Skip to main content

2020 | OriginalPaper | Buchkapitel

Performance Evaluation of ANOVA and RFE Algorithms for Classifying Microarray Dataset Using SVM

verfasst von : Sulaiman Olaniyi Abdulsalam, Abubakar Adamu Mohammed, Jumoke Falilat Ajao, Ronke S. Babatunde, Roseline Oluwaseun Ogundokun, Chiebuka T. Nnodim, Micheal Olaolu Arowolo

Erschienen in: Information Systems

Verlag: Springer International Publishing

Aktivieren Sie unsere intelligente Suche, um passende Fachinhalte oder Patente zu finden.

search-config
loading …

Abstract

A significant application of microarray gene expression data is the classification and prediction of biological models. An essential component of data analysis is dimension reduction. This study presents a comparison study on a reduced data using Analysis of Variance (ANOVA) and Recursive Feature Elimination (RFE) feature selection dimension reduction techniques, and evaluates the relative performance evaluation of classification procedures of Support Vector Machine (SVM) classification technique. In this study, an accuracy and computational performance metrics of the processes were carried out on a microarray colon cancer dataset for classification, SVM-RFE achieved 93% compared to ANOVA with 87% accuracy in the classification output result.

Sie haben noch keine Lizenz? Dann Informieren Sie sich jetzt über unsere Produkte:

Springer Professional "Wirtschaft+Technik"

Online-Abonnement

Mit Springer Professional "Wirtschaft+Technik" erhalten Sie Zugriff auf:

  • über 102.000 Bücher
  • über 537 Zeitschriften

aus folgenden Fachgebieten:

  • Automobil + Motoren
  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Elektrotechnik + Elektronik
  • Energie + Nachhaltigkeit
  • Finance + Banking
  • Management + Führung
  • Marketing + Vertrieb
  • Maschinenbau + Werkstoffe
  • Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

Springer Professional "Technik"

Online-Abonnement

Mit Springer Professional "Technik" erhalten Sie Zugriff auf:

  • über 67.000 Bücher
  • über 390 Zeitschriften

aus folgenden Fachgebieten:

  • Automobil + Motoren
  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Elektrotechnik + Elektronik
  • Energie + Nachhaltigkeit
  • Maschinenbau + Werkstoffe




 

Jetzt Wissensvorsprung sichern!

Springer Professional "Wirtschaft"

Online-Abonnement

Mit Springer Professional "Wirtschaft" erhalten Sie Zugriff auf:

  • über 67.000 Bücher
  • über 340 Zeitschriften

aus folgenden Fachgebieten:

  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Finance + Banking
  • Management + Führung
  • Marketing + Vertrieb
  • Versicherung + Risiko




Jetzt Wissensvorsprung sichern!

Literatur
3.
Zurück zum Zitat Levin, J.Z., et al.: Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat. Methods 7, 709–715 (2010)CrossRef Levin, J.Z., et al.: Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat. Methods 7, 709–715 (2010)CrossRef
4.
Zurück zum Zitat Pierson, E., Yau, C.: ZIFA: dimensionality reduction for zero-inflated single-cell gene expression analysis. Genome Biol. 16, 241–257 (2015)CrossRef Pierson, E., Yau, C.: ZIFA: dimensionality reduction for zero-inflated single-cell gene expression analysis. Genome Biol. 16, 241–257 (2015)CrossRef
6.
Zurück zum Zitat Junhyong, K.: Computational Analysis of RNA-Seq Data: From Quantification to High-Dimensional Analysis. University of Pennsylvania, pp. 35–43 (2012) Junhyong, K.: Computational Analysis of RNA-Seq Data: From Quantification to High-Dimensional Analysis. University of Pennsylvania, pp. 35–43 (2012)
7.
Zurück zum Zitat Bacher, R., and Kendziorski, C.: Design and computational analysis of single-cell RNA-seq experiments. Genome Biol. 17(63) (2016) Bacher, R., and Kendziorski, C.: Design and computational analysis of single-cell RNA-seq experiments. Genome Biol. 17(63) (2016)
8.
Zurück zum Zitat Alon, U., et al.: Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc. Natl. myAcad. Sci. USA 8; 96(12), 6745–6750 (1999) Alon, U., et al.: Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc. Natl. myAcad. Sci. USA 8; 96(12), 6745–6750 (1999)
10.
12.
Zurück zum Zitat Bezanson, J., Karpinski, S., Shah, V., Edelman, A.: Julia: a fast-dynamic language for technical computing (2012). arXiv:1209.5145 Bezanson, J., Karpinski, S., Shah, V., Edelman, A.: Julia: a fast-dynamic language for technical computing (2012). arXiv:​1209.​5145
13.
Zurück zum Zitat Gary, A.C.: Using ANOVA to analyze microarray data. Biotechn. Future Sci. 37(2), 1–5 (2018) Gary, A.C.: Using ANOVA to analyze microarray data. Biotechn. Future Sci. 37(2), 1–5 (2018)
14.
Zurück zum Zitat Mukesh, K., Nitish, K.R., Amitav, S., Santanu, K.R.: Feature selection and classification of microarray data using MapReduce Based ANOVA and KNN. Procedia Comput. Sci. 54, 301–310 (2015)CrossRef Mukesh, K., Nitish, K.R., Amitav, S., Santanu, K.R.: Feature selection and classification of microarray data using MapReduce Based ANOVA and KNN. Procedia Comput. Sci. 54, 301–310 (2015)CrossRef
15.
Zurück zum Zitat Ding, Y., Dawn, W.: Improving the performance of SVM-RFE to select genes in microarray data. BMC Bioinform. 2(12), 1–11 (2015) Ding, Y., Dawn, W.: Improving the performance of SVM-RFE to select genes in microarray data. BMC Bioinform. 2(12), 1–11 (2015)
16.
Zurück zum Zitat Shruti, M., Mishra, D.: SVM-BT-RFE: an improved gene selection framework using Bayesian T-test embedded in support vector machine (recursive feature elimination) algorithm. Karbala Int. J. Modern Sci. 1(2), 86–96 (2015)CrossRef Shruti, M., Mishra, D.: SVM-BT-RFE: an improved gene selection framework using Bayesian T-test embedded in support vector machine (recursive feature elimination) algorithm. Karbala Int. J. Modern Sci. 1(2), 86–96 (2015)CrossRef
17.
Zurück zum Zitat Rimah, A., Dorra, B.A., Noureddine, E.: An empirical comparison of SVM and some supervised learning algorithms for vowel recognition. Int. J. Intell. Inf. Process. (IJIIP) 3(1), 1–5 (2012) Rimah, A., Dorra, B.A., Noureddine, E.: An empirical comparison of SVM and some supervised learning algorithms for vowel recognition. Int. J. Intell. Inf. Process. (IJIIP) 3(1), 1–5 (2012)
19.
Zurück zum Zitat Chang, C., Lin, C.: LIBSVM: a library for support vector machines. ACM TIST. 2(3), 27 Chang, C., Lin, C.: LIBSVM: a library for support vector machines. ACM TIST. 2(3), 27
20.
Zurück zum Zitat Soofi, A.A., Awan, A.: Classification techniques in. machine learning: applications and issues. J. Basic Appl. Sci. 13, 459–465 (2017)CrossRef Soofi, A.A., Awan, A.: Classification techniques in. machine learning: applications and issues. J. Basic Appl. Sci. 13, 459–465 (2017)CrossRef
21.
Zurück zum Zitat Khan, A., Baharudin, B., Lee, L.H., Khan, K.: A review of machine learning algorithms for text-documents classification. J. Adv. Inf. Technol. 1(1), 1–17 (2010) Khan, A., Baharudin, B., Lee, L.H., Khan, K.: A review of machine learning algorithms for text-documents classification. J. Adv. Inf. Technol. 1(1), 1–17 (2010)
22.
Zurück zum Zitat Bhavsar, H., Panchal, M.H.: A review on support vector machine for data classification. Int. J. Adv. Res. Comput. Eng. Technol. (IJARCET) 1(2), 185–189 (2012) Bhavsar, H., Panchal, M.H.: A review on support vector machine for data classification. Int. J. Adv. Res. Comput. Eng. Technol. (IJARCET) 1(2), 185–189 (2012)
23.
Zurück zum Zitat Devi, A.V., Devaraj, D.V.: Gene expression data classification using support vector machine and mutual information-based gene selection. Procedia Comput. Sci. 47, 13–21 (2015)CrossRef Devi, A.V., Devaraj, D.V.: Gene expression data classification using support vector machine and mutual information-based gene selection. Procedia Comput. Sci. 47, 13–21 (2015)CrossRef
25.
Zurück zum Zitat Wenyan, Z., Xuewen, L., Jingjing, W.: Feature selection for cancer classification using microarray gene expression data. Biostat. Biometr. J. 1(2), 1–7 (2017) Wenyan, Z., Xuewen, L., Jingjing, W.: Feature selection for cancer classification using microarray gene expression data. Biostat. Biometr. J. 1(2), 1–7 (2017)
26.
Zurück zum Zitat Balamurugan, M., Nancy, A., Vijaykumar, S.: Alzheimer’s disease diagnosis by using dimensionality reduction based on KNN classifier. Biomed. Pharmacol. J. 10(4), 1823–1830 (2017)CrossRef Balamurugan, M., Nancy, A., Vijaykumar, S.: Alzheimer’s disease diagnosis by using dimensionality reduction based on KNN classifier. Biomed. Pharmacol. J. 10(4), 1823–1830 (2017)CrossRef
27.
Zurück zum Zitat Usman, A., Shazad, A., Javed, F.: Using PCA and factor analysis for dimensionality reduction of bio-informatics data. (IJACSA) Int. J. Adv. Comput. Sci. Appl. 8(5), 515–426 (2017) Usman, A., Shazad, A., Javed, F.: Using PCA and factor analysis for dimensionality reduction of bio-informatics data. (IJACSA) Int. J. Adv. Comput. Sci. Appl. 8(5), 515–426 (2017)
28.
Zurück zum Zitat Gökmen, Z., et al.: A comprehensive simulation study on classification of RNASeq data. PLoS ONE J. 12(8), 1–24 (2017) Gökmen, Z., et al.: A comprehensive simulation study on classification of RNASeq data. PLoS ONE J. 12(8), 1–24 (2017)
29.
Zurück zum Zitat Ian, T.J., Jorge, C.: Principal component analysis: a review and recent developments. Philosoph. Trans. Math. Phys. Eng. Sci. 374, 1–21 (2017) Ian, T.J., Jorge, C.: Principal component analysis: a review and recent developments. Philosoph. Trans. Math. Phys. Eng. Sci. 374, 1–21 (2017)
31.
Zurück zum Zitat Keerthi, K.V., Surendiran, B.: Dimensionality reduction using Principal Component Analysis for network intrusion detection. Perspect. Sci. 8, 510–512 (2016)CrossRef Keerthi, K.V., Surendiran, B.: Dimensionality reduction using Principal Component Analysis for network intrusion detection. Perspect. Sci. 8, 510–512 (2016)CrossRef
32.
Zurück zum Zitat Sofie, V.: A comparative review of dimensionality reduction methods for high-throughput single-cell transcriptomics. Master’s dissertation submitted to Ghent University to obtain the degree of Master of Science in Biochemistry and Biotechnology. Major Bioinformatics and Systems Biology, pp. 1–88 (2017) Sofie, V.: A comparative review of dimensionality reduction methods for high-throughput single-cell transcriptomics. Master’s dissertation submitted to Ghent University to obtain the degree of Master of Science in Biochemistry and Biotechnology. Major Bioinformatics and Systems Biology, pp. 1–88 (2017)
33.
Zurück zum Zitat Elavarasan, Mani, K.: A survey on feature extraction techniques. Int. J. Innov. Res. Comput. Commun. Eng. 3(1), 1–4 (2015)CrossRef Elavarasan, Mani, K.: A survey on feature extraction techniques. Int. J. Innov. Res. Comput. Commun. Eng. 3(1), 1–4 (2015)CrossRef
34.
Zurück zum Zitat Divya, J., Vijendra, S.: Feature selection and classification systems for chronic disease prediction: a review. Egyptian Inform. J. (2018). https://doi.org/10.1016/j.eij.2018.03.002 Divya, J., Vijendra, S.: Feature selection and classification systems for chronic disease prediction: a review. Egyptian Inform. J. (2018). https://​doi.​org/​10.​1016/​j.​eij.​2018.​03.​002
35.
Zurück zum Zitat Awotunde, J.B., Ogundokun, R.O., Ayo, Femi E., Ajamu, Gbemisola J., Adeniyi, E.A., Ogundokun, E.O.: Social media acceptance and use among university students for learning purpose using UTAUT model. In: Borzemski, L., Świątek, J., Wilimowska, Z. (eds.) ISAT 2019. AISC, vol. 1050, pp. 91–102. Springer, Cham (2020). https://doi.org/10.1007/978-3-030-30440-9_10CrossRef Awotunde, J.B., Ogundokun, R.O., Ayo, Femi E., Ajamu, Gbemisola J., Adeniyi, E.A., Ogundokun, E.O.: Social media acceptance and use among university students for learning purpose using UTAUT model. In: Borzemski, L., Świątek, J., Wilimowska, Z. (eds.) ISAT 2019. AISC, vol. 1050, pp. 91–102. Springer, Cham (2020). https://​doi.​org/​10.​1007/​978-3-030-30440-9_​10CrossRef
36.
Zurück zum Zitat Ogundokun, R.O.: Evaluation of the scholastic performance of students in 12 programs from a private university in the south-west geopolitical zone in Nigeria. Research 8 (2019) Ogundokun, R.O.: Evaluation of the scholastic performance of students in 12 programs from a private university in the south-west geopolitical zone in Nigeria. Research 8 (2019)
Metadaten
Titel
Performance Evaluation of ANOVA and RFE Algorithms for Classifying Microarray Dataset Using SVM
verfasst von
Sulaiman Olaniyi Abdulsalam
Abubakar Adamu Mohammed
Jumoke Falilat Ajao
Ronke S. Babatunde
Roseline Oluwaseun Ogundokun
Chiebuka T. Nnodim
Micheal Olaolu Arowolo
Copyright-Jahr
2020
DOI
https://doi.org/10.1007/978-3-030-63396-7_32

Premium Partner