Deep learning approaches for extracting adverse events and indications of dietary supplements from clinical text

Yadan Fan, Sicheng Zhou, Yifan Li, Rui Zhang

Research output: Contribution to journalArticlepeer-review

10 Scopus citations


Objective: We sought to demonstrate the feasibility of utilizing deep learning models to extract safety signals related to the use of dietary supplements (DSs) in clinical text. Materials and Methods: Two tasks were performed in this study. For the named entity recognition (NER) task, Bi-LSTM-CRF (bidirectional long short-Term memory conditional random field) and BERT (bidirectional encoder representations from transformers) models were trained and compared with CRF model as a baseline to recognize the named entities of DSs and events from clinical notes. In the relation extraction (RE) task, 2 deep learning models, including attention-based Bi-LSTM and convolutional neural network as well as a random forest model were trained to extract the relations between DSs and events, which were categorized into 3 classes: positive (ie, indication), negative (ie, adverse events), and not related. The best performed NER and RE models were further applied on clinical notes mentioning 88 DSs for discovering DSs adverse events and indications, which were compared with a DS knowledge base. Results: For the NER task, deep learning models achieved a better performance than CRF, with F1 scores above 0.860. The attention-based Bi-LSTM model performed the best in the RE task, with an F1 score of 0.893. When comparing DS event pairs generated by the deep learning models with the knowledge base for DSs and event, we found both known and unknown pairs. Conclusions: Deep learning models can detect adverse events and indication of DSs in clinical notes, which hold great potential for monitoring the safety of DS use.

Original languageEnglish (US)
Pages (from-to)569-577
Number of pages9
JournalJournal of the American Medical Informatics Association
Issue number3
StatePublished - Mar 1 2021

Bibliographical note

Publisher Copyright:
© 2020 The Author(s) 2020. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For permissions, please email:


  • clinical notes
  • deep learning
  • dietary supplements
  • named entity recognition
  • natural language processing
  • relation extraction


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