Using word embeddings to expand terminology of dietary supplements on clinical notes

Yadan Fan, Serguei Pakhomov, Reed McEwan, Wendi Zhao, Elizabeth Lindemann, Rui Zhang

Research output: Contribution to journalArticlepeer-review

17 Scopus citations


Objective: The objective of this study is to demonstrate the feasibility of applying word embeddings to expand the terminology of dietary supplements (DS) using over 26 million clinical notes. Methods: Word embedding models (ie, word2vec and GloVe) trained on clinical notes were used to predefine a list of top 40 semantically related terms for each of 14 commonly used DS. Each list was further evaluated by experts to generate semantically similar terms. We investigated the effect of corpus size and other settings (ie, vector size and window size) as well as the 2 word embedding models on performance for DS term expansion. We compared the number of clinical notes (and patients they represent) that were retrieved using the word embedding expanded terms to both the baseline terms and external DS sources expanded terms. Results: Using the word embedding models trained on clinical notes, we could identify 1-12 semantically similar terms for each DS. Using the word embedding expanded terms, we were able to retrieve averagely 8.39% more clinical notes and 11.68% more patients for each DS compared with 2 sets of terms. The increasing corpus size results in more misspellings, but not more semantic variants and brand names. Word2vec model is also found more capable of detecting semantically similar terms than GloVe. Conclusion: Our study demonstrates the utility of word embeddings on clinical notes for terminology expansion on 14 DS. We propose that this method can be potentially applied to create a DS vocabulary for downstream applications, such as information extraction.

Original languageEnglish (US)
Pages (from-to)246-253
Number of pages8
JournalJAMIA Open
Issue number2
StatePublished - 2019

Bibliographical note

Publisher Copyright:
© The Author(s) 2019.


  • Clinical notes
  • Dietary supplements
  • Natural language processing
  • Terminology expansion
  • Word embeddings


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