Recognition of medication information from discharge summaries using ensembles of classifiers.

BMC Medical Informatics and Decision Making
Son DoanMinh Phuong Tu

Abstract

Extraction of clinical information such as medications or problems from clinical text is an important task of clinical natural language processing (NLP). Rule-based methods are often used in clinical NLP systems because they are easy to adapt and customize. Recently, supervised machine learning methods have proven to be effective in clinical NLP as well. However, combining different classifiers to further improve the performance of clinical entity recognition systems has not been investigated extensively. Combining classifiers into an ensemble classifier presents both challenges and opportunities to improve performance in such NLP tasks. We investigated ensemble classifiers that used different voting strategies to combine outputs from three individual classifiers: a rule-based system, a support vector machine (SVM) based system, and a conditional random field (CRF) based system. Three voting methods were proposed and evaluated using the annotated data sets from the 2009 i2b2 NLP challenge: simple majority, local SVM-based voting, and local CRF-based voting. Evaluation on 268 manually annotated discharge summaries from the i2b2 challenge showed that the local CRF-based voting method achieved the best F-score of 90.84% (94.11% Pr...Continue Reading

References

May 21, 2003·Journal of Biomedical Informatics·Lynette HirschmanAlexander S Yeh
Nov 16, 2004·Journal of Biomedical Informatics·Michael Krauthammer, Goran Nenadic
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Oct 14, 2011·Journal of Biomedical Semantics·Scott Russell HalgrimOzlem Uzuner

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Citations

Oct 25, 2013·PloS One·Nigel CollierDietrich Rebholz-Schuhmann
Jul 31, 2012·Journal of the American Medical Informatics Association : JAMIA·Jonathan A Handler, James G Adams
Jan 15, 2016·BMC Bioinformatics·Eugene TseytlinRebecca S Jacobson
Jul 3, 2015·Journal of Biomedical Informatics·George KarystianisGoran Nenadic
Jul 10, 2019·Journal of the American Medical Informatics Association : JAMIA·Youngjun Kim, Stéphane M Meystre
Dec 23, 2017·International Journal of Methods in Psychiatric Research·George KarystianisGoran Nenadic
Oct 28, 2019·Journal of Biomedical Informatics·Cong LiuChunhua Weng

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Software Mentioned

TinySVM
Yamcha
NLTK
GM
CRF
BioTagger
Perl program
Linux
CoNLL
i2b2

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