Adapting Abstract Meaning Representation Parsing to the Clinical Narrative – the SPRING THYME parser
Jon Cai, Kristin Wright-Bettner, Martha Palmer, Guergana Savova, James Martin
Abstract
This paper is dedicated to the design and evaluation of the first AMR parser tailored for clinical notes. Our objective was to facilitate the precise transformation of the clinical notes into structured AMR expressions, thereby enhancing the interpretability and usability of clinical text data at scale. Leveraging the colon cancer dataset from the Temporal Histories of Your Medical Events (THYME) corpus, we adapted a state-of-the-art AMR parser utilizing continuous training. Our approach incorporates data augmentation techniques to enhance the accuracy of AMR structure predictions. Notably, through this learning strategy, our parser achieved an impressive F1 score of 88% on the THYME corpus’s colon cancer dataset. Moreover, our research delved into the efficacy of data required for domain adaptation within the realm of clinical notes, presenting domain adaptation data requirements for AMR parsing. This exploration not only underscores the parser’s robust performance but also highlights its potential in facilitating a deeper understanding of clinical narratives through structured semantic representations.- Anthology ID:
- 2024.clinicalnlp-1.23
- Volume:
- Proceedings of the 6th Clinical Natural Language Processing Workshop
- Month:
- June
- Year:
- 2024
- Address:
- Mexico City, Mexico
- Editors:
- Tristan Naumann, Asma Ben Abacha, Steven Bethard, Kirk Roberts, Danielle Bitterman
- Venues:
- ClinicalNLP | WS
- SIG:
- Publisher:
- Association for Computational Linguistics
- Note:
- Pages:
- 271–282
- Language:
- URL:
- https://aclanthology.org/2024.clinicalnlp-1.23
- DOI:
- Cite (ACL):
- Jon Cai, Kristin Wright-Bettner, Martha Palmer, Guergana Savova, and James Martin. 2024. Adapting Abstract Meaning Representation Parsing to the Clinical Narrative – the SPRING THYME parser. In Proceedings of the 6th Clinical Natural Language Processing Workshop, pages 271–282, Mexico City, Mexico. Association for Computational Linguistics.
- Cite (Informal):
- Adapting Abstract Meaning Representation Parsing to the Clinical Narrative – the SPRING THYME parser (Cai et al., ClinicalNLP-WS 2024)
- PDF:
- https://preview.aclanthology.org/jeptaln-2024-ingestion/2024.clinicalnlp-1.23.pdf