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Reconstructing Phylogenetic Networks via Cherry Picking and Machine Learning
- Source :
- 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022), 1-22, STARTPAGE=1;ENDPAGE=22;TITLE=22nd International Workshop on Algorithms in Bioinformatics (WABI 2022), Bernardini, G, van Iersel, L, Julien, E & Stougie, L 2022, Reconstructing Phylogenetic Networks via Cherry Picking and Machine Learning . in C Boucher & S Rahmann (eds), 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022) . Leibniz International Proceedings in Informatics, LIPIcs, vol. 242, Schloss Dagstuhl-Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, Dagstuhl, Germany, pp. 1-22, 22nd International Workshop on Algorithms in Bioinformatics, WABI 2022, Potsdam, Germany, 5/09/22 . https://doi.org/10.4230/LIPIcs.WABI.2022.16, WABI 2022-2nd International Workshop on Algorithms in Bioinformatics, WABI 2022-2nd International Workshop on Algorithms in Bioinformatics, Sep 2022, Potsdam, Germany. ⟨10.4230/LIPIcs.WABI.2022.16⟩, 22nd International Workshop on Algorithms in Bioinformatics, WABI 2022
- Publication Year :
- 2022
- Publisher :
- Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2022.
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Abstract
- Combining a set of phylogenetic trees into a single phylogenetic network that explains all of them is a fundamental challenge in evolutionary studies. In this paper, we apply the recently-introduced theoretical framework of cherry picking to design a class of heuristics that are guaranteed to produce a network containing each of the input trees, for practical-size datasets. The main contribution of this paper is the design and training of a machine learning model that captures essential information on the structure of the input trees and guides the algorithms towards better solutions. This is one of the first applications of machine learning to phylogenetic studies, and we show its promise with a proof-of-concept experimental study conducted on both simulated and real data consisting of binary trees with no missing taxa.<br />LIPIcs, Vol. 242, 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022), pages 16:1-16:22
Details
- Language :
- English
- Database :
- OpenAIRE
- Journal :
- 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022), 1-22, STARTPAGE=1;ENDPAGE=22;TITLE=22nd International Workshop on Algorithms in Bioinformatics (WABI 2022), Bernardini, G, van Iersel, L, Julien, E & Stougie, L 2022, Reconstructing Phylogenetic Networks via Cherry Picking and Machine Learning . in C Boucher & S Rahmann (eds), 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022) . Leibniz International Proceedings in Informatics, LIPIcs, vol. 242, Schloss Dagstuhl-Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, Dagstuhl, Germany, pp. 1-22, 22nd International Workshop on Algorithms in Bioinformatics, WABI 2022, Potsdam, Germany, 5/09/22 . https://doi.org/10.4230/LIPIcs.WABI.2022.16, WABI 2022-2nd International Workshop on Algorithms in Bioinformatics, WABI 2022-2nd International Workshop on Algorithms in Bioinformatics, Sep 2022, Potsdam, Germany. ⟨10.4230/LIPIcs.WABI.2022.16⟩, 22nd International Workshop on Algorithms in Bioinformatics, WABI 2022
- Accession number :
- edsair.doi.dedup.....9ea6310d4c5e2e4704835a633fc8baea