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Genetic Improvement of computational biology software

Langdon, WB; Zile, K; (2017) Genetic Improvement of computational biology software. In: GECCO '17: Proceedings of the Genetic and Evolutionary Computation Conference Companion. (pp. pp. 1657-1660). Association for Computing Machinery (ACM): New York, NY, USA. Green open access

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Abstract

There is a cultural divide between computer scientists and biologists that needs to be addressed. The two disciplines used to be quite unrelated but many new research areas have arisen from their synergy. We selectively review two multi-disciplinary problems: dealing with contamination in sequencing data repositories and improving software using biology inspired evolutionary computing. Through several examples, we show that ideas from biology may result in optimised code and provide surprising improvements that overcome challenges in speed and quality trade-offs. On the other hand, development of computational methods is essential for maintaining contamination free databases. Computer scientists and biologists must always be sceptical of each others data, just as they would be of their own.

Type: Proceedings paper
Title: Genetic Improvement of computational biology software
Event: Genetic and Evolutionary Computation Conference (GECCO '17)
ISBN-13: 9781450349390
Open access status: An open access version is available from UCL Discovery
DOI: 10.1145/3067695.3082540
Publisher version: https://doi.org/10.1145/3067695.3082540
Language: English
Additional information: This version is the author accepted manuscript. For information on re-use, please refer to the publisher’s terms and conditions.
Keywords: genetic programming, GP, genetic improvement, GI, GGGP, search based software engineering, SBSE, software engineering, bioinformatics, next generation sequencing, NGS, DNA sequences, microarray, genechip, NCBI GEO, molecular biology, data cleansing, in silico contamination, identification and correction of mislabelled genes, big data cleanup, hitchhiking genes, 1k geneomes, 1KGP
UCL classification: UCL > Provost and Vice Provost Offices
UCL > Provost and Vice Provost Offices > UCL BEAMS
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science > Dept of Computer Science
URI: https://discovery.ucl.ac.uk/id/eprint/10060281
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