Theory and practice of optimal mutation rate control in Hamming spaces of DNA sequences
Belavkin, Roman V. and Channon, Alastair and Aston, Elizabeth and Aston, John and Knight, Christopher (2011) Theory and practice of optimal mutation rate control in Hamming spaces of DNA sequences. In: Advances in artificial life, ECAL 2011: proceedings of the Eleventh European Conference on the Synthesis and Simulation of Living Systems. Lenaerts, Tom and Giacobini, Mario and Bersini, Hugues and Bourgine, Paul and Dorigo, Marco and Doursat, René, eds. MIT Press, pp. 8592. ISBN 9780262297141

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Abstract
We investigate the problem of optimal control of mutation by asexual selfreplicating organisms represented by points in a metric space. We introduce the notion of a relatively monotonic fitness landscape and consider a generalisation of Fisher's geometric model of adaptation for such spaces. Using a Hamming space as a prime example, we derive the probability of adaptation as a function of reproduction parameters (e.g. mutation size or rate). Optimal control rules for the parameters are derived explicitly for some relatively monotonic landscapes, and then a general informationbased heuristic is introduced. We then evaluate our theoretical control functions against optimal mutation functions evolved from a random population of functions using a meta genetic algorithm. Our experimental results show a close match between theory and experiment. We demonstrate this result both in artificial fitness landscapes, defined by a Hamming distance, and a natural landscape, where fitness is defined by a DNAprotein affinity. We discuss how a control of mutation rate could occur and evolve in natural organisms. We also outline future directions of this work.
Item Type:  Book Section 

Research Areas:  A. > School of Science and Technology > Computer Science A. > School of Science and Technology > Computer Science > Artificial Intelligence group 
Item ID:  8399 
Useful Links:  
Depositing User:  Dr Roman Belavkin 
Date Deposited:  17 Feb 2012 05:41 
Last Modified:  01 May 2015 05:37 
URI:  http://eprints.mdx.ac.uk/id/eprint/8399 
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