Regulatory Genes Through Robust-SNR for Binary Classification Within Functional Genomics Experiments

Muhammad Hamraz, Dost Muhammad Khan, Naz Gul, Amjad Ali, Zardad Khan, Shafiq Ahmad, Mejdal Alqahtani, Akber Abid Gardezi, Muhammad Shafiq

Research output: Contribution to journalArticlepeer-review

3 Citations (Scopus)

Abstract

The current study proposes a novel technique for feature selection by inculcating robustness in the conventional Signal to noise Ratio (SNR). The proposed method utilizes the robust measures of location i.e., the “Median” as well as the measures of variation i.e., “Median absolute deviation (MAD) and Interquartile range (IQR)” in the SNR. By this way, two independent robust signal-to-noise ratios have been proposed. The proposed method selects the most informative genes/features by combining the minimum subset of genes or features obtained via the greedy search approach with top-ranked genes selected through the robust signal-to-noise ratio (RSNR). The results obtained via the proposed method are compared with well-known gene/feature selection methods on the basis of performance metric i.e., classification error rate. A total of 5 gene expression datasets have been used in this study. Different subsets of informative genes are selected by the proposed and all the other methods included in the study, and their efficacy in terms of classification is investigated by using the classifier models such as support vector machine (SVM), Random forest (RF) and k-nearest neighbors (k-NN). The results of the analysis reveal that the proposed method (RSNR) produces minimum error rates than all the other competing feature selection methods in majority of the cases. For further assessment of the method, a detailed simulation study is also conducted.

Original languageEnglish
Pages (from-to)3663-3677
Number of pages15
JournalComputers, Materials and Continua
Volume74
Issue number2
DOIs
Publication statusPublished - 2023
Externally publishedYes

Keywords

  • classification
  • feature selection
  • high dimensional gene expression datasets
  • Median absolute deviation (MAD)
  • signal to noise ratio

ASJC Scopus subject areas

  • Biomaterials
  • Modelling and Simulation
  • Mechanics of Materials
  • Computer Science Applications
  • Electrical and Electronic Engineering

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