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
- 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)
- PDF:
- https://preview.aclanthology.org/ingestion-script-update/2022.naacl-main.233.pdf
- Code
- allenai/drug-combo-extraction
- Data
- BLUE