Dataset Information

Deep Learning Approach for Imputation of Missing Values in Actigraphy Data: Algorithm Development Study.

ABSTRACT: BACKGROUND:Data collected by an actigraphy device worn on the wrist or waist can provide objective measurements for studies related to physical activity; however, some data may contain intervals where values are missing. In previous studies, statistical methods have been applied to impute missing values on the basis of statistical assumptions. Deep learning algorithms, however, can learn features from the data without any such assumptions and may outperform previous approaches in imputation tasks. OBJECTIVE:The aim of this study was to impute missing values in data using a deep learning approach. METHODS:To develop an imputation model for missing values in accelerometer-based actigraphy data, a denoising convolutional autoencoder was adopted. We trained and tested our deep learning-based imputation model with the National Health and Nutrition Examination Survey data set and validated it with the external Korea National Health and Nutrition Examination Survey and the Korean Chronic Cerebrovascular Disease Oriented Biobank data sets which consist of daily records measuring activity counts. The partial root mean square error and partial mean absolute error of the imputed intervals (partial RMSE and partial MAE, respectively) were calculated using our deep learning-based imputation model (zero-inflated denoising convolutional autoencoder) as well as using other approaches (mean imputation, zero-inflated Poisson regression, and Bayesian regression). RESULTS:The zero-inflated denoising convolutional autoencoder exhibited a partial RMSE of 839.3 counts and partial MAE of 431.1 counts, whereas mean imputation achieved a partial RMSE of 1053.2 counts and partial MAE of 545.4 counts, the zero-inflated Poisson regression model achieved a partial RMSE of 1255.6 counts and partial MAE of 508.6 counts, and Bayesian regression achieved a partial RMSE of 924.5 counts and partial MAE of 605.8 counts. CONCLUSIONS:Our deep learning-based imputation model performed better than the other methods when imputing missing values in actigraphy data.

SUBMITTER: Jang JH

PROVIDER: S-EPMC7413283 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature

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Deep Learning Approach for Imputation of Missing Values in Actigraphy Data: Algorithm Development Study.

Jang Jong-Hwan JH Choi Junggu J Roh Hyun Woong HW Son Sang Joon SJ Hong Chang Hyung CH Kim Eun Young EY Kim Tae Young TY Yoon Dukyong D

JMIR mHealth and uHealth 20200723 7

<h4>Background</h4>Data collected by an actigraphy device worn on the wrist or waist can provide objective measurements for studies related to physical activity; however, some data may contain intervals where values are missing. In previous studies, statistical methods have been applied to impute missing values on the basis of statistical assumptions. Deep learning algorithms, however, can learn features from the data without any such assumptions and may outperform previous approaches in imputat ...[more]

PMID: 32445459

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Project description:The real-world data analysis and processing using data mining techniques often are facing observations that contain missing values. The main challenge of mining datasets is the existence of missing values. The missing values in a dataset should be imputed using the imputation method to improve the data mining methods' accuracy and performance. There are existing techniques that use k-nearest neighbors algorithm for imputing the missing values but determining the appropriate k value can be a challenging task. There are other existing imputation techniques that are based on hard clustering algorithms. When records are not well-separated, as in the case of missing data, hard clustering provides a poor description tool in many cases. In general, the imputation depending on similar records is more accurate than the imputation depending on the entire dataset's records. Improving the similarity among records can result in improving the imputation performance. This paper proposes two numerical missing data imputation methods. A hybrid missing data imputation method is initially proposed, called KI, that incorporates k-nearest neighbors and iterative imputation algorithms. The best set of nearest neighbors for each missing record is discovered through the records similarity by using the k-nearest neighbors algorithm (kNN). To improve the similarity, a suitable k value is estimated automatically for the kNN. The iterative imputation method is then used to impute the missing values of the incomplete records by using the global correlation structure among the selected records. An enhanced hybrid missing data imputation method is then proposed, called FCKI, which is an extension of KI. It integrates fuzzy c-means, k-nearest neighbors, and iterative imputation algorithms to impute the missing data in a dataset. The fuzzy c-means algorithm is selected because the records can belong to multiple clusters at the same time. This can lead to further improvement for similarity. FCKI searches a cluster, instead of the whole dataset, to find the best k-nearest neighbors. It applies two levels of similarity to achieve a higher imputation accuracy. The performance of the proposed imputation techniques is assessed by using fifteen datasets with variant missing ratios for three types of missing data; MCAR, MAR, MNAR. These different missing data types are generated in this work. The datasets with different sizes are used in this paper to validate the model. Therefore, proposed imputation techniques are compared with other missing data imputation methods by means of three measures; the root mean square error (RMSE), the normalized root mean square error (NRMSE), and the mean absolute error (MAE). The results show that the proposed methods achieve better imputation accuracy and require significantly less time than other missing data imputation methods.

Project description:BackgroundIncomplete categorical variables with more than two categories are common in public health data. However, most of the existing missing-data methods do not use the information from nonresponse (missingness) probabilities.MethodsWe propose a nearest-neighbour multiple imputation approach to impute a missing at random categorical outcome and to estimate the proportion of each category. The donor set for imputation is formed by measuring distances between each missing value with other non-missing values. The distance function is calculated based on a predictive score, which is derived from two working models: one fits a multinomial logistic regression for predicting the missing categorical outcome (the outcome model) and the other fits a logistic regression for predicting missingness probabilities (the missingness model). A weighting scheme is used to accommodate contributions from two working models when generating the predictive score. A missing value is imputed by randomly selecting one of the non-missing values with the smallest distances. We conduct a simulation to evaluate the performance of the proposed method and compare it with several alternative methods. A real-data application is also presented.ResultsThe simulation study suggests that the proposed method performs well when missingness probabilities are not extreme under some misspecifications of the working models. However, the calibration estimator, which is also based on two working models, can be highly unstable when missingness probabilities for some observations are extremely high. In this scenario, the proposed method produces more stable and better estimates. In addition, proper weights need to be chosen to balance the contributions from the two working models and achieve optimal results for the proposed method.ConclusionsWe conclude that the proposed multiple imputation method is a reasonable approach to dealing with missing categorical outcome data with more than two levels for assessing the distribution of the outcome. In terms of the choices for the working models, we suggest a multinomial logistic regression for predicting the missing outcome and a binary logistic regression for predicting the missingness probability.

Project description:When analyzing large datasets from high-throughput technologies, researchers often encounter missing quantitative measurements, which are particularly frequent in metabolomics datasets. Metabolomics, the comprehensive profiling of metabolite abundances, are typically measured using mass spectrometry technologies that often introduce missingness via multiple mechanisms: (1) the metabolite signal may be smaller than the instrument limit of detection; (2) the conditions under which the data are collected and processed may lead to missing values; (3) missing values can be introduced randomly. Missingness resulting from mechanism (1) would be classified as Missing Not At Random (MNAR), that from mechanism (2) would be Missing At Random (MAR), and that from mechanism (3) would be classified as Missing Completely At Random (MCAR). Two common approaches for handling missing data are the following: (1) omit missing data from the analysis; (2) impute the missing values. Both approaches may introduce bias and reduce statistical power in downstream analyses such as testing metabolite associations with clinical variables. Further, standard imputation methods in metabolomics often ignore the mechanisms causing missingness and inaccurately estimate missing values within a data set. We propose a mechanism-aware imputation algorithm that leverages a two-step approach in imputing missing values. First, we use a random forest classifier to classify the missing mechanism for each missing value in the data set. Second, we impute each missing value using imputation algorithms that are specific to the predicted missingness mechanism (i.e., MAR/MCAR or MNAR). Using complete data, we conducted simulations, where we imposed different missingness patterns within the data and tested the performance of combinations of imputation algorithms. Our proposed algorithm provided imputations closer to the original data than those using only one imputation algorithm for all the missing values. Consequently, our two-step approach was able to reduce bias for improved downstream analyses.

Project description:ObjectiveAssess the real-world performance of popular imputation algorithms on cochlear implant (CI) candidate audiometric data.Methods7,451 audiograms from patients undergoing CI candidacy evaluation were pooled from 32 institutions with complete case analysis yielding 1,304 audiograms. Imputation model performance was assessed with nested cross-validation on randomly generated sparse datasets with various amounts of missing data, distributions of sparsity, and dataset sizes. A threshold for safe imputation was defined as root mean square error (RMSE) <10dB. Models included univariate imputation, interpolation, multiple imputation by chained equations (MICE), k-nearest neighbors, gradient boosted trees, and neural networks.ResultsGreater quantities of missing data were associated with worse performance. Sparsity in audiometric data is not uniformly distributed, as inter-octave frequencies are less commonly tested. With 3-8 missing features per instance, a real-world sparsity distribution was associated with significantly better performance compared to other sparsity distributions (Δ RMSE 0.3 dB- 5.8 dB, non-overlapping 99% confidence intervals). With a real-world sparsity distribution, models were able to safely impute up to 6 missing datapoints in an 11-frequency audiogram. MICE consistently outperformed other models across all metrics and sparsity distributions (p < 0.01, Wilcoxon rank sum test). With sparsity capped at 6 missing features per audiogram but otherwise equivalent to the raw dataset, MICE imputed with RMSE of 7.83 dB [95% CI 7.81-7.86]. Imputing up to 6 missing features captures 99.3% of the audiograms in our dataset, allowing for a 5.7-fold increase in dataset size (1,304 to 7,399 audiograms) as compared with complete case analysis.ConclusionPrecision medicine will inevitably play an integral role in the future of hearing healthcare. These methods are data dependent, and rigorously validated imputation models are a key tool for maximizing datasets. Using the largest CI audiogram dataset to-date, we demonstrate that in a real-world scenario MICE can safely impute missing data for the vast majority (>99%) of audiograms with RMSE well below a clinically significant threshold of 10dB. Evaluation across a range of dataset sizes and sparsity distributions suggests a high degree of generalizability to future applications.

Dataset Information

Deep Learning Approach for Imputation of Missing Values in Actigraphy Data: Algorithm Development Study.

Publications

Deep Learning Approach for Imputation of Missing Values in Actigraphy Data: Algorithm Development Study.

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