title: Automatic prediction of rheumatoid arthritis disease activity from the electronic medical records.
abstract: OBJECTIVE
  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.
  
  
  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.
  
  
  CONCLUSIONS
  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.
authors: Informatics Program, Boston Children's Hospital, Boston, Massachusetts, United States of America.
authors: Chen
authors: C
authors: Lin
authors: Elizabeth W
authors: EW
authors: Karlson
authors: Helena
authors: H
authors: Canhao
authors: Timothy A
authors: TA
authors: Miller
authors: Dmitriy
authors: D
authors: Dligach
authors: Pei Jun
authors: PJ
authors: Chen
authors: Raul Natanael Guzman
authors: RN
authors: Perez
authors: Yuanyan
authors: Y
authors: Shen
authors: Michael E
authors: ME
authors: Weinblatt
authors: Nancy A
authors: NA
authors: Shadick
authors: Robert M
authors: RM
authors: Plenge
authors: Guergana K
authors: GK
authors: Savova
mesh_terms: D018501:Antirheumatic Agents / Q000627:therapeutic use; D001172:Arthritis, Rheumatoid / Q000175:diagnosis* / Q000188:drug therapy / Q000503:physiopathology; D001185:Artificial Intelligence; D057225:Data Mining / Q000379:methods; D018450:Disease Progression; D057286:Electronic Health Records / Q000295:instrumentation / Q000706:statistics & numerical data*; D006801:Humans; D012372:ROC Curve; D060388:Support Vector Machine
chemical_list: D018501:Antirheumatic Agents
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