Automatic recognition of abdominal lymph nodes from clinical text
Yifan Peng, Sungwon Lee, Daniel C. Elton, Thomas Shen, Yu-xing Tang, Qingyu Chen, Shuai Wang, Yingying Zhu, Ronald Summers, Zhiyong Lu
Abstract
Lymph node status plays a pivotal role in the treatment of cancer. The extraction of lymph nodes from radiology text reports enables large-scale training of lymph node detection on MRI. In this work, we first propose an ontology of 41 types of abdominal lymph nodes with a hierarchical relationship. We then introduce an end-to-end approach based on the combination of rules and transformer-based methods to detect these abdominal lymph node mentions and classify their types from the MRI radiology reports. We demonstrate the superior performance of a model fine-tuned on MRI reports using BlueBERT, called MriBERT. We find that MriBERT outperforms the rule-based labeler (0.957 vs 0.644 in micro weighted F1-score) as well as other BERT-based variations (0.913 - 0.928). We make the code and MriBERT publicly available at https://github.com/ncbi-nlp/bluebert, with the hope that this method can facilitate the development of medical report annotators to produce labels from scratch at scale.- Anthology ID:
- 2020.clinicalnlp-1.12
- 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:
- 101–110
- Language:
- URL:
- https://aclanthology.org/2020.clinicalnlp-1.12
- DOI:
- 10.18653/v1/2020.clinicalnlp-1.12
- Cite (ACL):
- Yifan Peng, Sungwon Lee, Daniel C. Elton, Thomas Shen, Yu-xing Tang, Qingyu Chen, Shuai Wang, Yingying Zhu, Ronald Summers, and Zhiyong Lu. 2020. Automatic recognition of abdominal lymph nodes from clinical text. In Proceedings of the 3rd Clinical Natural Language Processing Workshop, pages 101–110, Online. Association for Computational Linguistics.
- Cite (Informal):
- Automatic recognition of abdominal lymph nodes from clinical text (Peng et al., ClinicalNLP 2020)
- PDF:
- https://preview.aclanthology.org/emnlp-22-attachments/2020.clinicalnlp-1.12.pdf
- Code
- ncbi-nlp/bluebert
- Data
- BLUE, CheXpert