Interactive medical word sense disambiguation through informed learning

J Am Med Inform Assoc. 2018 Jul 1;25(7):800-808. doi: 10.1093/jamia/ocy013.


Objective: Medical word sense disambiguation (WSD) is challenging and often requires significant training with data labeled by domain experts. This work aims to develop an interactive learning algorithm that makes efficient use of expert's domain knowledge in building high-quality medical WSD models with minimal human effort.

Methods: We developed an interactive learning algorithm with expert labeling instances and features. An expert can provide supervision in 3 ways: labeling instances, specifying indicative words of a sense, and highlighting supporting evidence in a labeled instance. The algorithm learns from these labels and iteratively selects the most informative instances to ask for future labels. Our evaluation used 3 WSD corpora: 198 ambiguous terms from Medical Subject Headings (MSH) as MEDLINE indexing terms, 74 ambiguous abbreviations in clinical notes from the University of Minnesota (UMN), and 24 ambiguous abbreviations in clinical notes from Vanderbilt University Hospital (VUH). For each ambiguous term and each learning algorithm, a learning curve that plots the accuracy on the test set against the number of labeled instances was generated. The area under the learning curve was used as the primary evaluation metric.

Results: Our interactive learning algorithm significantly outperformed active learning, the previous fastest learning algorithm for medical WSD. Compared to active learning, it achieved 90% accuracy for the MSH corpus with 42% less labeling effort, 35% less labeling effort for the UMN corpus, and 16% less labeling effort for the VUH corpus.

Conclusions: High-quality WSD models can be efficiently trained with minimal supervision by inviting experts to label informative instances and provide domain knowledge through labeling/highlighting contextual features.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms*
  • Logistic Models
  • Machine Learning*
  • Medical Records
  • Medical Subject Headings
  • Medicine
  • Natural Language Processing*
  • Vocabulary