Ensemble of deep learning language models to support the creation of living systematic reviews for the COVID-19 literature

Julien Knafou*, Quetin Haas, Nikolay Borissov, Michel Counotte, Nicola Low, Hira Imeri, Aziz Mert Ipekci, Diana Buitrago-Garcia, Leonie Heron, Poorya Amini, Douglas Teodoro*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

1 Citation (Scopus)

Abstract

Background
The COVID-19 pandemic has led to an unprecedented amount of scientific publications, growing at a pace never seen before. Multiple living systematic reviews have been developed to assist professionals with up-to-date and trustworthy health information, but it is increasingly challenging for systematic reviewers to keep up with the evidence in electronic databases. We aimed to investigate deep learning-based machine learning algorithms to classify COVID-19-related publications to help scale up the epidemiological curation process.

Methods
In this retrospective study, five different pre-trained deep learning-based language models were fine-tuned on a dataset of 6365 publications manually classified into two classes, three subclasses, and 22 sub-subclasses relevant for epidemiological triage purposes. In a k-fold cross-validation setting, each standalone model was assessed on a classification task and compared against an ensemble, which takes the standalone model predictions as input and uses different strategies to infer the optimal article class. A ranking task was also considered, in which the model outputs a ranked list of sub-subclasses associated with the article.

Results
The ensemble model significantly outperformed the standalone classifiers, achieving a F1-score of 89.2 at the class level of the classification task. The difference between the standalone and ensemble models increases at the sub-subclass level, where the ensemble reaches a micro F1-score of 70% against 67% for the best-performing standalone model. For the ranking task, the ensemble obtained the highest recall@3, with a performance of 89%. Using an unanimity voting rule, the ensemble can provide predictions with higher confidence on a subset of the data, achieving detection of original papers with a F1-score up to 97% on a subset of 80% of the collection instead of 93% on the whole dataset.

Conclusion
This study shows the potential of using deep learning language models to perform triage of COVID-19 references efficiently and support epidemiological curation and review. The ensemble consistently and significantly outperforms any standalone model. Fine-tuning the voting strategy thresholds is an interesting alternative to annotate a subset with higher predictive confidence.
Original languageEnglish
Article number94
Number of pages16
JournalSystematic Reviews
Volume12
DOIs
Publication statusPublished - 5 Jun 2023

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