An interpretable machine learning model for covid-19 screening

Abstract

Introduction: the Coronavirus Disease 2019 (COVID-19) is a viral disease which has been declared a pandemic by the WHO. Diagnostic tests are expensive and are not always available. Researches using machine learning (ML) approach for diagnosing SARS-CoV-2 infection have been proposed in the literature to reduce cost and allow better control of the pandemic. Objective: we aim to develop a machine learning model to predict if a patient has COVID-19 with epidemiological data and clinical features. Methods: we used six ML algorithms for COVID-19 screening through diagnostic prediction and did an interpretative analysis using SHAP models and feature importances. Results: our best model was XGBoost (XGB) which obtained an area under the ROC curve of 0.752, a sensitivity of 90%, a specificity of 40%, a positive predictive value (PPV) of 42.16%, and a negative predictive value (NPV) of 91.0%. The best predictors were fever, cough, history of international travel less than 14 days ago, male gender, and nasal congestion, respectively. Conclusion: We conclude that ML is an important tool for screening with high sensitivity, compared to rapid tests, and can be used to empower clinical precision in COVID-19, a disease in which symptoms are very unspecific.