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How Certain are Clinical Assessments?: Annotating Swedish Clinical Text for (Un)certainties, Speculations and Negations
Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
2010 (English)In: Proceedings of the of the Seventh International Conference on Language Resources and Evaluation, LREC 2010 / [ed] Nicoletta Calzolari, 2010, 3071-3075 p.Conference paper, Published paper (Other academic)
Abstract [en]

Clinical texts contain a large amount of information. Some of this information is embedded in contexts where e.g. a patient status is reasoned about, which may lead to a considerable amount of statements that indicate uncertainty and speculation. We believe that distinguishing such instances from factual statements will be very beneficial for automatic information extraction. We have annotated a subset of the Stockholm Electronic Patient Record Corpus for certain and uncertain expressions as well as speculative and negation keywords, with the purpose of creating a resource for the development of automatic detection of speculative language in Swedish clinical text. We have analyzed the results from the initial annotation trial by means of pairwise Inter-Annotator Agreement (IAA) measured with F-score. Our main findings are that IAA results for certain expressions and negations are very high, but for uncertain expressions and speculative keywords results are less encouraging. These instances need to be defined in more detail. With this annotation trial, we have created an important resource that can be used to further analyze the properties of speculative language in Swedish clinical text. Our intention is to release this subset to other research groups in the future after removing identifiable information.

Place, publisher, year, edition, pages
2010. 3071-3075 p.
National Category
Information Science
Research subject
Computer and Systems Sciences
Identifiers
URN: urn:nbn:se:su:diva-51917ISBN: 2-9517408-6-7 (print)OAI: oai:DiVA.org:su-51917DiVA: diva2:386384
Conference
the Seventh International Conference on Language Resources and Evaluation, LREC 2010
Available from: 2011-01-12 Created: 2011-01-12 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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