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Neutrality and the Evolvability of Boolean Function Landscape [chapter]

Tina Yu, Julian Miller
2001 Lecture Notes in Computer Science  
We tested this method on a Boolean benchmark problem. The experimental results indicate that there is a positive relationship between neutrality and evolvability: neutrality improves evolvability.  ...  This work is a study of neutrality in the context of Evolutionary Computation systems.  ...  Acknowledgements We would like to thank Vesselin Vassilev and Jennifer Powell for their suggestions. The resource support by CITC Math Modeling Disciplines is also greatly appreciated.  ... 
doi:10.1007/3-540-45355-5_16 fatcat:4ktwnukzpfb5tk4phqpr3yos6u

Evolution of canalizing Boolean networks

A. Szejka, B. Drossel
2007 European Physical Journal B : Condensed Matter Physics  
Mutations change the connections and the functions of the nodes. Our fitness criterion is the robustness of the dynamical attractors against small perturbations.  ...  We find that with this fitness criterion the global maximum is always reached and that there is a huge neutral space of 100% fitness.  ...  In [8] , networks with connectivities of K = 2 and K = 10 are evolved by creating mutants through the rewiring of connections or the changing of bits of Boolean functions.  ... 
doi:10.1140/epjb/e2007-00135-2 fatcat:qjfjr2rearcfvkeoysj2hj26ky

Robustness as an evolutionary principle

S. Bornholdt, K. Sneppen
2000 Proceedings of the Royal Society of London. Biological Sciences  
We suggest simulating evolution of complex organisms using a model constrained solely by the requirement of robustness in its expression patterns.  ...  Evidence for dynamical features in the evolved networks is found that can be related to biological observables.  ...  We thank Stanley Brown for valuable comments on the manuscript.  ... 
doi:10.1098/rspb.2000.1280 pmid:11413644 pmcid:PMC1690809 fatcat:mag4qdkfxjd5nm7msmdtq7lh5m

A study of the neutrality of Boolean function landscapes in genetic programming

Leonardo Vanneschi, Yuri Pirola, Giancarlo Mauri, Marco Tomassini, Philippe Collard, Sébastien Verel
2012 Theoretical Computer Science  
The neutrality of genetic programming Boolean function landscapes is investigated in this paper.  ...  This study indicates the existence of a relationship between our neutrality measures and the performance of genetic programming for the problems studied.  ...  Finally, instead of using a fixed set of functions to build solutions, we compare the landscapes induced by different sets of Boolean operators ({nand} and {xor, not} for the even parity landscapes, and  ... 
doi:10.1016/j.tcs.2011.03.011 fatcat:xegh6llqy5cg5opd5anuaskhfi

Evolution of a population of random Boolean networks

T. Mihaljev, B. Drossel
2009 European Physical Journal B : Condensed Matter Physics  
We investigate the evolution of populations of random Boolean networks under selection for robustness of the dynamics with respect to the perturbation of the state of a node.  ...  The fitness landscape contains a huge plateau of maximum fitness that spans the entire network space.  ...  We have seen that in such a landscape networks can evolve without loss of dynamical robustness, i.e., of functionality.  ... 
doi:10.1140/epjb/e2009-00032-8 fatcat:dzchxlx52nckrkhper7xhj2k3q

Reliability of genetic networks is evolvable

Stefan Braunewell, Stefan Bornholdt
2008 Physical Review E  
Further, the evolvability of networks towards reliable dynamics while retaining their function is investigated and a high success rate is found.  ...  Control of the living cell functions with remarkable reliability despite the stochastic nature of the underlying molecular networks -- a property presumably optimized by biological evolution.  ...  The landscape can be easily shaped and robustness in dynamical functioning can be achieved after very few evolution steps.  ... 
doi:10.1103/physreve.77.060902 pmid:18643208 fatcat:5yyogrgmxfaxdiksnys6bw4dce

On the evolution of Boolean networks for computation: a guide RNA mechanism

Larry Bull
2015 International Journal of Parallel, Emergent and Distributed Systems  
) include a second set of B' connections to defined nodes and another Boolean update function.  ...  a functional role, rather it is maintained under drift/neutral processes.  ... 
doi:10.1080/17445760.2015.1057590 fatcat:asddqfnrmja3jdv5axopupuowq

The Role of Redundancy in the Robustness of Random Boolean Networks [article]

Carlos Gershenson, Stuart A. Kauffman, Ilya Shmulevich
2006 arXiv   pre-print
Evolution depends on the possibility of successfully exploring fitness landscapes via mutation and recombination.  ...  Random Boolean networks (RBNs), being general models, can be used to explore theories of how evolution can take place in rugged landscapes; or even change the landscapes.  ...  C.G. was partly supported by the Consejo Nacional de Ciencia y Teconolgía (CONACyT) of México.  ... 
arXiv:nlin/0511018v2 fatcat:cwp5hcqwq5adbmuf7xxtjagsjy

Evolving Boolean Networks with RNA Editing [article]

Larry Bull
2015 arXiv   pre-print
The editing of transcribed RNA by other molecules such that the form of the final product differs from that specified in the corresponding DNA sequence is ubiquitous.  ...  This paper uses an abstract, tunable Boolean genetic regulatory network model to explore aspects of RNA editing.  ...  ) include a second set of B' connections to defined nodes and another Boolean update function.  ... 
arXiv:1505.01980v1 fatcat:wpiv4ysm75ewdihlksmhph44uu

A quantitative study of neutrality in GP boolean landscapes

Leonardo Vanneschi, Yuri Pirola, Philippe Collard
2006 Proceedings of the 8th annual conference on Genetic and evolutionary computation - GECCO '06  
We compare the fitness landscape induced by two different sets of functional operators ({nand} and {xor ; not}).  ...  Neutrality of some boolean parity fitness landscapes is investigated in this paper.  ...  In [2] , Collard et al. studied synthetic neutrality and its effects on the evolvability of GAs.  ... 
doi:10.1145/1143997.1144152 dblp:conf/gecco/VanneschiPC06 fatcat:q76aqey3qnfntnc5kun52qw5fa

Program evolvability under environmental variations and neutrality

Tina Yu
2007 Proceedings of the 2007 GECCO conference companion on Genetic and evolutionary computation - GECCO '07  
Similar to biological evolution, the genetic programming populations exploit neutrality to cope with environmental fluctuations and evolve evolvability.  ...  One recent research reported that depending on the rates of environmental variation, populations evolve toward genotypes in different regions of the neutral networks to adapt to the changes.  ...  be easily switched into the other Boolean function with a small number of mutations.  ... 
doi:10.1145/1274000.1274041 dblp:conf/gecco/Yu07 fatcat:2z7krk2vfjhfpmcwargqbxkzla

Through the Interaction of Neutral and Adaptive Mutations, Evolutionary Search Finds a Way

Tina Yu, Julian Francis Miller
2006 Artificial Life  
An evolutionary system that supports the interaction of neutral and adaptive mutations is investigated.  ...  Experimental results on a Boolean function and needle-in-haystack problems show that this system enables evolutionary search to find better solutions faster.  ...  Experiments on a Boolean Function Landscape Even-3-parity is a Boolean function that takes three Boolean inputs and returns TRUE only if an even number of inputs are TRUE.  ... 
doi:10.1162/artl.2006.12.4.525 pmid:16953784 fatcat:2o3nv57v2je2rjkoszy3plv24e

Neutrality in evolutionary algorithms… What do we know?

Edgar Galván-López, Riccardo Poli, Ahmed Kattan, Michael O'Neill, Anthony Brabazon
2011 Evolving Systems  
Using as a framework the origin of neutrality and its study in different paradigms of EAs (e.g., Genetic Algorithms, Genetic Programming), we discuss the most significant works and findings on this topic  ...  Abstract Over the last years, the effects of neutrality have attracted the attention of many researchers in the Evolutionary Algorithms (EAs) community.  ...  Acknowledgments We would like to thank the editor, associate editor and reviewers for their fair and useful comments and ideas. The paper has been considerable strengthened thanks to their feedback.  ... 
doi:10.1007/s12530-011-9030-5 fatcat:oiao7sjqnbh2bj45c4nwebv43u

Robustness, Evolvability, and Accessibility in Linear Genetic Programming [chapter]

Ting Hu, Joshua L. Payne, Wolfgang Banzhaf, Jason H. Moore
2011 Lecture Notes in Computer Science  
Here, we argue that understanding the influence of neutrality on evolutionary optimization requires an understanding of the interplay between robustness and evolvability at the genotypic and phenotypic  ...  Using an ensemble of random walks, we demonstrate that the benefit of neutrality crucially depends upon its phenotypic distribution.  ...  Acknowledgments This work was partially supported by NIH grants R01-LM009012, R01-LM010098, and R01-AI59694. J.L.P. was supported by NIH grant K25-CA134286.  ... 
doi:10.1007/978-3-642-20407-4_2 fatcat:4mcgfgad5vca7oxwoc3loz6ila

Neutral Mutations and Punctuated Equilibrium in Evolving Genetic Networks

Stefan Bornholdt, Kim Sneppen
1998 Physical Review Letters  
We evolve connectivity in a single Boolean network, and demonstrate how the sole requirement of sequential matching of attractors may open for an evolution that exhibits punctuated equilibrium.  ...  Boolean networks may be viewed as idealizations of biological genetic networks, where each node is represented by an on-off switch which is a function of the binary output from some other nodes.  ...  ACKNOWLEDGMENTS S.B. thanks NORDITA, Copenhagen, for kind support and warm hospitality and the Deutsche Forschungsgemeinschaft for supporting this work. 8  ... 
doi:10.1103/physrevlett.81.236 fatcat:ebrpi3ekhbaqdoany5sewnldza
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