Extracting Clinical Findings from Swedish Health Record Text
2014 (English)Doctoral thesis, comprehensive summary (Other academic)
Information contained in the free text of health records is useful for the immediate care of patients as well as for medical knowledge creation. Advances in clinical language processing have made it possible to automatically extract this information, but most research has, until recently, been conducted on clinical text written in English. In this thesis, however, information extraction from Swedish clinical corpora is explored, particularly focusing on the extraction of clinical findings. Unlike most previous studies, Clinical Finding was divided into the two more granular sub-categories Finding (symptom/result of a medical examination) and Disorder (condition with an underlying pathological process). For detecting clinical findings mentioned in Swedish health record text, a machine learning model, trained on a corpus of manually annotated text, achieved results in line with the obtained inter-annotator agreement figures. The machine learning approach clearly outperformed an approach based on vocabulary mapping, showing that Swedish medical vocabularies are not extensive enough for the purpose of high-quality information extraction from clinical text. A rule and cue vocabulary-based approach was, however, successful for negation and uncertainty classification of detected clinical findings. Methods for facilitating expansion of medical vocabulary resources are particularly important for Swedish and other languages with less extensive vocabulary resources. The possibility of using distributional semantics, in the form of Random indexing, for semi-automatic vocabulary expansion of medical vocabularies was, therefore, evaluated. Distributional semantics does not require that terms or abbreviations are explicitly defined in the text, and it is, thereby, a method suitable for clinical corpora. Random indexing was shown useful for extending vocabularies with medical terms, as well as for extracting medical synonyms and abbreviation dictionaries.
Place, publisher, year, edition, pages
Stockholm University: Department of Computer and Systems Sciences, Stockholm University , 2014. , 128 p.
Report Series / Department of Computer & Systems Sciences, ISSN 1101-8526 ; 15-001
Named entity recognition, Corpora development, Clinical text processing, Distributional semantics, Random indexing, Vocabulary expansion, Assertion classification, Clinical text mining, Electronic health records, Swedish
Information Systems, Social aspects
Research subject Computer and Systems Sciences
IdentifiersURN: urn:nbn:se:su:diva-109254ISBN: 978-91-7649-054-9OAI: oai:DiVA.org:su-109254DiVA: diva2:763910
2015-01-23, Lilla hörsalen, NOD-huset, Borgarfjordsgatan 12, Kista, 13:00 (English)
Salakoski, Tapio, Professor
Dalianis, Hercules, ProfessorNilsson, Gunnar, ProfessorKvist, Maria, MD PhD
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