A Dataset for N-ary Relation Extraction of Drug Combinations

Aryeh Tiktinsky, Vijay Viswanathan, Danna Niezni, Dana Meron Azagury, Yosi Shamay, Hillel Taub-Tabib, Tom Hope, Yoav Goldberg


Abstract
Combination therapies have become the standard of care for diseases such as cancer, tuberculosis, malaria and HIV. However, the combinatorial set of available multi-drug treatments creates a challenge in identifying effective combination therapies available in a situation.To assist medical professionals in identifying beneficial drug-combinations, we construct an expert-annotated dataset for extracting information about the efficacy of drug combinations from the scientific literature. Beyond its practical utility, the dataset also presents a unique NLP challenge, as the first relation extraction dataset consisting of variable-length relations. Furthermore, the relations in this dataset predominantly require language understanding beyond the sentence level, adding to the challenge of this task. We provide a promising baseline model and identify clear areas for further improvement. We release our dataset (https://huggingface.co/datasets/allenai/drug-combo-extraction), code (https://github.com/allenai/drug-combo-extraction) and baseline models (https://huggingface.co/allenai/drug-combo-classifier-pubmedbert-dapt) publicly to encourage the NLP community to participate in this task.
Anthology ID:
2022.naacl-main.233
Volume:
Proceedings of the 2022 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies
Month:
July
Year:
2022
Address:
Seattle, United States
Venue:
NAACL
SIG:
Publisher:
Association for Computational Linguistics
Note:
Pages:
3190–3203
Language:
URL:
https://aclanthology.org/2022.naacl-main.233
DOI:
10.18653/v1/2022.naacl-main.233
Bibkey:
Cite (ACL):
Aryeh Tiktinsky, Vijay Viswanathan, Danna Niezni, Dana Meron Azagury, Yosi Shamay, Hillel Taub-Tabib, Tom Hope, and Yoav Goldberg. 2022. A Dataset for N-ary Relation Extraction of Drug Combinations. In Proceedings of the 2022 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, pages 3190–3203, Seattle, United States. Association for Computational Linguistics.
Cite (Informal):
A Dataset for N-ary Relation Extraction of Drug Combinations (Tiktinsky et al., NAACL 2022)
Copy Citation:
PDF:
https://aclanthology.org/2022.naacl-main.233.pdf
Code
 allenai/drug-combo-extraction
Data
BLUE