Evaluating Knowledge Fusion Models on Detecting Adverse Drug Events in Text

Background Detecting adverse drug events (ADE) of drugs that are already available on the market is an essential part of the pharmacovigilance work conducted by both medical regulatory bodies and the pharmaceutical industry. Concerns regarding drug safety and economic interests serve as motivating factors for the efforts to identify ADEs. Hereby, social media platforms play an important role as a valuable source of reports on ADEs, particularly through collecting posts discussing adverse events associated with specific drugs. Methodology We aim with our study to assess the effectiveness of knowledge fusion approaches in combination with transformer-based NLP models to extract ADE mentions from diverse datasets, for instance, texts from Twitter, websites like askapatient.com, and drug labels. The extraction task is formulated as a named entity recognition (NER) problem. The proposed methodology involves applying fusion learning methods to enhance the performance of transformer-based language models with additional contextual knowledge from ontologies or knowledge graphs. Additionally, the study introduces a multi-modal architecture that combines transformer-based language models with graph attention networks (GAT) to identify ADE spans in textual data. Results A multi-modality model consisting of the ERNIE model with knowledge on drugs reached an F1-score of 71.84% on CADEC corpus. Additionally, a combination of a graph attention network with BERT resulted in an F1-score of 65.16% on SMM4H corpus. Impressively, the same model achieved an F1-score of 72.50% on the PSYTAR corpus, 79.54% on the ADE corpus, and 94.15% on the TAC corpus. Except for the CADEC corpus, the knowledge fusion models consistently outperformed the baseline model, BERT. Conclusion Our study demonstrates the significance of context knowledge in improving the performance of knowledge fusion models for detecting ADEs from various types of textual data. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement The author(s) received no specific funding for this work. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: N/A I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes The data underlying the results presented in the study are available from various study owners. These studies have been linked in the main manuscript.