Dataset Information

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

ABSTRACT:

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.

SUBMITTER: Fan Y

PROVIDER: S-EPMC7936508 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BACKGROUND:Dietary supplements, such as herbal or complementary nutritional products and micronutrients (vitamins and minerals), are commonly used in the United States, yet national data on adverse effects are limited. METHODS:We used nationally representative surveillance data from 63 emergency departments obtained from 2004 through 2013 to describe visits to U.S. emergency departments because of adverse events related to dietary supplements. RESULTS:On the basis of 3667 cases, we estimated that 23,005 (95% confidence interval [CI], 18,611 to 27,398) emergency department visits per year were attributed to adverse events related to dietary supplements. These visits resulted in an estimated 2154 hospitalizations (95% CI, 1342 to 2967) annually. Such visits frequently involved young adults between the ages of 20 and 34 years (28.0% of visits; 95% CI, 25.1 to 30.8) and unsupervised children (21.2% of visits; 95% CI, 18.4 to 24.0). After the exclusion of unsupervised ingestion of dietary supplements by children, 65.9% (95% CI, 63.2 to 68.5) of emergency department visits for single-supplement-related adverse events involved herbal or complementary nutritional products; 31.8% (95% CI, 29.2 to 34.3) involved micronutrients. Herbal or complementary nutritional products for weight loss (25.5%; 95% CI, 23.1 to 27.9) and increased energy (10.0%; 95% CI, 8.0 to 11.9) were commonly implicated. Weight-loss or energy products caused 71.8% (95% CI, 67.6 to 76.1) of supplement-related adverse events involving palpitations, chest pain, or tachycardia, and 58.0% (95% CI, 52.2 to 63.7) involved persons 20 to 34 years of age. Among adults 65 years of age or older, choking or pill-induced dysphagia or globus caused 37.6% (95% CI, 29.1 to 46.2) of all emergency department visits for supplement-related adverse events; micronutrients were implicated in 83.1% (95% CI, 73.3 to 92.9) of these visits. CONCLUSIONS:An estimated 23,000 emergency department visits in the United States every year are attributed to adverse events related to dietary supplements. Such visits commonly involve cardiovascular manifestations from weight-loss or energy products among young adults and swallowing problems, often associated with micronutrients, among older adults. (Funded by the Department of Health and Human Services.).