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    Automatic design of deterministic and non-halting membrane systems by tuning syntactical ingredients

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    Publication date
    2014
    Author
    Zhang, G.
    Rong, H.
    Ou, Z.
    Perez-Jimenez, M.J.
    Gheorghe, Marian
    Keyword
    Algorithms: Cell membrane; Communication; Computers, Molecular; Models, Biological
    Rights
    © 2014 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.
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    Abstract
    To solve the programmability issue of membrane computing models, the automatic design of membrane systems is a newly initiated and promising research direction. In this paper, we propose an automatic design method, Permutation Penalty Genetic Algorithm (PPGA), for a deterministic and non-halting membrane system by tuning membrane structures, initial objects and evolution rules. The main ideas of PPGA are the introduction of the permutation encoding technique for a membrane system, a penalty function evaluation approach for a candidate membrane system and a genetic algorithm for evolving a population of membrane systems toward a successful one fulfilling a given computational task. Experimental results show that PPGA can successfully accomplish the automatic design of a cell-like membrane system for computing the square of n ( n >/= 1 is a natural number) and can find the minimal membrane systems with respect to their membrane structures, alphabet, initial objects, and evolution rules for fulfilling the given task. We also provide the guidelines on how to set the parameters of PPGA.
    URI
    http://hdl.handle.net/10454/10828
    Version
    Accepted manuscript
    Citation
    Zhang, G., Rong, H., Ou, Z., Perez-Jimenez, M.J. and Gheorghe, M. (2014) Automatic design of deterministic and non-halting membrane systems by tuning syntactical ingredients. IEEE Transactions on Nanobioscience. 13 (3), 363-71.
    Link to publisher’s version
    https://doi.org/10.1109/TNB.2014.2341618
    Type
    Journal Article
    Collections
    Engineering and Informatics Publications

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