Leveraging natural language processing for efficient information extraction from breast cancer pathology reports: Single-institution study.
<h4>Background</h4>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.<h4>Objective</h4>For the data extraction of breas...
Saved in:
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2025-01-01
|
| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0318726 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849323353923387392 |
|---|---|
| author | Phillip Park Yeonho Choi Nayoung Han Ye-Lin Park Juyeon Hwang Heejung Chae Chong Woo Yoo Kui Son Choi Hyun-Jin Kim |
| author_facet | Phillip Park Yeonho Choi Nayoung Han Ye-Lin Park Juyeon Hwang Heejung Chae Chong Woo Yoo Kui Son Choi Hyun-Jin Kim |
| author_sort | Phillip Park |
| collection | DOAJ |
| description | <h4>Background</h4>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.<h4>Objective</h4>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).<h4>Methods</h4>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.<h4>Results</h4>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).<h4>Conclusions</h4>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. |
| format | Article |
| id | doaj-art-e78be3a4002b4a74976f32debea09841 |
| institution | Kabale University |
| issn | 1932-6203 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj-art-e78be3a4002b4a74976f32debea098412025-08-20T03:49:03ZengPublic Library of Science (PLoS)PLoS ONE1932-62032025-01-01202e031872610.1371/journal.pone.0318726Leveraging natural language processing for efficient information extraction from breast cancer pathology reports: Single-institution study.Phillip ParkYeonho ChoiNayoung HanYe-Lin ParkJuyeon HwangHeejung ChaeChong Woo YooKui Son ChoiHyun-Jin Kim<h4>Background</h4>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.<h4>Objective</h4>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).<h4>Methods</h4>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.<h4>Results</h4>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).<h4>Conclusions</h4>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.https://doi.org/10.1371/journal.pone.0318726 |
| spellingShingle | Phillip Park Yeonho Choi Nayoung Han Ye-Lin Park Juyeon Hwang Heejung Chae Chong Woo Yoo Kui Son Choi Hyun-Jin Kim Leveraging natural language processing for efficient information extraction from breast cancer pathology reports: Single-institution study. PLoS ONE |
| title | Leveraging natural language processing for efficient information extraction from breast cancer pathology reports: Single-institution study. |
| title_full | Leveraging natural language processing for efficient information extraction from breast cancer pathology reports: Single-institution study. |
| title_fullStr | Leveraging natural language processing for efficient information extraction from breast cancer pathology reports: Single-institution study. |
| title_full_unstemmed | Leveraging natural language processing for efficient information extraction from breast cancer pathology reports: Single-institution study. |
| title_short | Leveraging natural language processing for efficient information extraction from breast cancer pathology reports: Single-institution study. |
| title_sort | leveraging natural language processing for efficient information extraction from breast cancer pathology reports single institution study |
| url | https://doi.org/10.1371/journal.pone.0318726 |
| work_keys_str_mv | AT phillippark leveragingnaturallanguageprocessingforefficientinformationextractionfrombreastcancerpathologyreportssingleinstitutionstudy AT yeonhochoi leveragingnaturallanguageprocessingforefficientinformationextractionfrombreastcancerpathologyreportssingleinstitutionstudy AT nayounghan leveragingnaturallanguageprocessingforefficientinformationextractionfrombreastcancerpathologyreportssingleinstitutionstudy AT yelinpark leveragingnaturallanguageprocessingforefficientinformationextractionfrombreastcancerpathologyreportssingleinstitutionstudy AT juyeonhwang leveragingnaturallanguageprocessingforefficientinformationextractionfrombreastcancerpathologyreportssingleinstitutionstudy AT heejungchae leveragingnaturallanguageprocessingforefficientinformationextractionfrombreastcancerpathologyreportssingleinstitutionstudy AT chongwooyoo leveragingnaturallanguageprocessingforefficientinformationextractionfrombreastcancerpathologyreportssingleinstitutionstudy AT kuisonchoi leveragingnaturallanguageprocessingforefficientinformationextractionfrombreastcancerpathologyreportssingleinstitutionstudy AT hyunjinkim leveragingnaturallanguageprocessingforefficientinformationextractionfrombreastcancerpathologyreportssingleinstitutionstudy |