Extracting medication changes in clinical narratives using pre-trained language models

J Biomed Inform. 2023 Mar:139:104302. doi: 10.1016/j.jbi.2023.104302. Epub 2023 Feb 6.


An accurate and detailed account of patient medications, including medication changes within the patient timeline, is essential for healthcare providers to provide appropriate patient care. Healthcare providers or the patients themselves may initiate changes to patient medication. Medication changes take many forms, including prescribed medication and associated dosage modification. These changes provide information about the overall health of the patient and the rationale that led to the current care. Future care can then build on the resulting state of the patient. This work explores the automatic extraction of medication change information from free-text clinical notes. The Contextual Medication Event Dataset (CMED) is a corpus of clinical notes with annotations that characterize medication changes through multiple change-related attributes, including the type of change (start, stop, increase, etc.), initiator of the change, temporality, change likelihood, and negation. Using CMED, we identify medication mentions in clinical text and propose three novel high-performing BERT-based systems that resolve the annotated medication change characteristics. We demonstrate that our proposed systems improve medication change classification performance over the initial work exploring CMED.

Keywords: Information extraction; Machine learning; Medication information; Natural language processing.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Humans
  • Language*
  • Narration
  • Natural Language Processing*