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Named entity recognition of follow-up and time information in 20,000 radiology reports

Yan Xu, Junichi Tsujii, and Eric Chang

Abstract

Objective: To develop a system to extract follow-up information from radiology reports. The method may be used as a component in a system which automatically generates follow-up information in a timely fashion. Methods: A novel method of combining an LSP (labeled sequential pattern) classifier with a CRF (conditional random field) recognizer was devised. The LSP classifier filters out irrelevant sentences, while the CRF recognizer extracts follow-up and time phrases from candidate sentences presented by the LSP classifier. Measurements: The standard performance metrics of precision (P), recall (R), and F measure (F) in the exact and inexact matching settings were used for evaluation. Results: Four experiments conducted using 20 000 radiology reports showed that the CRF recognizer achieved high performance without time-consuming feature engineering and that the LSP classifier further improved the performance of the CRF recognizer. The performance of the current system is P¼0.90, R¼0.86, F¼0.88 in the exact matching setting and P¼0.98, R¼0.93, F¼0.95 in the inexact matching setting. Conclusion: The experiments demonstrate that the system performs far better than a baseline rule-based system and is worth considering for deployment trials in an alert generation system. The LSP classifier successfully compensated for the inherent weakness of CRF, that is, its inability to use global information.

Details

Publication typeArticle
Published inJournal of the American Medical Informatics Association
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