Computational Intelligence in Bioinformatics

Preface. Contributors. Part One Gene Expression Analysis and Systems Biology. 1. Hybrid of Neural Classifi er and Swarm Intelligence in Multiclass Cancer Diagnosis with Gene Expression Signatures (Rui Xu, Georgios C. Anagnostopoulos, and Donald C. Wunsch II). 1.1 Introduction. 1.2 Methods and Systems. 1.3 Experimental Results. 1.4 Conclusions. 2. Classifying Gene Expression Profi les with Evolutionary Computation (Jin Hyuk Hong and Sung Bae Cho). 2.1 DNA Microarray Data Classifi cation. 2.2 Evolutionary Approach to the Problem. 2.3 Gene Selection with Speciated Genetic Algorithm. 2.4 Cancer Classifi ction Based on Ensemble Genetic Programming. 2.5 Conclusion. 3. Finding Clusters in Gene Expression Data Using EvoCluster (Patrick C. H. Ma, Keith C. C. Chan, and Xin Yao). 3.1 Introduction. 3.2 Related Work. 3.3 Evolutionary Clustering Algorithm. 3.4 Experimental Results. 3.5 Conclusions. 4. Gene Networks and Evolutionary Computation (Jennifer Hallinan). 4.1 Introduction. 4.2 Evolutionary Optimization. 4.3 Computational Network Modeling. 4.4 Extending Reach of Gene Networks. 4.5 Network Topology Analysis. 4.6 Summary. Part Two Sequence Analysis and Feature Detection. 5. Fuzzy Granular Methods for Identifying Marker Genes from Microarray Expression Data (Yuanchen He, Yuchun Tang, Yan Qing Zhang, and Rajshekhar Sunderraman). 5.1 Introduction. 5.2 Traditional Algorithms for Gene Selection. 5.3 New Fuzzy Granular Based Algorithm for Gene Selection. 5.4 Simulation. 5.5 Conclusions. 6. Evolutionary Feature Selection for Bioinformatics (Laetitia Jourdan, Clarisse Dhaenens, and El Ghazali Talbi). 6.1 Introduction. 6.2 Evolutionary Algorithms for Feature Selection. 6.3 Feature Selection for Clustering in Bioinformatics. 6.4 Feature Selection for Classifi cation in Bioinformatics. 6.5 Frameworks and Data Sets. 6.6 Conclusion. 7. Fuzzy Approaches for the Analysis CpG Island Methylation Patterns (Ozy Sjahputera, Mihail Popescu, James M. Keller, and Charles W. Caldwell). 7.1

Gary B. Fogel, PhD, is Vice President of Natural Selection, Inc., and his current research interests focus on the application of computational intelligence methods to problems in the biomedical sciences. He is a senior member of the IEEE and serves as an Associate Editor on three IEEE journals.

David W. Corne holds a Chair in Computer Science at Heriot-Watt University, Edinburgh, Scotland, and his research interests include evolutionary computation, multi-objective optimization, bioinformatics, telecommunications, and general aspects and applications of nature-inspired computation.

Yi Pan, PhD, is Chair and Professor of Computer Science at Georgia State University and his research interests include high-performance computing, networking, and bioinformatics. Dr. Pan has coedited over twenty books and his recent research has been supported by the NSF, NIH, NSFC, AFOSR, AFRL, JSPS, IISF, and the states of Georgia and Ohio.