Adapting and evaluating a deep learning language model for clinical why-question answering

Andrew Wen, Mohamed Y. Elwazir, Sungrim Moon, Jungwei Fan

Research output: Contribution to journalArticlepeer-review


Objectives: To adapt and evaluate a deep learning language model for answering why-questions based on patient-specific clinical text. Materials and Methods: Bidirectional encoder representations from transformers (BERT) models were trained with varying data sources to perform SQuAD 2.0 style why-question answering (why-QA) on clinical notes. The evaluation focused on: (1) comparing the merits from different training data and (2) error analysis. Results: The best model achieved an accuracy of 0.707 (or 0.760 by partial match). Training toward customization for the clinical language helped increase 6% in accuracy. Discussion: The error analysis suggested that the model did not really perform deep reasoning and that clinical why-QA might warrant more sophisticated solutions. Conclusion: The BERT model achieved moderate accuracy in clinical why-QA and should benefit from the rapidly evolving technology. Despite the identified limitations, it could serve as a competent proxy for questiondriven clinical information extraction.

Original languageEnglish (US)
Pages (from-to)16-20
Number of pages5
JournalJAMIA Open
Issue number1
StatePublished - 2021


  • Artificial intelligence
  • Clinical decision-making
  • Evaluation studies
  • Natural language processing
  • Question answering

ASJC Scopus subject areas

  • Health Informatics


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