Background Textual datasets (corpora) are crucial for the application of natural language processing (NLP) models. However, corpus creation in the medical field is challenging, primarily because of privacy issues with raw clinical data such as health records. Thus, the existing clinical corpora are generally small and scarce. Medical NLP (MedNLP) methodologies perform well with limited data availability.

Objectives We present the outcomes of the Real-MedNLP workshop, which was conducted using limited and parallel medical corpora. Real-MedNLP exhibits three distinct characteristics: (1) limited annotated documents: the training data comprise only a small set (∼100) of case reports (CRs) and radiology reports (RRs) that have been annotated. (2) Bilingually parallel: the constructed corpora are parallel in Japanese and English. (3) Practical tasks: the workshop addresses fundamental tasks, such as named entity recognition (NER) and applied practical tasks.

Methods We propose three tasks: NER of ∼100 available documents (Task 1), NER based only on annotation guidelines for humans (Task 2), and clinical applications (Task 3) consisting of adverse drug effect (ADE) detection for CRs and identical case identification (CI) for RRs.

Results Nine teams participated in this study. The best systems achieved 0.65 and 0.89 F1-scores for CRs and RRs in Task 1, whereas the top scores in Task 2 decreased by 50 to 70%. In Task 3, ADE reports were detected by up to 0.64 F1-score, and CI scored up to 0.96 binary accuracy.

Conclusion Most systems adopt medical-domain–specific pretrained language models using data augmentation methods. Despite the challenge of limited corpus size in Tasks 1 and 2, recent approaches are promising because the partial match scores reached ∼0.8–0.9 F1-scores. Task 3 applications revealed that the different availabilities of external language resources affected the performance per language.

This study did not require the participants to be involved in any physical or mental intervention. Furthermore, as it did not utilize personally identifiable information, the study was exempt from institutional review board approval in accordance with the Ethical Guidelines for Medical and Health Research Involving Human Subjects outlined by the Japanese national government.

Received: 07 June 2023

Accepted: 23 August 2024

Accepted Manuscript online:
29 August 2024

Article published online:
29 October 2024

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