Deleger, LouiseMolnar, KatalinSavova, GuerganaXia, FeiLingren, ToddLi, QiMarsolo, KeithJegga, AnilKaiser, MeganStoutenborough, LauraSolti, Imre2014-03-112012Deleger, L., K. Molnar, G. Savova, F. Xia, T. Lingren, Q. Li, K. Marsolo, et al. 2012. “Large-scale evaluation of automated clinical note de-identification and its impact on information extraction.” Journal of the American Medical Informatics Association : JAMIA 20 (1): 84-94. doi:10.1136/amiajnl-2012-001012. http://dx.doi.org/10.1136/amiajnl-2012-001012.1067-5027http://nrs.harvard.edu/urn-3:HUL.InstRepos:11879366Objective: (1) To evaluate a state-of-the-art natural language processing (NLP)-based approach to automatically de-identify a large set of diverse clinical notes. (2) To measure the impact of de-identification on the performance of information extraction algorithms on the de-identified documents. Material and methods A cross-sectional study that included 3503 stratified, randomly selected clinical notes (over 22 note types) from five million documents produced at one of the largest US pediatric hospitals. Sensitivity, precision, F value of two automated de-identification systems for removing all 18 HIPAA-defined protected health information elements were computed. Performance was assessed against a manually generated ‘gold standard’. Statistical significance was tested. The automated de-identification performance was also compared with that of two humans on a 10% subsample of the gold standard. The effect of de-identification on the performance of subsequent medication extraction was measured. Results: The gold standard included 30 815 protected health information elements and more than one million tokens. The most accurate NLP method had 91.92% sensitivity (R) and 95.08% precision (P) overall. The performance of the system was indistinguishable from that of human annotators (annotators' performance was 92.15%(R)/93.95%(P) and 94.55%(R)/88.45%(P) overall while the best system obtained 92.91%(R)/95.73%(P) on same text). The impact of automated de-identification was minimal on the utility of the narrative notes for subsequent information extraction as measured by the sensitivity and precision of medication name extraction. Discussion and conclusion NLP-based de-identification shows excellent performance that rivals the performance of human annotators. Furthermore, unlike manual de-identification, the automated approach scales up to millions of documents quickly and inexpensively.en-USNatural language processingprivacy of patient datahealth insurance portability and accountability actautomated de-identificationprotected health informationNLPtext mininghuman-computer interaction and human-centered computingproviding just-in-time access to the biomedical literature and other health informationapplications that link biomedical knowledge from diverse primary sources (includes automated indexing)linking the genotype and phenotypediscoverybionlpmedical informaticsbiomedical informaticsdisease networkstranslational medicinedrug repositioningrare diseasesJournal Article2014-03-1110.1136/amiajnl-2012-001012