Developing a natural language processing system using transformer-based models for adverse drug event detection in electronic health records
Jingyuan Wu, Xiaodi Ruan, Elizabeth A. McNeer, Katelyn M. Rossow, Leena Choi · PLoS ONE · 2026
OBJECTIVE: To develop a transformer-based natural language processing (NLP) system for detecting adverse drug events (ADEs) from clinical notes in electronic health records (EHRs). MATERIALS AND METHODS: We fine-tuned BERT Short-Formers and Clinical-Longformer using the processed dataset from the 2018 National NLP Clinical Challenges (n2c2) shared task Track 2. Two data processing methods, window-based and split-based approaches, were compared to identify the optimal processing method. Model generalizability was evaluated on a dataset extracted from Vanderbilt University Medical Center (VUMC) EHRs. RESULTS: On the n2c2 dataset, the best 5-fold cross-validation AUPRC, micro F1, and macro F1 scores were 0.840 (Clinical-Longformer, 4-chunk split), 0.965 (BioBERT, 15-word window), and 0.852 (Clinical-Longformer, 10-chunk split). On the VUMC dataset, the best AUPRC, micro F1, and macro F1 scores were 0.536 (Clinical-Longformer, 6-chunk split), 0.966 (BERT-base-uncased, 6-chunk split), and 0.762 (Clinical-Longformer, 4-chunk split). DISCUSSION: Transformer-based models demonstrated strong performance for ADE detection, with split-based processing generally outperforming window-based methods. Clinical-Longformer combined with a practical split-based approach showed promise for real-world implementation. Beyond token limits, chunk size substantially influenced model performance, even when text length remained within limits. CONCLUSION: Our findings provide practical guidance for developing transformer-based ADE detection systems from clinical notes. The selection of both text preprocessing strategies and model architectures should be guided by note characteristics and practical considerations such as annotation burden.