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Register a new userDeriving information from missing data: implications for mood prediction
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Yue Wu
Publication date
2020
fields
Mathematical Statistics
and research's language is
English
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The availability of mobile technologies has enabled the efficient collection prospective longitudinal, ecologically valid self-reported mood data from psychiatric patients. These data streams have potential for improving the efficiency and accuracy of psychiatric diagnosis as well predicting future mood states enabling earlier intervention. However, missing responses are common in such datasets and there is little consensus as to how this should be dealt with in practice. A signature-based method was used to capture different elements of self-reported mood alongside missing data to both classify diagnostic group and predict future mood in patients with bipolar disorder, borderline personality disorder and healthy controls. The missing-response-incorporated signature-based method achieves roughly 66% correct diagnosis, with f1 scores for three different clinic groups 59% (bipolar disorder), 75% (healthy control) and 61% (borderline personality disorder) respectively. This was significantly more efficient than the naive model which excluded missing data. Accuracies of predicting subsequent mood states and scores were also improved by inclusion of missing responses. The signature method provided an effective approach to the analysis of prospectively collected mood data where missing data was common and should be considered as an approach in other similar datasets.
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Missing data are a common problem for both the construction and implementation of a prediction algorithm. Pattern mixture kernel submodels (PMKS) - a series of submodels for every missing data pattern that are fit using only data from that pattern - are a computationally efficient remedy for both stages. Here we show that PMKS yield the most predictive algorithm among all standard missing data strategies. Specifically, we show that the expected loss of a forecasting algorithm is minimized when each pattern-specific loss is minimized. Simulations and a re-analysis of the SUPPORT study confirms that PMKS generally outperforms zero-imputation, mean-imputation, complete-case analysis, complete-case submodels, and even multiple imputation (MI). The degree of improvement is highly dependent on the missingness mechanism and the effect size of missing predictors. When the data are Missing at Random (MAR) MI can yield comparable forecasting performance but generally requires a larger computational cost. We see that predictions from the PMKS are equivalent to the limiting predictions for a MI procedure that uses a mean model dependent on missingness indicators (the MIMI model). Consequently, the MIMI model can be used to assess the MAR assumption in practice. The focus of this paper is on out-of-sample prediction behavior, implications for model inference are only briefly explored.
Background: All-in-one station-based health monitoring devices are implemented in elder homes in Hong Kong to support the monitoring of vital signs of the elderly. During a pilot study, it was discovered that the systolic blood pressure was incorrectly measured during multiple weeks. A real-time solution was needed to identify future data quality issues as soon as possible. Methods: Control charts are an effective tool for real-time monitoring and signaling issues (changes) in data. In this study, as in other healthcare applications, many observations are missing. Few methods are available for monitoring data with missing observations. A data quality monitoring method is developed to signal issues with the accuracy of the collected data quickly. This method has the ability to deal with missing observations. A Hotellings T-squared control chart is selected as the basis for our proposed method. Findings: The proposed method is retrospectively validated on a case study with a known measurement error in the systolic blood pressure measurements. The method is able to adequately detect this data quality problem. The proposed method was integrated into a personalized telehealth monitoring system and prospectively implemented in a second case study. It was found that the proposed scheme supports the control of data quality. Conclusions: Data quality is an important issue and control charts are useful for real-time monitoring of data quality. However, these charts must be adjusted to account for missing data that often occur in healthcare context.
Quantitatively predicting phenotype variables by the expression changes in a set of candidate genes is of great interest in molecular biology but it is also a challenging task for several reasons. First, the collected biological observations might be heterogeneous and correspond to different biological mechanisms. Secondly, the gene expression variables used to predict the phenotype are potentially highly correlated since genes interact though unknown regulatory networks. In this paper, we present a novel approach designed to predict quantitative trait from transcriptomic data, taking into account the heterogeneity in biological samples and the hidden gene regulatory networks underlying different biological mechanisms. The proposed model performs well on prediction but it is also fully parametric, which facilitates the downstream biological interpretation. The model provides clusters of individuals based on the relation between gene expression data and the phenotype, and also leads to infer a gene regulatory network specific for each cluster of individuals. We perform numerical simulations to demonstrate that our model is competitive with other prediction models, and we demonstrate the predictive performance and the interpretability of our model to predict alcohol sensitivity from transcriptomic data on real data from Drosophila Melanogaster Genetic Reference Panel (DGRP).
Association testing aims to discover the underlying relationship between genotypes (usually Single Nucleotide Polymorphisms, or SNPs) and phenotypes (attributes, or traits). The typically large data sets used in association testing often contain missing values. Standard statistical methods either impute the missing values using relatively simple assumptions, or delete them, or both, which can generate biased results. Here we describe the Bayesian hierarchical model BAMD (Bayesian Association with Missing Data). BAMD is a Gibbs sampler, in which missing values are multiply imputed based upon all of the available information in the data set. We estimate the parameters and prove that updating one SNP at each iteration preserves the ergodic property of the Markov chain, and at the same time improves computational speed. We also implement a model selection option in BAMD, which enables potential detection of SNP interactions. Simulations show that unbiased estimates of SNP effects are recovered with missing genotype data. Also, we validate associations between SNPs and a carbon isotope discrimination phenotype that were previously reported using a family based method, and discover an additional SNP associated with the trait. BAMD is available as an R-package from http://cran.r-project.org/package=BAMD
During the semiconductor manufacturing process, predicting the yield of the semiconductor is an important problem. Early detection of defective product production in the manufacturing process can save huge production cost. The data generated from the semiconductor manufacturing process have characteristics of highly non-normal distributions, complicated missing patterns and high missing rate, which complicate the prediction of the yield. We propose Dirichlet process - naive Bayes model (DPNB), a classification method based on the mixtures of Dirichlet process and naive Bayes model. Since the DPNB is based on the mixtures of Dirichlet process and learns the joint distribution of all variables involved, it can handle highly non-normal data and can make predictions for the test dataset with any missing patterns. The DPNB also performs well for high missing rates since it uses all information of observed components. Experiments on various real datasets including semiconductor manufacturing data show that the DPNB has better performance than MICE and MissForest in terms of predicting missing values as percentage of missing values increases.
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