Automatic prediction of rheumatoid arthritis disease activity from the electronic medical records

• Published in: PloS one Vol. 8; no. 8; p. e69932
• Main Authors: Lin, Chen, Karlson, Elizabeth W, Canhao, Helena, Miller, Timothy A, Dligach, Dmitriy, Chen, Pei Jun, Perez, Raul Natanael Guzman, Shen, Yuanyan, Weinblatt, Michael E, Shadick, Nancy A, Plenge, Robert M, Savova, Guergana K
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 16.08.2013; Public Library of Science (PLoS)
• Subjects: Algorithms; Antirheumatic Agents - therapeutic use; Arthritis; Arthritis, Rheumatoid - diagnosis; Arthritis, Rheumatoid - drug therapy; Arthritis, Rheumatoid - physiopathology; Artificial Intelligence; Bioindicators; Biology; Children & youth; Clinical trials; Computer Science; Data mining; Data Mining - methods; Disease Progression; Electronic health records; Electronic Health Records - instrumentation; Electronic Health Records - statistics & numerical data; Electronic medical records; Electronic records; Genomes; Health risk assessment; Hospitals; Human factors; Human performance; Humans; Immunology; Inflammation; Informatics; Laboratories; Learning algorithms; Machine learning; Mathematics; Medical materials; Medical records; Medical schools; Medicine; Natural language processing; Ontology; Patients; Pharmacology; Pneumonia; Remission; Rheumatoid arthritis; Rheumatoid factor; Rheumatology; ROC Curve; Statistical analysis; Support Vector Machine; Support vector machines; Text analysis; Womens health; United States > US; Massachusetts
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0069932

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. 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. 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. 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.