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Semi-supervised clustering for gene-expression data in multiobjective optimization framework

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Abstract

Studying the patterns hidden in gene expression data helps to understand the functionality of genes. But due to the large volume of genes and the complexity of biological networks it is difficult to study the resulting mass of data which often consists of millions of measurements. In order to reveal natural structures and to identify interesting patterns from the given gene expression data set, clustering techniques are applied. Semi-supervised classification is a new direction of machine learning. It requires huge unlabeled data and a few labeled data. Semi-supervised classification in general performs better than unsupervised classification. But to the best of our knowledge there are no works for solving gene expression data clustering problem using semi-supervised classification techniques. In the current paper we have made an attempt to solve the gene expression data clustering problem using a multiobjective optimization based semi-supervised classification technique with the aim to attain good quality partitions by using few labeled data. In order to generate the labeled data, initially Fuzzy C-means clustering technique is applied. In order to automatically determine the partitioning, multiple cluster centers corresponding to a cluster are encoded in the form of a string. In order to compute the quality of the obtained partitioning, values of five objective functions are computed. The effectiveness of this proposed semi-supervised clustering technique is demonstrated on five publicly available benchmark gene expression data sets. Comparison results with the existing techniques for gene expression data clustering prove that the proposed method is the most effective one. Statistical and biological significance tests have also been carried out.

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Notes

  1. http://anirbanmukhopadhyay.50webs.com/mogasvm.html.

  2. http://db.yeastgenome.org/cgi-bin/GO/goTermFinder.

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  1. Computer Science Engineering, Indian Institute of Technology, Patna, India

    Abhay Kumar Alok, Sriparna Saha & Asif Ekbal

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  1. Abhay Kumar Alok
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Correspondence to Abhay Kumar Alok.

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Alok, A.K., Saha, S. & Ekbal, A. Semi-supervised clustering for gene-expression data in multiobjective optimization framework. Int. J. Mach. Learn. & Cyber. 8, 421–439 (2017). https://doi.org/10.1007/s13042-015-0335-8

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