Text Mining of Adverse Events in Clinical Trials: Deep Learning Approach (Preprint)

Abstract

Pharmacovigilance and safety reporting, which involve processes for monitoring the use of medicines in clinical trials, play a critical role in the identification of previously unrecognized adverse events or changes in the patterns of adverse events.

This study aims to demonstrate the feasibility of automating the coding of adverse events described in the narrative section of the serious adverse event report forms to enable statistical analysis of the aforementioned patterns.

We used the Unified Medical Language System (UMLS) as the coding scheme, which integrates 217 source vocabularies, thus enabling coding against other relevant terminologies such as the International Classification of Diseases–10th Revision, Medical Dictionary for Regulatory Activities, and Systematized Nomenclature of Medicine). We used MetaMap, a highly configurable dictionary lookup software, to identify the mentions of the UMLS concepts. We trained a binary classifier using Bidirectional Encoder Representations from Transformers (BERT), a transformer-based language model that captures contextual relationships, to differentiate between mentions of the UMLS concepts that represented adverse events and those that did not.

The model achieved a high F1 score of 0.8080, despite the class imbalance. This is 10.15 percent points lower than human-like performance but also 17.45 percent points higher than that of the baseline approach.

These results confirmed that automated coding of adverse events described in the narrative section of serious adverse event reports is feasible. Once coded, adverse events can be statistically analyzed so that any correlations with the trialed medicines can be estimated in a timely fashion.