Upon the analogy of definition of heterosis and inbreeding depresstion in terms of population genetics, the heterosis is thought to be evaluated overall with fitness. By establishing a mathematical model, the equilibr...Upon the analogy of definition of heterosis and inbreeding depresstion in terms of population genetics, the heterosis is thought to be evaluated overall with fitness. By establishing a mathematical model, the equilibrium status of three genotypes of random mating population （i. e. RR, Rr and rr） under different fitness, which exposes that heterosis is the precondition for multiallele to exist in the population. The heterosis protects the genetic diversity and makes the population owning a stronger self-control and evolution potential by improving the hetemzygote＇s fithess so as not to wash out different types of genes. It deepens Darwin＇s thoughts of individual section by making the individual fitness consonant with population fitness.展开更多
A novel immune genetic algorithm with the elitist selection and elitist crossover was proposed, which is called the immune genetic algorithm with the elitism （IGAE）. In IGAE, the new methods for computing antibody s...A novel immune genetic algorithm with the elitist selection and elitist crossover was proposed, which is called the immune genetic algorithm with the elitism （IGAE）. In IGAE, the new methods for computing antibody similarity, expected reproduction probability, and clonal selection probability were given. IGAE has three features. The first is that the similarities of two antibodies in structure and quality are all defined in the form of percentage, which helps to describe the similarity of two antibodies more accurately and to reduce the computational burden effectively. The second is that with the elitist selection and elitist crossover strategy IGAE is able to find the globally optimal solution of a given problem. The third is that the formula of expected reproduction probability of antibody can be adjusted through a parameter r, which helps to balance the population diversity and the convergence speed of IGAE so that IGAE can find the globally optimal solution of a given problem more rapidly. Two different complex multi-modal functions were selected to test the validity of IGAE. The experimental results show that IGAE can find the globally maximum/minimum values of the two functions rapidly. The experimental results also confirm that IGAE is of better performance in convergence speed, solution variation behavior, and computational efficiency compared with the canonical genetic algorithm with the elitism and the immune genetic algorithm with the information entropy and elitism.展开更多
There has been a growing interest in mathematical models to character the evolutionary algorithms. The best-known one of such models is the axiomatic model called the abstract evolutionary algorithm （AEA）, which uni...There has been a growing interest in mathematical models to character the evolutionary algorithms. The best-known one of such models is the axiomatic model called the abstract evolutionary algorithm （AEA）, which unifies most of the currently known evolutionary algorithms and describes the evolution as an abstract stochastic process composed of two fundamental abstract operators： abstract selection and evolution operators. In this paper, we first introduce the definitions of the generalized abstract selection and evolution operators. Then we discuss the characterization of some parameters related to generalized abstract selection and evolution operators. Based on these operators, we finally give the strong convergence of the generalized abstract evolutionary algorithm. The present work provides a big step toward the establishment of a unified theory of evolutionary computation.展开更多
HIV-1 evolves strongly and undergoes geographic differentiation as it spreads in diverse host populations around the world.For instance,distinct genomic backgrounds can be observed between the pandemic subtype B,preva...HIV-1 evolves strongly and undergoes geographic differentiation as it spreads in diverse host populations around the world.For instance,distinct genomic backgrounds can be observed between the pandemic subtype B,prevalent in Europe and North-America,and its offspring clade B＇ in East Asia.Here we ask whether this differentiation affects the selection pressure experienced by the virus.To answer this question we evaluate selection pressure on the HIV-1 envelope protein gp120 at the level of individual codons using a simple and fast estimation method based on the ratio ka/ks of amino acid changes to synonymous changes.To validate the approach we compare results to those from a state-of-the-art mixed-effect method.The agreement is acceptable,but the analysis also demonstrates some limitations of the simpler approach.Further,we find similar distributions of codons under stabilizing and directional selection pressure in gp120 for subtypes B and B＇ with more directional selection pressure in variable loops and more stabilizing selection in the constant regions.Focusing on codons with increased ka/ks values in B＇,we show that these codons are scattered over the whole of gp120,with remarkable clusters of higher density in regions flanking the variable loops.We identify a significant statistical association of glycosylation sites and codons with increased ka/ks values.展开更多
文摘Upon the analogy of definition of heterosis and inbreeding depresstion in terms of population genetics, the heterosis is thought to be evaluated overall with fitness. By establishing a mathematical model, the equilibrium status of three genotypes of random mating population （i. e. RR, Rr and rr） under different fitness, which exposes that heterosis is the precondition for multiallele to exist in the population. The heterosis protects the genetic diversity and makes the population owning a stronger self-control and evolution potential by improving the hetemzygote＇s fithess so as not to wash out different types of genes. It deepens Darwin＇s thoughts of individual section by making the individual fitness consonant with population fitness.
基金Project(50275150) supported by the National Natural Science Foundation of ChinaProjects(20040533035, 20070533131) supported by the National Research Foundation for the Doctoral Program of Higher Education of China
文摘A novel immune genetic algorithm with the elitist selection and elitist crossover was proposed, which is called the immune genetic algorithm with the elitism （IGAE）. In IGAE, the new methods for computing antibody similarity, expected reproduction probability, and clonal selection probability were given. IGAE has three features. The first is that the similarities of two antibodies in structure and quality are all defined in the form of percentage, which helps to describe the similarity of two antibodies more accurately and to reduce the computational burden effectively. The second is that with the elitist selection and elitist crossover strategy IGAE is able to find the globally optimal solution of a given problem. The third is that the formula of expected reproduction probability of antibody can be adjusted through a parameter r, which helps to balance the population diversity and the convergence speed of IGAE so that IGAE can find the globally optimal solution of a given problem more rapidly. Two different complex multi-modal functions were selected to test the validity of IGAE. The experimental results show that IGAE can find the globally maximum/minimum values of the two functions rapidly. The experimental results also confirm that IGAE is of better performance in convergence speed, solution variation behavior, and computational efficiency compared with the canonical genetic algorithm with the elitism and the immune genetic algorithm with the information entropy and elitism.
基金Supported by the National Science Foundation of China(60133010)Supported by the Science Foundation of Henan Province(2000110019)
文摘There has been a growing interest in mathematical models to character the evolutionary algorithms. The best-known one of such models is the axiomatic model called the abstract evolutionary algorithm （AEA）, which unifies most of the currently known evolutionary algorithms and describes the evolution as an abstract stochastic process composed of two fundamental abstract operators： abstract selection and evolution operators. In this paper, we first introduce the definitions of the generalized abstract selection and evolution operators. Then we discuss the characterization of some parameters related to generalized abstract selection and evolution operators. Based on these operators, we finally give the strong convergence of the generalized abstract evolutionary algorithm. The present work provides a big step toward the establishment of a unified theory of evolutionary computation.
基金Deutsche Forschungsgemeinschaft(http://www.dfg.de),grant TRR60/A6the University of Duisburg-Essen(http://www.uni-due.de)the Chinese Key National Science and Technology Program in the 12th Five-YearPeriod,grant 2012ZX10001006-002
文摘HIV-1 evolves strongly and undergoes geographic differentiation as it spreads in diverse host populations around the world.For instance,distinct genomic backgrounds can be observed between the pandemic subtype B,prevalent in Europe and North-America,and its offspring clade B＇ in East Asia.Here we ask whether this differentiation affects the selection pressure experienced by the virus.To answer this question we evaluate selection pressure on the HIV-1 envelope protein gp120 at the level of individual codons using a simple and fast estimation method based on the ratio ka/ks of amino acid changes to synonymous changes.To validate the approach we compare results to those from a state-of-the-art mixed-effect method.The agreement is acceptable,but the analysis also demonstrates some limitations of the simpler approach.Further,we find similar distributions of codons under stabilizing and directional selection pressure in gp120 for subtypes B and B＇ with more directional selection pressure in variable loops and more stabilizing selection in the constant regions.Focusing on codons with increased ka/ks values in B＇,we show that these codons are scattered over the whole of gp120,with remarkable clusters of higher density in regions flanking the variable loops.We identify a significant statistical association of glycosylation sites and codons with increased ka/ks values.
