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Updated: May 27, 2025
A Metadata Extraction Approach for Clinical Case Reports to Enable Advanced Understanding of Biomedical Concepts
Published on: September 20, 2018
Leveraging natural language processing for efficient information extraction from breast cancer pathology reports:
Phillip Park1,2, Yeonho Choi2, Nayoung Han3
1Department of Digital Health, Samsung Advanced Institute for Health Sciences and Technology, Sung Kyun Kwan University, Seoul, Korea.
Background:
Pathology reports provide important information for accurate diagnosis of cancer and optimal treatment decision making. In particular, breast cancer has known to be the most common cancer in women worldwide.
Objective:
For the data extraction of breast cancer pathology reports in a single institute, we assessed the accuracy of methods between regular expression and natural language processing (NLP).
Methods:
A total of 1,215 breast cancer pathology reports were annotated for NLP model development. As NLP models, we considered three BERT models with specific vocabularies including BERT-basic, BioBERT, and ClinicalBERT. K-fold cross-validation was used to verify the performance of the BERT model. The results between the regular expression and the BERT model were compared using the named entity recognition (NER) techniques.
Results:
Among three BERT models, BioBERT was the most accurate parsing model (average performance = 0.99901) for breast cancer pathology when set to k = 5. BioBERT also had the lowest error rate for all items in the breast cancer pathology report compared to other BERT models (accuracy for all variables ≥ 0.9). Therefore, we finally selected BioBERT as the NLP model. When comparing the results of BioBERT and regular expressions using NER, we identified that BioBERT was more accurate than regular expression method, especially for some items such as intraductal component (BioBERT: 1.0, RegEx: 0.1644), lymph node (BioBERT: 0.9886, RegEx: 0.4792), and lymphovascular invasion (BioBERT: 0.9918, RegEx: 0.3759).
Conclusions:
Our results showed that the NLP model, BioBERT, had higher accuracy than regular expression, suggesting the importance of BioBERT in the processing of breast cancer pathology reports.
