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Oversampling techniques for predicting COVID-19 patient length of stay

Farahany, Zachariah, Wu, Jiawei, Islam, K M Sajjadul, Madiraju, Praveen

arXiv.org Artificial Intelligence

Abstract--COVID-19 is a respiratory disease that caused a global pandemic in 2019. It is highly infectious and has the following symptoms: fever or chills, cough, shortness of breath, fatigue, muscle or body aches, headache, the new loss of taste or smell, sore throat, congestion or runny nose, nausea or vomiting, and diarrhea. These symptoms vary in severity; some people with many risk factors have been known to have lengthy hospital stays or die from the disease. In this paper, we analyze patients' electronic health records (EHR) to predict the severity of their COVID-19 infection using the length of stay (LOS) as our measurement of severity. This is an imbalanced classification problem, as many people have a shorter LOS rather than a longer one. T o combat this problem, we synthetically create alternate oversampled training data sets. Once we have this oversampled data, we run it through an Artificial Neural Network (ANN), which during training has its hyperparameters tuned by using bayesian optimization. We select the model with the best F1 score and then evaluate it and discuss it. COVID-19 is defined by the Centers for Disease Control and Prevention (CDC) as "a respiratory disease caused by SARS-CoV -2, a coronavirus discovered in 2019. The virus spreads mainly from person to person through respiratory droplets produced when an infected person coughs, sneezes, or talks" [1]. Furthermore, they add, "For people who have symptoms, illness can range from mild to severe. Adults 65 years and older and people of any age with underlying medical conditions are at higher risk for severe illness" [1].In 2019 this novel coronavirus was first detected. The highly infectious nature of this disease, combined with the respiratory nature of the infection, caused a pandemic. Along with being highly contagious, COVID-19 also has an extensive range of symptoms such as fever or chills, cough, shortness of breath, fatigue, muscle or body aches, headache, the new loss of taste or smell, sore throat, congestion or runny nose, nausea or vomiting, and diarrhea [2]. Along with a long list of symptoms, COVID-19 has many risk factors, which may increase the severity of the infection.


A Study of Left Before Treatment Complete Emergency Department Patients: An Optimized Explanatory Machine Learning Framework

Ahmed, Abdulaziz, Aram, Khalid Y., Tutun, Salih

arXiv.org Artificial Intelligence

The issue of left before treatment complete (LBTC) patients is common in emergency departments (EDs). This issue represents a medico-legal risk and may cause a revenue loss. Thus, understanding the factors that cause patients to leave before treatment is complete is vital to mitigate and potentially eliminate these adverse effects. This paper proposes a framework for studying the factors that affect LBTC outcomes in EDs. The framework integrates machine learning, metaheuristic optimization, and model interpretation techniques. Metaheuristic optimization is used for hyperparameter optimization--one of the main challenges of machine learning model development. Three metaheuristic optimization algorithms are employed for optimizing the parameters of extreme gradient boosting (XGB), which are simulated annealing (SA), adaptive simulated annealing (ASA), and adaptive tabu simulated annealing (ATSA). The optimized XGB models are used to predict the LBTC outcomes for the patients under treatment in ED. The designed algorithms are trained and tested using four data groups resulting from the feature selection phase. The model with the best predictive performance is interpreted using SHaply Additive exPlanations (SHAP) method. The findings show that ATSA-XGB outperformed other mode configurations with an accuracy, area under the curve (AUC), sensitivity, specificity, and F1-score of 86.61%, 87.50%, 85.71%, 87.51%, and 86.60%, respectively. The degree and the direction of effects of each feature were determined and explained using the SHAP method.


Cascading Neural Network Methodology for Artificial Intelligence-Assisted Radiographic Detection and Classification of Lead-Less Implanted Electronic Devices within the Chest

Demirer, Mutlu, White, Richard D., Gupta, Vikash, Sebro, Ronnie A., Erdal, Barbaros S.

arXiv.org Artificial Intelligence

Background & Purpose: Chest X-Ray (CXR) use in pre-MRI safety screening for Lead-Less Implanted Electronic Devices (LLIEDs), easily overlooked or misidentified on a frontal view (often only acquired), is common. Although most LLIED types are "MRI conditional": 1. Some are stringently conditional; 2. Different conditional types have specific patient- or device- management requirements; and 3. Particular types are "MRI unsafe". This work focused on developing CXR interpretation-assisting Artificial Intelligence (AI) methodology with: 1. 100% detection for LLIED presence/location; and 2. High classification in LLIED typing. Materials & Methods: Data-mining (03/1993-02/2021) produced an AI Model Development Population (1,100 patients/4,871 images) creating 4,924 LLIED Region-Of-Interests (ROIs) (with image-quality grading) used in Training, Validation, and Testing. For developing the cascading neural network (detection via Faster R-CNN and classification via Inception V3), "ground-truth" CXR annotation (ROI labeling per LLIED), as well as inference display (as Generated Bounding Boxes (GBBs)), relied on a GPU-based graphical user interface. Results: To achieve 100% LLIED detection, probability threshold reduction to 0.00002 was required by Model 1, resulting in increasing GBBs per LLIED-related ROI. Targeting LLIED-type classification following detection of all LLIEDs, Model 2 multi-classified to reach high-performance while decreasing falsely positive GBBs. Despite 24% suboptimal ROI image quality, classification was correct in 98.9% and AUCs for the 9 LLIED-types were 1.00 for 8 and 0.92 for 1. For all misclassification cases: 1. None involved stringently conditional or unsafe LLIEDs; and 2. Most were attributable to suboptimal images. Conclusion: This project successfully developed a LLIED-related AI methodology supporting: 1. 100% detection; and 2. Typically 100% type classification.


Large expert-curated database for benchmarking document similarity detection in biomedical literature search

#artificialintelligence

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations.


Using Multitask Learning to Improve 12-Lead Electrocardiogram Classification

Hughes, J. Weston, Sittler, Taylor, Joseph, Anthony D., Olgin, Jeffrey E., Gonzalez, Joseph E., Tison, Geoffrey H.

arXiv.org Machine Learning

We develop a multi-task convolutional neural network (CNN) to classify multiple diagnoses from 12-lead electrocardiograms (ECGs) using a dataset comprised of over 40,000 ECGs, with labels derived from cardiologist clinical interpretations. Since many clinically important classes can occur in low frequencies, approaches are needed to improve performance on rare classes. We compare the performance of several single-class classifiers on rare classes to a multi-headed classifier across all available classes. We demonstrate that the addition of common classes can significantly improve CNN performance on rarer classes when compared to a model trained on the rarer class in isolation. Using this method, we develop a model with high performance as measured by F1 score on multiple clinically relevant classes compared against the gold-standard cardiologist interpretation.


Method to Annotate Arrhythmias by Deep Network

Lu, Weijia, Shuai, Jie, Gu, Shuyan, Xue, Joel

arXiv.org Artificial Intelligence

This study targets to automatically annotate on arrhythmia by deep network. The investigated types include sinus rhythm, asystole (Asys), supraventricular tachycardia (Tachy), ventricular flutter or fibrillation (VF/VFL), ventricular tachycardia (VT). Methods: 13s limb lead ECG chunks from MIT malignant ventricular arrhythmia database (VFDB) and MIT normal sinus rhythm database were partitioned into subsets for 5-fold cross validation. These signals were resampled to 200Hz, filtered to remove baseline wandering, projected to 2D gray spectrum and then fed into a deep network with brand-new structure. In this network, a feature vector for a single time point was retrieved by residual layers, from which latent representation was extracted by variational autoencoder (VAE). These front portions were trained to meet a certain threshold in loss function, then fixed while training procedure switched to remaining bidirectional recurrent neural network (RNN), the very portions to predict an arrhythmia category. Attention windows were polynomial lumped on RNN outputs for learning from details to outlines. And over sampling was employed for imbalanced data. The trained model was wrapped into docker image for deployment in edge or cloud. Conclusion: Promising sensitivities were achieved in four arrhythmias and good precision rates in two ventricular arrhythmias were also observed. Moreover, it was proven that latent representation by VAE, can significantly boost the speed of convergence and accuracy.