Context-Aware Biomedical Word Embeddings Enhance ADR Prediction: A Shift from Word2Vec to BERT (Preprint)
Authors: Jeon Woohyuk , Park Minjae , An Doyeon , Nam Wonshik , Shin Ju-Young , Lee Seunghee , Lee Suehyun 
Published: October 2024

BACKGROUND

Adverse drug reactions (ADRs) pose serious risks to patient health, and effectively predicting and managing them is an important public health challenge. Given the complexity and specificity of biomedical text data, the traditional context-independent language model, Word2Vec, has limitations in fully reflecting the domain specificity of such data. Therefore, to predict drug-side effect relationships more accurately, we applied a Bidirectional Encoder Representations from Transformers (BERT) model specialized for biomedical applications.

OBJECTIVE

This study aimed to propose a method for extracting drug-side effect relationships from embedding vectors generated by biomedical language models, specifically BERT-based models pre-trained on biomedical corpora. This approach aims to overcome the limitations of the traditional Word2Vec model in accurately capturing complex relationships in biomedical data.

METHODS

Using data from 158,096 pairs of drug-side effect relationships from the Side Effect Resource (SIDER) database, we generated an adjacency matrix and calculated the cosine similarity between the word embedding vectors of drugs and side effects. Relation scores were calculated for a total of 8,235,435 drug-side effect pairs using this similarity. To evaluate the prediction accuracy of drug-side effect relationships, the area under the curve (AUC) value was measured using the calculated relation score and 158,096 known drug-side effect relationships provided by SIDER.

RESULTS

The clagator/biobert_v1.1 model achieved an AUC of 0.915 at an optimal threshold of 0.289, largely outperforming the existing Word2Vec model, which had an AUC of 0.848. The BERT-based model pre-trained on the biomedical corpus outperformed the vanilla BERT model, with an AUC of 0.857. Furthermore, external validation with the FDA Adverse Event Reporting System (FAERS) data, using Fisher’s exact test based on 8,235,435 predicted drug-side effect pairs and 901,361 known relationships, confirmed high statistical significance (P<.001) with an odds ratio of 4.830. Additionally, a literature review was conducted for predicted drug-side effect relationships. This review reveals that these relationships have been reported in recent studies published after 2016.

CONCLUSIONS

This study introduces a method for extracting drug-side effect relationship data embedded in the pre-trained parameters of language models pre-trained on biomedical corpora and using this information to predict the probability of previously unknown drug-side effect relationships. We improved the accuracy of predicting drug-side effect relationships by using BERT-based models instead of the Word2Vec model. We found that BERT-based models pre-trained with biomedical corpora consider contextual information and achieve better performance in drug-side effect relationship prediction. External validation using the FAERS dataset combined with a literature review of certain cases confirmed high statistical significance, demonstrating the practical applicability of this approach. These results highlight the utility of natural language processing-based approaches for predicting and managing ADRs.