Journal of Data Science

Obesity rates continue to exhibit an upward trajectory, particularly in the US, and is the underlying cause of several comorbidities, including but not limited to high blood pressure, high cholesterol, diabetes, heart disease, stroke, and cancers. To monitor obesity, body mass index (BMI) and proportion body fat (PBF) are two commonly used measurements. Although BMI and PBF changes over time in an individual’s lifespan and their relationship may also change dynamically, existing work has mostly remained cross-sectional, or separately modeling BMI and PBF. A combined longitudinal assessment is expected to be more effective in unravelling their complex interplay. To mitigate this, we consider Bayesian cross-domain latent growth curve models within a structural equation modeling framework, which simultaneously handles issues such as individually varying time metrics, proportion data, and potential missing not at random data for joint assessment of the longitudinal changes of BMI and PBF. Through simulation studies, we observe that our proposed models and estimation method yielded parameter estimates with small bias and mean squared error in general, however, a mis-specified missing data mechanism may cause inaccurate and inefficient parameter estimates. Furthermore, we demonstrate application of our method to a motivating longitudinal obesity study, controlling for both time-invariant (such as, sex), and time-varying (such as diastolic and systolic blood pressure, biceps skinfold, bioelectrical impedance, and waist circumference) covariates in separate models. Under time-invariance, we observe that the initial BMI level and the rate of change in BMI influenced PBF. However, in presence of time-varying covariates, only the initial BMI level influenced the initial PBF. The added-on selection model estimation indicated that observations with higher PBF values were less likely to be missing.

Clinical risk prediction models are commonly developed in a post-hoc and passive fashion, capitalizing on convenient data from completed clinical trials or retrospective cohorts. Impacts of the models often end at their publication rather than with the patients. The field of clinical risk prediction is rapidly improving in a progressively more transparent data science era. Based on collective experience over the past decade by the Prostate Biopsy Collaborative Group (PBCG), this paper proposes the following four data science-driven strategies for improving clinical risk prediction to the benefit of clinical practice and research. The first proposed strategy is to actively design prospective data collection, monitoring, analysis and validation of risk tools following the same standards as for clinical trials in order to elevate the quality of training data. The second suggestion is to make risk tools and model formulas available online. User-friendly risk tools will bring quantitative information to patients and their clinicians for improved knowledge-based decision-making. As past experience testifies, online tools expedite independent validation, providing helpful information as to whether the tools are generalizable to new populations. The third proposal is to dynamically update and localize risk tools to adapt to changing demographic and clinical landscapes. The fourth strategy is to accommodate systematic missing data patterns across cohorts in order to maximize the statistical power in model training, as well as to accommodate missing information on the end-user side too, in order to maximize utility for the public.

Researchers and practitioners of many areas of knowledge frequently struggle with missing data. Missing data is a problem because almost all standard statistical methods assume that the information is complete. Consequently, missing value imputation offers a solution to this problem. The main contribution of this paper lies on the development of a random forest-based imputation method (TI-FS) that can handle any type of data, including high-dimensional data with nonlinear complex interactions. The premise behind the proposed scheme is that a variable can be imputed considering only those variables that are related to it using feature selection. This work compares the performance of the proposed scheme with other two imputation methods commonly used in literature: KNN and missForest. The results suggest that the proposed method can be useful in complex scenarios with categorical variables and a high volume of missing values, while reducing the amount of variables used and their corresponding preliminary imputations.

Abstract: This paper considers the statistical problems of editing and imputing data of multiple time series generated by repetitive surveys. The case under study is that of the Survey of Cattle Slaughter in Mexico’s Municipal Abattoirs. The proposed procedure consists of two phases; firstly the data of each abattoir are edited to correct them for gross inconsistencies. Secondly, the missing data are imputed by means of restricted forecasting. This method uses all the historical and current information available for the abattoir, as well as multiple time series models from which efficient estimates of the missing data are obtained. Some empirical examples are shown to illustrate the usefulness of the method in practice.

Abstract: Missing data are a common problem for researchers working with surveys and other types of questionnaires. Often, respondents do not respond to one or more items, making the conduct of statistical analyses, as well as the calculation of scores difficult. A number of methods have been developed for dealing with missing data, though most of these have focused on continuous variables. It is not clear that these techniques for imputation are appropriate for the categorical items that make up surveys. However, methods of imputation specifically designed for categorical data are either limited in terms of the number of variables they can accommodate, or have not been fully compared with the continuous data approaches used with categorical variables. The goal of the current study was to compare the performance of these explicitly categorical imputation approaches with the more well established continuous method used with categorical item responses. Results of the simulation study based on real data demonstrate that the continuous based imputation approach and a categorical method based on stochastic regression appear to perform well in terms of creating data that match the complete datasets in terms of logistic regression results.

Longitudinal data analysis had been widely developed in the past three decades. Longitudinal data are common in many fields such as public health, medicine, biological and social sciences. Longitudinal data have special nature as the individual may be observed during a long period of time. Hence, missing values are common in longitudinal data. The presence of missing values leads to biased results and complicates the analysis. The missing values have two patterns: intermittent and dropout. The missing data mechanisms are missing completely at random (MCAR), missing at random (MAR), and missing not at random (MNAR). The appropriate analysis relies heavily on the assumed mechanism and pattern. The parametric fractional imputation is developed to handle longitudinal data with intermittent missing pattern. The maximum likelihood estimates are obtained and the Jackkife method is used to obtain the standard errors of the parameters estimates. Finally a simulation study is conducted to validate the proposed approach. Also, the proposed approach is applied to a real data.

Abstract: Latent class analysis (LCA) is a popular method for analyzing multiple categorical outcomes. Given the potential for LCA model assump tions to influence inference, model diagnostics are a particulary important part of LCA. We suggest using the rate of missing information as an addi tional diagnostic tool. The rate of missing information gives an indication of the amount of information missing as a result of observing multiple sur rogates in place of the underlying latent variable of interest and provides a measure of how confident one can be in the model results. Simulation studies and real data examples are presented to explore the usefulness of the proposed measure.

Social network data often contain missing values because of the sensitive nature of the information collected and the dependency among the network actors. As a response, network imputation methods including simple ones constructed from network structural characteristics and more complicated model-based ones have been developed. Although past studies have explored the influence of missing data on social networks and the effectiveness of imputation procedures in many missing data conditions, the current study aims to evaluate a more extensive set of eight network imputation techniques (i.e., null-tie, Reconstruction, Preferential Attachment, Constrained Random Dot Product Graph, Multiple Imputation by Bayesian Exponential Random Graph Models or BERGMs, k-Nearest Neighbors, Random Forest, and Multiple Imputation by Chained Equations) under more practical conditions through comprehensive simulation. A factorial design for missing data conditions is adopted with factors including missing data types, missing data mechanisms, and missing data proportions, which are applied to generated social networks with varying numbers of actors based on 4 different sets of coefficients in ERGMs. Results show that the effectiveness of imputation methods differs by missing data types, missing data mechanisms, the evaluation criteria used, and the complexity of the social networks. More complex methods such as the BERGMs have consistently good performances in recovering missing edges that should have been present. While simpler methods like Reconstruction work better in recovering network statistics when the missing proportion of present edges is low, the BERGMs work better when more present edges are missing. The BERGMs also work well in recovering ERGM coefficients when the networks are complex and the missing data type is actor non-response. In conclusion, researchers analyzing social networks with incomplete data should identify the network structures of interest and the potential missing data types before selecting appropriate imputation methods.

We consider a continuous outcome subject to nonresponse and a fully observed covariate. We propose a spline proxy pattern-mixture model (S-PPMA), an extension of the proxy pattern-mixture model (PPMA) (Andridge and Little, 2011), to estimate the mean of the outcome under varying assumptions about nonresponse. S-PPMA improves the robustness of PPMA, which assumes bivariate normality between the outcome and the covariate, by modeling the relationship via a spline. Simulations indicate that S-PPMA outperforms PPMA when the data deviate from normality and are missing not at random, with minor losses of efficiency when the data are normal.

Early in the course of the pandemic in Colorado, researchers wished to fit a sparse predictive model to intubation status for newly admitted patients. Unfortunately, the training data had considerable missingness which complicated the modeling process. I developed a quick solution to this problem: Median Aggregation of penaLized Coefficients after Multiple imputation (MALCoM). This fast, simple solution proved successful on a prospective validation set. In this manuscript, I show how MALCoM performs comparably to a popular alternative (MI-lasso), and can be implemented in more general penalized regression settings. A simulation study and application to local COVID-19 data is included.