Predicting Emerging Themes in Rapidly Expanding COVID-19 Literature With Unsupervised Word Embeddings and Machine Learning: Evidence-Based Study

• Published in: Journal of medical Internet research Vol. 24; no. 11; p. e34067
• Main Authors: Pal, Ridam, Chopra, Harshita, Awasthi, Raghav, Bandhey, Harsh, Nagori, Aditya, Sethi, Tavpritesh
• Format: Journal Article
• Language: English
• Published: Canada Journal of Medical Internet Research 02.11.2022; Gunther Eysenbach MD MPH, Associate Professor; JMIR Publications
• Subjects: Analysis; Complications; Computational linguistics; Coronaviruses; COVID-19; Data mining; Diagrams; Forecasts and trends; Health aspects; Humans; Language processing; Machine Learning; Medical research; Multimedia; Natural language; Natural language interfaces; Original Paper; Post-Acute COVID-19 Syndrome; Prediction models; Semantics; Supervised Machine Learning; Symptoms; Trends; Vaccines; COVID-19; named entity recognition; machine learning; natural language preprocessing; unsupervised word embeddings
• ISSN: 1438-8871; 1439-4456; 1438-8871
• DOI: 10.2196/34067

Evidence from peer-reviewed literature is the cornerstone for designing responses to global threats such as COVID-19. In massive and rapidly growing corpuses, such as COVID-19 publications, assimilating and synthesizing information is challenging. Leveraging a robust computational pipeline that evaluates multiple aspects, such as network topological features, communities, and their temporal trends, can make this process more efficient. We aimed to show that new knowledge can be captured and tracked using the temporal change in the underlying unsupervised word embeddings of the literature. Further imminent themes can be predicted using machine learning on the evolving associations between words. Frequently occurring medical entities were extracted from the abstracts of more than 150,000 COVID-19 articles published on the World Health Organization database, collected on a monthly interval starting from February 2020. Word embeddings trained on each month's literature were used to construct networks of entities with cosine similarities as edge weights. Topological features of the subsequent month's network were forecasted based on prior patterns, and new links were predicted using supervised machine learning. Community detection and alluvial diagrams were used to track biomedical themes that evolved over the months. We found that thromboembolic complications were detected as an emerging theme as early as August 2020. A shift toward the symptoms of long COVID complications was observed during March 2021, and neurological complications gained significance in June 2021. A prospective validation of the link prediction models achieved an area under the receiver operating characteristic curve of 0.87. Predictive modeling revealed predisposing conditions, symptoms, cross-infection, and neurological complications as dominant research themes in COVID-19 publications based on the patterns observed in previous months. Machine learning-based prediction of emerging links can contribute toward steering research by capturing themes represented by groups of medical entities, based on patterns of semantic relationships over time.