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.
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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 UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences 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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