Natural language processing (NLP) to facilitate abstract review in medical research: the application of BioBERT to exploring the 20-year use of NLP in medical research

Abstract

Background review is a time and labor-consuming step in the systematic and scoping literature review in medicine. Text mining methods, typically natural language processing (NLP), may efficiently replace manual abstract screening. This study applies NLP to a deliberately selected literature review problem, the trend of using NLP in medical research, to demonstrate the performance of this automated abstract review model.MethodsScanning PubMed, Embase, PsycINFO, and CINAHL databases, we identified 22,294 with a final selection of 12,817 English abstracts published between 2000 and 2021. We invented a manual classification of medical fields, three variables, i.e., the context of use (COU), text source (TS), and primary research field (PRF). A training dataset was developed after reviewing 485 abstracts. We used a language model called Bidirectional Encoder Representations from Transformers to classify the abstracts. To evaluate the performance of the trained models, we report a micro f1-score and accuracy.Results The trained models’ micro f1-score for classifying abstracts, into three variables were 77.35% for COU, 76.24% for TS, and 85.64% for PRF.The average annual growth rate (AAGR) of the publications was 20.99% between 2000 and 2020 (72.01 articles (95% CI: 56.80–78.30) yearly increase), with 81.76% of the abstracts published between 2010 and 2020. Studies on neoplasms constituted 27.66% of the entire corpus with an AAGR of 42.41%, followed by studies on mental conditions (AAGR = 39.28%). While electronic health or medical records comprised the highest proportion of text sources (57.12%), omics databases had the highest growth among all text sources with an AAGR of 65.08%. The most common NLP application was clinical decision support (25.45%).ConclusionsBioBERT showed an acceptable performance in the abstract review. If future research shows the high performance of this language model, it can reliably replace manual abstract reviews.