Coreference analysis in clinical notes: a multi-pass sieve with alternate anaphora resolution modules

Journal of the American Medical Informatics Association : JAMIA
Siddhartha JonnalagaddaHongfang Liu

Abstract

This paper describes the coreference resolution system submitted by Mayo Clinic for the 2011 i2b2/VA/Cincinnati shared task Track 1C. The goal of the task was to construct a system that links the markables corresponding to the same entity. The task organizers provided progress notes and discharge summaries that were annotated with the markables of treatment, problem, test, person, and pronoun. We used a multi-pass sieve algorithm that applies deterministic rules in the order of preciseness and simultaneously gathers information about the entities in the documents. Our system, MedCoref, also uses a state-of-the-art machine learning framework as an alternative to the final, rule-based pronoun resolution sieve. The best system that uses a multi-pass sieve has an overall score of 0.836 (average of B(3), MUC, Blanc, and CEAF F score) for the training set and 0.843 for the test set. A supervised machine learning system that typically uses a single function to find coreferents cannot accommodate irregularities encountered in data especially given the insufficient number of examples. On the other hand, a completely deterministic system could lead to a decrease in recall (sensitivity) when the rules are not exhaustive. The sieve-based f...Continue Reading

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Citations

Dec 5, 2013·Journal of the American Medical Informatics Association : JAMIA·Jyotishman PathakJoshua C Denny
May 17, 2014·Journal of the American Medical Informatics Association : JAMIA·Stephen WuHongfang Liu
Apr 6, 2013·Journal of the American Medical Informatics Association : JAMIA·Sunghwan SohnHongfang Liu
Mar 1, 2012·Journal of the American Medical Informatics Association : JAMIA·Ozlem UzunerBrett R South
Sep 13, 2015·Journal of Biomedical Informatics·Qingcai ChenJingfeng Wang
Apr 15, 2014·Journal of the American Society for Information Science and Technology : JASIST·Graciela RosemblatThomas C Rindflesch
Apr 6, 2016·Journal of Biomedical Informatics·Duy Duc An BuiSiddhartha Jonnalagadda
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Jul 8, 2016·Biomedical Informatics Insights·Vinod C KaggalHongfang Liu
May 10, 2017·Journal of Biomedical Informatics·Duy Duc An BuiJames J Cimino

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Knowledge Representation (Computer)
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