Interpreting a Genotype-Phenotype Map with Rich Representations in XMLGE

11

[1]  D. Federici.  Using Embryonic Stages to increase the evolvability of development , 2004 .

[2]  Una-May O'Reilly,et al.  Genetic Programming II: Automatic Discovery of Reusable Programs. , 1994, Artificial Life.

[3]  Michael O'Neill,et al.  Coevolving antibodies with a rich representation of grammatical evolution , 2005, 2005 IEEE Congress on Evolutionary Computation.

[4]  Daniel E. Goldberg.  The design of innovation: Lessons from genetic algorithms , 1998 .

[5]  Daniel Roggen,et al.  Multi-cellular Development: Is There Scalability and Robustness to Gain? , 2004, PPSN.

[6]  Peter J. Bentley,et al.  Three Ways to Grow Designs: A Comparison of Embryogenies for an Evolutionary Design Problem , 1999, GECCO.

[7]  Michael O'Neill,et al.  No Coercion and No Prohibition, a Position Independent Encoding Scheme for Evolutionary Algorithms - The Chorus System , 2001, EuroGP.

[8]  D. Goldberg,et al.  Probabilistic Model Building and Competent Genetic Programming , 2003 .

[9]  Andy M Tyrrell,et al.  Modelling biological evolvability: implicit context and variation filtering in enzyme genetic programming. , 2004, Bio Systems.

[10]  Hidefumi Sawai,et al.  Chemical genetic algorithms: coevolution between codes and code translation , 2002 .

[11]  Kenneth Alan De Jong,et al.  An analysis of the behavior of a class of genetic adaptive systems. , 1975 .

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

[13]  W. Banzhaf,et al.  Genetic Programming of an Algorithmic Chemistry , 2005 .

[14]  Wolfgang Banzhaf,et al.  Evolving Dynamics in an Artificial Regulatory Network Model , 2004, PPSN.

[15]  Conor Ryan,et al.  Structural Emergence with Order Independent Representations , 2003, GECCO.

[16]  Wojciech Piaseczny,et al.  Chemical Genetic Programming - Coevolution Between Genotypic Strings and Phenotypic Trees , 2004, GECCO.

[17]  K. Dejong,et al.  An analysis of the behavior of a class of genetic adaptive systems , 1975 .

[18]  Kalyanmoy Deb,et al.  Messy Genetic Algorithms: Motivation, Analysis, and First Results , 1989, Complex Syst..

[19]  Jan van Leeuwen,et al.  The emergent computational potential of evolving artificial living systems , 2002, AI Commun..

[20]  Per Kristian Lehre,et al.  Developmental mappings and phenotypic complexity , 2003, The 2003 Congress on Evolutionary Computation, 2003. CEC '03..

[21]  Julian Francis Miller,et al.  Evolving Developmental Programs for Adaptation, Morphogenesis, and Self-Repair , 2003, ECAL.

[22]  Annie S. Wu,et al.  A Comparison of the Fixed and Floating Building Block Representation in the Genetic Algorithm , 1996, Evolutionary Computation.

[23]  Gregory S. Hornby,et al.  The advantages of generative grammatical encodings for physical design , 2001, Proceedings of the 2001 Congress on Evolutionary Computation (IEEE Cat. No.01TH8546).

[24]  Andreas Zell,et al.  Evolving the Ability of Limited Growth and Self-Repair for Artificial Embryos , 2003, ECAL.

[25]  S. Wolfram.  Statistical mechanics of cellular automata , 1983 .

[26]  Marc Ebner,et al.  How neutral networks influence evolvability , 2001, Complex..

[27]  D. Goldberg,et al.  BOA: the Bayesian optimization algorithm , 1999 .

[28]  M. Pelikán,et al.  The Bivariate Marginal Distribution Algorithm , 1999 .

[29]  Hitoshi Iba,et al.  Multimodal Search with Immune Based Genetic Programming , 2004, ICARIS.

[30]  Anthony Brabazon,et al.  Grammatical Swarm , 2004, GECCO.

[31]  Kalyanmoy Deb,et al.  RapidAccurate Optimization of Difficult Problems Using Fast Messy Genetic Algorithms , 1993, ICGA.

[32]  L. Segel,et al.  Design Principles for the Immune System and Other Distributed Autonomous Systems , 2001 .

[33]  Jordan B. Pollack,et al.  The Emergence of Ontogenic Scaffolding in a Stochastic Development Environment , 2004, GECCO.

[34]  Stuart A. Kauffman,et al.  The origins of order , 1993 .

[35]  Dirk Thierens,et al.  Hierarchical Genetic Algorithms , 2004, PPSN.

[36]  P. Hogeweg,et al.  Evolving mechanisms of morphogenesis: on the interplay between differential adhesion and cell differentiation. , 2000, Journal of theoretical biology.

[37]  M. Conrad.  The geometry of evolution. , 1990, Bio Systems.

[38]  J. Pollack,et al.  A computational model of symbiotic composition in evolutionary transitions. , 2003, Bio Systems.

[39]  Dirk Thierens,et al.  Toward a Better Understanding of Mixing in Genetic Algorithms , 1993 .

[40]  Peter J. Bentley,et al.  Adaptive Fractal Gene Reguatory Networks for Robot Control , 2005 .

[41]  H. Van Dyke Parunak,et al.  Entropy and self-organization in multi-agent systems , 2001, AGENTS '01.

[42]  I. Cohen.  Tending Adam's Garden: Evolving the Cognitive Immune Self , 2004 .

[43]  Eric van der Vlist,et al.  XML Schema , 2002 .

[44]  Michael O'Neill,et al.  Grammatical evolution - evolutionary automatic programming in an arbitrary language , 2003, Genetic programming.

[45]  Eric Bonabeau,et al.  From Classical Models of Morphogenesis to Agent-Based Models of Pattern Formation , 1997, Artificial Life.

[46]  Hussein A. Abbass,et al.  Grammar model-based program evolution , 2004, Proceedings of the 2004 Congress on Evolutionary Computation (IEEE Cat. No.04TH8753).

[47]  Robert Richards.  Extensible Stylesheet Language Transformations (XSLT) , 2006 .

[48]  Conor Ryan,et al.  Grammatical Evolution by Grammatical Evolution: The Evolution of Grammar and Genetic Code , 2004, EuroGP.

[49]  Wolfgang Banzhaf,et al.  Genotype-Phenotype-Mapping and Neutral Variation - A Case Study in Genetic Programming , 1994, PPSN.

[50]  G. Zipf,et al.  The Psycho-Biology of Language , 1936 .

[51]  David E. Goldberg,et al.  The Design of Innovation: Lessons from and for Competent Genetic Algorithms , 2002 .

[52]  Sang Joon Kim,et al.  A Mathematical Theory of Communication , 2006 .

[53]  Annie S. Wu,et al.  Winnowing Wheat from Chaff: The Chunking GA , 2004, GECCO.

[54]  Maarten Keijzer,et al.  Improving Symbolic Regression with Interval Arithmetic and Linear Scaling , 2003, EuroGP.

[55]  Anthony Brabazon,et al.  pi-Grammatical Evolution , 2004, GECCO.

[56]  Shumeet Baluja,et al.  A Method for Integrating Genetic Search Based Function Optimization and Competitive Learning , 1994 .

[57]  Marco Dorigo,et al.  From Natural to Artificial Swarm Intelligence , 1999 .

[58]  H. D. Garis.  The Genetic Programming of an Artificial Embryo , 1992 .

[59]  W. Banzhaf.  Artificial Regulatory Networks and Genetic Programming , 2003 .

[60]  Jonathan Timmis,et al.  A Fractal Immune Network , 2004, ICARIS.

[61]  Edwin D. de Jong,et al.  Representation Development from Pareto-Coevolution , 2003, GECCO.

[62]  Peter F. Stadler,et al.  On the Evolution of Primitive Genetic Codes , 2003, Origins of life and evolution of the biosphere.

[63]  Seth Lloyd,et al.  Information measures, effective complexity, and total information , 1996, Complex..

[64]  G. Harik.  Learning gene linkage to efficiently solve problems of bounded difficulty using genetic algorithms , 1997 .

[65]  Emma Hart,et al.  Immunology as a metaphor for computational information processing : fact or fiction , 2002 .

[66]  Steven J. DeRose,et al.  XML Path Language (XPath) , 1999 .

[67]  Annie S. Wu,et al.  Testing the Robustness of the Genetic Algorithm on the Floating Building Block Representation , 1996, AAAI/IAAI, Vol. 1.

[68]  Uri Hershberg,et al.  THE EMERGENCE OF MEANING IN BIOLOGICAL SYSTEMS , 2003 .

[69]  Steven M. Gustafson.  An analysis of diversity in genetic programming , 2004 .

[70]  Paul M. B. Vitányi,et al.  Meaningful Information , 2001, IEEE Transactions on Information Theory.

[71]  R. Matthews,et al.  Ants. , 1898, Science.

[72]  Stephanie Forrest,et al.  An immunological model of distributed detection and its application to computer security , 1999 .

[73]  M. Huynen.  Exploring phenotype space through neutral evolution , 1996, Journal of Molecular Evolution.

[74]  Hiroaki Kitano,et al.  Designing Neural Networks Using Genetic Algorithms with Graph Generation System , 1990, Complex Syst..

[75]  Michael Conrad,et al.  The effect of weak interactions on the structure of adaptive surfaces , 1997, Soft Comput..

[76]  Jordan B. Pollack,et al.  Incremental commitment in genetic algorithms , 1999 .

[77]  Anthony Brabazon,et al.  mGGA: The meta-Grammar Genetic Algorithm , 2005, EuroGP.

[78]  Wolfgang Banzhaf,et al.  The evolution of genetic code in Genetic Programming , 1999 .

[79]  R. Pfeifer,et al.  Repeated structure and dissociation of genotypic and phenotypic complexity in artificial ontogeny , 2001 .

[80]  Annie S. Wu,et al.  Effects of Module Encapsulation in Repetitively Modular Genotypes on the Search Space , 2004, GECCO.

[81]  Kunihiko Kaneko,et al.  Origin of multicellular organisms as an inevitable consequence of dynamical systems , 2002, The Anatomical record.

[82]  Peter J. Bentley,et al.  Fractal Proteins , 2004, Genetic Programming and Evolvable Machines.

[83]  C. Adami,et al.  Evolution of Biological Complexity , 2000, Proc. Natl. Acad. Sci. USA.

[84]  Michael A. Lones,et al.  Crossover and bloat in the functionality model of enzyme genetic programming , 2002, Proceedings of the 2002 Congress on Evolutionary Computation. CEC'02 (Cat. No.02TH8600).

[85]  M. F.,et al.  Bibliography , 1985, Experimental Gerontology.

[86]  Daniel Polani,et al.  Meaningful Information, Sensor Evolution, and the Temporal Horizon of Embodied Organisms , 2002 .

[87]  Seth Lloyd,et al.  Information measures, effective complexity, and total information , 1996 .

[88]  V. Bedian,et al.  Self-description and the origin of the genetic code. , 2001, Bio Systems.

[89]  K. De Jong,et al.  An examination of building block dynamics in different representations , 1999, Proceedings of the 1999 Congress on Evolutionary Computation-CEC99 (Cat. No. 99TH8406).

[90]  Annie S. Wu,et al.  The Modular Genetic Algorithm: Exploiting Regularities in the Problem Space , 2003, ISCIS.

[91]  James P. Crutchfield,et al.  The Evolutionary Design of Collective Computation in Cellular Automata , 1998, adap-org/9809001.

[92]  R. Lewontin.  ‘The Selfish Gene’ , 1977, Nature.

[93]  Volkert,et al.  The Role of Weak Interactions in Biological Systems: the Dual Dynamics Model. , 1998, Journal of theoretical biology.

[94]  Arantxa Etxeverria.  The Origins of Order , 1993 .

[95]  L. G. Volkert,et al.  Enhancing evolvability with mutation buffering mediated through multiple weak interactions. , 2003, Bio Systems.

[96]  Günter P. Wagner,et al.  Complex Adaptations and the Evolution of Evolvability , 2005 .

[97]  Larry D. Pyeatt,et al.  A comparison between cellular encoding and direct encoding for genetic neural networks , 1996 .

[98]  Annie S. Wu,et al.  The Proportional Genetic Algorithm: Gene Expression in a Genetic Algorithm , 2002, Genetic Programming and Evolvable Machines.

[99]  Dirk Thierens,et al.  On the complexity of hierarchical problem solving , 2005, GECCO '05.

[100]  Peter Eggenberger,et al.  Evolving Morphologies of Simulated 3d Organisms Based on Differential Gene Expression , 1997 .

[101]  Uri Hershberg,et al.  The immune system and other cognitive systems , 2001, Complex..

[102]  Dietmar Saupe,et al.  Chaos and fractals - new frontiers of science , 1992 .

[103]  Mauro Birattari,et al.  Swarm Intelligence , 2012, Lecture Notes in Computer Science.

[104]  Michael O’Neill,et al.  An Evolutionary Approach to Complex System Regulation Using Grammatical Evolution , 2004 .

[105]  Marcus Hutter,et al.  Algorithmic Information Theory , 1977, IBM J. Res. Dev..

[106]  Alan S. Perelson,et al.  The Evolution of Emergent Organization in Immune System Gene Libraries , 1995, ICGA.

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

[108]  Conor Ryan,et al.  Ripple Crossover in Genetic Programming , 2001, EuroGP.

[109]  S. Forrest,et al.  Antibody repertoires and pathogen recognition: the role of germline diversity and somatic hypermutation , 1999 .

[110]  Jim Melton,et al.  XML schema , 2003, SGMD.

[111]  Phil Husbands,et al.  An Evolutionary Approach to Complex System Regulation Using Grammatical Evolution , 2004 .

[112]  Christoph Adami,et al.  Sequence complexity in Darwinian evolution , 2002, Complex..

[113]  Rich Caruana,et al.  Removing the Genetics from the Standard Genetic Algorithm , 1995, ICML.

[114]  V.,et al.  Social Insects , 1990, Springer Berlin Heidelberg.

[115]  Seth Lloyd,et al.  Effective Complexity , 1995 .

[116]  C. M. Sperberg-McQueen,et al.  Extensible Markup Language (XML) , 1997, World Wide Web J..

[117]  Martin Pelikan,et al.  Hierarchical Bayesian optimization algorithm: toward a new generation of evolutionary algorithms , 2010, SICE 2003 Annual Conference (IEEE Cat. No.03TH8734).

[118]  David E. Goldberg,et al.  Learning Linkage , 1996, FOGA.

[119]  Uri Hershberg,et al.  Optimal exemplar learning in cognitive systems , 2003 .

[120]  Regina Dunlea,et al.  Simple Object Access Protocol (SOAP) , 2005 .

[121]  C. Tsallis,et al.  Nonextensive Entropy: Interdisciplinary Applications , 2004 .

[122]  Michael Adam Lones,et al.  Enzyme genetic programming : modelling biological evolvability in genetic programming , 2003 .