COVID-19 SEVERITY PREDICTOR

Project Description/Objectives

WARNING: This tool is strictly prohibited from clinical use. It has not been externally validated and is under no circumstance to be used to guide decision making in the healthcare context.

Background

• The COVID-19 pandemic is profoundly impacting healthcare institutions worldwide
• At present, little is known about its clinical course and discovery is ongoing daily
• A model which predicts a patient’s future in-hospital mortality from the time of initial presentation could afford clinicians early prognostic information and inform decisions for admission to the intensive care unit.

Design

• Read in COVID-19 risk factors from published literature (1): boolean, calculate and store relative risk of mortality; continuous, store ranges of values
• Simulate patient database based on risk factors
• Display risk calculator, accept user input (GUI)
• Pass input to machine learning model (Weka)
• Display results panel
• Weka prediction (mortality risk)
• Graphs showing trends in patient data

How to run this application

To run this application, please follow the instructions below:

0. From the terminal/command line (or git bash), navigate to your preferred folder location and create a new directory called COVID: type mkdir COVID in the terminal and hit enter.
1. Type cd COVID and hit enter
2. Type git init and hit enter
3. Clone the covid project repo from the terminal by entering the following command git clone git@github.com:UPenn-CIT599/final-project-team_37_covid_19.git and hit enter.
4. Open up Eclipse IDE
5. To load the project, go to: File --> New --> Java Project
6. When the "New Java Project" dialog box opens, uncheck Use default location and hit Browse
7. Navigate into the COVID folder created in step 1 to see the final-project-team_37_covid_19 subfolder. Select this subfolder and click open. Eclipse should load the project into your workspace.
8. Follow the steps below to load Weka and JFreeChart BEFORE running the program

To get Weka working on your local, Please download stable-3-8.zip from https://www.cs.waikato.ac.nz/ml/weka/snapshots/weka_snapshots.html

Unzip the file, add weka.jar to your library path of Java project in Eclipse following these instructions:

To import jar file in your Eclipse IDE, follow the steps given below.

• Right click on your project
• Select Build Path
• Click on Configure Build Path
• Click on Libraries and select Add External JARs
• Select the jar file from the required folder
• Click and Apply and Ok

Source: https://www.edureka.co/community/4028/how-to-import-a-jar-file-in-eclipse

To enable the JFreeChart library, go to https://sourceforge.net/projects/jfreechart/files/

• Click the green "download latest version" button.
• Unzip the file, open the uncompressed file, navigate to the lib folder where you will find the .jar files.
• Use the same steps outlined above (how to import weka.jar in to Eclipse IDE) to add both jfreechart.jar and jcommon.jar to the library path of your Java project in Eclipse.

9. In your Eclipse IDE workspace, under the Package Explorer tab, click the down arrow left of final-project-team_37_covid_19 to access the drop-down list showing the folder content.

10. Click src --> default package --> Runner.java to open the Runner class.

11. Hit Run (Shift+Cmd+F11). The application should load. If it doesn't go over the steps above to be sure every step was carried out correctly.

12. The COVID 19 Severity Predictor dialog box should appear showing risk factors for covid mortality.

13. Please fill all fields-- numbers in the text input fields, and select radio buttons for each risk factor as appropriate.

14. Hit calculate

15. The application will return the patient mortality risk based on the inputs provided along with trend plots for important features on which the classifier (multilayer perceptron) was trained.

References

1. F Zhou, et al. Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study. Lancet (2020 Mar 11), 10.1016/S0140-6736(20)30566-3