A Hybrid Metaheuristic for Biclustering Based on Scatter Search and Genetic Algorithms

In this paper a hybrid metaheuristic for biclustering based on Scatter Search and Genetic Algorithms is presented. A general scheme of Scatter Search has been used to obtain high---quality biclusters, but a way of generating the initial population and a method of combination based on Genetic Algorithms have been chosen. Experimental results from yeast cell cycle and human B-cell lymphoma are reported. Finally, the performance of the proposed hybrid algorithm is compared with a genetic algorithm recently published.

[1]  Padraig Cunningham,et al.  Biclustering of expression data using simulated annealing , 2005, 18th IEEE Symposium on Computer-Based Medical Systems (CBMS'05).

[2]  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.

[3]  Jesús S. Aguilar-Ruiz,et al.  Shifting and scaling patterns from gene expression data , 2005, Bioinform..

[4]  Concha Bielza,et al.  Machine Learning in Bioinformatics , 2008, Encyclopedia of Database Systems.

[5]  Ash A. Alizadeh,et al.  Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling , 2000, Nature.

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

[7]  Yang Li,et al.  Analysis of Tiling Microarray Data by Learning Vector Quantization and Relevance Learning , 2007, IDEAL.

[8]  Robert M. Haralick,et al.  Exploiting the Geometry of Gene Expression Patterns for Unsupervised Learning , 2006, 18th International Conference on Pattern Recognition (ICPR'06).

[9]  Juan A. Nepomuceno,et al.  Biclusters Evaluation Based on Shifting and Scaling Patterns , 2007, IDEAL.

[10]  Sushmita Mitra,et al.  Multi-objective evolutionary biclustering of gene expression data , 2006, Pattern Recognit..

[11]  Philip S. Yu,et al.  Enhanced biclustering on expression data , 2003, Third IEEE Symposium on Bioinformatics and Bioengineering, 2003. Proceedings..

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

[13]  G. Getz,et al.  Coupled two-way clustering analysis of gene microarray data. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

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

[15]  Federico Divina,et al.  Biclustering of expression data with evolutionary computation , 2006, IEEE Transactions on Knowledge and Data Engineering.

[16]  Roded Sharan,et al.  Discovering statistically significant biclusters in gene expression data , 2002, ISMB.

[17]  Rafael Martí,et al.  Scatter Search: Diseño Básico y Estrategias avanzadas , 2002, Inteligencia Artif..