Risk Stratification of COVID-19 Using Routine Laboratory Tests: A Machine Learning Approach

Abstract

The COVID-19 pandemic placed significant stress on an already overburdened health system. The diagnosis was based on detection of a positive RT-PCR test, which may be delayed when there is peak demand for testing. Rapid risk stratification of high-risk patients allows for the prioritization of resources for patient care. The study aims were to classify patients as severe or not severe based on outcomes using machine learning on routine laboratory tests. Data were extracted for all individuals who had at least one SARS-CoV-2 PCR test conducted via the NHLS between the periods of 1 March 2020 to 7 July 2020. Exclusion criteria: those 18 years, and those with indeterminate PCR tests. Results for 15437 patients (3301 positive and 12,136 negative) were used to fit six machine learning models, namely the logistic regression (LR) (the base model), decision trees (DT), random forest (RF), extreme gradient boosting (XGB), convolutional neural network (CNN) and self-normalising neural network (SNN). Model development was carried out by splitting the data into training and testing set of a ratio 70:30, together with a 10-fold cross-validation re-sampling technique. For risk stratification, admission to high care or ICU was the outcome for severe disease. Performance of the models varied: sensitivity was best for RF at 75% and accuracy of 75% for CNN. The area under the curve ranged from 57% for CNN to 75% for RF. RF and SNN were the best-performing models. Machine Learning (ML) can be incorporated into the laboratory information system and offers promise for early identification and risk stratification of COVID-19 patients, particularly in areas of resource-poor settings.