A bio-inspired convolution neural network architecture for automatic breast cancer detection and classification using RNA-Seq gene expression data
Abstract Breast cancer is considered one of the significant health challenges and ranks among the most prevalent and dangerous cancer types affecting women globally. Early breast cancer detection and diagnosis are crucial for effective treatment and personalized therapy. Early detection and diagnosi...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-09-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-41731-z |
| _version_ | 1797576924964323328 |
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| author | Tehnan I. A. Mohamed Absalom E. Ezugwu Jean Vincent Fonou-Dombeu Abiodun M. Ikotun Mohanad Mohammed |
| author_facet | Tehnan I. A. Mohamed Absalom E. Ezugwu Jean Vincent Fonou-Dombeu Abiodun M. Ikotun Mohanad Mohammed |
| author_sort | Tehnan I. A. Mohamed |
| collection | DOAJ |
| description | Abstract Breast cancer is considered one of the significant health challenges and ranks among the most prevalent and dangerous cancer types affecting women globally. Early breast cancer detection and diagnosis are crucial for effective treatment and personalized therapy. Early detection and diagnosis can help patients and physicians discover new treatment options, provide a more suitable quality of life, and ensure increased survival rates. Breast cancer detection using gene expression involves many complexities, such as the issue of dimensionality and the complicatedness of the gene expression data. This paper proposes a bio-inspired CNN model for breast cancer detection using gene expression data downloaded from the cancer genome atlas (TCGA). The data contains 1208 clinical samples of 19,948 genes with 113 normal and 1095 cancerous samples. In the proposed model, Array-Array Intensity Correlation (AAIC) is used at the pre-processing stage for outlier removal, followed by a normalization process to avoid biases in the expression measures. Filtration is used for gene reduction using a threshold value of 0.25. Thereafter the pre-processed gene expression dataset was converted into images which were later converted to grayscale to meet the requirements of the model. The model also uses a hybrid model of CNN architecture with a metaheuristic algorithm, namely the Ebola Optimization Search Algorithm (EOSA), to enhance the detection of breast cancer. The traditional CNN and five hybrid algorithms were compared with the classification result of the proposed model. The competing hybrid algorithms include the Whale Optimization Algorithm (WOA-CNN), the Genetic Algorithm (GA-CNN), the Satin Bowerbird Optimization (SBO-CNN), the Life Choice-Based Optimization (LCBO-CNN), and the Multi-Verse Optimizer (MVO-CNN). The results show that the proposed model determined the classes with high-performance measurements with an accuracy of 98.3%, a precision of 99%, a recall of 99%, an f1-score of 99%, a kappa of 90.3%, a specificity of 92.8%, and a sensitivity of 98.9% for the cancerous class. The results suggest that the proposed method has the potential to be a reliable and precise approach to breast cancer detection, which is crucial for early diagnosis and personalized therapy. |
| first_indexed | 2024-03-10T22:01:43Z |
| format | Article |
| id | doaj.art-be337eb958634bfb8e11b1cc6fc0792b |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-03-10T22:01:43Z |
| publishDate | 2023-09-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-be337eb958634bfb8e11b1cc6fc0792b2023-11-19T12:57:18ZengNature PortfolioScientific Reports2045-23222023-09-0113111910.1038/s41598-023-41731-zA bio-inspired convolution neural network architecture for automatic breast cancer detection and classification using RNA-Seq gene expression dataTehnan I. A. Mohamed0Absalom E. Ezugwu1Jean Vincent Fonou-Dombeu2Abiodun M. Ikotun3Mohanad Mohammed4School of Mathematics, Statistics, and Computer Science, University of KwaZulu-NatalUnit for Data Science and Computing, North-West UniversitySchool of Mathematics, Statistics, and Computer Science, University of KwaZulu-NatalSchool of Mathematics, Statistics, and Computer Science, University of KwaZulu-NatalSchool of Mathematics, Statistics, and Computer Science, University of KwaZulu-NatalAbstract Breast cancer is considered one of the significant health challenges and ranks among the most prevalent and dangerous cancer types affecting women globally. Early breast cancer detection and diagnosis are crucial for effective treatment and personalized therapy. Early detection and diagnosis can help patients and physicians discover new treatment options, provide a more suitable quality of life, and ensure increased survival rates. Breast cancer detection using gene expression involves many complexities, such as the issue of dimensionality and the complicatedness of the gene expression data. This paper proposes a bio-inspired CNN model for breast cancer detection using gene expression data downloaded from the cancer genome atlas (TCGA). The data contains 1208 clinical samples of 19,948 genes with 113 normal and 1095 cancerous samples. In the proposed model, Array-Array Intensity Correlation (AAIC) is used at the pre-processing stage for outlier removal, followed by a normalization process to avoid biases in the expression measures. Filtration is used for gene reduction using a threshold value of 0.25. Thereafter the pre-processed gene expression dataset was converted into images which were later converted to grayscale to meet the requirements of the model. The model also uses a hybrid model of CNN architecture with a metaheuristic algorithm, namely the Ebola Optimization Search Algorithm (EOSA), to enhance the detection of breast cancer. The traditional CNN and five hybrid algorithms were compared with the classification result of the proposed model. The competing hybrid algorithms include the Whale Optimization Algorithm (WOA-CNN), the Genetic Algorithm (GA-CNN), the Satin Bowerbird Optimization (SBO-CNN), the Life Choice-Based Optimization (LCBO-CNN), and the Multi-Verse Optimizer (MVO-CNN). The results show that the proposed model determined the classes with high-performance measurements with an accuracy of 98.3%, a precision of 99%, a recall of 99%, an f1-score of 99%, a kappa of 90.3%, a specificity of 92.8%, and a sensitivity of 98.9% for the cancerous class. The results suggest that the proposed method has the potential to be a reliable and precise approach to breast cancer detection, which is crucial for early diagnosis and personalized therapy.https://doi.org/10.1038/s41598-023-41731-z |
| spellingShingle | Tehnan I. A. Mohamed Absalom E. Ezugwu Jean Vincent Fonou-Dombeu Abiodun M. Ikotun Mohanad Mohammed A bio-inspired convolution neural network architecture for automatic breast cancer detection and classification using RNA-Seq gene expression data Scientific Reports |
| title | A bio-inspired convolution neural network architecture for automatic breast cancer detection and classification using RNA-Seq gene expression data |
| title_full | A bio-inspired convolution neural network architecture for automatic breast cancer detection and classification using RNA-Seq gene expression data |
| title_fullStr | A bio-inspired convolution neural network architecture for automatic breast cancer detection and classification using RNA-Seq gene expression data |
| title_full_unstemmed | A bio-inspired convolution neural network architecture for automatic breast cancer detection and classification using RNA-Seq gene expression data |
| title_short | A bio-inspired convolution neural network architecture for automatic breast cancer detection and classification using RNA-Seq gene expression data |
| title_sort | bio inspired convolution neural network architecture for automatic breast cancer detection and classification using rna seq gene expression data |
| url | https://doi.org/10.1038/s41598-023-41731-z |
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