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Mod/Resc Parsimony Inference

Igor Nor 1, 2 Danny Hermelin 3 Sylvain Charlat 4 Jan Engelstadter 5 Max Reuter 6 Olivier Duron 7 Marie-France Sagot 1, 2, * 
* Corresponding author
1 Baobab
PEGASE - Département PEGASE [LBBE]
2 BAMBOO - An algorithmic view on genomes, cells, and environments
Inria Grenoble - Rhône-Alpes, LBBE - Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
4 Génétique et évolution des interactions hôtes-parasites
GINSENG - Département génétique, interactions et évolution des génomes [LBBE]
Abstract : We address in this paper a new computational biology problem that aims at understanding a mechanism that could potentially be used to genetically manipulate natural insect populations infected by inherited, intra-cellular parasitic bacteria. In this problem, that we denote by Mod/Resc Parsimony Inference, we are given a boolean matrix and the goal is to find two other boolean matrices with a minimum number of columns such that an appropriately defined operation on these matrices gives back the input. We show that this is formally equivalent to the Bipartite Biclique Edge Cover problem and derive some complexity results for our problem using this equivalence. We provide a new, fixed-parameter tractability approach for solving both that slightly improves upon a previously published algorithm for the Bipartite Biclique Edge Cover. Finally, we present experimental results where we applied some of our techniques to a real-life data set.
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Submitted on : Thursday, March 22, 2012 - 3:34:21 PM
Last modification on : Friday, August 5, 2022 - 10:38:04 AM
Long-term archiving on: : Saturday, June 23, 2012 - 2:35:39 AM


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Igor Nor, Danny Hermelin, Sylvain Charlat, Jan Engelstadter, Max Reuter, et al.. Mod/Resc Parsimony Inference. Combinatorial Pattern Matching, Jun 2010, New York, United States. pp.202--213, ⟨10.1007/978-3-642-13509-5_19⟩. ⟨hal-00681830⟩



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