Biomarker detection using corrected degree of domesticity in hybrid social network feature selection for improving classifier performance

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BMC Bioinformatics, vol.24, no.1, 2023 (SCI-Expanded) identifier identifier

  • Publication Type: Article / Article
  • Volume: 24 Issue: 1
  • Publication Date: 2023
  • Doi Number: 10.1186/s12859-023-05540-5
  • Journal Name: BMC Bioinformatics
  • Journal Indexes: Science Citation Index Expanded (SCI-EXPANDED), Scopus, Academic Search Premier, BIOSIS, Biotechnology Research Abstracts, Compendex, EMBASE, INSPEC, MEDLINE, Veterinary Science Database, Directory of Open Access Journals
  • Keywords: Biomarkers, Classification, Dimension reduction, Genomics, R genomics, Social network feature selection
  • Hacettepe University Affiliated: Yes


Background: Dimension reduction, especially feature selection, is an important step in improving classification performance for high-dimensional data. Particularly in cancer research, when reducing the number of features, i.e., genes, it is important to select the most informative features/potential biomarkers that could affect the diagnostic accuracy. Therefore, researchers continuously try to explore more efficient ways to reduce the large number of features/genes to a small but informative subset before the classification task. Hybrid methods have been extensively investigated for this purpose, and research to find the optimal approach is ongoing. Social network analysis is used as a part of a hybrid method, although there are several issues that have arisen when using social network tools, such as using a single environment for computing, constructing an adjacency matrix or computing network measures. Therefore, in our study, we apply a hybrid feature selection method consisting of several machine learning algorithms in addition to social network analysis with our proposed network metric, called the corrected degree of domesticity, in a single environment, R, to improve the support vector machine classifier’s performance. In addition, we evaluate and compare the performances of several combinations used in the different steps of the method with a simulation experiment. Results: The proposed method improves the classifier’s performance compared to using the whole feature set in all the cases we investigate. Additionally, in terms of the area under the receiver operating characteristic (ROC) curve, our approach improves classification performance compared to several approaches in the literature. Conclusion: When using the corrected degree of domesticity as a network degree centrality measure, it is important to use our correction to compare nodes/features with no connection outside of their community since it provides a more accurate ranking among the features. Due to the nature of the hybrid method, which includes social network analysis, it is necessary to investigate possible combinations to provide an optimal solution for the microarray data used in the research.