ArticleJournal of the American Medical Informatics Association : JAMIA
Coreference analysis in clinical notes: a multi-pass sieve with alternate anaphora resolution modules.
Article in Journal of the American Medical Informatics Association : JAMIA. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- The UAB Informatics Institute and 2016 CEGS N-GRID de-identification shared task challenge.Journal of biomedical informatics · 2017Article
- Automated annotation and classification of BI-RADS assessment from radiology reports.Journal of biomedical informatics · 2017Article
- Towards generalizable entity-centric clinical coreference resolution.Journal of biomedical informatics · 2017Article
- PDF text classification to leverage information extraction from publication reports.Journal of biomedical informatics · 2016Article
- PIPE: a protein-protein interaction passage extraction module for BioCreative challenge.Database : the journal of biological databases and curation · 2016Article
- Bio-SCoRes: A Smorgasbord Architecture for Coreference Resolution in Biomedical Text.PloS one · 2016Article
- An Infinite Mixture Model for Coreference Resolution in Clinical Notes.AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science · 2016Article
- A Natural Language Processing Tool for Large-Scale Data Extraction from Echocardiography Reports.PloS one · 2016Article
- Toward a Learning Health-care System - Knowledge Delivery at the Point of Care Empowered by Big Data and NLP.Biomedical informatics insights · 2016Article
- An automatic system to identify heart disease risk factors in clinical texts over time.Journal of biomedical informatics · 2015Article
- "Big data" and the electronic health record.Yearbook of medical informatics · 2014Review
- Electronic health records-driven phenotyping: challenges, recent advances, and perspectives.Journal of the American Medical Informatics Association : JAMIA · 2013Article
- Developing a self-service query interface for re-using de-identified electronic health record data.Studies in health technology and informatics · 2013Article
- Comprehensive temporal information detection from clinical text: medical events, time, and TLINK identification.Journal of the American Medical Informatics Association : JAMIAArticle
- Patient-level temporal aggregation for text-based asthma status ascertainment.Journal of the American Medical Informatics Association : JAMIAArticle
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7 authors.
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Abstract
objectiveThis 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
methodsThe 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.
resultsThe 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.
conclusionUsing 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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.