Danish Clinical Named Entity Recognition and Relation Extraction

Martin Sundahl Laursen, Jannik Skyttegaard Pedersen, Rasmus Søgaard Hansen, Thiusius Rajeeth Savarimuthu, Pernille Just Vinholt

Keywords: electronic health records, named entity recognition, relation extraction

TL;DR: This paper presents the first Danish clinical named entity recognition and relation extraction dataset for extraction of six types of clinical events, six types of attributes, and three types of relations.

Abstract: Electronic health records contain important information regarding the patients' medical history but much of this information is stored in unstructured narrative text. This paper presents the first Danish clinical named entity recognition and relation extraction dataset for extraction of six types of clinical events, six types of attributes, and three types of relations. The dataset contains 11,607 paragraphs from Danish electronic health records containing 54,631 clinical events, 41,954 attributes, and 14,604 relations. We detail the methodology of developing the annotation scheme, and train a transformer-based architecture on the developed dataset with macro F1 performance of 60.05%, 44.85%, and 70.64% for clinical events, attributes, and relations, respectively.

Student Paper: Yes, the first author is a student