Population Exploration on Genotype Networks in Genetic Programming

Redundant genotype-to-phenotype mappings are pervasive in evolutionary computation. Such redundancy allows populations to expand in neutral genotypic regions where mutations to a genotype do not alter the phenotypic outcome. Genotype networks have been proposed as a useful framework to characterize the distribution of neutrality among genotypes and phenotypes. In this study, we examine a simple Genetic Programming model that has a finite and compact genotype space by characterizing its genotype networks. We study the topology of individual genotype networks underlying unique phenotypes, investigate the genotypic properties as vertices in genotype networks, and discuss the correlation of these network properties with robustness and evolvability. Using GP simulations of a population, we demonstrate how an evolutionary population diffuses on genotype networks.

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

[2]  P. Turner,et al.  Robustness promotes evolvability of thermotolerance in an RNA virus , 2008, BMC Evolutionary Biology.

[3]  C. Ofria,et al.  EVOLUTION AND DETECTION OF GENETIC ROBUSTNESS , 2003 .

[4]  Jeffrey E. Barrick,et al.  Balancing Robustness and Evolvability , 2006, PLoS biology.

[5]  Ting Hu,et al.  Neutrality and variability: two sides of evolvability in linear genetic programming , 2009, GECCO.

[6]  Alex Bavelas,et al.  Communication Patterns in Task‐Oriented Groups , 1950 .

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

[8]  Leslie G. Valiant,et al.  Evolvability , 2009, JACM.

[9]  W. Banzhaf,et al.  Evolvability and Speed of Evolutionary Algorithms in Light of Recent Developments in Biology , 2010, Journal of Artificial Evolution and Applications.

[10]  Reinhard Männer,et al.  Parallel Problem Solving from Nature — PPSN III , 1994, Lecture Notes in Computer Science.

[11]  A. Wagner,et al.  Innovation and robustness in complex regulatory gene networks , 2007, Proceedings of the National Academy of Sciences.

[12]  Eric L. Miller,et al.  The Ascent of the Abundant: How Mutational Networks Constrain Evolution , 2008, PLoS Comput. Biol..

[13]  Gert Sabidussi,et al.  The centrality index of a graph , 1966 .

[14]  Scott A. Rifkin,et al.  Genetic Properties Influencing the Evolvability of Gene Expression , 2007, Science.

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

[16]  Ting Hu,et al.  Evolutionary dynamics on multiple scales: a quantitative analysis of the interplay between genotype, phenotype, and fitness in linear genetic programming , 2012, Genetic Programming and Evolvable Machines.

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

[18]  A. Wagner.  Robustness and evolvability: a paradox resolved , 2008, Proceedings of the Royal Society B: Biological Sciences.

[19]  G. Wagner,et al.  Mutational robustness can facilitate adaptation , 2010, Nature.

[20]  G. Wagner,et al.  EVOLUTION AND DETECTION OF GENETIC ROBUSTNESS , 2003 .

[21]  Meredith V. Trotter,et al.  Robustness and evolvability. , 2010, Trends in genetics : TIG.

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

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

[24]  M. Pigliucci.  Is evolvability evolvable? , 2008, Nature Reviews Genetics.

[25]  Terence Soule,et al.  Resilient Individuals Improve Evolutionary Search , 2006, Artificial Life.

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

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

[28]  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.

[29]  Claus O. Wilke,et al.  Adaptive evolution on neutral networks , 2001, Bulletin of mathematical biology.