Cancer Registry Information Extraction via Transfer Learning
Yan-Jie Lin, Hong-Jie Dai, You-Chen Zhang, Chung-Yang Wu, Yu-Cheng Chang, Pin-Jou Lu, Chih-Jen Huang, Yu-Tsang Wang, Hui-Min Hsieh, Kun-San Chao, Tsang-Wu Liu, I-Shou Chang, Yi-Hsin Connie Yang, Ti-Hao Wang, Ko-Jiunn Liu, Li-Tzong Chen, Sheau-Fang Yang
Abstract
A cancer registry is a critical and massive database for which various types of domain knowledge are needed and whose maintenance requires labor-intensive data curation. In order to facilitate the curation process for building a high-quality and integrated cancer registry database, we compiled a cross-hospital corpus and applied neural network methods to develop a natural language processing system for extracting cancer registry variables buried in unstructured pathology reports. The performance of the developed networks was compared with various baselines using standard micro-precision, recall and F-measure. Furthermore, we conducted experiments to study the feasibility of applying transfer learning to rapidly develop a well-performing system for processing reports from different sources that might be presented in different writing styles and formats. The results demonstrate that the transfer learning method enables us to develop a satisfactory system for a new hospital with only a few annotations and suggest more opportunities to reduce the burden of cancer registry curation.- Anthology ID:
- 2020.clinicalnlp-1.22
- Volume:
- Proceedings of the 3rd Clinical Natural Language Processing Workshop
- Month:
- November
- Year:
- 2020
- Address:
- Online
- Editors:
- Anna Rumshisky, Kirk Roberts, Steven Bethard, Tristan Naumann
- Venue:
- ClinicalNLP
- SIG:
- Publisher:
- Association for Computational Linguistics
- Note:
- Pages:
- 201–208
- Language:
- URL:
- https://aclanthology.org/2020.clinicalnlp-1.22
- DOI:
- 10.18653/v1/2020.clinicalnlp-1.22
- Cite (ACL):
- Yan-Jie Lin, Hong-Jie Dai, You-Chen Zhang, Chung-Yang Wu, Yu-Cheng Chang, Pin-Jou Lu, Chih-Jen Huang, Yu-Tsang Wang, Hui-Min Hsieh, Kun-San Chao, Tsang-Wu Liu, I-Shou Chang, Yi-Hsin Connie Yang, Ti-Hao Wang, Ko-Jiunn Liu, Li-Tzong Chen, and Sheau-Fang Yang. 2020. Cancer Registry Information Extraction via Transfer Learning. In Proceedings of the 3rd Clinical Natural Language Processing Workshop, pages 201–208, Online. Association for Computational Linguistics.
- Cite (Informal):
- Cancer Registry Information Extraction via Transfer Learning (Lin et al., ClinicalNLP 2020)
- PDF:
- https://preview.aclanthology.org/emnlp-22-attachments/2020.clinicalnlp-1.22.pdf