Slot Filling for Biomedical Information Extraction
Yannis Papanikolaou, Marlene Staib, Justin Joshua Grace, Francine Bennett
Abstract
Information Extraction (IE) from text refers to the task of extracting structured knowledge from unstructured text. The task typically consists of a series of sub-tasks such as Named Entity Recognition and Relation Extraction. Sourcing entity and relation type specific training data is a major bottleneck in domains with limited resources such as biomedicine. In this work we present a slot filling approach to the task of biomedical IE, effectively replacing the need for entity and relation-specific training data, allowing us to deal with zero-shot settings. We follow the recently proposed paradigm of coupling a Tranformer-based bi-encoder, Dense Passage Retrieval, with a Transformer-based reading comprehension model to extract relations from biomedical text. We assemble a biomedical slot filling dataset for both retrieval and reading comprehension and conduct a series of experiments demonstrating that our approach outperforms a number of simpler baselines. We also evaluate our approach end-to-end for standard as well as zero-shot settings. Our work provides a fresh perspective on how to solve biomedical IE tasks, in the absence of relevant training data. Our code, models and datasets are available at https://github.com/tba.- Anthology ID:
- 2022.bionlp-1.7
- Volume:
- Proceedings of the 21st Workshop on Biomedical Language Processing
- Month:
- May
- Year:
- 2022
- Address:
- Dublin, Ireland
- Venue:
- BioNLP
- SIG:
- Publisher:
- Association for Computational Linguistics
- Note:
- Pages:
- 82–90
- Language:
- URL:
- https://aclanthology.org/2022.bionlp-1.7
- DOI:
- 10.18653/v1/2022.bionlp-1.7
- Cite (ACL):
- Yannis Papanikolaou, Marlene Staib, Justin Joshua Grace, and Francine Bennett. 2022. Slot Filling for Biomedical Information Extraction. In Proceedings of the 21st Workshop on Biomedical Language Processing, pages 82–90, Dublin, Ireland. Association for Computational Linguistics.
- Cite (Informal):
- Slot Filling for Biomedical Information Extraction (Papanikolaou et al., BioNLP 2022)
- PDF:
- https://preview.aclanthology.org/auto-file-uploads/2022.bionlp-1.7.pdf
- Code
- ypapanik/biomedical-slot-filling + additional community code
- Data
- KILT, Natural Questions