Neutrality in evolutionary algorithms… What do we know?

Over the last years, the effects of neutrality have attracted the attention of many researchers in the Evolutionary Algorithms (EAs) community. A mutation from one gene to another is considered as neutral if this modification does not affect the phenotype. This article provides a general overview on the work carried out on neutrality in EAs. 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. This work points towards open issues, which we belive the community needs to address.

[1]  Julian Francis Miller Cartesian Genetic Programming , 2011, Cartesian Genetic Programming.

[2]  M. Newman,et al.  Effects of selective neutrality on the evolution of molecular species , 1998, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[3]  P. Schuster,et al.  Genotypes with phenotypes: adventures in an RNA toy world. , 1997, Biophysical chemistry.

[4]  W. Fontana,et al.  Neutrality in Technological Landscapes , 2004 .

[5]  Christian M. Reidys,et al.  Neutrality in fitness landscapes , 2001, Appl. Math. Comput..

[6]  Phil Husbands,et al.  Neutral Networks and Evolvability with Complex Genotype-Phenotype Mapping , 2001, ECAL.

[7]  N. Kasabov,et al.  Evolving Systems , 2005 .

[8]  Phil Husbands,et al.  Fitness Landscapes and Evolvability , 2002, Evolutionary Computation.

[9]  Kalyanmoy Deb,et al.  Massive Multimodality, Deception, and Genetic Algorithms , 1992, PPSN.

[10]  Peter Nordin,et al.  Genetic programming - An Introduction: On the Automatic Evolution of Computer Programs and Its Applications , 1998 .

[11]  Tim Jones Evolutionary Algorithms, Fitness Landscapes and Search , 1995 .

[12]  Anthony Brabazon,et al.  Defining locality in genetic programming to predict performance , 2010, IEEE Congress on Evolutionary Computation.

[13]  Riccardo Poli,et al.  The Effects of Constant and Bit-Wise Neutrality on Problem Hardness, Fitness Distance Correlation and Phenotypic Mutation Rates , 2012, IEEE Transactions on Evolutionary Computation.

[14]  Kazuhiro Ohkura,et al.  Estimating the Degree of Neutrality in Fitness Landscapes by the Nei’s Standard Genetic Distance – An Application to Evolutionary Robotics – , 2006, 2006 IEEE International Conference on Evolutionary Computation.

[15]  Kazuhiro Ohkura,et al.  An Approach to Evolutionary Robotics Using a Genetic Algorithm with a Variable Mutation Rate Strategy , 2004, PPSN.

[16]  Marc Toussaint,et al.  On the Evolution of Phenotypic Exploration Distributions , 2002, FOGA.

[17]  M. Huynen,et al.  Neutral evolution of mutational robustness. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[18]  J. B. S. Haldane,et al.  The cost of natural selection , 1957, Journal of Genetics.

[19]  David E. Goldberg,et al.  Construction of high-order deceptive functions using low-order Walsh coefficients , 1992, Annals of Mathematics and Artificial Intelligence.

[20]  Riccardo Poli,et al.  An empirical investigation of how and why neutrality affects evolutionary search , 2006, GECCO '06.

[21]  Julian Francis Miller,et al.  Information Characteristics and the Structure of Landscapes , 2000, Evolutionary Computation.

[22]  John R. Koza,et al.  Genetic programming - on the programming of computers by means of natural selection , 1993, Complex adaptive systems.

[23]  Per Kristian Lehre,et al.  Phenotypic complexity and local variations in neutral degree , 2007, Biosyst..

[24]  Anthony Brabazon,et al.  Defining locality as a problem difficulty measure in genetic programming , 2011, Genetic Programming and Evolvable Machines.

[25]  James P. Crutchfield,et al.  Statistical Dynamics of the Royal Road Genetic Algorithm , 1999, Theor. Comput. Sci..

[26]  Lionel Barnett,et al.  Netcrawling-optimal evolutionary search with neutral networks , 2001, Proceedings of the 2001 Congress on Evolutionary Computation (IEEE Cat. No.01TH8546).

[27]  P. Husbands,et al.  Neutral networks in an evolutionary robotics search space , 2001, Proceedings of the 2001 Congress on Evolutionary Computation (IEEE Cat. No.01TH8546).

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

[29]  Frank Neumann,et al.  A rigorous view on neutrality , 2007, 2007 IEEE Congress on Evolutionary Computation.

[30]  Edmund K. Burke,et al.  Parallel Problem Solving from Nature - PPSN IX: 9th International Conference, Reykjavik, Iceland, September 9-13, 2006, Proceedings , 2006, Parallel Problem Solving from Nature.

[31]  C. Ofria,et al.  Evolution of digital organisms at high mutation rates leads to survival of the flattest , 2001, Nature.

[32]  M. Collins Finding needles in haystacks is harder with neutrality , 2006, Genetic Programming and Evolvable Machines.

[33]  M. Ebner On the search space of genetic programming and its relation to nature's search space , 1999, Proceedings of the 1999 Congress on Evolutionary Computation-CEC99 (Cat. No. 99TH8406).

[34]  M. Huynen,et al.  Smoothness within ruggedness: the role of neutrality in adaptation. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[35]  Franz Rothlauf,et al.  Redundant Representations in Evolutionary Computation , 2003, Evolutionary Computation.

[36]  Sébastien Vérel,et al.  Scuba search: when selection meets innovation , 2004, Proceedings of the 2004 Congress on Evolutionary Computation (IEEE Cat. No.04TH8753).

[37]  K. Holsinger The neutral theory of molecular evolution , 2004 .

[38]  A. E. Eiben,et al.  Introduction to Evolutionary Computing , 2003, Natural Computing Series.

[39]  Zbigniew Michalewicz,et al.  Parameter Control in Evolutionary Algorithms , 2007, Parameter Setting in Evolutionary Algorithms.

[40]  Yuri Pirola,et al.  A quantitative study of neutrality in GP boolean landscapes , 2006, GECCO '06.

[41]  Richard A. Watson,et al.  On the Utility of Redundant Encodings in Mutation-Based Evolutionary Search , 2002, PPSN.

[42]  Rick Chow,et al.  Evolving Genotype to Phenotype Mappings with a Multiple-Chromosome Genetic Algorithm , 2004, GECCO.

[43]  Leonardo Vanneschi,et al.  Fitness Distance Correlation in Structural Mutation Genetic Programming , 2003, EuroGP.

[44]  C. Darwin The Origin of Species by Means of Natural Selection, Or, The Preservation of Favoured Races in the Struggle for Life , 1859 .

[45]  A. Wagner Robustness, evolvability, and neutrality , 2005, FEBS letters.

[46]  Richard MarkDowning Evolving Binary Decision Diagrams using Implicit Neutrality , 2005 .

[47]  Riccardo Poli,et al.  A Field Guide to Genetic Programming , 2008 .

[48]  Inman Harvey,et al.  Through the Labyrinth Evolution Finds a Way: A Silicon Ridge , 1996, ICES.

[49]  Yuri Pirola,et al.  A Comprehensive View of Fitness Landscapes with Neutrality and Fitness Clouds , 2007, EuroGP.

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

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

[52]  Riccardo Poli,et al.  On the effects of bit-wise neutrality on fitness distance correlation, phenotypic mutation rates and problem hardness , 2007, FOGA'07.

[53]  Sébastien Vérel,et al.  Fitness Clouds and Problem Hardness in Genetic Programming , 2004, GECCO.

[54]  Marc Toussaint,et al.  Neutrality: a necessity for self-adaptation , 2002, Proceedings of the 2002 Congress on Evolutionary Computation. CEC'02 (Cat. No.02TH8600).

[55]  P. Schuster,et al.  IR-98-039 / April Continuity in Evolution : On the Nature of Transitions , 1998 .

[56]  Wolfgang Banzhaf,et al.  Evolution on Neutral Networks in Genetic Programming , 2006 .

[57]  P. Schuster,et al.  From sequences to shapes and back: a case study in RNA secondary structures , 1994, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[58]  Anthony Brabazon,et al.  Towards an understanding of locality in genetic programming , 2010, GECCO '10.

[59]  Riccardo Poli,et al.  Some Steps Towards Understanding How Neutrality Affects Evolutionary Search , 2006, PPSN.

[60]  Riccardo Poli,et al.  Fitness-proportional negative slope coefficient as a hardness measure for genetic algorithms , 2007, GECCO '07.

[61]  R. Shipman,et al.  Genetic Redundancy: Desirable or Problematic for Evolutionary Adaptation? , 1999, ICANNGA.

[62]  Melanie Mitchell,et al.  The royal road for genetic algorithms: Fitness landscapes and GA performance , 1991 .

[63]  M. Newman,et al.  Effects of neutral selection on the evolution of molecular species , 1997, adap-org/9712005.

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

[65]  Dipankar Dasgupta,et al.  Nonstationary Function Optimization using the Structured Genetic Algorithm , 1992, PPSN.

[66]  Julian Francis Miller,et al.  The Advantages of Landscape Neutrality in Digital Circuit Evolution , 2000, ICES.

[67]  Julian Francis Miller,et al.  The Role of Neutral and Adaptive Mutation in an Evolutionary Search on the OneMax Problem , 2002, GECCO Late Breaking Papers.

[68]  Riccardo Poli,et al.  Foundations of Genetic Programming , 1999, Springer Berlin Heidelberg.

[69]  Karsten Weicker,et al.  Burden and Benefits of Redundancy , 2000, FOGA.

[70]  J. L. King,et al.  Non-Darwinian evolution. , 1969, Science.

[71]  R. A. Fisher,et al.  On the dominance ratio , 1990 .

[72]  J. Miller An empirical study of the efficiency of learning boolean functions using a Cartesian Genetic Programming approach , 1999 .

[73]  Pietro Corsi The age of Lamarck , 1988 .

[74]  Hans-Georg Beyer,et al.  The Theory of Evolution Strategies , 2001, Natural Computing Series.

[75]  Carlos M. Fonseca,et al.  Developing redundant binary representations for genetic search , 2005, 2005 IEEE Congress on Evolutionary Computation.

[76]  Janet Wiles,et al.  A comparison of neutral landscapes - NK, NKp and NKq , 2002, Proceedings of the 2002 Congress on Evolutionary Computation. CEC'02 (Cat. No.02TH8600).

[77]  M. Kimura Evolutionary Rate at the Molecular Level , 1968, Nature.

[78]  N. Packard,et al.  Neutral search spaces for artificial evolution: a lesson from life , 2000 .

[79]  Per Kristian Lehre,et al.  Accessibility between neutral networks in indirect genotype-phenotype mappings , 2005, 2005 IEEE Congress on Evolutionary Computation.

[80]  Riccardo Poli,et al.  The Effects of Constant Neutrality on Performance and Problem Hardness in GP , 2008, EuroGP.

[81]  Julian Francis Miller,et al.  Redundancy and computational efficiency in Cartesian genetic programming , 2006, IEEE Transactions on Evolutionary Computation.

[82]  Leonardo Vanneschi Fitness landscapes and problem hardness in genetic programming , 2009, GECCO '09.

[83]  M. Kimura The Neutral Theory of Molecular Evolution: Introduction , 1983 .

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

[85]  Kalyanmoy Deb,et al.  Ordering Genetic Algorithms and Deception , 1992, PPSN.

[86]  Leonardo Vanneschi,et al.  Fitness Distance Correlation And Problem Difficulty For Genetic Programming , 2002, GECCO.

[87]  L. Barnett Ruggedness and neutrality—the NKp family of fitness landscapes , 1998 .

[88]  R. Chow,et al.  Effects of phenotypic feedback and the coupling of genotypic and phenotypic spaces in genetic searches , 2004, Proceedings of the 2004 Congress on Evolutionary Computation (IEEE Cat. No.04TH8753).

[89]  Sébastien Vérel,et al.  Deceptiveness and neutrality the ND family of fitness landscapes , 2006, GECCO.

[90]  N. Packard,et al.  Neutral Search Spaces for Artificial Evolution: A Lesson From Life , 2000 .

[91]  Kazuhiro Ohkura,et al.  Analysis on topologies of fitness landscapes with both neutrality and ruggedness based on neutral networks , 2009, GECCO '09.

[92]  Leonardo Vanneschi Investigating Problem Hardness of Real Life Applications , 2008 .

[93]  David B. Fogel,et al.  Evolution-ary Computation 1: Basic Algorithms and Operators , 2000 .

[94]  Julian Francis Miller,et al.  Neutrality and the Evolvability of Boolean Function Landscape , 2001, EuroGP.

[95]  Kazuhiro Ohkura,et al.  Estimating the Degree of Neutrality in Fitness Landscapes by the Nei's Standard Genetic Distance-An Application to Evolutionary Robotics , 2005 .

[96]  Marc Ebner,et al.  On neutral networks and evolvability , 2001, Proceedings of the 2001 Congress on Evolutionary Computation (IEEE Cat. No.01TH8546).

[97]  Leonardo Vanneschi,et al.  Theory and practice for efficient genetic programming , 2004 .

[98]  P. Schuster,et al.  Generic properties of combinatory maps: neutral networks of RNA secondary structures. , 1997, Bulletin of mathematical biology.

[99]  Riccardo Poli,et al.  Limitations of the fitness-proportional negative slope coefficient as a difficulty measure , 2009, GECCO '09.

[100]  Julian Francis Miller,et al.  Finding Needles in Haystacks Is Not Hard with Neutrality , 2002, EuroGP.

[101]  M. Shackleton,et al.  An investigation of redundant genotype-phenotype mappings and their role in evolutionary search , 2000, Proceedings of the 2000 Congress on Evolutionary Computation. CEC00 (Cat. No.00TH8512).

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