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dc.contributor.authorLin, Chenen_US
dc.contributor.authorKarlson, Elizabeth W.en_US
dc.contributor.authorCanhao, Helenaen_US
dc.contributor.authorMiller, Timothy A.en_US
dc.contributor.authorDligach, Dmitriyen_US
dc.contributor.authorChen, Pei Junen_US
dc.contributor.authorPerez, Raul Natanael Guzmanen_US
dc.contributor.authorShen, Yuanyanen_US
dc.contributor.authorWeinblatt, Michael E.en_US
dc.contributor.authorShadick, Nancy A.en_US
dc.contributor.authorPlenge, Robert M.en_US
dc.contributor.authorSavova, Guergana K.en_US
dc.date.accessioned2014-03-01T02:25:00Z
dc.date.issued2013en_US
dc.identifier.citationLin, C., E. W. Karlson, H. Canhao, T. A. Miller, D. Dligach, P. J. Chen, R. N. G. Perez, et al. 2013. “Automatic Prediction of Rheumatoid Arthritis Disease Activity from the Electronic Medical Records.” PLoS ONE 8 (8): e69932. doi:10.1371/journal.pone.0069932. http://dx.doi.org/10.1371/journal.pone.0069932.en
dc.identifier.issn1932-6203en
dc.identifier.urihttp://nrs.harvard.edu/urn-3:HUL.InstRepos:11855841
dc.description.abstractObjective: We aimed to mine the data in the Electronic Medical Record to automatically discover patients' Rheumatoid Arthritis disease activity at discrete rheumatology clinic visits. We cast the problem as a document classification task where the feature space includes concepts from the clinical narrative and lab values as stored in the Electronic Medical Record. Materials and Methods The Training Set consisted of 2792 clinical notes and associated lab values. Test Set 1 included 1749 clinical notes and associated lab values. Test Set 2 included 344 clinical notes for which there were no associated lab values. The Apache clinical Text Analysis and Knowledge Extraction System was used to analyze the text and transform it into informative features to be combined with relevant lab values. Results: Experiments over a range of machine learning algorithms and features were conducted. The best performing combination was linear kernel Support Vector Machines with Unified Medical Language System Concept Unique Identifier features with feature selection and lab values. The Area Under the Receiver Operating Characteristic Curve (AUC) is 0.831 (σ = 0.0317), statistically significant as compared to two baselines (AUC = 0.758, σ = 0.0291). Algorithms demonstrated superior performance on cases clinically defined as extreme categories of disease activity (Remission and High) compared to those defined as intermediate categories (Moderate and Low) and included laboratory data on inflammatory markers. Conclusion: Automatic Rheumatoid Arthritis disease activity discovery from Electronic Medical Record data is a learnable task approximating human performance. As a result, this approach might have several research applications, such as the identification of patients for genome-wide pharmacogenetic studies that require large sample sizes with precise definitions of disease activity and response to therapies.en
dc.language.isoen_USen
dc.publisherPublic Library of Scienceen
dc.relation.isversionofdoi:10.1371/journal.pone.0069932en
dc.relation.hasversionhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC3745469/pdf/en
dash.licenseLAAen_US
dc.subjectBiologyen
dc.subjectComputational Biologyen
dc.subjectGenomicsen
dc.subjectPharmacogenomicsen
dc.subjectGeneticsen
dc.subjectHeredityen
dc.subjectPhenotypesen
dc.subjectGenomic Medicineen
dc.subjectComputer Scienceen
dc.subjectAlgorithmsen
dc.subjectNatural Language Processingen
dc.subjectText Miningen
dc.subjectMathematicsen
dc.subjectApplied Mathematicsen
dc.subjectStatisticsen
dc.subjectBiostatisticsen
dc.subjectStatistical Methodsen
dc.subjectMedicineen
dc.subjectClinical Immunologyen
dc.subjectAutoimmune Diseasesen
dc.subjectRheumatoid Arthritisen
dc.subjectEpidemiologyen
dc.subjectDisease Informaticsen
dc.subjectRheumatologyen
dc.titleAutomatic Prediction of Rheumatoid Arthritis Disease Activity from the Electronic Medical Recordsen
dc.typeJournal Articleen_US
dc.description.versionVersion of Recorden
dc.relation.journalPLoS ONEen
dash.depositing.authorKarlson, Elizabeth W.en_US
dc.date.available2014-03-01T02:25:00Z
dc.identifier.doi10.1371/journal.pone.0069932*
dash.authorsorderedfalse
dash.contributor.affiliatedMiller, Timothy
dash.contributor.affiliatedDligach, Dmitriy
dash.contributor.affiliatedShadick, Nancy
dash.contributor.affiliatedWeinblatt, Michael
dash.contributor.affiliatedPlenge, Robert M.
dash.contributor.affiliatedSavova, Guergana
dash.contributor.affiliatedKarlson, Elizabeth


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