Graph data science and machine learning for the detection of COVID-19 infection from symptoms

Eman Alqaissi; Fahd Alotaibi; Muhammad Sher Ramzan

doi:10.7717/peerj-cs.1333

Graph data science and machine learning for the detection of COVID-19 infection from symptoms

PeerJ Comput Sci. 2023 Apr 10:9:e1333. doi: 10.7717/peerj-cs.1333. eCollection 2023.

Authors

Eman Alqaissi^{1

2}, Fahd Alotaibi¹, Muhammad Sher Ramzan¹

Affiliations

¹ Faculty of Computing and Information Technology, King Abdulaziz University, Jeddah, Saudi Arabia.
² Information Systems, King Khalid University, Abha, Saudi Arabia.

Abstract

Background: COVID-19 is an infectious disease caused by SARS-CoV-2. The symptoms of COVID-19 vary from mild-to-moderate respiratory illnesses, and it sometimes requires urgent medication. Therefore, it is crucial to detect COVID-19 at an early stage through specific clinical tests, testing kits, and medical devices. However, these tests are not always available during the time of the pandemic. Therefore, this study developed an automatic, intelligent, rapid, and real-time diagnostic model for the early detection of COVID-19 based on its symptoms.

Methods: The COVID-19 knowledge graph (KG) constructed based on literature from heterogeneous data is imported to understand the COVID-19 different relations. We added human disease ontology to the COVID-19 KG and applied a node-embedding graph algorithm called fast random projection to extract an extra feature from the COVID-19 dataset. Subsequently, experiments were conducted using two machine learning (ML) pipelines to predict COVID-19 infection from its symptoms. Additionally, automatic tuning of the model hyperparameters was adopted.

Results: We compared two graph-based ML models, logistic regression (LR) and random forest (RF) models. The proposed graph-based RF model achieved a small error rate = 0.0064 and the best scores on all performance metrics, including specificity = 98.71%, accuracy = 99.36%, precision = 99.65%, recall = 99.53%, and F1-score = 99.59%. Furthermore, the Matthews correlation coefficient achieved by the RF model was higher than that of the LR model. Comparative analysis with other ML algorithms and with studies from the literature showed that the proposed RF model exhibited the best detection accuracy.

Conclusion: The graph-based RF model registered high performance in classifying the symptoms of COVID-19 infection, thereby indicating that the graph data science, in conjunction with ML techniques, helps improve performance and accelerate innovations.

Keywords: Automatic tuning; COVID-19; Detection; Graph algorithm; Knowledge graph; Machine learning; Ontology; Symptoms.

Grants and funding

The authors received no funding for this work.