An Empirical Comparison of Multiple Imputation Methods for Categorical Data

Multiple imputation is a common approach for dealing with missing values in statistical databases. The imputer fills in missing values with draws from predictive models estimated from the observed data, resulting in multiple, completed versions of the database. Researchers have developed a variety of default routines to implement multiple imputation; however, there has been limited research comparing the performance of these methods, particularly for categorical data. We use simulation studies to compare repeated sampling properties of three default multiple imputation methods for categorical data, including chained equations using generalized linear models, chained equations using classification and regression trees, and a fully Bayesian joint distribution based on Dirichlet Process mixture models. We base the simulations on categorical data from the American Community Survey. In the circumstances of this study, the results suggest that default chained equations approaches based on generalized linear models are dominated by the default regression tree and Bayesian mixture model approaches. They also suggest competing advantages for the regression tree and Bayesian mixture model approaches, making both reasonable default engines for multiple imputation of categorical data. A supplementary material for this article is available online

High Dimensional Classification with combined Adaptive Sparse PLS and Logistic Regression

Motivation: The high dimensionality of genomic data calls for the development of specific classification methodologies, especially to prevent over-optimistic predictions. This challenge can be tackled by compression and variable selection, which combined constitute a powerful framework for classification, as well as data visualization and interpretation. However, current proposed combinations lead to instable and non convergent methods due to inappropriate computational frameworks. We hereby propose a stable and convergent approach for classification in high dimensional based on sparse Partial Least Squares (sparse PLS). Results: We start by proposing a new solution for the sparse PLS problem that is based on proximal operators for the case of univariate responses. Then we develop an adaptive version of the sparse PLS for classification, which combines iterative optimization of logistic regression and sparse PLS to ensure convergence and stability. Our results are confirmed on synthetic and experimental data. In particular we show how crucial convergence and stability can be when cross-validation is involved for calibration purposes. Using gene expression data we explore the prediction of breast cancer relapse. We also propose a multicategorial version of our method on the prediction of cell-types based on single-cell expression data. Availability: Our approach is implemented in the plsgenomics R-package.Comment: 9 pages, 3 figures, 4 tables + Supplementary Materials 8 pages, 3 figures, 10 table

The chopthin algorithm for resampling

Resampling is a standard step in particle filters and more generally sequential Monte Carlo methods. We present an algorithm, called chopthin, for resampling weighted particles. In contrast to standard resampling methods the algorithm does not produce a set of equally weighted particles; instead it merely enforces an upper bound on the ratio between the weights. Simulation studies show that the chopthin algorithm consistently outperforms standard resampling methods. The algorithms chops up particles with large weight and thins out particles with low weight, hence its name. It implicitly guarantees a lower bound on the effective sample size. The algorithm can be implemented efficiently, making it practically useful. We show that the expected computational effort is linear in the number of particles. Implementations for C++, R (on CRAN), Python and Matlab are available.Comment: 14 pages, 4 figure

Variable Selection in General Multinomial Logit Models

The use of the multinomial logit model is typically restricted to applications with few predictors, because in high-dimensional settings maximum likelihood estimates tend to deteriorate. In this paper we are proposing a sparsity-inducing penalty that accounts for the special structure of multinomial models. In contrast to existing methods, it penalizes the parameters that are linked to one variable in a grouped way and thus yields variable selection instead of parameter selection. We develop a proximal gradient method that is able to efficiently compute stable estimates. In addition, the penalization is extended to the important case of predictors that vary across response categories. We apply our estimator to the modeling of party choice of voters in Germany including voter-specific variables like age and gender but also party-specific features like stance on nuclear energy and immigration

Binary and Ordinal Random Effects Models Including Variable Selection

A likelihood-based boosting approach for fitting binary and ordinal mixed models is presented. In contrast to common procedures it can be used in high-dimensional settings where a large number of potentially influential explanatory variables is available. Constructed as a componentwise boosting method it is able to perform variable selection with the complexity of the resulting estimator being determined by information criteria. The method is investigated in simulation studies both for cumulative and sequential models and is illustrated by using real data sets

A method of moments estimator for semiparametric index models

We propose an easy to use derivative based two-step estimation procedure for semi-parametric index models. In the first step various functionals involving the derivatives of the unknown function are estimated using nonparametric kernel estimators. The functionals used provide moment conditions for the parameters of interest, which are used in the second step within a method-of-moments framework to estimate the parameters of interest. The estimator is shown to be root N consistent and asymptotically normal. We extend the procedure to multiple equation models. Our identification conditions and estimation framework provide natural tests for the number of indices in the model. In addition we discuss tests of separability, additivity, and linearity of the influence of the indices.Semiparametric estimation, multiple index models, average derivative functionals, generalized methods of moments estimator, rank testing

Hazard function models to estimate mortality rates affecting fish populations with application to the sea mullet (Mugil cephalus) fishery on the Queensland coast (Australia)

Fisheries management agencies around the world collect age data for the purpose of assessing the status of natural resources in their jurisdiction. Estimates of mortality rates represent a key information to assess the sustainability of fish stocks exploitation. Contrary to medical research or manufacturing where survival analysis is routinely applied to estimate failure rates, survival analysis has seldom been applied in fisheries stock assessment despite similar purposes between these fields of applied statistics. In this paper, we developed hazard functions to model the dynamic of an exploited fish population. These functions were used to estimate all parameters necessary for stock assessment (including natural and fishing mortality rates as well as gear selectivity) by maximum likelihood using age data from a sample of catch. This novel application of survival analysis to fisheries stock assessment was tested by Monte Carlo simulations to assert that it provided un-biased estimations of relevant quantities. The method was applied to data from the Queensland (Australia) sea mullet (Mugil cephalus) commercial fishery collected between 2007 and 2014. It provided, for the first time, an estimate of natural mortality affecting this stock: 0.22 $\pm$ 0.08 year$^{-1}$