Machine learning based natural language processing of radiology reports in orthopaedic trauma. (September 2021)

• Record Type: Journal Article
• Authors: Olthof, A.W.; Shouche, P.; Fennema, E.M.; IJpma, F.F.A.; Koolstra, R.H.C.; Stirler, V.M.A.; van Ooijen, P.M.A.; Cornelissen, L.J.
• Is Part Of: Computer methods and programs in biomedicine. Volume 208(2021)
• Publication Date: 2021-09
• Subjects: (MeSH) -- Natural language processing -- Machine learning -- Informatics -- Radiology -- Orthopaedic trauma; Medicine -- Computer programs -- Periodicals; Biology -- Computer programs -- Periodicals; Computers -- Periodicals; Medicine -- Periodicals; Médecine -- Logiciels -- Périodiques; Biologie -- Logiciels -- Périodiques; Biology -- Computer programs; Medicine -- Computer programs; Periodicals; Electronic journals; 610.28
• DOI: 10.1016/j.cmpb.2021.106304
• Languages: English
• ISSNs: 0169-2607

Abstract

Highlights: BERT Natural Language Processing (NLP) outperforms traditional ML and rule-based classifiers when applied to radiology reports in orthopaedic trauma. Traditional ML classification performance is mostly determined by the extracted features rather than classifier-type, and more complex features are not always better than simple methods. Positivity rate assessment and automated label generation from radiology reports are feasible with NLP. Abstract: Objectives: To compare different Machine Learning (ML) Natural Language Processing (NLP) methods to classify radiology reports in orthopaedic trauma for the presence of injuries. Assessing NLP performance is a prerequisite for downstream tasks and therefore of importance from a clinical perspective (avoiding missed injuries, quality check, insight in diagnostic yield) as well as from a research perspective (identification of patient cohorts, annotation of radiographs). Methods: Datasets of Dutch radiology reports of injured extremities ( n = 2469, 33% fractures) and chest radiographs ( n = 799, 20% pneumothorax) were collected in two different hospitals and labeled by radiologists and trauma surgeons for the presence or absence of injuries. NLP classification was applied and optimized by testing different preprocessing steps and different classifiers (Rule-based, ML, and Bidirectional Encoder Representations from Transformers (BERT)). Performance was assessed by F1-score, AUC, sensitivity, specificity and accuracy. Results: The deep learning based BERT model outperforms all other classification methods which were assessed. The model achieved an F1-score of (95 ± 2)% and accuracy of (96 ± 1)% on a dataset of simple reports (n= 2469), and an F1 of (83 ± 7)% with accuracy (93 ± 2)% on a dataset of complex reports (n= 799). Conclusion: BERT NLP outperforms traditional ML and rule-base classifiers when applied to Dutch radiology reports in orthopaedic trauma.