EBIC: a next-generation evolutionary-based parallel biclustering method

In this paper we present the recent accomplishments in developing a biclustering method based on evolutionary computation. In one of the recent papers we demonstrated the supremacy of our method over several state-of-the-art algorithms. We highlight the evolutionary fundamentals of the method and discuss potential future directions.

[1]  Zhenjia Wang,et al.  UniBic: Sequential row-based biclustering algorithm for analysis of gene expression data , 2016, Scientific Reports.

[2]  Ying Xu,et al.  QUBIC: a qualitative biclustering algorithm for analyses of gene expression data , 2009, Nucleic acids research.

[3]  Ümit V. Çatalyürek,et al.  A Biclustering Method to Discover Co-regulated Genes Using Diverse Gene Expression Datasets , 2009, BICoB.

[4]  Fred Glover,et al.  Tabu Search - Part II , 1989, INFORMS J. Comput..

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

[6]  Riccardo Poli,et al.  A Field Guide to Genetic Programming , 2008 .

[7]  Richard M. Karp,et al.  Discovering local structure in gene expression data: the order-preserving submatrix problem , 2002, RECOMB '02.

[8]  Krzysztof Boryczko,et al.  Hybrid Biclustering Algorithms for Data Mining , 2016, EvoApplications.

[9]  Fred W. Glover,et al.  Tabu Search - Part I , 1989, INFORMS J. Comput..

[10]  Sven Bergmann,et al.  Iterative signature algorithm for the analysis of large-scale gene expression data. , 2002, Physical review. E, Statistical, nonlinear, and soft matter physics.

[11]  Mehmet Deveci,et al.  A comparative analysis of biclustering algorithms for gene expression data , 2013, Briefings Bioinform..

[12]  T. M. Murali,et al.  Extracting Conserved Gene Expression Motifs from Gene Expression Data , 2002, Pacific Symposium on Biocomputing.

[13]  Lothar Thiele,et al.  A systematic comparison and evaluation of biclustering methods for gene expression data , 2006, Bioinform..

[14]  L. Lazzeroni Plaid models for gene expression data , 2000 .

[15]  Bruno Sareni,et al.  Fitness sharing and niching methods revisited , 1998, IEEE Trans. Evol. Comput..

[16]  Anindya Bhattacharya,et al.  A GPU-accelerated algorithm for biclustering analysis and detection of condition-dependent coexpression network modules , 2017, Scientific Reports.

[17]  Jason H. Moore,et al.  EBIC: an artificial intelligence-based parallel biclustering algorithm for pattern discovery , 2018, ArXiv.

[18]  Ulrich Bodenhofer,et al.  FABIA: factor analysis for bicluster acquisition , 2010, Bioinform..

[19]  John R. Koza,et al.  Genetic programming - on the programming of computers by means of natural selection , 1993, Complex adaptive systems.

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

[21]  Riccardo Poli,et al.  Elitism reduces bloat in genetic programming , 2008, GECCO '08.