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Methods Inf Med 2015; 54(02): 164-170
DOI: 10.3414/ME13-01-0130
Original Articles
Schattauer GmbH

Adaptive Semantic Tag Mining from Heterogeneous Clinical Research Texts[*]

T. Hao
1   Department of Biomedical Informatics, Columbia University, New York, NY, USA
2   Key Laboratory of Language Engineering and Computing of Guangdong Province, Guangdong University of Foreign Studies, Guangzhou, China
,
C. Weng
1   Department of Biomedical Informatics, Columbia University, New York, NY, USA
› Author Affiliations
Further Information

Publication History

received: 29 November 2013

accepted: 15 September 2014

Publication Date:
22 January 2018 (online)

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Summary

Objectives: To develop an adaptive approach to mine frequent semantic tags (FSTs) from heterogeneous clinical research texts.

Methods: We develop a “plug-n-play” framework that integrates replaceable un-supervised kernel algorithms with formatting, functional, and utility wrappers for FST mining. Temporal information identification and semantic equivalence detection were two example functional wrappers. We first compared this approach’s recall and efficiency for mining FSTs from ClinicalTrials.gov to that of a recently published tag-mining algorithm. Then we assessed this approach’s adaptability to two other types of clinical research texts: clinical data requests and clinical trial protocols, by comparing the prevalence trends of FSTs across three texts.

Results: Our approach increased the average recall and speed by 12.8% and 47.02% respectively upon the baseline when mining FSTs from ClinicalTrials.gov, and maintained an overlap in relevant FSTs with the baseline ranging between 76.9% and 100% for varying FST frequency thresholds. The FSTs saturated when the data size reached 200 documents. Consistent trends in the prevalence of FST were observed across the three texts as the data size or frequency threshold changed.

Conclusions: This paper contributes an adaptive tag-mining framework that is scalable and adaptable without sacrificing its recall. This component-based architectural design can be potentially generalizable to improve the adaptability of other clinical text mining methods.

Keywords

Medical informatics - text mining - clinical trials - semantic tags - component-based architecture

* Supplementary material published on our web-site www.methods-online.com