An interpretable machine learning framework for diagnosis and prognosis of COVID-19

PLoS One. 2023 Sep 21;18(9):e0291961. doi: 10.1371/journal.pone.0291961. eCollection 2023.

Abstract

Coronaviruses have affected the lives of people around the world. Increasingly, studies have indicated that the virus is mutating and becoming more contagious. Hence, the pressing priority is to swiftly and accurately predict patient outcomes. In addition, physicians and patients increasingly need interpretability when building machine models in healthcare. We propose an interpretable machine framework(KISM) that can diagnose and prognose patients based on blood test datasets. First, we use k-nearest neighbors, isolated forests, and SMOTE to pre-process the original blood test datasets. Seven machine learning tools Support Vector Machine, Extra Tree, Random Forest, Gradient Boosting Decision Tree, eXtreme Gradient Boosting, Logistic Regression, and ensemble learning were then used to diagnose and predict COVID-19. In addition, we used SHAP and scikit-learn post-hoc interpretability to report feature importance, allowing healthcare professionals and artificial intelligence models to interact to suggest biomarkers that some doctors may have missed. The 10-fold cross-validation of two public datasets shows that the performance of KISM is better than that of the current state-of-the-art methods. In the diagnostic COVID-19 task, an AUC value of 0.9869 and an accuracy of 0.9787 were obtained, and ultimately Leukocytes, platelets, and Proteina C reativa mg/dL were found to be the most indicative biomarkers for the diagnosis of COVID-19. An AUC value of 0.9949 and an accuracy of 0.9677 were obtained in the prognostic COVID-19 task and Age, LYMPH, and WBC were found to be the most indicative biomarkers for identifying the severity of the patient.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Artificial Intelligence
  • Blood Platelets
  • COVID-19 Testing
  • COVID-19* / diagnosis
  • Humans
  • Machine Learning
  • Prognosis

Grants and funding

This work was supported in part by the National Natural Science Foundation of China under Grant 62162015 and Grant 61762026, in part by the Guangxi Natural Science Foundation under Grant 2023GXNSFAA026054, in part by the Innovation Project of GUET Graduate Education under Grant 2021YCXS062, in part by the Innovation Project of GUET Graduate Education under Grant 2023YCXS071. The funders had no role in study design, data collection, and analysis, the decision to publish, or the preparation of the manuscript.