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Efficient Non-Coding Rna Gene Searches Through Classical And Evolutionary Methods, Jennifer Smith
Efficient Non-Coding Rna Gene Searches Through Classical And Evolutionary Methods, Jennifer Smith
Jennifer A. Smith
Successful non-coding RNA gene searching requires examination of long-range intramolecular base pairing possibilities. This results in search algorithms with extremely long run times such that large-scale use of the algorithms often becomes computationally infeasible. Methods for the efficient search of the solution space are examined. A review of the standard dynamic-programming covariance model search algorithm is given. An analysis of the statistically probable regions of the search space is undertaken and a method of limiting the traditional dynamic-programming algorithm to this region is shown. An alternative search method using a Genetic Algorithm (GA) which favours the probable region of the …
The Crowding Approach To Niching In Genetic Algorithms, Ole J. Mengshoel, David E. Goldberg
The Crowding Approach To Niching In Genetic Algorithms, Ole J. Mengshoel, David E. Goldberg
Ole J Mengshoel
A wide range of niching techniques have been investigated in evolutionary and genetic algorithms. In this article, we focus on niching using crowding techniques in the context of what we call local tournament algorithms. In addition to deterministic and probabilistic crowding, the family of local tournament algorithms includes the Metropolis algorithm, simulated annealing, restricted tournament selection, and parallel recombinative simulated annealing. We describe an algorithmic and analytical framework which is applicable to a wide range of crowding algorithms. As an example of utilizing this framework, we present and analyze the probabilistic crowding niching algorithm. Like the closely related deterministic crowding …