Optimizing Brain Networks Topologies Using Multi-objective Evolutionary Computation

The analysis of brain network topological features has served to better understand these networks and reveal particular characteristics of their functional behavior. The distribution of brain network motifs is particularly useful for detecting and describing differences between brain networks and random and computationally optimized artificial networks. In this paper we use a multi-objective evolutionary optimization approach to generate optimized artificial networks that have a number of topological features resembling brain networks. The Pareto set approximation of the optimized networks is used to extract network descriptors that are compared to brain and random network descriptors. To analyze the networks, the clustering coefficient, the average path length, the modularity and the betweenness centrality are computed. We argue that the topological complexity of a brain network can be estimated using the number of evaluations needed by an optimization algorithm to output artificial networks of similar complexity. For the analyzed network examples, our results indicate that while original brain networks have a reduced structural motif number and a high functional motif number, they are not optimal with respect to these two topological features. We also investigate the correlation between the structural and functional motif numbers, the average path length and the clustering coefficient in random, optimized and brain networks.

[1]  Eckart Zitzler,et al.  Dimensionality Reduction in Multiobjective Optimization: The Minimum Objective Subset Problem , 2006, OR.

[2]  O. Sporns,et al.  Motifs in Brain Networks , 2004, PLoS biology.

[3]  Concha Bielza,et al.  Mateda-2.0: Estimation of Distribution Algorithms in MATLAB , 2010 .

[4]  Naonori Ueda,et al.  Visualization of Documents and Concepts in Neuroinformatics with the 3D-SE Viewer , 2007, Frontiers Neuroinformatics.

[5]  Raul Rodriguez-Esteban,et al.  Global optimization of cerebral cortex layout. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[6]  E A Leicht,et al.  Community structure in directed networks. , 2007, Physical review letters.

[7]  H. Berendse,et al.  The application of graph theoretical analysis to complex networks in the brain , 2007, Clinical Neurophysiology.

[8]  O. Sporns,et al.  Complex brain networks: graph theoretical analysis of structural and functional systems , 2009, Nature Reviews Neuroscience.

[9]  Duncan J. Watts,et al.  Collective dynamics of ‘small-world’ networks , 1998, Nature.

[10]  D. J. Felleman,et al.  Distributed hierarchical processing in the primate cerebral cortex. , 1991, Cerebral cortex.

[11]  John H. Holland,et al.  Adaptation in Natural and Artificial Systems: An Introductory Analysis with Applications to Biology, Control, and Artificial Intelligence , 1992 .

[12]  C Cherniak,et al.  Component placement optimization in the brain , 1991, The Journal of neuroscience : the official journal of the Society for Neuroscience.

[13]  Thomas K. Berger,et al.  Evaluating automated parameter constraining procedures of neuron models by experimental and surrogate data , 2008, Biological Cybernetics.

[14]  Robert J. Butera,et al.  Genetic Algorithm for Optimization and Specification of a Neuron Model , 2006, 2005 IEEE Engineering in Medicine and Biology 27th Annual Conference.

[15]  Olli Yli-Harja,et al.  Comparison of automated parameter estimation methods for neuronal signaling networks , 2006, Neurocomputing.

[16]  Luciano da Fontoura Costa,et al.  Signal Propagation in Cortical Networks: A Digital Signal Processing Approach , 2009, Front. Neuroinform..

[17]  Lucas Antiqueira,et al.  Correlations between structure and random walk dynamics in directed complex networks , 2007, Applied physics letters.

[18]  M. Young The organization of neural systems in the primate cerebral cortex , 1993, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[19]  O. Sporns,et al.  Hierarchical features of large-scale cortical connectivity , 2005, q-bio/0508007.

[20]  Luciano da Fontoura Costa,et al.  Predicting the connectivity of primate cortical networks from topological and spatial node properties , 2007, BMC Systems Biology.

[21]  Shao-Ping Wang,et al.  Random walks on the neural network of C.elegans , 2008, 2008 International Conference on Neural Networks and Signal Processing.

[22]  Carlos A. Coello Coello,et al.  Objective reduction using a feature selection technique , 2008, GECCO '08.

[23]  Luciano da Fontoura Costa,et al.  A structure–dynamic approach to cortical organization: Number of paths and accessibility , 2009, Journal of Neuroscience Methods.

[24]  P. Goldman-Rakic,et al.  Preface: Cerebral Cortex Has Come of Age , 1991 .

[25]  Olaf Sporns,et al.  Network structure of cerebral cortex shapes functional connectivity on multiple time scales , 2007, Proceedings of the National Academy of Sciences.

[26]  Karl-Heinz Waldmann,et al.  Operations Research Proceedings 2006 , 2007 .

[27]  Peter J. Fleming,et al.  Conflict, Harmony, and Independence: Relationships in Evolutionary Multi-criterion Optimisation , 2003, EMO.

[28]  S. Shen-Orr,et al.  Network motifs: simple building blocks of complex networks. , 2002, Science.

[29]  David E. Goldberg,et al.  Genetic Algorithms in Search Optimization and Machine Learning , 1988 .

[30]  Sergey N. Dorogovtsev,et al.  Critical phenomena in complex networks , 2007, ArXiv.

[31]  U. Alon,et al.  Spontaneous evolution of modularity and network motifs. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[32]  J. S. Barlow The mindful brain: B.M. Edelman and V.B. Mountcastle (MIT Press, Cambridge, Mass., 1978, 100 p., U.S. $ 10.00) , 1979 .

[33]  Christos Faloutsos,et al.  Kronecker Graphs: An Approach to Modeling Networks , 2008, J. Mach. Learn. Res..

[34]  K. Deb,et al.  On Finding Pareto-Optimal Solutions Through Dimensionality Reduction for Certain Large-Dimensional Multi-Objective Optimization Problems , 2022 .

[35]  L. da F. Costa,et al.  Characterization of complex networks: A survey of measurements , 2005, cond-mat/0505185.

[36]  M. Montuori,et al.  Topological approach to neural complexity. , 2004, Physical review. E, Statistical, nonlinear, and soft matter physics.

[37]  William M. Gelbart,et al.  Recombination of Genes , 1999 .

[38]  Michael L. Hines,et al.  Neuroinformatics Original Research Article Neuron and Python , 2022 .

[39]  Pedro Larrañaga,et al.  Research topics in discrete estimation of distribution algorithms based on factorizations , 2009, Memetic Comput..

[40]  J. A. Lozano,et al.  Estimation of Distribution Algorithms: A New Tool for Evolutionary Computation , 2001 .

[41]  R. K. Ursem Multi-objective Optimization using Evolutionary Algorithms , 2009 .

[42]  Pedro Larrañaga,et al.  Estimation of Distribution Algorithms , 2002, Genetic Algorithms and Evolutionary Computation.

[43]  H. Mühlenbein,et al.  From Recombination of Genes to the Estimation of Distributions I. Binary Parameters , 1996, PPSN.

[44]  Henry Markram,et al.  A Novel Multiple Objective Optimization Framework for Constraining Conductance-Based Neuron Models by Experimental Data , 2007, Front. Neurosci..

[45]  Michael Defoin-Platel,et al.  Quantum-Inspired Evolutionary Algorithm: A Multimodel EDA , 2009, IEEE Transactions on Evolutionary Computation.