Automatic Prediction of Rheumatoid Arthritis Disease Activity from the Electronic Medical Records.docVIP

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Automatic Prediction of Rheumatoid Arthritis Disease Activity from the Electronic Medical Records.doc

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Automatic Prediction of Rheumatoid Arthritis Disease Activity from the Electronic Medical Records

AutomaticPredictionofRheumatoidArthritisDisease ActivityfromtheElectronicMedicalRecords ChenLin1*,ElizabethW.Karlson2,3,HelenaCanhao4,TimothyA.Miller1,3,DmitriyDligach1,3 ,Pei JunChen1,RaulNatanaelGuzmanPerez2,YuanyanShen5,MichaelE.Weinblatt2,3,NancyA.Shadick2,3 RobertM.Plenge2,3,GuerganaK.Savova1,3 , 1Informatics Program, Boston Children’s Hospital, Boston, Massachusetts, United States of America, 2Rheumatology and Immunology Department, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America, 3Harvard Medical School, Harvard University, Boston, Massachusetts, United States of America, 4RheumatologyResearchUnit,InstitutodeMedicinaMolecular,FaculdadedeMedicinadaUniversidadedeLisboa,Lisbon,Portugal,5SchoolofPublicHealth,Harvard University,Boston,Massachusetts,UnitedStatesofAmerica Abstract Objective: We aimed to mine the data in the Electronic Medical Record to automatically discover patients’ Rheumatoid Arthritisdiseaseactivityatdiscreterheumatologyclinicvisits.Wecasttheproblemasadocumentclassificationtaskwhere thefeaturespaceincludesconceptsfromtheclinicalnarrativeandlabvaluesasstoredintheElectronicMedicalRecord. Materials andMethods: TheTraining Setconsistedof2792 clinicalnotesandassociated labvalues. TestSet1included 1749clinicalnotesandassociatedlabvalues.TestSet2included344clinicalnotesforwhichtherewerenoassociatedlab values.TheApacheclinicalTextAnalysisandKnowledgeExtractionSystemwasusedtoanalyzethetextandtransformit intoinformativefeaturestobecombinedwithrelevantlabvalues. Results: Experiments over a range of machine learning algorithms and features were conducted. The best performing combinationwaslinearkernelSupportVectorMachineswithUnifiedMedicalLanguageSystemConceptUniqueIdentifier featureswithfeatureselectionandlabvalues.TheAreaUndertheReceiverOperatingCharacteristicCurve(AUC)is0.831 (s=0.0317), statistically significant as compared to two baselines (AUC=0.758, s=0.0291). Algorithms demonstrated superiorperformanceoncasesclinic