A sequence-to-sequence approach for document-level relation extraction

John Giorgi, Gary Bader, Bo Wang


Abstract
Motivated by the fact that many relations cross the sentence boundary, there has been increasing interest in document-level relation extraction (DocRE). DocRE requires integrating information within and across sentences, capturing complex interactions between mentions of entities. Most existing methods are pipeline-based, requiring entities as input. However, jointly learning to extract entities and relations can improve performance and be more efficient due to shared parameters and training steps. In this paper, we develop a sequence-to-sequence approach, seq2rel, that can learn the subtasks of DocRE (entity extraction, coreference resolution and relation extraction) end-to-end, replacing a pipeline of task-specific components. Using a simple strategy we call entity hinting, we compare our approach to existing pipeline-based methods on several popular biomedical datasets, in some cases exceeding their performance. We also report the first end-to-end results on these datasets for future comparison. Finally, we demonstrate that, under our model, an end-to-end approach outperforms a pipeline-based approach. Our code, data and trained models are available at https://github.com/johngiorgi/seq2rel. An online demo is available at https://share.streamlit.io/johngiorgi/seq2rel/main/demo.py.
Anthology ID:
2022.bionlp-1.2
Volume:
Proceedings of the 21st Workshop on Biomedical Language Processing
Month:
May
Year:
2022
Address:
Dublin, Ireland
Venues:
ACL | BioNLP
SIG:
Publisher:
Association for Computational Linguistics
Note:
Pages:
10–25
Language:
URL:
https://aclanthology.org/2022.bionlp-1.2
DOI:
10.18653/v1/2022.bionlp-1.2
Bibkey:
Cite (ACL):
John Giorgi, Gary Bader, and Bo Wang. 2022. A sequence-to-sequence approach for document-level relation extraction. In Proceedings of the 21st Workshop on Biomedical Language Processing, pages 10–25, Dublin, Ireland. Association for Computational Linguistics.
Cite (Informal):
A sequence-to-sequence approach for document-level relation extraction (Giorgi et al., BioNLP 2022)
Copy Citation:
PDF:
https://aclanthology.org/2022.bionlp-1.2.pdf
Code
 johngiorgi/seq2rel +  additional community code
Data
BC5CDRCDRDocRED