Effective information extraction framework for heterogeneous clinical reports using online machine learning and controlled vocabularies

Shuai Zheng, James J. Lu, Nima Ghasemzadeh, Salim S. Hayek, Arshed A. Quyyumi, Fusheng Wang

Research output: Contribution to journalArticlepeer-review

18 Scopus citations


Background: Extracting structured data from narrated medical reports is challenged by the complexity of heterogeneous structures and vocabularies and often requires significant manual effort. Traditional machine-based approaches lack the capability to take user feedbacks for improving the extraction algorithm in real time. Objective: Our goal was to provide a generic information extraction framework that can support diverse clinical reports and enables a dynamic interaction between a human and a machine that produces highly accurate results. Methods: A clinical information extraction system IDEAL-X has been built on top of online machine learning. It processes one document at a time, and user interactions are recorded as feedbacks to update the learning model in real time. The updated model is used to predict values for extraction in subsequent documents. Once prediction accuracy reaches a user-acceptable threshold, the remaining documents may be batch processed. A customizable controlled vocabulary may be used to support extraction. Results: Three datasets were used for experiments based on report styles: 100 cardiac catheterization procedure reports, 100 coronary angiographic reports, and 100 integrated reports-each combines history and physical report, discharge summary, outpatient clinic notes, outpatient clinic letter, and inpatient discharge medication report. Data extraction was performed by 3 methods: Online machine learning, controlled vocabularies, and a combination of these. The system delivers results with F1 scores greater than 95%. Conclusions: IDEAL-X adopts a unique online machine learning-based approach combined with controlled vocabularies to support data extraction for clinical reports. The system can quickly learn and improve, thus it is highly adaptable.

Original languageEnglish (US)
Article numbere12
JournalJMIR Medical Informatics
Issue number2
StatePublished - Apr 2017
Externally publishedYes


  • Controlled vocabulary
  • Electronic medical records
  • Information extraction
  • Natural language processing

ASJC Scopus subject areas

  • Health Informatics
  • Health Information Management


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