A Novel Corpus of Annotated Medical Imaging Reports and Information Extraction Results Using BERT-based Language Models

Namu Park, Kevin Lybarger, Giridhar Kaushik Ramachandran, Spencer Lewis, Aashka Damani, Özlem Uzuner, Martin Gunn, Meliha Yetisgen


Abstract
Medical imaging is critical to the diagnosis, surveillance, and treatment of many health conditions, including oncological, neurological, cardiovascular, and musculoskeletal disorders, among others. Radiologists interpret these complex, unstructured images and articulate their assessments through narrative reports that remain largely unstructured. This unstructured narrative must be converted into a structured semantic representation to facilitate secondary applications such as retrospective analyses or clinical decision support. Here, we introduce the Corpus of Annotated Medical Imaging Reports (CAMIR), which includes 609 annotated radiology reports from three imaging modality types: Computed Tomography, Magnetic Resonance Imaging, and Positron Emission Tomography-Computed Tomography. Reports were annotated using an event-based schema that captures clinical indications, lesions, and medical problems. Each event consists of a trigger and multiple arguments, and a majority of the argument types, including anatomy, normalize the spans to pre-defined concepts to facilitate secondary use. CAMIR uniquely combines a granular event structure and concept normalization. To extract CAMIR events, we explored two BERT (Bi-directional Encoder Representation from Transformers)-based architectures, including an existing architecture (mSpERT) that jointly extracts all event information and a multi-step approach (PL-Marker++) that we augmented for the CAMIR schema.
Anthology ID:
2024.lrec-main.115
Volume:
Proceedings of the 2024 Joint International Conference on Computational Linguistics, Language Resources and Evaluation (LREC-COLING 2024)
Month:
May
Year:
2024
Address:
Torino, Italia
Editors:
Nicoletta Calzolari, Min-Yen Kan, Veronique Hoste, Alessandro Lenci, Sakriani Sakti, Nianwen Xue
Venues:
LREC | COLING
SIG:
Publisher:
ELRA and ICCL
Note:
Pages:
1280–1292
Language:
URL:
https://aclanthology.org/2024.lrec-main.115
DOI:
Bibkey:
Cite (ACL):
Namu Park, Kevin Lybarger, Giridhar Kaushik Ramachandran, Spencer Lewis, Aashka Damani, Özlem Uzuner, Martin Gunn, and Meliha Yetisgen. 2024. A Novel Corpus of Annotated Medical Imaging Reports and Information Extraction Results Using BERT-based Language Models. In Proceedings of the 2024 Joint International Conference on Computational Linguistics, Language Resources and Evaluation (LREC-COLING 2024), pages 1280–1292, Torino, Italia. ELRA and ICCL.
Cite (Informal):
A Novel Corpus of Annotated Medical Imaging Reports and Information Extraction Results Using BERT-based Language Models (Park et al., LREC-COLING 2024)
Copy Citation:
PDF:
https://aclanthology.org/2024.lrec-main.115.pdf