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Annie S. Wu
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Journal Articles
Publisher: Journals Gateway
Evolutionary Computation (1998) 6 (4): 387–410.
Published: 01 December 1998
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The majority of current genetic algorithms (GAs), while inspired by natural evolutionary systems, are seldom viewed as biologically plausible models. This is not a criticism of GAs, but rather a reflection of choices made regarding the level of abstraction at which biological mechanisms are modeled, and a reflection of the more engineering-oriented goals of the evolutionary computation community. Understanding better and reducing this gap between GAs and genetics has been a central issue in an interdisciplinary project whose goal is to build GA-based computational models of viral evolution. The result is a system called Virtual Virus (VIV). VIV incorporates a number of more biologically plausible mechanisms, including a more flexible genotype-to-phenotype mapping. In VIV the genes are independent of position, and genomes can vary in length and may contain noncoding regions, as well as duplicative or competing genes. Initial computational studies with VIV have already revealed several emergent phenomena of both biological and computational interest. In the absence of any penalty based on genome length, VIV develops individuals with long genomes and also performs more poorly (from a problem-solving viewpoint) than when a length penalty is used. With a fixed linear length penalty, genome length tends to increase dramatically in the early phases of evolution and then decrease to a level based on the mutation rate. The plateau genome length (i.e., the average length of individuals in the final population) generally increases in response to an increase in the base mutation rate. When VIV converges, there tend to be many copies of good alternative genes within the individuals. We observed many instances of switching between active and inactive genes during the entire evolutionary process. These observations support the conclusion that noncoding regions serve as scratch space in which VIV can explore alternative gene values. These results represent a positive step in understanding how GAs might exploit more of the power and flexibility of biological evolution while simultaneously providing better tools for understanding evolving biological systems.
Journal Articles
Publisher: Journals Gateway
Evolutionary Computation (1998) 6 (4): iii–vi.
Published: 01 December 1998
Journal Articles
Publisher: Journals Gateway
Evolutionary Computation (1996) 4 (2): 169–193.
Published: 01 June 1996
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This article compares the traditional, fixed problem representation style of a genetic algorithm (GA) with a new floating representation in which the building blocks of a problem are not fixed at specific locations on the individuals of the population. In addition, the effects of noncoding segments on both of these representations is studied. Noncoding segments are a computational model of noncoding deoxyribonucleic acid, and floating building blocks mimic the location independence of genes. The fact that these structures are prevalent in natural genetic systems suggests that they may provide some advantages to the evolutionary process. Our results show that there is a significant difference in how GAs solve a problem in the fixed and floating representations. Genetic algorithms are able to maintain a more diverse population with the floating representation. The combination of noncoding segments and floating building blocks appears to encourage a GA to take advantage of its parallel search and recombination abilities.
Journal Articles
Publisher: Journals Gateway
Evolutionary Computation (1995) 3 (2): 121–147.
Published: 01 June 1995
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The genetic algorithm (GA) is a problem-solving method that is modeled after the process of natural selection. We are interested in studying a specific aspect of the GA: the effect of noncoding segments on GA performance. Noncoding segments are segments of bits in an individual that provide no contribution, positive or negative, to the fitness of that individual. Previous research on noncoding segments suggests that including these structures in the GA may improve GA performance. Understanding when and why this improvement occurs will help us to use the GA to its full potential. In this article we discuss our hypotheses on noncoding segments and describe the results of our experiments. The experiments may be separated into two categories: testing our program on problems from previous related studies, and testing new hypotheses on the effect of noncoding segments.