4 Search Results for "Bérard, Béatrice"


Document
Reconstructing Rearrangement Phylogenies of Natural Genomes

Authors: Leonard Bohnenkämper, Jens Stoye, and Daniel Dörr

Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)


Abstract
We study the classical problem of inferring ancestral genomes from a set of extant genomes under a given phylogeny, known as the Small Parsimony Problem (SPP). Genomes are represented as sequences of oriented markers, organized in one or more linear or circular chromosomes. Any marker may appear in several copies, without restriction on orientation or genomic location, known as the natural genomes model. Evolutionary events along the branches of the phylogeny encompass large scale rearrangements, including segmental inversions, translocations, gain and loss (DCJ-indel model). Even under simpler rearrangement models, such as the classical breakpoint model without duplicates, the SPP is computationally intractable. Nevertheless, the SPP for natural genomes under the DCJ-indel model has been studied recently, with limited success. Here, we improve on that earlier work, giving a highly optimized ILP that is able to solve the SPP for sufficiently small phylogenies and gene families. A notable improvement w.r.t. the previous result is an optimized way of handling both circular and linear chromosomes. This is especially relevant to the SPP, since the chromosomal structure of ancestral genomes is unknown and the solution space for this chromosomal structure is typically large. We benchmark our method on simulated and real data. On simulated phylogenies we observe a considerable performance improvement on problems that include linear chromosomes. And even when the ground truth contains only one circular chromosome per genome, our method outperforms its predecessor due to its optimized handling of the solution space. The practical advantage becomes also visible in an analysis of seven Anopheles taxa.

Cite as

Leonard Bohnenkämper, Jens Stoye, and Daniel Dörr. Reconstructing Rearrangement Phylogenies of Natural Genomes. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 12:1-12:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)


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@InProceedings{bohnenkamper_et_al:LIPIcs.WABI.2024.12,
  author =	{Bohnenk\"{a}mper, Leonard and Stoye, Jens and D\"{o}rr, Daniel},
  title =	{{Reconstructing Rearrangement Phylogenies of Natural Genomes}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{12:1--12:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-340-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{312},
  editor =	{Pissis, Solon P. and Sung, Wing-Kin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2024.12},
  URN =		{urn:nbn:de:0030-drops-206564},
  doi =		{10.4230/LIPIcs.WABI.2024.12},
  annote =	{Keywords: genome rearrangement, ancestral reconstruction, small parsimony, integer linear programming, double-cut-and-join}
}
Document
Hyper Partial Order Logic

Authors: Béatrice Bérard, Stefan Haar, and Loic Hélouët

Published in: LIPIcs, Volume 122, 38th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2018)


Abstract
We define HyPOL, a local hyper logic for partial order models, expressing properties of sets of runs. These properties depict shapes of causal dependencies in sets of partially ordered executions, with similarity relations defined as isomorphisms of past observations. Unsurprisingly, since comparison of projections are included, satisfiability of this logic is undecidable. We then address model checking of HyPOL and show that, already for safe Petri nets, the problem is undecidable. Fortunately, sensible restrictions of observations and nets allow us to bring back model checking of HyPOL to a decidable problem, namely model checking of MSO on graphs of bounded treewidth.

Cite as

Béatrice Bérard, Stefan Haar, and Loic Hélouët. Hyper Partial Order Logic. In 38th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 122, pp. 20:1-20:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)


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@InProceedings{berard_et_al:LIPIcs.FSTTCS.2018.20,
  author =	{B\'{e}rard, B\'{e}atrice and Haar, Stefan and H\'{e}lou\"{e}t, Loic},
  title =	{{Hyper Partial Order Logic}},
  booktitle =	{38th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2018)},
  pages =	{20:1--20:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-093-4},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{122},
  editor =	{Ganguly, Sumit and Pandya, Paritosh},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FSTTCS.2018.20},
  URN =		{urn:nbn:de:0030-drops-99190},
  doi =		{10.4230/LIPIcs.FSTTCS.2018.20},
  annote =	{Keywords: Partial orders, logic, hyper-logic}
}
Document
Finite Bisimulations for Dynamical Systems with Overlapping Trajectories

Authors: Béatrice Bérard, Patricia Bouyer, and Vincent Jugé

Published in: LIPIcs, Volume 119, 27th EACSL Annual Conference on Computer Science Logic (CSL 2018)


Abstract
Having a finite bisimulation is a good feature for a dynamical system, since it can lead to the decidability of the verification of reachability properties. We investigate a new class of o-minimal dynamical systems with very general flows, where the classical restrictions on trajectory intersections are partly lifted. We identify conditions, that we call Finite and Uniform Crossing: When Finite Crossing holds, the time-abstract bisimulation is computable and, under the stronger Uniform Crossing assumption, this bisimulation is finite and definable.

Cite as

Béatrice Bérard, Patricia Bouyer, and Vincent Jugé. Finite Bisimulations for Dynamical Systems with Overlapping Trajectories. In 27th EACSL Annual Conference on Computer Science Logic (CSL 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 119, pp. 26:1-26:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)


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@InProceedings{berard_et_al:LIPIcs.CSL.2018.26,
  author =	{B\'{e}rard, B\'{e}atrice and Bouyer, Patricia and Jug\'{e}, Vincent},
  title =	{{Finite Bisimulations for Dynamical Systems with Overlapping Trajectories}},
  booktitle =	{27th EACSL Annual Conference on Computer Science Logic (CSL 2018)},
  pages =	{26:1--26:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-088-0},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{119},
  editor =	{Ghica, Dan R. and Jung, Achim},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CSL.2018.26},
  URN =		{urn:nbn:de:0030-drops-96932},
  doi =		{10.4230/LIPIcs.CSL.2018.26},
  annote =	{Keywords: Reachability properties, dynamical systems, o-minimal structures, intersecting trajectories, finite bisimulations}
}
Document
Probabilistic Disclosure: Maximisation vs. Minimisation

Authors: Béatrice Bérard, Serge Haddad, and Engel Lefaucheux

Published in: LIPIcs, Volume 93, 37th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2017)


Abstract
We consider opacity questions where an observation function provides to an external attacker a view of the states along executions and secret executions are those visiting some state from a fixed subset. Disclosure occurs when the observer can deduce from a finite observation that the execution is secret, the epsilon-disclosure variant corresponding to the execution being secret with probability greater than 1 - epsilon. In a probabilistic and non deterministic setting, where an internal agent can choose between actions, there are two points of view, depending on the status of this agent: the successive choices can either help the attacker trying to disclose the secret, if the system has been corrupted, or they can prevent disclosure as much as possible if these choices are part of the system design. In the former situation, corresponding to a worst case, the disclosure value is the supremum over the strategies of the probability to disclose the secret (maximisation), whereas in the latter case, the disclosure is the infimum (minimisation). We address quantitative problems (comparing the optimal value with a threshold) and qualitative ones (when the threshold is zero or one) related to both forms of disclosure for a fixed or finite horizon. For all problems, we characterise their decidability status and their complexity. We discover a surprising asymmetry: on the one hand optimal strategies may be chosen among deterministic ones in maximisation problems, while it is not the case for minimisation. On the other hand, for the questions addressed here, more minimisation problems than maximisation ones are decidable.

Cite as

Béatrice Bérard, Serge Haddad, and Engel Lefaucheux. Probabilistic Disclosure: Maximisation vs. Minimisation. In 37th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 93, pp. 13:1-13:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)


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@InProceedings{berard_et_al:LIPIcs.FSTTCS.2017.13,
  author =	{B\'{e}rard, B\'{e}atrice and Haddad, Serge and Lefaucheux, Engel},
  title =	{{Probabilistic Disclosure: Maximisation vs. Minimisation}},
  booktitle =	{37th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2017)},
  pages =	{13:1--13:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-055-2},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{93},
  editor =	{Lokam, Satya and Ramanujam, R.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FSTTCS.2017.13},
  URN =		{urn:nbn:de:0030-drops-83844},
  doi =		{10.4230/LIPIcs.FSTTCS.2017.13},
  annote =	{Keywords: Partially observed systems, Opacity, Markov chain, Markov decision process}
}
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