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arXiv · 2506.14900

Adverse Event Extraction from Discharge Summaries: A New Dataset, Annotation Scheme, and Initial Findings

Imane Guellil·Salomé Andres·Atul Anand·Bruce Guthrie·Huayu Zhang·Abul Hasan·Honghan Wu·Beatrice Alex
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Abstract

In this work, we present a manually annotated corpus for Adverse Event (AE) extraction from discharge summaries of elderly patients, a population often underrepresented in clinical NLP resources. The dataset includes 14 clinically significant AEs-such as falls, delirium, and intracranial haemorrhage, along with contextual attributes like negation, diagnosis type, and in-hospital occurrence. Uniquely, the annotation schema supports both discontinuous and overlapping entities, addressing challenges rarely tackled in prior work. We evaluate multiple models using FlairNLP across three annotation granularities: fine-grained, coarse-grained, and coarse-grained with negation. While transformer-based models (e.g., BERT-cased) achieve strong performance on document-level coarse-grained extraction (F1 = 0.943), performance drops notably for fine-grained entity-level tasks (e.g., F1 = 0.675), particularly for rare events and complex attributes. These results demonstrate that despite high-level scores, significant challenges remain in detecting underrepresented AEs and capturing nuanced clinical language. Developed within a Trusted Research Environment (TRE), the dataset is available upon request via DataLoch and serves as a robust benchmark for evaluating AE extraction methods and supporting future cross-dataset generalisation.

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Imane Guellil, Salomé Andres, Atul Anand, Bruce Guthrie, Huayu Zhang, Abul Hasan, Honghan Wu, Beatrice Alex. 2025-06-17. Adverse Event Extraction from Discharge Summaries: A New Dataset, Annotation Scheme, and Initial Findings. https://arxiv.org/abs/2506.14900

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