"covid_IIS" is a Python app developed to predict the outcome of COVID-19 patients in the moment of hospital admission. It returns the probability given by our machine learning model (XGBOOST) of unfavorable outcome (ICU admission or death) and the corresponding value (as a Cut-off analysis was performed and a probability greater than 0.4 is considered high enought to be 'severe') It is designed to use as less variables as possible (only 20). All such variables as selected between the most common ones, available in many hospitals. It is released under European Union Public License (EUPL).
This project includes:
- A Jupyter-notebook file containing the App code.
- A Pix folder containing the logos of the different institutions and organizations involved in the project.
- A Model folder containing our best model, selected for the app.
- A environment.yml containing the requirements for creating a conda environment to run the jupyter notebook.
- A README.md file containing the explanations.
To be able to install the environment.yml file, Anaconda and Python should be installed previously in your computer/server.
Once cloned the repository, allocate on the main folder and execute:
conda env create -f environment.yml
This will create the environment covid_ITA_IIS. Activate it by executing:
conda activate covid_ITA_IIS
With the environment activated, run the app with the command:
voila VoilaApp.ipynb --VoilaConfiguration.file_whitelist="['.*.(png)']" --MappingKernelManager.cull_interval=120 --MappingKernelManager.cull_idle_timeout=120 --port={port}
Where {port} is the selected port on your server/computer that will give acces to the app.
Shap values are not represented in this demo-app due to privacy and data protection. The 20 variables considered are: Age, Oxygen saturation, Diagnosed dementia, Obesity, Cerebrovascular disease, Intermittent claudication, Red blood cells, MCV, % of neutrophils, % of lymphocytes, % of monocytes, % of eosinophils, Lymphocytes, Eosiniphils, INR-TP, Basal glucose, Urea, Creatinine, Chloride, LDH
- Rocío Aznar Gimeno - raznar@itainnova.es
- Rafael del Hoyo Alonso - rdelhoyo@itainnova.es
- David Abadía Gallego - dabadia@gmail.com
- Gorka Labata Lezaun - glabata@itainnova.es
Esta actuación está cofinanciada por el Fondo Europeo de Desarrollo regional en el marco del Programa Operativo FEDER Aragón 2014-2020, cuyo lema es “Construyendo Europa desde Aragón”.