Feature engineering combined with machine learning and rule-based methods for structured information extraction from narrative clinical discharge summaries.

Journal of the American Medical Informatics Association : JAMIA
Yan XuEric I-Chao Chang

Abstract

A system that translates narrative text in the medical domain into structured representation is in great demand. The system performs three sub-tasks: concept extraction, assertion classification, and relation identification. The overall system consists of five steps: (1) pre-processing sentences, (2) marking noun phrases (NPs) and adjective phrases (APs), (3) extracting concepts that use a dosage-unit dictionary to dynamically switch two models based on Conditional Random Fields (CRF), (4) classifying assertions based on voting of five classifiers, and (5) identifying relations using normalized sentences with a set of effective discriminating features. Macro-averaged and micro-averaged precision, recall and F-measure were used to evaluate results. The performance is competitive with the state-of-the-art systems with micro-averaged F-measure of 0.8489 for concept extraction, 0.9392 for assertion classification and 0.7326 for relation identification. The system exploits an array of common features and achieves state-of-the-art performance. Prudent feature engineering sets the foundation of our systems. In concept extraction, we demonstrated that switching models, one of which is especially designed for telegraphic sentences, impr...Continue Reading

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Citations

Jul 31, 2012·Journal of the American Medical Informatics Association : JAMIA·Jonathan A Handler, James G Adams
Aug 13, 2013·Journal of the American Medical Informatics Association : JAMIA·Yan XuEric I Chang
Dec 5, 2013·Journal of the American Medical Informatics Association : JAMIA·Jyotishman PathakJoshua C Denny
Mar 8, 2013·Journal of the American Medical Informatics Association : JAMIA·Yan XuEric I-Chao Chang
Jul 3, 2015·Journal of Biomedical Informatics·George KarystianisGoran Nenadic
May 27, 2014·Journal of Biomedical Informatics·Xinbo LvBenyang Deng
Jul 31, 2013·Journal of Biomedical Informatics·Myungjae KwakJeffrey Harwell
Jul 14, 2010·Journal of Biomedical Semantics·Hutchatai Chanlekha, Nigel Collier
Nov 10, 2015·BMC Bioinformatics·Slavko ŽitnikMarko Bajec
May 7, 2019·Frontiers in Medicine·Michela AssaleFederico Cabitza
Sep 15, 2020·BMC Bioinformatics·Timofey V IvanisenkoVladimir A Ivanisenko
Aug 10, 2020·Journal of Biomedical Informatics·Sunyang FuHongfang Liu

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