Homology and linkage in crossover for linear genomes of variable length
Merlevede, Adriaan LU ; Åhl, Henrik and Troein, Carl LU
(2019)
In PLoS ONE
14(1).
- Abstract
The use of variable-length genomes in evolutionary computation has applications in optimisation when the size of the search space is unknown, and provides a unique environment to study the evolutionary dynamics of genome structure. Here, we revisit crossover for linear genomes of variable length, identifying two crucial attributes of successful recombination algorithms: the ability to retain homologous structure, and to reshuffle variant information. We introduce direct measures of these properties—homology score and linkage score—and use them to review existing crossover algorithms, as well as two novel ones. In addition, we measure the performance of these crossover methods on three different benchmark problems, and find that... (More)
The use of variable-length genomes in evolutionary computation has applications in optimisation when the size of the search space is unknown, and provides a unique environment to study the evolutionary dynamics of genome structure. Here, we revisit crossover for linear genomes of variable length, identifying two crucial attributes of successful recombination algorithms: the ability to retain homologous structure, and to reshuffle variant information. We introduce direct measures of these properties—homology score and linkage score—and use them to review existing crossover algorithms, as well as two novel ones. In addition, we measure the performance of these crossover methods on three different benchmark problems, and find that variable-length genomes out-perform fixed-length variants in all three cases. Our homology and linkage scores successfully explain the difference in performance between different crossover methods, providing a simple and insightful framework for crossover in a variable-length setting.
(Less)
- author
- Merlevede, Adriaan
LU
; Åhl, Henrik
and Troein, Carl
LU
- organization
- publishing date
- 2019
- type
- Contribution to journal
- publication status
- published
- subject
- in
- PLoS ONE
- volume
- 14
- issue
- 1
- article number
- e0209712
- publisher
- Public Library of Science (PLoS)
- external identifiers
-
- scopus:85059471099
- pmid:30605463
- ISSN
- 1932-6203
- DOI
- 10.1371/journal.pone.0209712
- project
- Crossover in evolutionary algorithms with dynamic linear genome representations
- language
- English
- LU publication?
- yes
- id
- 57ccf594-58a9-46f0-ad6c-6327e2f3fa9b
- date added to LUP
- 2019-01-11 09:28:15
- date last changed
- 2024-04-01 17:40:58
@article{57ccf594-58a9-46f0-ad6c-6327e2f3fa9b,
abstract = {{<p>The use of variable-length genomes in evolutionary computation has applications in optimisation when the size of the search space is unknown, and provides a unique environment to study the evolutionary dynamics of genome structure. Here, we revisit crossover for linear genomes of variable length, identifying two crucial attributes of successful recombination algorithms: the ability to retain homologous structure, and to reshuffle variant information. We introduce direct measures of these properties—homology score and linkage score—and use them to review existing crossover algorithms, as well as two novel ones. In addition, we measure the performance of these crossover methods on three different benchmark problems, and find that variable-length genomes out-perform fixed-length variants in all three cases. Our homology and linkage scores successfully explain the difference in performance between different crossover methods, providing a simple and insightful framework for crossover in a variable-length setting.</p>}},
author = {{Merlevede, Adriaan and Åhl, Henrik and Troein, Carl}},
issn = {{1932-6203}},
language = {{eng}},
number = {{1}},
publisher = {{Public Library of Science (PLoS)}},
series = {{PLoS ONE}},
title = {{Homology and linkage in crossover for linear genomes of variable length}},
url = {{http://dx.doi.org/10.1371/journal.pone.0209712}},
doi = {{10.1371/journal.pone.0209712}},
volume = {{14}},
year = {{2019}},
}