arXiv subjects

James G. Booth

Publications and source records attributed to James G. Booth.

8 recordsLinked to original sources

arXiv2021

Mixed Models and Shrinkage Estimation for Balanced and Unbalanced Designs

The known connection between shrinkage estimation, empirical Bayes, and mixed effects models is explored and applied to balanced and unbalanced designs in which the responses are correlated. As an illustration, a mixed model is proposed for predicting the outcome of English Premier League games that takes into account both home and away team effects. Results based on empirical best linear unbiased predictors obtained from fitting mixed linear models are compared with fully Bayesian predictors that utilize prior information from the previous season.

stat.ME↗

arXiv2021

Quantile Regression Modelling via Location and Scale Mixtures of Normal Distributions

We show that the estimating equations for quantile regression can be solved using a simple EM algorithm in which the M-step is computed via weighted least squares, with weights computed at the E-step as the expectation of independent generalized inverse-Gaussian variables. We compute the variance-covariance matrix for the quantile regression coefficients using a kernel density estimator that results in more stable standard errors than those produced by existing software. A natural modification of the EM algorithm that involves fitting a linear mixed model at the M-step extends the methodology to mixed effects quantile regression models. In this case, the fitting method can be justified as a generalized alternating minimization algorithm. Obtaining quantile regression estimates via the weighted least squares method enables model diagnostic techniques similar to the ones used in the linear regression setting. The computational approach is compared with existing software using simulated data, and the methodology is illustrated with several case studies.

stat.ME↗

arXiv2018

Rank-based approach for estimating correlations in mixed ordinal data

High-dimensional mixed data as a combination of both continuous and ordinal variables are widely seen in many research areas such as genomic studies and survey data analysis. Estimating the underlying correlation among mixed data is hence crucial for further inferring dependence structure. We propose a semiparametric latent Gaussian copula model for this problem. We start with estimating the association among ternary-continuous mixed data via a rank-based approach and generalize the methodology to p-level-ordinal and continuous mixed data. Concentration rate of the estimator is also provided and proved. At last, we demonstrate the performance of the proposed estimator by extensive simulations and two case studies of real data examples of algorithmic risk score evaluation and cancer patients survival data.

stat.ME↗

arXiv2015

A Scalable Empirical Bayes Approach to Variable Selection

We develop a model-based empirical Bayes approach to variable selection problems in which the number of predictors is very large, possibly much larger than the number of responses (the so-called 'large p, small n' problem). We consider the multiple linear regression setting, where the response is assumed to be a continuous variable and it is a linear function of the predictors plus error. The explanatory variables in the linear model can have a positive effect on the response, a negative effect, or no effect. We model the effects of the linear predictors as a three-component mixture in which a key assumption is that only a small (unknown) fraction of the candidate predictors have a non-zero effect on the response variable. By treating the coefficients as random effects we develop an approach that is computationally efficient because the number of parameters that have to be estimated is small, and remains constant regardless of the number of explanatory variables. The model parameters are estimated using the EM algorithm which is scalable and leads to significantly faster convergence, compared with simulation-based methods.

stat.ME↗

arXiv2015

Simultaneous sparse estimation of canonical vectors in the p>>N setting

This article considers the problem of sparse estimation of canonical vectors in linear discriminant analysis when $p\gg N$. Several methods have been proposed in the literature that estimate one canonical vector in the two-group case. However, $G-1$ canonical vectors can be considered if the number of groups is $G$. In the multi-group context, it is common to estimate canonical vectors in a sequential fashion. Moreover, separate prior estimation of the covariance structure is often required. We propose a novel methodology for direct estimation of canonical vectors. In contrast to existing techniques, the proposed method estimates all canonical vectors at once, performs variable selection across all the vectors and comes with theoretical guarantees on the variable selection and classification consistency. First, we highlight the fact that in the $N>p$ setting the canonical vectors can be expressed in a closed form up to an orthogonal transformation. Secondly, we propose an extension of this form to the $p\gg N$ setting and achieve feature selection by using a group penalty. The resulting optimization problem is convex and can be solved using a block-coordinate descent algorithm. The practical performance of the method is evaluated through simulation studies as well as real data applications.

stat.ME↗

arXiv2014

Supervised Classification Using Sparse Fisher's LDA

It is well known that in a supervised classification setting when the number of features is smaller than the number of observations, Fisher's linear discriminant rule is asymptotically Bayes. However, there are numerous modern applications where classification is needed in the high-dimensional setting. Naive implementation of Fisher's rule in this case fails to provide good results because the sample covariance matrix is singular. Moreover, by constructing a classifier that relies on all features the interpretation of the results is challenging. Our goal is to provide robust classification that relies only on a small subset of important features and accounts for the underlying correlation structure. We apply a lasso-type penalty to the discriminant vector to ensure sparsity of the solution and use a shrinkage type estimator for the covariance matrix. The resulting optimization problem is solved using an iterative coordinate ascent algorithm. Furthermore, we analyze the effect of nonconvexity on the sparsity level of the solution and highlight the difference between the penalized and the constrained versions of the problem. The simulation results show that the proposed method performs favorably in comparison to alternatives. The method is used to classify leukemia patients based on DNA methylation features.

stat.ML↗

arXiv2012

Integrative Model-based clustering of microarray methylation and expression data

In many fields, researchers are interested in large and complex biological processes. Two important examples are gene expression and DNA methylation in genetics. One key problem is to identify aberrant patterns of these processes and discover biologically distinct groups. In this article we develop a model-based method for clustering such data. The basis of our method involves the construction of a likelihood for any given partition of the subjects. We introduce cluster specific latent indicators that, along with some standard assumptions, impose a specific mixture distribution on each cluster. Estimation is carried out using the EM algorithm. The methods extend naturally to multiple data types of a similar nature, which leads to an integrated analysis over multiple data platforms, resulting in higher discriminating power.

stat.AP↗

arXiv2010

A Multivariate Variance Components Model for Analysis of Covariance in Designed Experiments

Traditional methods for covariate adjustment of treatment means in designed experiments are inherently conditional on the observed covariate values. In order to develop a coherent general methodology for analysis of covariance, we propose a multivariate variance components model for the joint distribution of the response and covariates. It is shown that, if the design is orthogonal with respect to (random) blocking factors, then appropriate adjustments to treatment means can be made using the univariate variance components model obtained by conditioning on the observed covariate values. However, it is revealed that some widely used models are incorrectly specified, leading to biased estimates and incorrect standard errors. The approach clarifies some issues that have been the source of ongoing confusion in the statistics literature.

stat.ME↗