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Algorithmic investigations of the dynamics of species interactions

Abstract : To understand the dynamics of interaction between groups of species, for example, in a hosts/parasites (or hosts/symbionts) system, it is essential to consider the process of coevolution. The cophylogeny reconciliation model formulates the coevolution question as an optimization problem. The set of optimal solutions represents different scenarios of coevolution which need to be analyzed separately. The main result of this thesis is a novel approach that addresses the issue of the often huge number of optimal solutions which makes it difficult to analyze the results. We introduce several biologically motivated equivalence relations, each one splitting the solution space into equivalence classes. We propose polynomial-delay algorithms that enumerate the equivalence classes, and the representative solutions, i.e., the solutions taken from each equivalence class. Experimental results are then presented to illustrate the practical benefits of considering equivalence classes as a means of efficiently exploring the solution space of cophylogeny reconciliation. Based on the algorithmic results, a software called Capybara has been developed as a practical tool for analyzing cophylogeny datasets. More generally, in the area of enumeration algorithms, the problem of efficiently enumerating representative solutions is of theoretical importance. In the second part of this thesis, we provide a general framework for the enumeration of the equivalence classes of solutions for a family of optimization problems. We show that this framework can be applied to various dynamic programming problems, of which the cophylogeny problem is a special case.
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Submitted on : Monday, April 4, 2022 - 11:17:18 AM
Last modification on : Sunday, September 25, 2022 - 3:57:22 AM


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  • HAL Id : tel-03499342, version 2


Yishu Wang. Algorithmic investigations of the dynamics of species interactions. Bioinformatics [q-bio.QM]. Université de Lyon, 2021. English. ⟨NNT : 2021LYSE1196⟩. ⟨tel-03499342v2⟩



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