals from one generation. Consideration of genotype information as a fixed effect in the model resulted in overestimation of polygenic heritability of the QTL trait, but increased accuracy of estimated additive genetic correlations of the QTL trait.
Conclusion
Combined use of phenotype and genotype information on parents and offspring will help to identify agonistic and antagonistic genetic correlations between traits of interests, facilitating design of effective multiple trait selection schemes.
doi:10.1186/1471-2156-8-19
PMCID: PMC1876470  PMID: 17490471

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