Dependent Missingness Research Articles

Labeling Self-Tracked Menstrual Health Records With Hidden Semi-Markov Models.

Globally, millions of women track their menstrual cycle and fertility via smartphone-based health apps, generating multivariate time series with frequent missing data. To leverage this type of data for studies of fertility or studies of the effect of the menstrual cycle on symptoms and diseases, it is critical to have methods for identifying reproductive events, such as ovulation, pregnancy losses or births. Here, we present a hierarchical approach relying on hidden semi-Markov models that adapts to changes in tracking behavior, explicitly captures variable- and state- dependent missingness, allows for variables of different type, and quantifies uncertainty. The accuracy on simulated data reaches 98% with no missing data and 90% with realistic missingness. On our partially labeled real-world time series, the accuracy reaches 93%. Our method also accurately predicts cycle length by learning user characteristics. Its implementation is publicly available (HiddenSemiMarkov R package) and transferable to any health time series, including self-reported symptoms and occasional tests.

Bayesian Approach to Non-ignorable Missingness in Latent Growth Models

Latent growth curve models (LGCMs) are becoming increasingly important among growth models because they can effectively capture individuals' latent growth trajectories and also explain the factors that influence such growth by analyzing the repeatedly measured manifest variables. However, with the increase in complexity of LGCMs, there is an increase in issues on model estimation. This research proposes a Bayesian approach to LGCMs to address the perennial problem of almost all longitudinal research, namely, missing data. First, different missingness models are formulated. We focus on non-ignorable missingness in this article. Specifically, these models include the latent intercept dependent missingness, the latent slope dependent missingness, and the potential outcome dependent missingness. To implement the model estimation, this study proposes a full Bayesian approach through data augmentation algorithm and Gibbs sampling procedure. Simulation studies are conducted and results show that the proposed method accurately recover model parameters and the mis-specified missingness may result in severely misleading conclusions. Finally, the implications of the approach and future research directions are discussed.

Robust Summarization and Inference in Proteome-wide Label-free Quantification

Label-Free Quantitative mass spectrometry based workflows for differential expression (DE) analysis of proteins impose important challenges on the data analysis because of peptide-specific effects and context dependent missingness of peptide intensities. Peptide-based workflows, like MSqRob, test for DE directly from peptide intensities and outperform summarization methods which first aggregate MS1 peptide intensities to protein intensities before DE analysis. However, these methods are computationally expensive, often hard to understand for the non-specialized end-user, and do not provide protein summaries, which are important for visualization or downstream processing. In this work, we therefore evaluate state-of-the-art summarization strategies using a benchmark spike-in dataset and discuss why and when these fail compared with the state-of-the-art peptide based model, MSqRob. Based on this evaluation, we propose a novel summarization strategy, MSqRobSum, which estimates MSqRob's model parameters in a two-stage procedure circumventing the drawbacks of peptide-based workflows. MSqRobSum maintains MSqRob's superior performance, while providing useful protein expression summaries for plotting and downstream analysis. Summarizing peptide to protein intensities considerably reduces the computational complexity, the memory footprint and the model complexity, and makes it easier to disseminate DE inferred on protein summaries. Moreover, MSqRobSum provides a highly modular analysis framework, which provides researchers with full flexibility to develop data analysis workflows tailored toward their specific applications.

Clustering with missing features: a penalized dissimilarity measure based approach

Many real-world clustering problems are plagued by incomplete data characterized by missing or absent features for some or all of the data instances. Traditional clustering methods cannot be directly applied to such data without preprocessing by imputation or marginalization techniques. In this article, we overcome this drawback by utilizing a penalized dissimilarity measure which we refer to as the feature weighted penalty based dissimilarity (FWPD). Using the FWPD measure, we modify the traditional k-means clustering algorithm and the standard hierarchical agglomerative clustering algorithms so as to make them directly applicable to datasets with missing features. We present time complexity analyses for these new techniques and also undertake a detailed theoretical analysis showing that the new FWPD based k-means algorithm converges to a local optimum within a finite number of iterations. We also present a detailed method for simulating random as well as feature dependent missingness. We report extensive experiments on various benchmark datasets for different types of missingness showing that the proposed clustering techniques have generally better results compared to some of the most well-known imputation methods which are commonly used to handle such incomplete data. We append a possible extension of the proposed dissimilarity measure to the case of absent features (where the unobserved features are known to be undefined).

Handling missing items in the Hospital Anxiety and Depression Scale (HADS): a simulation study.

BackgroundThe Hospital Anxiety and Depression Scale (HADS) is a widely used questionnaire in health research, but there is little guidance on how to handle missing items. We aimed to investigate approaches to handling item non-response, varying sample size, proportion of subjects with missing items, proportion of missing items per subject, and the missingness mechanism.MethodsWe performed a simulation study based on anxiety and depression data among cancer survivors and patients. Item level data were deleted according to random, demographic, and subscale dependent missingness mechanisms. Seven methods for handling missing items were assessed for bias and imprecision. Imputation, imputation conditional on the number of non-missing items, and complete case approaches were used. One thousand datasets were simulated for each parameter combination.ResultsAll methods were most sensitive when missingness was dependent on the subscale (i.e., higher values of depression leads to higher levels of missingness). The worst performing approach was to analyze only individuals with complete data. The best performing imputation methods depended on whether inference was targeted at the individual or at the population.ConclusionsWe recommend the ‘half rule’ using individual subscale means when using the HADS scores at the individual level (e.g. screening). For population inference, we recommend relaxing the requirement that at least half the items be answered to minimize missing scores.Electronic supplementary materialThe online version of this article (doi:10.1186/s13104-016-2284-z) contains supplementary material, which is available to authorized users.

Missing continuous outcomes under covariate dependent missingness in cluster randomised trials.

Attrition is a common occurrence in cluster randomised trials which leads to missing outcome data. Two approaches for analysing such trials are cluster-level analysis and individual-level analysis. This paper compares the performance of unadjusted cluster-level analysis, baseline covariate adjusted cluster-level analysis and linear mixed model analysis, under baseline covariate dependent missingness in continuous outcomes, in terms of bias, average estimated standard error and coverage probability. The methods of complete records analysis and multiple imputation are used to handle the missing outcome data. We considered four scenarios, with the missingness mechanism and baseline covariate effect on outcome either the same or different between intervention groups. We show that both unadjusted cluster-level analysis and baseline covariate adjusted cluster-level analysis give unbiased estimates of the intervention effect only if both intervention groups have the same missingness mechanisms and there is no interaction between baseline covariate and intervention group. Linear mixed model and multiple imputation give unbiased estimates under all four considered scenarios, provided that an interaction of intervention and baseline covariate is included in the model when appropriate. Cluster mean imputation has been proposed as a valid approach for handling missing outcomes in cluster randomised trials. We show that cluster mean imputation only gives unbiased estimates when missingness mechanism is the same between the intervention groups and there is no interaction between baseline covariate and intervention group. Multiple imputation shows overcoverage for small number of clusters in each intervention group.

Comparison of population-averaged and cluster-specific models for the analysis of cluster randomized trials with missing binary outcomes: a simulation study

sBackgroundThe objective of this simulation study is to compare the accuracy and efficiency of population-averaged (i.e. generalized estimating equations (GEE)) and cluster-specific (i.e. random-effects logistic regression (RELR)) models for analyzing data from cluster randomized trials (CRTs) with missing binary responses.MethodsIn this simulation study, clustered responses were generated from a beta-binomial distribution. The number of clusters per trial arm, the number of subjects per cluster, intra-cluster correlation coefficient, and the percentage of missing data were allowed to vary. Under the assumption of covariate dependent missingness, missing outcomes were handled by complete case analysis, standard multiple imputation (MI) and within-cluster MI strategies. Data were analyzed using GEE and RELR. Performance of the methods was assessed using standardized bias, empirical standard error, root mean squared error (RMSE), and coverage probability.ResultsGEE performs well on all four measures — provided the downward bias of the standard error (when the number of clusters per arm is small) is adjusted appropriately — under the following scenarios: complete case analysis for CRTs with a small amount of missing data; standard MI for CRTs with variance inflation factor (VIF) <3; within-cluster MI for CRTs with VIF≥3 and cluster size>50. RELR performs well only when a small amount of data was missing, and complete case analysis was applied.ConclusionGEE performs well as long as appropriate missing data strategies are adopted based on the design of CRTs and the percentage of missing data. In contrast, RELR does not perform well when either standard or within-cluster MI strategy is applied prior to the analysis.