EBST: An Evolutionary Multi-Objective Optimization Based Tool for Discovering Potential Biomarkers in Ovarian Cancer
| Autor: | Bashdar Mahmud Hussen, Esmaeil Babaei, Ali Emami, Hanif Yaghoobi |
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| Rok vydání: | 2020 |
| Předmět: |
Computer science
0206 medical engineering Data classification 02 engineering and technology Machine learning computer.software_genre Multi-objective optimization Machine Learning Genetics medicine Biomarkers Tumor Humans Cluster analysis Ovarian Neoplasms business.industry Applied Mathematics Imperialist competitive algorithm Computational Biology Cancer signaling medicine.disease body regions MicroRNAs Potential biomarkers embryonic structures Female Artificial intelligence Ovarian cancer business Transcriptome Classifier (UML) computer 020602 bioinformatics Algorithms Biotechnology |
| Zdroj: | IEEE/ACM transactions on computational biology and bioinformatics. 18(6) |
| ISSN: | 1557-9964 |
| Popis: | Ovarian cancer is the deadliest gynecologic malignancy, mainly due to limitations in early diagnosis. With advances in high-throughput technologies, research interest in identifying novel and customized tumor biomarkers for early detection and diagnosis is rapidly growing. Here we introduce a new tool called EBST to select microRNAs with biomarker potency in ovarian cancer. This tool has pre-processing options and Its core is the use of Modified Multi Objective Imperialist Competitive Algorithm and six objective functions based on the classifier performance/structure evaluation, clustering error and mRMR filter. In this paper, we used the FDR filter in the pre-processing stage and considered five objective functions, four of which relate to the l1-SVM classifier performance and one to the average mRMR ranking. The proposed method has identified 11 microRNAs including hsa-miR-6784-5p, hsa-miR-1228-5p, hsa-miR-8073, hsa-miR-6756-5p, hsa-miR-1307-3p, hsa-miR-4697-5p, hsa-miR-3663-3p, hsa-miR-328-5p, hsa-miR-1228-3p, hsa-miR-6821-5p, hsa-miR-1268a. Data classification by the proposed model showed 100% sensitivity, 99.38% specificity, 99.69% accuracy and 99.39% positive predictive value. In comparison with routine state-of-the-art methods, superiority of our method was confirmed. The biological evaluation of selected microRNAs using bioinformatics tools and published articles confirms their role in cancer signaling pathways. The tool and its MATLAB code are freely available at https://github.com/hanif-y. |
| Databáze: | OpenAIRE |
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