A Stack-based Ensemble Framework for Detecting Cancer MicroRNA Biomarkers
MicroRNA (miRNA) plays vital roles in biological processes like RNA splicing and regulation of gene expression. Studies have revealed that there might be possible links between oncogenesis and expression profiles of some miRNAs, due to their differential expression between normal and tumor tissues....
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Oxford University Press
2017-12-01
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| Series: | Genomics, Proteomics & Bioinformatics |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S1672022917301705 |
| _version_ | 1827158735181578240 |
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| author | Sriparna Saha Sayantan Mitra Ravi Kant Yadav |
| author_facet | Sriparna Saha Sayantan Mitra Ravi Kant Yadav |
| author_sort | Sriparna Saha |
| collection | DOAJ |
| description | MicroRNA (miRNA) plays vital roles in biological processes like RNA splicing and regulation of gene expression. Studies have revealed that there might be possible links between oncogenesis and expression profiles of some miRNAs, due to their differential expression between normal and tumor tissues. However, the automatic classification of miRNAs into different categories by considering the similarity of their expression values has rarely been addressed. This article proposes a solution framework for solving some real-life classification problems related to cancer, miRNA, and mRNA expression datasets. In the first stage, a multiobjective optimization based framework, non-dominated sorting genetic algorithm II, is proposed to automatically determine the appropriate classifier type, along with its suitable parameter and feature combinations, pertinent for classifying a given dataset. In the second page, a stack-based ensemble technique is employed to get a single combinatorial solution from the set of solutions obtained in the first stage. The performance of the proposed two-stage approach is evaluated on several cancer and RNA expression profile datasets. Compared to several state-of-the-art approaches for classifying different datasets, our method shows supremacy in the accuracy of classification. |
| first_indexed | 2024-03-08T17:51:34Z |
| format | Article |
| id | doaj.art-e81db9159407445e8c7d9f8f3339b8e0 |
| institution | Directory Open Access Journal |
| issn | 1672-0229 |
| language | English |
| last_indexed | 2025-03-20T23:45:57Z |
| publishDate | 2017-12-01 |
| publisher | Oxford University Press |
| record_format | Article |
| series | Genomics, Proteomics & Bioinformatics |
| spelling | doaj.art-e81db9159407445e8c7d9f8f3339b8e02024-08-03T12:47:41ZengOxford University PressGenomics, Proteomics & Bioinformatics1672-02292017-12-0115638138810.1016/j.gpb.2016.10.006A Stack-based Ensemble Framework for Detecting Cancer MicroRNA BiomarkersSriparna SahaSayantan MitraRavi Kant YadavMicroRNA (miRNA) plays vital roles in biological processes like RNA splicing and regulation of gene expression. Studies have revealed that there might be possible links between oncogenesis and expression profiles of some miRNAs, due to their differential expression between normal and tumor tissues. However, the automatic classification of miRNAs into different categories by considering the similarity of their expression values has rarely been addressed. This article proposes a solution framework for solving some real-life classification problems related to cancer, miRNA, and mRNA expression datasets. In the first stage, a multiobjective optimization based framework, non-dominated sorting genetic algorithm II, is proposed to automatically determine the appropriate classifier type, along with its suitable parameter and feature combinations, pertinent for classifying a given dataset. In the second page, a stack-based ensemble technique is employed to get a single combinatorial solution from the set of solutions obtained in the first stage. The performance of the proposed two-stage approach is evaluated on several cancer and RNA expression profile datasets. Compared to several state-of-the-art approaches for classifying different datasets, our method shows supremacy in the accuracy of classification.http://www.sciencedirect.com/science/article/pii/S1672022917301705Sequential minimal optimizerNon-dominated sorting genetic algorithmMultiobjective optimizationMicroRNA |
| spellingShingle | Sriparna Saha Sayantan Mitra Ravi Kant Yadav A Stack-based Ensemble Framework for Detecting Cancer MicroRNA Biomarkers Genomics, Proteomics & Bioinformatics Sequential minimal optimizer Non-dominated sorting genetic algorithm Multiobjective optimization MicroRNA |
| title | A Stack-based Ensemble Framework for Detecting Cancer MicroRNA Biomarkers |
| title_full | A Stack-based Ensemble Framework for Detecting Cancer MicroRNA Biomarkers |
| title_fullStr | A Stack-based Ensemble Framework for Detecting Cancer MicroRNA Biomarkers |
| title_full_unstemmed | A Stack-based Ensemble Framework for Detecting Cancer MicroRNA Biomarkers |
| title_short | A Stack-based Ensemble Framework for Detecting Cancer MicroRNA Biomarkers |
| title_sort | stack based ensemble framework for detecting cancer microrna biomarkers |
| topic | Sequential minimal optimizer Non-dominated sorting genetic algorithm Multiobjective optimization MicroRNA |
| url | http://www.sciencedirect.com/science/article/pii/S1672022917301705 |
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