The utility of a deep learning-based approach in Her-2/neu assessment in breast cancer
<p>Introduction HER-2/neu is a protein present on the surface of specific cancer cells and has been linked to the development and progression of certain cancer types. It is present in 15 to 20% of breast cancers and is clinically significant due to the availability of multiple anti-Her2 treatm...
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2024
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| _version_ | 1864513532073082880 |
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| author | Saidul Kabir (15302407) |
| author2 | Semir Vranic (3353012) Rafif Mahmood Al Saady (17632263) Muhammad Salman Khan (17632266) Rusab Sarmun (17632269) Abdulrahman Alqahtani (6056309) Tariq O. Abbas (11247771) Muhammad E.H. Chowdhury (17151154) |
| author2_role | author author author author author author author |
| author_facet | Saidul Kabir (15302407) Semir Vranic (3353012) Rafif Mahmood Al Saady (17632263) Muhammad Salman Khan (17632266) Rusab Sarmun (17632269) Abdulrahman Alqahtani (6056309) Tariq O. Abbas (11247771) Muhammad E.H. Chowdhury (17151154) |
| author_role | author |
| dc.creator.none.fl_str_mv | Saidul Kabir (15302407) Semir Vranic (3353012) Rafif Mahmood Al Saady (17632263) Muhammad Salman Khan (17632266) Rusab Sarmun (17632269) Abdulrahman Alqahtani (6056309) Tariq O. Abbas (11247771) Muhammad E.H. Chowdhury (17151154) |
| dc.date.none.fl_str_mv | 2024-03-15T03:00:00Z |
| dc.identifier.none.fl_str_mv | 10.1016/j.eswa.2023.122051 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/journal_contribution/The_utility_of_a_deep_learning-based_approach_in_Her-2_neu_assessment_in_breast_cancer/24805239 |
| dc.rights.none.fl_str_mv | CC BY 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Biomedical and clinical sciences Clinical sciences Oncology and carcinogenesis Information and computing sciences Artificial intelligence Machine learning Her-2/neu Breast cancer Immunohistochemistry (IHC) Hematoxylin-eosin (H&E) Artificial intelligence Deep learning Classification |
| dc.title.none.fl_str_mv | The utility of a deep learning-based approach in Her-2/neu assessment in breast cancer |
| dc.type.none.fl_str_mv | Text Journal contribution info:eu-repo/semantics/publishedVersion text contribution to journal |
| description | <p>Introduction HER-2/neu is a protein present on the surface of specific cancer cells and has been linked to the development and progression of certain cancer types. It is present in 15 to 20% of breast cancers and is clinically significant due to the availability of multiple anti-Her2 treatment options. Immunohistochemistry (IHC) is the most commonly used method to evaluate and quantify the expression of Her-2/neu. Although IHC is well-standardized in clinical practice, it is still subjected to inter-observer variability. Automating Her-2/neu scoring can improve accuracy, efficiency, consistency, and cost-effectiveness while reducing pathologists' workload. Materials and Methods A deep learning-based automatic framework was utilized for the automatic detection of Her-2/neu score from whole slide images (WSI). The framework consists of three phases: identification of tumor patches, scoring of tumor patches, and Her-2/neu score prediction for whole slide images (WSI) based on the distribution of each score. This work used the dataset from the University of Warwick HER2 challenge contest. Two expert pathologists evaluated all 86 WSIs and assigned Her-2/neu scores to them. In addition, patches were generated from 50 WSIs and annotated individually by the pathologists. A total of 6641 extracted patches were generated out of which, 947 were labeled as 0, 327 as 1+, 1401 as 2+, 2950 as 3+, and 1016 were marked for discarding. Four pre-trained image classification models, namely DenseNet201, GoogleNet, MobileNet_v2, and a Vision Transformer based model, were fine-tuned, and tested on the generated patches. In order to predict the Her-2/neu score of the entire WSI, a random forest classifier was trained to predict the Her-2/neu score from the percentages of patches of each score present in the whole slide image. Results In patch classification performances, the vision transformer-based model outperformed the other models by achieving an accuracy of 92.6% on tumor patch classification and 91.15% on patch score classification. The random forest classifier achieved an accuracy of 88% on four score classification (0, 1+, 2 + and 3 + ) and 96% on three score classification (0/1+, 2 + and 3 + ). Conclusion The proposed deep learning-based framework for the automatic detection and evaluation of Her-2/neu expression in breast cancer obtained encouraging results. This framework has the potential to be used as a prognostic tool, providing a cost-effective and time-efficient alternative for generating clinically relevant results. However, additional research is required to assess the applicability of this pipeline in different contexts.</p><h2>Other Information</h2> <p> Published in: Expert Systems with Applications<br> License: <a href="http://creativecommons.org/licenses/by/4.0/" target="_blank">http://creativecommons.org/licenses/by/4.0/</a><br>See article on publisher's website: <a href="https://dx.doi.org/10.1016/j.eswa.2023.122051" target="_blank">https://dx.doi.org/10.1016/j.eswa.2023.122051</a></p> |
| eu_rights_str_mv | openAccess |
| id | Manara2_ed6c1c5b8d74c569c9db5cc6fa7bd69a |
| identifier_str_mv | 10.1016/j.eswa.2023.122051 |
| network_acronym_str | Manara2 |
| network_name_str | Manara2 |
| oai_identifier_str | oai:figshare.com:article/24805239 |
| publishDate | 2024 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | The utility of a deep learning-based approach in Her-2/neu assessment in breast cancerSaidul Kabir (15302407)Semir Vranic (3353012)Rafif Mahmood Al Saady (17632263)Muhammad Salman Khan (17632266)Rusab Sarmun (17632269)Abdulrahman Alqahtani (6056309)Tariq O. Abbas (11247771)Muhammad E.H. Chowdhury (17151154)Biomedical and clinical sciencesClinical sciencesOncology and carcinogenesisInformation and computing sciencesArtificial intelligenceMachine learningHer-2/neuBreast cancerImmunohistochemistry (IHC)Hematoxylin-eosin (H&E)Artificial intelligenceDeep learningClassification<p>Introduction HER-2/neu is a protein present on the surface of specific cancer cells and has been linked to the development and progression of certain cancer types. It is present in 15 to 20% of breast cancers and is clinically significant due to the availability of multiple anti-Her2 treatment options. Immunohistochemistry (IHC) is the most commonly used method to evaluate and quantify the expression of Her-2/neu. Although IHC is well-standardized in clinical practice, it is still subjected to inter-observer variability. Automating Her-2/neu scoring can improve accuracy, efficiency, consistency, and cost-effectiveness while reducing pathologists' workload. Materials and Methods A deep learning-based automatic framework was utilized for the automatic detection of Her-2/neu score from whole slide images (WSI). The framework consists of three phases: identification of tumor patches, scoring of tumor patches, and Her-2/neu score prediction for whole slide images (WSI) based on the distribution of each score. This work used the dataset from the University of Warwick HER2 challenge contest. Two expert pathologists evaluated all 86 WSIs and assigned Her-2/neu scores to them. In addition, patches were generated from 50 WSIs and annotated individually by the pathologists. A total of 6641 extracted patches were generated out of which, 947 were labeled as 0, 327 as 1+, 1401 as 2+, 2950 as 3+, and 1016 were marked for discarding. Four pre-trained image classification models, namely DenseNet201, GoogleNet, MobileNet_v2, and a Vision Transformer based model, were fine-tuned, and tested on the generated patches. In order to predict the Her-2/neu score of the entire WSI, a random forest classifier was trained to predict the Her-2/neu score from the percentages of patches of each score present in the whole slide image. Results In patch classification performances, the vision transformer-based model outperformed the other models by achieving an accuracy of 92.6% on tumor patch classification and 91.15% on patch score classification. The random forest classifier achieved an accuracy of 88% on four score classification (0, 1+, 2 + and 3 + ) and 96% on three score classification (0/1+, 2 + and 3 + ). Conclusion The proposed deep learning-based framework for the automatic detection and evaluation of Her-2/neu expression in breast cancer obtained encouraging results. This framework has the potential to be used as a prognostic tool, providing a cost-effective and time-efficient alternative for generating clinically relevant results. However, additional research is required to assess the applicability of this pipeline in different contexts.</p><h2>Other Information</h2> <p> Published in: Expert Systems with Applications<br> License: <a href="http://creativecommons.org/licenses/by/4.0/" target="_blank">http://creativecommons.org/licenses/by/4.0/</a><br>See article on publisher's website: <a href="https://dx.doi.org/10.1016/j.eswa.2023.122051" target="_blank">https://dx.doi.org/10.1016/j.eswa.2023.122051</a></p>2024-03-15T03:00:00ZTextJournal contributioninfo:eu-repo/semantics/publishedVersiontextcontribution to journal10.1016/j.eswa.2023.122051https://figshare.com/articles/journal_contribution/The_utility_of_a_deep_learning-based_approach_in_Her-2_neu_assessment_in_breast_cancer/24805239CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/248052392024-03-15T03:00:00Z |
| spellingShingle | The utility of a deep learning-based approach in Her-2/neu assessment in breast cancer Saidul Kabir (15302407) Biomedical and clinical sciences Clinical sciences Oncology and carcinogenesis Information and computing sciences Artificial intelligence Machine learning Her-2/neu Breast cancer Immunohistochemistry (IHC) Hematoxylin-eosin (H&E) Artificial intelligence Deep learning Classification |
| status_str | publishedVersion |
| title | The utility of a deep learning-based approach in Her-2/neu assessment in breast cancer |
| title_full | The utility of a deep learning-based approach in Her-2/neu assessment in breast cancer |
| title_fullStr | The utility of a deep learning-based approach in Her-2/neu assessment in breast cancer |
| title_full_unstemmed | The utility of a deep learning-based approach in Her-2/neu assessment in breast cancer |
| title_short | The utility of a deep learning-based approach in Her-2/neu assessment in breast cancer |
| title_sort | The utility of a deep learning-based approach in Her-2/neu assessment in breast cancer |
| topic | Biomedical and clinical sciences Clinical sciences Oncology and carcinogenesis Information and computing sciences Artificial intelligence Machine learning Her-2/neu Breast cancer Immunohistochemistry (IHC) Hematoxylin-eosin (H&E) Artificial intelligence Deep learning Classification |