Variable selection models based on multiple imputation with an application for predicting median effective dose and maximum effect

The statistical methods for variable selection and prediction could be challenging when missing covariates exist. Although multiple imputation (MI) is a universally accepted technique for solving missing data problem, how to combine the MI results for variable selection is not quite clear, because different imputations may result in different selections. The widely applied variable selection methods include the sparse partial least-squares (SPLS) method and the penalized least-squares method, e.g. the elastic net (ENet) method. In this paper, we propose an MI-based weighted elastic net (MI-WENet) method that is based on stacked MI data and a weighting scheme for each observation in the stacked data set. In the MI-WENet method, MI accounts for sampling and imputation uncertainty for missing values, and the weight accounts for the observed information. Extensive numerical simulations are carried out to compare the proposed MI-WENet method with the other competing alternatives, such as the SPLS and ENet. In addition, we applied the MI-WENet method to examine the predictor variables for the endothelial function that can be characterized by median effective dose (ED50) and maximum effect (Emax) in an ex-vivo phenylephrine-induced extension and acetylcholine-induced relaxation experiment.     

Latent class based multiple imputation approach for missing categorical data

In this paper we propose a latent class based multiple imputation approach for analyzing missing categorical covariate data in a highly stratified data model. In this approach, we impute the missing data assuming a latent class imputation model and we use likelihood methods to analyze the imputed data. Via extensive simulations, we study its statistical properties and make comparisons with complete case analysis, multiple imputation, saturated log-linear multiple imputation and the Expectation–Maximization approach under seven missing data mechanisms (including missing completely at random, missing at random and not missing at random). These methods are compared with respect to bias, asymptotic standard error, type I error, and 95% coverage probabilities of parameter estimates. Simulations show that, under many missingness scenarios, latent class multiple imputation performs favorably when jointly considering these criteria. A data example from a matched case–control study of the association between multiple myeloma and polymorphisms of the Inter-Leukin 6 genes is considered.     

Statistical inference under imputation for proportional hazard model with missing covariates

Missing covariate data are common in biomedical studies. In this article, by using the non parametric kernel regression technique, a new imputation approach is developed for the Cox-proportional hazard regression model with missing covariates. This method achieves the same efficiency as the fully augmented weighted estimators (Qi et al. 2005. Journal of the American Statistical Association, 100:1250) and has a simpler form. The asymptotic properties of the proposed estimator are derived and analyzed. The comparisons between the proposed imputation method and several other existing methods are conducted via a number of simulation studies and a mouse leukemia data.     

A semiparametric method of multiple imputation

In this paper, we describe how to use multiple imputation semiparametrically to obtain estimates of parameters and their standard errors when some individuals have missing data. The methods given require the investigator to know or be able to estimate the process generating the missing data but requires no full distributional form for the data. The method is especially useful for non-standard problems, such as estimating the median when data are missing.     

A Degrees-Of-Freedom approximation in Multiple imputation

When using multiple imputation to form confidence intervals with missing data, Rubin and Schenker (1986) proposed using a t -distribution with approximate degrees-of-freedom which is a function of the number of multiple imputations and the within and between imputation variance. In this t -approximation, Rubin and Schenker assume there are a finite number of multiple imputations, but an infinite number of observations in the sample. We propose a further degrees-of-freedom approximation which is a function of the within and between imputation variance, the number of multiple imputations, and the number of observations in the sample. When the number of observations in the sample is small, our approximate degrees-of-freedom may be more appropriate, as seen in our simulations.     

Multiple imputation using multivariate gh transformations

Multiple imputation has emerged as a popular approach to handling data sets with missing values. For incomplete continuous variables, imputations are usually produced using multivariate normal models. However, this approach might be problematic for variables with a strong non-normal shape, as it would generate imputations incoherent with actual distributions and thus lead to incorrect inferences. For non-normal data, we consider a multivariate extension of Tukey's gh distribution/transformation [38] to accommodate skewness and/or kurtosis and capture the correlation among the variables. We propose an algorithm to fit the incomplete data with the model and generate imputations. We apply the method to a national data set for hospital performance on several standard quality measures, which are highly skewed to the left and substantially correlated with each other. We use Monte Carlo studies to assess the performance of the proposed approach. We discuss possible generalizations and give some advices to practitioners on how to handle non-normal incomplete data.     

Tukey's gh Distribution for Multiple Imputation

Tukey proposed a class of distributions, the g-and-h family (gh family), based on a transformation of a standard normal variable to accommodate different skewness and elongation in the distribution of variables arising in practical applications. It is easy to draw values from this distribution even though it is hard to explicitly state the probability density function. Given this flexibility, the gh family may be extremely useful in creating multiple imputations for missing data. This article demonstrates how this family, as well as its generalizations, can be used in the multiple imputation analysis of incomplete data. The focus of this article is on a scalar variable with missing values. In the absence of any additional information, data are missing completely at random, and hence the correct analysis is the complete-case analysis. Thus, the application of the gh multiple imputation to the scalar cases affords comparison with the correct analysis and with other model-based multiple imputation methods. Comparisons are made using simulated datasets and the data from a survey of adolescents ascertaining driving after drinking alcohol.     

A Simulation Study Comparing Multiple Imputation Methods for Incomplete Longitudinal Ordinal Data

Multiple imputation (MI) is now a reference solution for handling missing data. The default method for MI is the Multivariate Normal Imputation (MNI) algorithm that is based on the multivariate normal distribution. In the presence of longitudinal ordinal missing data, where the Gaussian assumption is no longer valid, application of the MNI method is questionable. This simulation study compares the performance of the MNI and ordinal imputation regression model for incomplete longitudinal ordinal data for situations covering various numbers of categories of the ordinal outcome, time occasions, sample sizes, rates of missingness, well-balanced, and skewed data.     

Consistency of information criteria for model selection with missing data

ABSTRACT

In this paper, we investigate the consistency of the Expectation Maximization (EM) algorithm-based information criteria for model selection with missing data. The criteria correspond to a penalization of the conditional expectation of the complete data log-likelihood given the observed data and with respect to the missing data conditional density. We present asymptotic properties related to maximum likelihood estimation in the presence of incomplete data and we provide sufficient conditions for the consistency of model selection by minimizing the information criteria. Their finite sample performance is illustrated through simulation and real data studies.     

A Simple Method to Ensure Plausible Multiple Imputation for Continuous Multivariate Data

Multiple Imputation (MI) is an established approach for handling missing values. We show that MI for continuous data under the multivariate normal assumption is susceptible to generating implausible values. Our proposed remedy, is to: (1) transform the observed data into quantiles of the standard normal distribution; (2) obtain a functional relationship between the observed data and it's corresponding standard normal quantiles; (3) undertake MI using the quantiles produced in step 1; and finally, (4) use the functional relationship to transform the imputations into their original domain. In conclusion, our approach safeguards MI from imputing implausible values.     

MIMCA: multiple imputation for categorical variables with multiple correspondence analysis

We propose a multiple imputation method to deal with incomplete categorical data. This method imputes the missing entries using the principal component method dedicated to categorical data: multiple correspondence analysis (MCA). The uncertainty concerning the parameters of the imputation model is reflected using a non-parametric bootstrap. Multiple imputation using MCA (MIMCA) requires estimating a small number of parameters due to the dimensionality reduction property of MCA. It allows the user to impute a large range of data sets. In particular, a high number of categories per variable, a high number of variables or a small number of individuals are not an issue for MIMCA. Through a simulation study based on real data sets, the method is assessed and compared to the reference methods (multiple imputation using the loglinear model, multiple imputation by logistic regressions) as well to the latest works on the topic (multiple imputation by random forests or by the Dirichlet process mixture of products of multinomial distributions model). The proposed method provides a good point estimate of the parameters of the analysis model considered, such as the coefficients of a main effects logistic regression model, and a reliable estimate of the variability of the estimators. In addition, MIMCA has the great advantage that it is substantially less time consuming on data sets of high dimensions than the other multiple imputation methods.     

Navigating choices when applying multiple imputation in the presence of multi-level categorical interaction effects

Multiple imputation (MI) is an appealing option for handling missing data. When implementing MI, however, users need to make important decisions to obtain estimates with good statistical properties. One such decision involves the choice of imputation model–the joint modeling (JM) versus fully conditional specification (FCS) approach. Another involves the choice of method to handle interactions. These include imputing the interaction term as any other variable (active imputation), or imputing the main effects and then deriving the interaction (passive imputation). Our study investigates the best approach to perform MI in the presence of interaction effects involving two categorical variables. Such effects warrant special attention as they involve multiple correlated parameters that are handled differently under JM and FCS modeling. Through an extensive simulation study, we compared active, passive and an improved passive approach under FCS, as JM precludes passive imputation. We additionally compared JM and FCS techniques using active imputation. Performance between active and passive imputation was comparable. The improved passive approach proved superior to the other two particularly when the number of parameters corresponding to the interaction was large. JM without rounding and FCS using active imputation were also mostly comparable, with JM outperforming FCS when the number of parameters was large. In a direct comparison of JM active and FCS improved passive, the latter was the clear winner. We recommend improved passive imputation under FCS along with sensitivity analyses to handle multi-level interaction terms.     

Comparison of alternative imputation methods for ordinal data

In this article, we compare alternative missing imputation methods in the presence of ordinal data, in the framework of CUB (Combination of Uniform and (shifted) Binomial random variable) models. Various imputation methods are considered, as are univariate and multivariate approaches. The first step consists of running a simulation study designed by varying the parameters of the CUB model, to consider and compare CUB models as well as other methods of missing imputation. We use real datasets on which to base the comparison between our approach and some general methods of missing imputation for various missing data mechanisms.     

Calibrated random imputation for qualitative data

In official statistics, when a file of microdata must be delivered to external users, it is very difficult to propose them a file where missing values has been treated by multiple imputations. In order to overcome this difficulty, we propose a method of single imputation for qualitative data that respect numerous constraints. The imputation is balanced on totals previously estimated; editing rules can be respected; the imputation is random, but the totals are not affected by an imputation variance.     

A multiple imputation approach to deal with the unity measure error

Unity measure errors (UME) in numerical survey data can determine serious bias in the estimates of interest. In this paper, a finite Gaussian mixture model is used to identify observations affected by UME and to robustly estimate the target parameters in presence of this type of error. In the proposed model, the mixture components are associated to the different error patterns across the variables. We follow a multiple imputation approach in a Bayesian setting that allows us to handle missing values in data. In this framework, the assessment of the uncertainty associated with both errors and missingness is based on repeatedly drawing from the predictive distribution of the true non contaminated data given the observed data. The draws are obtained through a suitable version of the data augmentation algorithm. Applications to both simulated and real data are presented.     

M-Estimators Based on Inverse Probability Weighted Estimating Equations with Response Missing at Random

Asymptotic properties of M-estimators with complete data are investigated extensively. In the presence of missing data, however, the standard inference procedures for complete data cannot be applied directly. In this article, the inverse probability weighted method is applied to missing response problem to define M-estimators. The existence of M-estimators is established under very general regularity conditions. Consistency and asymptotic normality of the M-estimators are proved, respectively. An iterative algorithm is applied to calculating the M-estimators. It is shown that one step iteration suffices and the resulting one-step M-estimate has the same limit distribution as in the fully iterated M-estimators.     

Diagnostics for multivariate imputations

Summary.  We consider three sorts of diagnostics for random imputations: displays of the completed data, which are intended to reveal unusual patterns that might suggest problems with the imputations, comparisons of the distributions of observed and imputed data values and checks of the fit of observed data to the model that is used to create the imputations. We formulate these methods in terms of sequential regression multivariate imputation, which is an iterative procedure in which the missing values of each variable are randomly imputed conditionally on all the other variables in the completed data matrix. We also consider a recalibration procedure for sequential regression imputations. We apply these methods to the 2002 environmental sustainability index, which is a linear aggregation of 64 environmental variables on 142 countries.     

A numerical study of multiple imputation methods using nonparametric multivariate outlier identifiers and depth-based performance criteria with clinical laboratory data

It is well known that if a multivariate outlier has one or more missing component values, then multiple imputation (MI) methods tend to impute nonextreme values and make the outlier become less extreme and less likely to be detected. In this paper, nonparametric depth-based multivariate outlier identifiers are used as criteria in a numerical study comparing several established methods of MI as well as a new proposed one, nine in all, in a setting of several actual clinical laboratory data sets of different dimensions. Two criteria, an ‘outlier recovery probability’ and a ‘relative accuracy measure’, are developed, based on depth functions. Three outlier identifiers, based on Mahalanobis distance, robust Mahalanobis distance, and generalized principle component analysis are also included in the study. Consequently, not only the comparison of imputation methods but also the comparison of outlier detection methods is accomplished in this study. Our findings show that the performance of an MI method depends on the choice of depth-based outlier detection criterion, as well as the size and dimension of the data and the fraction of missing components. By taking these features into account, an MI method for a given data set can be selected more optimally.     

Nonparametric curve estimation with missing data: A general empirical process approach

A general nonparametric imputation procedure, based on kernel regression, is proposed to estimate points as well as set- and function-indexed parameters when the data are missing at random (MAR). The proposed method works by imputing a specific function of a missing value (and not the missing value itself), where the form of this specific function is dictated by the parameter of interest. Both single and multiple imputations are considered. The associated empirical processes provide the right tool to study the uniform convergence properties of the resulting estimators. Our estimators include, as special cases, the imputation estimator of the mean, the estimator of the distribution function proposed by Cheng and Chu [1996. Kernel estimation of distribution functions and quantiles with missing data. Statist. Sinica 6, 63–78], imputation estimators of a marginal density, and imputation estimators of regression functions.     

Empirical Likelihood in a Semi-Parametric Model for Missing Response Data

Let Y be a response and, given covariate X,Y has a conditional density f(y | x, θ), where θ is a unknown p-dimensional vector of parameters and the marginal distribution of X is unknown. When responses are missing at random, with auxiliary information and imputation, we define an adjusted empirical log-likelihood ratio for the mean of Y and obtain its asymptotic distribution. A simulation study is conducted to compare the adjusted empirical log-likelihood and the normal approximation method in terms of coverage accuracies.