Skip to main content
Top

2015 | OriginalPaper | Chapter

Automatic Teaching–Learning-Based Optimization: A Novel Clustering Method for Gene Functional Enrichments

Authors : Ramachandra Rao Kurada, K. Karteeka Pavan, Allam Appa Rao

Published in: Computational Intelligence Techniques for Comparative Genomics

Publisher: Springer Singapore

Activate our intelligent search to find suitable subject content or patents.

search-config
loading …

Abstract

Multi-objective optimization emerged as a significant research area in engineering studies because most of the real-world problems require optimization with a group of objectives. The most recently developed meta-heuristics called the teaching–learning-based optimization (TLBO) and its variant algorithms belongs to this category. This paper provokes the importance of hybrid methodology by illuminating this meta-heuristic over microarray datasets to attain functional enrichments of genes in the biological process. This paper persuades a novel automatic clustering algorithm (AutoTLBO) with a credible prospect by coalescing automatic assignment of k value in partitioned clustering algorithms and cluster validations into TLBO. The objectives of the algorithm were thoroughly tested over microarray datasets. The investigation results that endorse AutoTLBO were impeccable in obtaining optimal number of clusters, co-expressed cluster profiles, and gene patterns. The work was further extended by inputting the AutoTLBO algorithm outcomes into benchmarked bioinformatics tools to attain optimal gene functional enrichment scores. The concessions from these tools indicate excellent implications and significant results, justifying that the outcomes of AutoTLBO were incredible. Thus, both these rendezvous investigations give a lasting impression that AutoTLBO arises as an impending colonizer in this hybrid approach.

Dont have a licence yet? Then find out more about our products and how to get one now:

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!

Literature
1.
go back to reference Rao RV, Savsani VJ, Vakharia DP (2011) Teaching–learning-based optimization: a novel method for constrained mechanical design optimization problems. Computer Aided Des 43:303–315. doi:10.1016/j.cad.2010.12.015 Rao RV, Savsani VJ, Vakharia DP (2011) Teaching–learning-based optimization: a novel method for constrained mechanical design optimization problems. Computer Aided Des 43:303–315. doi:10.​1016/​j.​cad.​2010.​12.​015
3.
go back to reference Rao RV, Patel V (2013) Comparative performance of an elitist teaching-learning-based optimization algorithm for solving unconstrained optimization problems. Int J Ind Eng Comput 4: 29–50. doi:10.5267/j.ijiec.2012.09.001 Rao RV, Patel V (2013) Comparative performance of an elitist teaching-learning-based optimization algorithm for solving unconstrained optimization problems. Int J Ind Eng Comput 4: 29–50. doi:10.​5267/​j.​ijiec.​2012.​09.​001
5.
go back to reference Rand WM (1971) Objective criteria for the evaluation of clustering methods. J Am Stat Assoc 66(336):846–850CrossRef Rand WM (1971) Objective criteria for the evaluation of clustering methods. J Am Stat Assoc 66(336):846–850CrossRef
6.
go back to reference Hubert Lawrence, Schultz James (1976) Quadratic assignment as a general data analysis strategy. Br J Math Stat Psychol 29(2):190–241CrossRefMATHMathSciNet Hubert Lawrence, Schultz James (1976) Quadratic assignment as a general data analysis strategy. Br J Math Stat Psychol 29(2):190–241CrossRefMATHMathSciNet
7.
go back to reference Rousseeuw PJ (1987) Silhouettes: a graphical aid to the interpretation and validation of cluster analysis. J Comput Appl Math 20:53–65 Rousseeuw PJ (1987) Silhouettes: a graphical aid to the interpretation and validation of cluster analysis. J Comput Appl Math 20:53–65
8.
go back to reference Davies DL, Bouldin DW (1979) A cluster separation measure. Pattern Anal Mach Intell IEEE Trans On 2:224–227CrossRef Davies DL, Bouldin DW (1979) A cluster separation measure. Pattern Anal Mach Intell IEEE Trans On 2:224–227CrossRef
9.
go back to reference Chou C-H, Su M-C, Lai Eugene (2004) A new cluster validity measure and its application to image compression. Pattern Anal Appl 7(2):205–220CrossRefMathSciNet Chou C-H, Su M-C, Lai Eugene (2004) A new cluster validity measure and its application to image compression. Pattern Anal Appl 7(2):205–220CrossRefMathSciNet
11.
go back to reference Rao RV, Waghmare GG (2014) A comparative study of a teaching–learning-based optimization algorithm on multi-objective unconstrained and constrained functions. J King Saud University—Comput Inf Sci 26: 332–346. doi:10.1016/j.jksuci.2013.12.004 Rao RV, Waghmare GG (2014) A comparative study of a teaching–learning-based optimization algorithm on multi-objective unconstrained and constrained functions. J King Saud University—Comput Inf Sci 26: 332–346. doi:10.​1016/​j.​jksuci.​2013.​12.​004
12.
go back to reference Amiri Babak (2012) Application of teaching-learning-based optimization algorithm on cluster analysis. J Basic Appl Sci Res 2(11):11795–11802 Amiri Babak (2012) Application of teaching-learning-based optimization algorithm on cluster analysis. J Basic Appl Sci Res 2(11):11795–11802
13.
go back to reference Suresh K, Kundu D, Ghosh S, Das S, Abraham A (2009) Automatic clustering with multi-objective differential evolution algorithms. In: Evolutionary computation, 2009, IEEE Congress on CEC’09. IEEE, pp 2590–2597 Suresh K, Kundu D, Ghosh S, Das S, Abraham A (2009) Automatic clustering with multi-objective differential evolution algorithms. In: Evolutionary computation, 2009, IEEE Congress on CEC’09. IEEE, pp 2590–2597
14.
go back to reference Kundu D, Suresh K, Ghosh S, Das S, Abraham A, Badr Y (2009) Automatic clustering using a synergy of genetic algorithm and multi-objective differential evolution. In: Hybrid artificial intelligence systems. Springer, Berlin, pp 177–186 Kundu D, Suresh K, Ghosh S, Das S, Abraham A, Badr Y (2009) Automatic clustering using a synergy of genetic algorithm and multi-objective differential evolution. In: Hybrid artificial intelligence systems. Springer, Berlin, pp 177–186
15.
go back to reference Liu Yimin, Özyer Tansel, Alhajj Reda, Barker Ken (2005) Integrating multi-objective genetic algorithm and validity analysis for locating and ranking alternative clustering. Informatica 29:33–40MATH Liu Yimin, Özyer Tansel, Alhajj Reda, Barker Ken (2005) Integrating multi-objective genetic algorithm and validity analysis for locating and ranking alternative clustering. Informatica 29:33–40MATH
16.
go back to reference Satapathy SC, Naik A, Parvathi K (2013) A teaching learning based optimization based on orthogonal design for solving global optimization problems. SpringerPlus 2:130 Satapathy SC, Naik A, Parvathi K (2013) A teaching learning based optimization based on orthogonal design for solving global optimization problems. SpringerPlus 2:130
19.
go back to reference Suresh Kaushik, Kundu Debarati, Ghosh Sayan, Das Swagatam, Abraham A, Han SY (2009) Multi-objective differential evolution for automatic clustering with application to micro-array data analysis. Sensors 9:3981–4004. doi:10.3390/s90503981 CrossRef Suresh Kaushik, Kundu Debarati, Ghosh Sayan, Das Swagatam, Abraham A, Han SY (2009) Multi-objective differential evolution for automatic clustering with application to micro-array data analysis. Sensors 9:3981–4004. doi:10.​3390/​s90503981 CrossRef
20.
go back to reference Pavan KK, Rao AA, Dattatreya Rao AV, Sridhar GR (2011) Robust seed selection algorithm for k-means type algorithms. Int J Comput Sci Inf Technol (IJCSIT) 3(5). doi:10.5121/ijcsit.2011.3513 Pavan KK, Rao AA, Dattatreya Rao AV, Sridhar GR (2011) Robust seed selection algorithm for k-means type algorithms. Int J Comput Sci Inf Technol (IJCSIT) 3(5). doi:10.​5121/​ijcsit.​2011.​3513
21.
go back to reference Deb Kalyanmoy (2000) An efficient constraint handling method for genetic algorithms. Comput Methods Appl Mech Eng 186(2):311–338CrossRefMATH Deb Kalyanmoy (2000) An efficient constraint handling method for genetic algorithms. Comput Methods Appl Mech Eng 186(2):311–338CrossRefMATH
22.
go back to reference Wilkinson L, Friendly M (2009) The history of the cluster heat map. The American Statistician 63(2) Wilkinson L, Friendly M (2009) The history of the cluster heat map. The American Statistician 63(2)
23.
go back to reference Al-Shahrour F, Minguez P, Tárraga J, Medina I, Alloza E, Montaner D, Dopazo J (2007) FatiGO+: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments. Nucleic Acids Research 35 (Web Server issue):W91–W96 Al-Shahrour F, Minguez P, Tárraga J, Medina I, Alloza E, Montaner D, Dopazo J (2007) FatiGO+: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments. Nucleic Acids Research 35 (Web Server issue):W91–W96
24.
go back to reference Dennis G, Sherman BT, Hosack DA, Yang J, Baseler MW, Lane HC, Lempicki RA (2003) DAVID: database for annotation, visualization, and integrated discovery. Genome Biology 4(5):P3 Dennis G, Sherman BT, Hosack DA, Yang J, Baseler MW, Lane HC, Lempicki RA (2003) DAVID: database for annotation, visualization, and integrated discovery. Genome Biology 4(5):P3
Metadata
Title
Automatic Teaching–Learning-Based Optimization: A Novel Clustering Method for Gene Functional Enrichments
Authors
Ramachandra Rao Kurada
K. Karteeka Pavan
Allam Appa Rao
Copyright Year
2015
Publisher
Springer Singapore
DOI
https://doi.org/10.1007/978-981-287-338-5_2

Premium Partner