Deep Learning-Based Approach for Missing Data Imputation

The missing values in the datasets are a problem that will decrease the machine learning performance. New methods arerecommended every day to overcome this problem. The methods of statistical, machine learning, evolutionary and deeplearning are among these methods. Although deep learning methods is one of the popular subjects of today, there are limitedstudies in the missing data imputation. Several deep learning techniques have been used to handling missing data, one of themis the autoencoder and its denoising and stacked variants. In this study, the missing value in three different real-world datasetswas estimated by using denoising autoencoder (DAE), k-nearest neighbor (kNN) and multivariate imputation by chainedequations (MICE) methods. The estimation success of the methods was compared according to the root mean square error(RMSE) criterion. It was observed that the DAE method was more successful than other statistical methods in estimating themissing values for large datasets

Predicting the need for intubation in the first 24 h after critical care admission using machine learning approaches

Early and accurate prediction of the need for intubation may provide more time for preparation and increase safety margins by avoiding high risk late intubation. This study evaluates whether machine learning can predict the need for intubation within 24 h using commonly available bedside and laboratory parameters taken at critical care admission. We extracted data from 2 large critical care databases (MIMIC-III and eICU-CRD). Missing variables were imputed using autoencoder. Machine learning classifiers using logistic regression and random forest were trained using 60% of the data and tested using the remaining 40% of the data. We compared the performance of logistic regression and random forest models to predict intubation in critically ill patients. After excluding patients with limitations of therapy and missing data, we included 17,616 critically ill patients in this retrospective cohort. Within 24 h of admission, 2,292 patients required intubation, whilst 15,324 patients were not intubated. Blood gas parameters (PaO2, PaCO2, HCO3-), Glasgow Coma Score, respiratory variables (respiratory rate, SpO2), temperature, age, and oxygen therapy were used to predict intubation. Random forest had AUC 0.86 (95% CI 0.85-0.87) and logistic regression had AUC 0.77 (95% CI 0.76-0.78) for intubation prediction performance. Random forest model had sensitivity of 0.88 (95% CI 0.86-0.90) and specificity of 0.66 (95% CI 0.63-0.69), with good calibration throughout the range of intubation risks. The results showed that machine learning could predict the need for intubation in critically ill patients using commonly collected bedside clinical parameters and laboratory results. It may be used in real-time to help clinicians predict the need for intubation within 24 h of intensive care unit admission.Peer reviewe

Multi-Output Gaussian Processes for Crowdsourced Traffic Data Imputation

Traffic speed data imputation is a fundamental challenge for data-driven transport analysis. In recent years, with the ubiquity of GPS-enabled devices and the widespread use of crowdsourcing alternatives for the collection of traffic data, transportation professionals increasingly look to such user-generated data for many analysis, planning, and decision support applications. However, due to the mechanics of the data collection process, crowdsourced traffic data such as probe-vehicle data is highly prone to missing observations, making accurate imputation crucial for the success of any application that makes use of that type of data. In this article, we propose the use of multi-output Gaussian processes (GPs) to model the complex spatial and temporal patterns in crowdsourced traffic data. While the Bayesian nonparametric formalism of GPs allows us to model observation uncertainty, the multi-output extension based on convolution processes effectively enables us to capture complex spatial dependencies between nearby road segments. Using 6 months of crowdsourced traffic speed data or "probe vehicle data" for several locations in Copenhagen, the proposed approach is empirically shown to significantly outperform popular state-of-the-art imputation methods.Comment: 10 pages, IEEE Transactions on Intelligent Transportation Systems, 201

Machine Learning Methods To Identify Hidden Phenotypes In The Electronic Health Record

The widespread adoption of Electronic Health Records (EHRs) means an unprecedented amount of patient treatment and outcome data is available to researchers. Research is a tertiary priority in the EHR, where the priorities are patient care and billing. Because of this, the data is not standardized or formatted in a manner easily adapted to machine learning approaches. Data may be missing for a large variety of reasons ranging from individual input styles to differences in clinical decision making, for example, which lab tests to issue. Few patients are annotated at a research quality, limiting sample size and presenting a moving gold standard. Patient progression over time is key to understanding many diseases but many machine learning algorithms require a snapshot, at a single time point, to create a usable vector form. In this dissertation, we develop new machine learning methods and computational workflows to extract hidden phenotypes from the Electronic Health Record (EHR). In Part 1, we use a semi-supervised deep learning approach to compensate for the low number of research quality labels present in the EHR. In Part 2, we examine and provide recommendations for characterizing and managing the large amount of missing data inherent to EHR data. In Part 3, we present an adversarial approach to generate synthetic data that closely resembles the original data while protecting subject privacy. We also introduce a workflow to enable reproducible research even when data cannot be shared. In Part 4, we introduce a novel strategy to first extract sequential data from the EHR and then demonstrate the ability to model these sequences with deep learning

Missing Features Reconstruction Using a Wasserstein Generative Adversarial Imputation Network

Missing data is one of the most common preprocessing problems. In this paper, we experimentally research the use of generative and non-generative models for feature reconstruction. Variational Autoencoder with Arbitrary Conditioning (VAEAC) and Generative Adversarial Imputation Network (GAIN) were researched as representatives of generative models, while the denoising autoencoder (DAE) represented non-generative models. Performance of the models is compared to traditional methods k-nearest neighbors (k-NN) and Multiple Imputation by Chained Equations (MICE). Moreover, we introduce WGAIN as the Wasserstein modification of GAIN, which turns out to be the best imputation model when the degree of missingness is less than or equal to 30%. Experiments were performed on real-world and artificial datasets with continuous features where different percentages of features, varying from 10% to 50%, were missing. Evaluation of algorithms was done by measuring the accuracy of the classification model previously trained on the uncorrupted dataset. The results show that GAIN and especially WGAIN are the best imputers regardless of the conditions. In general, they outperform or are comparative to MICE, k-NN, DAE, and VAEAC.Comment: Preprint of the conference paper (ICCS 2020), part of the Lecture Notes in Computer Scienc

Establishing strong imputation performance of a denoising autoencoder in a wide range of missing data problems

Dealing with missing data in data analysis is inevitable. Although powerful imputation methods that address this problem exist, there is still much room for improvement. In this study, we examined single imputation based on deep autoencoders, motivated by the apparent success of deep learning to efficiently extract useful dataset features. We have developed a consistent framework for both training and imputation. Moreover, we benchmarked the results against state-of-the-art imputation methods on different data sizes and characteristics. The work was not limited to the one-type variable dataset; we also imputed missing data with multi-type variables, e.g., a combination of binary, categorical, and continuous attributes. To evaluate the imputation methods, we randomly corrupted the complete data, with varying degrees of corruption, and then compared the imputed and original values. In all experiments, the developed autoencoder obtained the smallest error for all ranges of initial data corruption

Recovering Loss to Followup Information Using Denoising Autoencoders

Loss to followup is a significant issue in healthcare and has serious consequences for a study's validity and cost. Methods available at present for recovering loss to followup information are restricted by their expressive capabilities and struggle to model highly non-linear relations and complex interactions. In this paper we propose a model based on overcomplete denoising autoencoders to recover loss to followup information. Designed to work with high volume data, results on various simulated and real life datasets show our model is appropriate under varying dataset and loss to followup conditions and outperforms the state-of-the-art methods by a wide margin ($\ge 20\%$ in some scenarios) while preserving the dataset utility for final analysis.Comment: Copyright IEEE 2017, IEEE International Conference on Big Data (Big Data