title: Ensembles of NLP Tools for Data Element Extraction from Clinical Notes.
abstract: Natural Language Processing (NLP) is essential for concept extraction from narrative text in electronic health records (EHR). To extract numerous and diverse concepts, such as data elements (i.e., important concepts related to a certain medical condition), a plausible solution is to combine various NLP tools into an ensemble to improve extraction performance. However, it is unclear to what extent ensembles of popular NLP tools improve the extraction of numerous and diverse concepts. Therefore, we built an NLP ensemble pipeline to synergize the strength of popular NLP tools using seven ensemble methods, and to quantify the improvement in performance achieved by ensembles in the extraction of data elements for three very different cohorts. Evaluation results show that the pipeline can improve the performance of NLP tools, but there is high variability depending on the cohort.
authors.affiliation: University of California San Diego, La Jolla, CA.
authors.forename: Tsung-Ting
authors.initials: TT
authors.lastname: Kuo
authors.affiliation: University of California, Davis, CA.
authors.forename: Pallavi
authors.initials: P
authors.lastname: Rao
authors.affiliation: University of California, Los Angeles, CA.
authors.forename: Cleo
authors.initials: C
authors.lastname: Maehara
authors.affiliation: University of California San Diego, La Jolla, CA.
authors.forename: Son
authors.initials: S
authors.lastname: Doan
authors.affiliation: University of California San Diego, La Jolla, CA.
authors.forename: Juan D
authors.initials: JD
authors.lastname: Chaparro
authors.affiliation: University of California San Diego, La Jolla, CA.
authors.forename: Michele E
authors.initials: ME
authors.lastname: Day
authors.affiliation: University of California San Diego, La Jolla, CA.
authors.forename: Claudiu
authors.initials: C
authors.lastname: Farcas
authors.affiliation: University of California San Diego, La Jolla, CA.
authors.forename: Lucila
authors.initials: L
authors.lastname: Ohno-Machado
authors.affiliation: University of California San Diego, La Jolla, CA.
authors.forename: Chun-Nan
authors.initials: CN
authors.lastname: Hsu
mesh_terms: D003625:Data Collection; D057286:Electronic Health Records; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods*; D009323:Natural Language Processing