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Factuality Levels of Diagnoses in Swedish Clinical Text
Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
2011 (English)In: User Centred Networked Health Care - Proceedings of MIE 2011 / [ed] Anne Moen, Stig Kjær Andersen, Jos Aarts, Petter Hurlen, 2011, 559-563 p.Conference paper, Published paper (Refereed)
Abstract [en]

Different levels of knowledge certainty, or factuality levels, are expressed in clinical health record documentation. This information is currently not fully exploited, as the subtleties expressed in natural language cannot easily be machine analyzed. Extracting relevant information from knowledge-intensive resources such as electronic health records can be used for improving health care in general by e.g. building automated information access systems. We present an annotation model of six factuality levels linked to diagnoses in Swedish clinical assessments from an emergency ward. Our main findings are that overall agreement is fairly high (0.7/0.58 F-measure, 0.73/0.6 Cohen's κ, Intra/Inter). These distinctions are important for knowledge models, since only approx. 50% of the diagnoses are affirmed with certainty. Moreover, our results indicate that there are patterns inherent in the diagnosis expressions themselves conveying factuality levels, showing that certainty is not only dependent on context cues.

Place, publisher, year, edition, pages
2011. 559-563 p.
Keyword [en]
Diagnosis reasoning, factuality levels, annotation, Swedish, clinical text, electronic health records
National Category
Information Science
Research subject
Computer and Systems Sciences
Identifiers
URN: urn:nbn:se:su:diva-62347DOI: 10.3233/978-1-60750-806-9-559ISBN: 978-1-60750-805-2 (print)OAI: oai:DiVA.org:su-62347DiVA: diva2:441272
Conference
MIME 2011
Available from: 2011-09-15 Created: 2011-09-15 Last updated: 2012-03-27Bibliographically approved
In thesis
1. Shades of Certainty: Annotation and Classification of Swedish Medical Records
Open this publication in new window or tab >>Shades of Certainty: Annotation and Classification of Swedish Medical Records
2012 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Access to information is fundamental in health care. This thesis presents research on Swedish medical records with the overall goal of building intelligent information access tools that can aid health personnel, researchers and other professions in their daily work, and, ultimately, improve health care in general.

The issue of ethics and identifiable information is addressed by creating an annotated gold standard corpus and porting an existing de-identification system to Swedish from English. The aim is to move towards making textual resources available to researchers without risking exposure of patients’ confidential information. Results for the rule-based system are not encouraging, but results for the gold standard are fairly high.

Affirmed, uncertain and negated information needs to be distinguished when building accurate information extraction tools. Annotation models are created, with the aim of building automated systems. One model distinguishes certain and uncertain sentences, and is applied on medical records from several clinical departments. In a second model, two polarities and three levels of certainty are applied on diagnostic statements from an emergency department. Overall results are promising. Differences are seen depending on clinical practice, annotation task and level of domain expertise among the annotators.

Using annotated resources for automatic classification is studied. Encouraging overall results using local context information are obtained. The fine-grained certainty levels are used for building classifiers for real-world e-health scenarios.

This thesis contributes two annotation models of certainty and one of identifiable information, applied on Swedish medical records. A deeper understanding of the language use linked to conveying certainty levels is gained. Three annotated resources that can be used for further research have been created, and implications for automated systems are presented.

Place, publisher, year, edition, pages
Stockholm: Department of Computer and Systems Sciences, Stockholm University, 2012. 78 p.
Series
Report Series / Department of Computer & Systems Sciences, ISSN 1101-8526 ; 12-002
Keyword
Clinical documentation, Certainty level classification, Annotation, E-health, Corpus creation, De-identification, Speculative language, Medical Records, Swedish, Natural Language Processing, Language Technology
National Category
Information Systems, Social aspects
Research subject
Computer and Systems Sciences
Identifiers
urn:nbn:se:su:diva-74828 (URN)978-91-7447-444-2 (ISBN)
Public defence
2012-04-27, Sal C, Forum 100, Isafjordsgatan 39, Kista, 13:00 (English)
Opponent
Supervisors
Available from: 2012-04-05 Created: 2012-03-27 Last updated: 2012-03-28Bibliographically approved

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