C Cano1, A Blanco, L Peshkin. 1. University of Granada, Department of Computer Science and A.I., Spain.
Abstract
OBJECTIVES: Automated understanding of clinical records is a challenging task involving various legal and technical difficulties. Clinical free text is inherently redundant, unstructured, and full of acronyms, abbreviations and domain-specific language which make it challenging to mine automatically. There is much effort in the field focused on creating specialized ontology, lexicons and heuristics based on expert knowledge of the domain. However, ad-hoc solutions poorly generalize across diseases or diagnoses. This paper presents a successful approach for a rapid prototyping of a diagnosis classifier based on a popular computational linguistics platform. METHODS: The corpus consists of several hundred of full length discharge summaries provided by Partners Healthcare. The goal is to identify a diagnosis and assign co-morbidi-ty. Our approach is based on the rapid implementation of a logistic regression classifier using an existing toolkit: LingPipe (http://alias-i.com/lingpipe). We implement and compare three different classifiers. The baseline approach uses character 5-grams as features. The second approach uses a bag-of-words representation enriched with a small additional set of features. The third approach reduces a feature set to the most informative features according to the information content. RESULTS: The proposed systems achieve high performance (average F-micro 0.92) for the task. We discuss the relative merit of the three classifiers. Supplementary material with detailed results is available at: http:// decsai.ugr.es/~ccano/LR/supplementary_ material/ CONCLUSIONS: We show that our methodology for rapid prototyping of a domain-unaware system is effective for building an accurate classifier for clinical records.
OBJECTIVES: Automated understanding of clinical records is a challenging task involving various legal and technical difficulties. Clinical free text is inherently redundant, unstructured, and full of acronyms, abbreviations and domain-specific language which make it challenging to mine automatically. There is much effort in the field focused on creating specialized ontology, lexicons and heuristics based on expert knowledge of the domain. However, ad-hoc solutions poorly generalize across diseases or diagnoses. This paper presents a successful approach for a rapid prototyping of a diagnosis classifier based on a popular computational linguistics platform. METHODS: The corpus consists of several hundred of full length discharge summaries provided by Partners Healthcare. The goal is to identify a diagnosis and assign co-morbidi-ty. Our approach is based on the rapid implementation of a logistic regression classifier using an existing toolkit: LingPipe (http://alias-i.com/lingpipe). We implement and compare three different classifiers. The baseline approach uses character 5-grams as features. The second approach uses a bag-of-words representation enriched with a small additional set of features. The third approach reduces a feature set to the most informative features according to the information content. RESULTS: The proposed systems achieve high performance (average F-micro 0.92) for the task. We discuss the relative merit of the three classifiers. Supplementary material with detailed results is available at: http:// decsai.ugr.es/~ccano/LR/supplementary_ material/ CONCLUSIONS: We show that our methodology for rapid prototyping of a domain-unaware system is effective for building an accurate classifier for clinical records.
Authors: Elizabeth Ford; John A Carroll; Helen E Smith; Donia Scott; Jackie A Cassell Journal: J Am Med Inform Assoc Date: 2016-02-05 Impact factor: 4.497