Ensemble cuckoo search biclustering of the gene expression data

Many biclustering algorithms have been proposed in analyzing the gene expression data and ensemble biclustering methods can improve performance of the biclustering algorithm. We propose a new method of obtaining a variety of constituent biclusters which use different quality measures of bicluster. To demonstrate the efficiency of our methods, experiment on six real gene expression data shows the diversity and biological significance of the biclusters obtained by our methods are higher than that of the compared methods.

[1]  Neelima Gupta,et al.  BEMI Bicluster Ensemble Using Mutual Information , 2013, 2013 12th International Conference on Machine Learning and Applications.

[2]  Kenneth Steiglitz,et al.  Combinatorial Optimization: Algorithms and Complexity , 1981 .

[3]  Xin-She Yang,et al.  Cuckoo Search via Lévy flights , 2009, 2009 World Congress on Nature & Biologically Inspired Computing (NaBIC).

[4]  Joydeep Ghosh,et al.  Cluster Ensembles --- A Knowledge Reuse Framework for Combining Multiple Partitions , 2002, J. Mach. Learn. Res..

[5]  Jesús S. Aguilar-Ruiz,et al.  Biclustering on expression data: A review , 2015, J. Biomed. Informatics.

[6]  Arlindo L. Oliveira,et al.  Biclustering algorithms for biological data analysis: a survey , 2004, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[7]  D. Botstein,et al.  Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[8]  Panos M. Pardalos,et al.  Biclustering in data mining , 2008, Comput. Oper. Res..

[9]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[10]  Federico Divina,et al.  An effective measure for assessing the quality of biclusters , 2012, Comput. Biol. Medicine.

[11]  Blaise Hanczar,et al.  Using the bagging approach for biclustering of gene expression data , 2011, Neurocomputing.

[12]  Kathleen Marchal,et al.  An ensemble biclustering approach for querying gene expression compendia with experimental lists , 2011, Bioinform..

[13]  Lusheng Wang,et al.  Computing the maximum similarity bi-clusters of gene expression data , 2007, Bioinform..

[14]  Mahmoud Mounir,et al.  On biclustering of gene expression data , 2015, 2015 IEEE Seventh International Conference on Intelligent Computing and Information Systems (ICICIS).

[15]  George M. Church,et al.  Biclustering of Expression Data , 2000, ISMB.

[16]  Li Teng,et al.  Discovering Biclusters by Iteratively Sorting with Weighted Correlation Coefficient in Gene Expression Data , 2008, J. Signal Process. Syst..

[17]  Robert Gentleman,et al.  Using GOstats to test gene lists for GO term association , 2007, Bioinform..

[18]  Blaise Hanczar,et al.  Ensemble methods for biclustering tasks , 2012, Pattern Recognit..

[19]  Ronald W. Davis,et al.  A genome-wide transcriptional analysis of the mitotic cell cycle. , 1998, Molecular cell.

[20]  Michael L. Bittner,et al.  Clustering analysis for gene expression data , 1999, Photonics West - Biomedical Optics.

[21]  Ujjwal Maulik,et al.  A Novel Coherence Measure for Discovering Scaling Biclusters from Gene Expression Data , 2009, J. Bioinform. Comput. Biol..

[22]  Michael K. Ng,et al.  HARP: a practical projected clustering algorithm , 2004, IEEE Transactions on Knowledge and Data Engineering.

[23]  Beatriz Pontes,et al.  Quality Measures for Gene Expression Biclusters , 2015, PloS one.

[24]  Blaise Hanczar,et al.  Unsupervised Consensus Functions Applied to Ensemble Biclustering , 2014, ICPRAM.

[25]  Pedro Larrañaga,et al.  A new measure for gene expression biclustering based on non-parametric correlation , 2013, Comput. Methods Programs Biomed..

[26]  J. Hartigan Direct Clustering of a Data Matrix , 1972 .

[27]  Yongguo Liu,et al.  Biclustering of the Gene Expression Data by Coevolution Cuckoo Search , 2015 .

[28]  Neelima Gupta,et al.  BiETopti-BiClustering Ensemble Using Optimization Techniques , 2013, ICDM.