Classification based extraction of numeric values from clinical narratives

Maximilian Zubke

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Abstract
The robust extraction of numeric values from clinical narratives is a well known problem in clinical data warehouses. In this paper we describe a dynamic and domain-independent approach to deliver numerical described values from clinical narratives. In contrast to alternative systems, we neither use manual defined rules nor any kind of ontologies or nomenclatures. Instead we propose a topic-based system, that tackles the information extraction as a text classification problem. Hence we use machine learning to identify the crucial context features of a topic-specific numeric value by a given set of example sentences, so that the manual effort reduces to the selection of appropriate sample sentences. We describe context features of a certain numeric value by term frequency vectors which are generated by multiple document segmentation procedures. Due to this simultaneous segmentation approaches, there can be more than one context vector for a numeric value. In those cases, we choose the context vector with the highest classification confidence and suppress the rest. To test our approach, we used a dataset from a german hospital containing 12,743 narrative reports about laboratory results of Leukemia patients. We used Support Vector Machines (SVM) for classification and achieved an average accuracy of 96% on a manually labeled subset of 2073 documents, using 10-fold cross validation. This is a significant improvement over an alternative rule based system.
Anthology ID:
W17-8004
Volume:
Proceedings of the Biomedical NLP Workshop associated with RANLP 2017
Month:
September
Year:
2017
Address:
Varna, Bulgaria
Editors:
Svetla Boytcheva, Kevin Bretonnel Cohen, Guergana Savova, Galia Angelova
Venue:
RANLP
SIG:
Publisher:
INCOMA Ltd.
Note:
Pages:
24–31
Language:
URL:
https://doi.org/10.26615/978-954-452-044-1_004
DOI:
10.26615/978-954-452-044-1_004
Bibkey:
Cite (ACL):
Maximilian Zubke. 2017. Classification based extraction of numeric values from clinical narratives. In Proceedings of the Biomedical NLP Workshop associated with RANLP 2017, pages 24–31, Varna, Bulgaria. INCOMA Ltd..
Cite (Informal):
Classification based extraction of numeric values from clinical narratives (Zubke, RANLP 2017)
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PDF:
https://doi.org/10.26615/978-954-452-044-1_004
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