OBJECTIVE: 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. MATERIALS AND METHODS: 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. RESULTS: 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. DISCUSSION: 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 framework allows one to combine reliable machine learning components with rules designed by experts. CONCLUSION: Using relatively simple rules, part-of-speech information, and semantic type properties, an effective coreference resolution system could be designed. The source code of the system described is available at https://sourceforge.net/projects/ohnlp/files/MedCoref.
OBJECTIVE: 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. MATERIALS AND METHODS: 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. RESULTS: 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. DISCUSSION: 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 framework allows one to combine reliable machine learning components with rules designed by experts. CONCLUSION: Using relatively simple rules, part-of-speech information, and semantic type properties, an effective coreference resolution system could be designed. The source code of the system described is available at https://sourceforge.net/projects/ohnlp/files/MedCoref.
Authors: Ozlem Uzuner; Andreea Bodnari; Shuying Shen; Tyler Forbush; John Pestian; Brett R South Journal: J Am Med Inform Assoc Date: 2012-02-24 Impact factor: 4.497
Authors: Joshua C Denny; Anderson Spickard; Kevin B Johnson; Neeraja B Peterson; Josh F Peterson; Randolph A Miller Journal: J Am Med Inform Assoc Date: 2009-08-28 Impact factor: 4.497
Authors: Jeff Friedlin; Marc Overhage; Mohammed A Al-Haddad; Joshua A Waters; J Juan R Aguilar-Saavedra; Joe Kesterson; Max Schmidt Journal: AMIA Annu Symp Proc Date: 2010-11-13
Authors: Ozlem Uzuner; Andreea Bodnari; Shuying Shen; Tyler Forbush; John Pestian; Brett R South Journal: J Am Med Inform Assoc Date: 2012-02-24 Impact factor: 4.497
Authors: Sunghwan Sohn; Kavishwar B Wagholikar; Dingcheng Li; Siddhartha R Jonnalagadda; Cui Tao; Ravikumar Komandur Elayavilli; Hongfang Liu Journal: J Am Med Inform Assoc Date: 2013-04-04 Impact factor: 4.497