PHEE: A Dataset for Pharmacovigilance Event Extraction from Text

Zhaoyue Sun, Jiazheng Li, Gabriele Pergola, Byron Wallace, Bino John, Nigel Greene, Joseph Kim, Yulan He


Abstract
The primary goal of drug safety researchers and regulators is to promptly identify adverse drug reactions. Doing so may in turn prevent or reduce the harm to patients and ultimately improve public health. Evaluating and monitoring drug safety (i.e., pharmacovigilance) involves analyzing an ever growing collection of spontaneous reports from health professionals, physicians, and pharmacists, and information voluntarily submitted by patients. In this scenario, facilitating analysis of such reports via automation has the potential to rapidly identify safety signals. Unfortunately, public resources for developing natural language models for this task are scant. We present PHEE, a novel dataset for pharmacovigilance comprising over 5000 annotated events from medical case reports and biomedical literature, making it the largest such public dataset to date. We describe the hierarchical event schema designed to provide coarse and fine-grained information about patients’ demographics, treatments and (side) effects. Along with the discussion of the dataset, we present a thorough experimental evaluation of current state-of-the-art approaches for biomedical event extraction, point out their limitations, and highlight open challenges to foster future research in this area.
Anthology ID:
2022.emnlp-main.376
Volume:
Proceedings of the 2022 Conference on Empirical Methods in Natural Language Processing
Month:
December
Year:
2022
Address:
Abu Dhabi, United Arab Emirates
Editors:
Yoav Goldberg, Zornitsa Kozareva, Yue Zhang
Venue:
EMNLP
SIG:
Publisher:
Association for Computational Linguistics
Note:
Pages:
5571–5587
Language:
URL:
https://aclanthology.org/2022.emnlp-main.376
DOI:
10.18653/v1/2022.emnlp-main.376
Bibkey:
Cite (ACL):
Zhaoyue Sun, Jiazheng Li, Gabriele Pergola, Byron Wallace, Bino John, Nigel Greene, Joseph Kim, and Yulan He. 2022. PHEE: A Dataset for Pharmacovigilance Event Extraction from Text. In Proceedings of the 2022 Conference on Empirical Methods in Natural Language Processing, pages 5571–5587, Abu Dhabi, United Arab Emirates. Association for Computational Linguistics.
Cite (Informal):
PHEE: A Dataset for Pharmacovigilance Event Extraction from Text (Sun et al., EMNLP 2022)
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PDF:
https://aclanthology.org/2022.emnlp-main.376.pdf