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2016 | OriginalPaper | Chapter

Unsupervised Machine Learning Approach for Gene Expression Microarray Data Using Soft Computing Technique

Authors : Madhurima Rana, Prachi Vijayeeta, Utsav Kar, Madhabananda Das, B. S. P. Mishra

Published in: Proceedings of 3rd International Conference on Advanced Computing, Networking and Informatics

Publisher: Springer India

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Abstract

Machine learning is a burgeoning technology used for extractions of knowledge from an ocean of data. It has robust binding with optimization and artificial intelligence that delivers theory, methodologies and application domain to the field of statistics and computer science. Machine learning tasks are broadly classified into two groups namely supervised learning and unsupervised learning. The analysis of the unsupervised data requires thorough computational activities using different clustering algorithms. Microarray gene expression data are taken into consideration for cluster regulating genes from non-regulating genes. In our work optimization technique (Cat Swarm Optimization) is used to minimize the number of cluster by evaluating the Euclidean distance among the centroids. A comparative study is being carried out by clustering the regulating genes before optimization and after optimization. In our work Principal component analysis (PCA) is incorporated for dimensionality reduction of vast dataset to ensure qualitative cluster analysis.

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Literature
1.
go back to reference Ma, P.C.H., Chan, K.C.C., Xin, Y., Chiu, D.K.Y.: An evolutionary clustering algorithm for gene expression microarray data analysis. IEEE Trans. Evol. Comput. 10(3), 296–314 (2006) Ma, P.C.H., Chan, K.C.C., Xin, Y., Chiu, D.K.Y.: An evolutionary clustering algorithm for gene expression microarray data analysis. IEEE Trans. Evol. Comput. 10(3), 296–314 (2006)
2.
go back to reference Witten, I.H., Frank, E., Hall, M.A.: Data Mining—Practical Machine Learning Tools and Techniques. Morgan Kaufmann (2005) Witten, I.H., Frank, E., Hall, M.A.: Data Mining—Practical Machine Learning Tools and Techniques. Morgan Kaufmann (2005)
3.
go back to reference Thamaraiselvi, G., Kaliammal, A.: A data mining: concepts and techniques. SRELS J. Inform. Manage. 41(4), 339–348 (2004) Thamaraiselvi, G., Kaliammal, A.: A data mining: concepts and techniques. SRELS J. Inform. Manage. 41(4), 339–348 (2004)
4.
go back to reference Roy, S., Chakraborty, U.: Introduction to soft computing: NeuroFuzzy and Genetic Algorithms. Pearson Publication Roy, S., Chakraborty, U.: Introduction to soft computing: NeuroFuzzy and Genetic Algorithms. Pearson Publication
5.
go back to reference Dudoit, S., Gentleman, R.: Cluster analysis in DNA microarray experiments. Bioconductor Short Course Winter (2002) Dudoit, S., Gentleman, R.: Cluster analysis in DNA microarray experiments. Bioconductor Short Course Winter (2002)
6.
go back to reference Gibbons, F.D., Roth, F.P.: Judging the quality of gene expression-based clustering methods using gene annotation. Genome Res. 12(10), 1574–1581 (2002)CrossRef Gibbons, F.D., Roth, F.P.: Judging the quality of gene expression-based clustering methods using gene annotation. Genome Res. 12(10), 1574–1581 (2002)CrossRef
7.
go back to reference Deng, Y., Kayarat, D., Elasri, M.O., Brown, S.J.: Microarray data clustering using particle swarm optimization K-means algorithm. In: Proceedings 8th JCIS, pp. 1730–1734 (2005) Deng, Y., Kayarat, D., Elasri, M.O., Brown, S.J.: Microarray data clustering using particle swarm optimization K-means algorithm. In: Proceedings 8th JCIS, pp. 1730–1734 (2005)
8.
go back to reference Lee, K.M., Chung, T.S., Kim, J.H.: Global optimization of clusters in gene expression data of DNA microarrays by deterministic annealing. Genom. Inform. 1(1), 20–24 (2003) Lee, K.M., Chung, T.S., Kim, J.H.: Global optimization of clusters in gene expression data of DNA microarrays by deterministic annealing. Genom. Inform. 1(1), 20–24 (2003)
9.
go back to reference Dudoit, S., Gentleman, R.: Cluster analysis in DNA microarray experiments. Bioconductor Short Course Winter (2002) Dudoit, S., Gentleman, R.: Cluster analysis in DNA microarray experiments. Bioconductor Short Course Winter (2002)
10.
go back to reference Rousseeuw, P.J.: Silhouettes: a graphical aid to the interpretation and validation of cluster analysis. J. Comput. Appl. Math. 20, 53–65 (1987) Rousseeuw, P.J.: Silhouettes: a graphical aid to the interpretation and validation of cluster analysis. J. Comput. Appl. Math. 20, 53–65 (1987)
11.
go back to reference Jiang, D., Chun, T., Aidong, Z.: Cluster analysis for gene expression data: A survey. IEEE Trans. Knowled. Data Eng. 16(11), 1370–1386 (2004)CrossRef Jiang, D., Chun, T., Aidong, Z.: Cluster analysis for gene expression data: A survey. IEEE Trans. Knowled. Data Eng. 16(11), 1370–1386 (2004)CrossRef
12.
go back to reference Dey, L., Mukhopadhyay, A.: Microarray gene expression data clustering using PSO based K-means algorithm. UACEE Int. J. Comput. Sci. Appl. 1(1), 232–236 (2009) Dey, L., Mukhopadhyay, A.: Microarray gene expression data clustering using PSO based K-means algorithm. UACEE Int. J. Comput. Sci. Appl. 1(1), 232–236 (2009)
13.
go back to reference Andreopoulos, B., An, A., Wang, X., Schroeder, M.: A roadmap of clustering algorithms: finding a match for a biomedical application. Briefings Bioinform. 10(3), 297–314 (2009)CrossRef Andreopoulos, B., An, A., Wang, X., Schroeder, M.: A roadmap of clustering algorithms: finding a match for a biomedical application. Briefings Bioinform. 10(3), 297–314 (2009)CrossRef
14.
go back to reference Santosa, B., Ningrum, M.K.: Cat swarm optimization for clustering and pattern recognition. In: International Conference of Soft Computing SOCPAR’09, pp. 54–59. 20 (2009) Santosa, B., Ningrum, M.K.: Cat swarm optimization for clustering and pattern recognition. In: International Conference of Soft Computing SOCPAR’09, pp. 54–59. 20 (2009)
15.
go back to reference Yin, L., Huang, C.H., Ni, J.: Clustering of gene expression data: performance and similarity analysis. BMC Bioinform. (2006) Yin, L., Huang, C.H., Ni, J.: Clustering of gene expression data: performance and similarity analysis. BMC Bioinform. (2006)
16.
go back to reference Priscilla, R., Swamynathan, S.: Efficient two dimensional clustering of microarray gene expression data by means of hybrid similarity measure. In Proceedings of the International Conference on Advances in Computing, Communications and Informatics, pp. 1047–1053. ACM (2012) Priscilla, R., Swamynathan, S.: Efficient two dimensional clustering of microarray gene expression data by means of hybrid similarity measure. In Proceedings of the International Conference on Advances in Computing, Communications and Informatics, pp. 1047–1053. ACM (2012)
17.
go back to reference Santosa, B., Ningrum, M.K.: Cat swarm optimization for clustering. In: International Conference of in Soft Computing and Pattern Recognition, pp. 54–59 (2009) Santosa, B., Ningrum, M.K.: Cat swarm optimization for clustering. In: International Conference of in Soft Computing and Pattern Recognition, pp. 54–59 (2009)
18.
go back to reference Iassargir, M., Ahhmad, A.: A hybrid multi-objective PSO method discover biclusters in microarray data. Mohsen. Int. J. Comput. (2009) Iassargir, M., Ahhmad, A.: A hybrid multi-objective PSO method discover biclusters in microarray data. Mohsen. Int. J. Comput. (2009)
19.
go back to reference Karaboga, D., Ozturk, C.: A novel clustering approach: artificial bee colony (ABC) algorithm. Appl. Soft Comput. 652–657 (2011) Karaboga, D., Ozturk, C.: A novel clustering approach: artificial bee colony (ABC) algorithm. Appl. Soft Comput. 652–657 (2011)
20.
go back to reference Castellanos-Garzón, J.A., Diaz, F.: An evolutionary and visual framework for clustering of DNA microarray data. J. Integr. Bioinform. 10, 232–232 (2012) Castellanos-Garzón, J.A., Diaz, F.: An evolutionary and visual framework for clustering of DNA microarray data. J. Integr. Bioinform. 10, 232–232 (2012)
Metadata
Title
Unsupervised Machine Learning Approach for Gene Expression Microarray Data Using Soft Computing Technique
Authors
Madhurima Rana
Prachi Vijayeeta
Utsav Kar
Madhabananda Das
B. S. P. Mishra
Copyright Year
2016
Publisher
Springer India
DOI
https://doi.org/10.1007/978-81-322-2538-6_51

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