5 Search Results for "Baste, Julien"

Document
DOI: 10.4230/LIPIcs.WABI.2021.7
Tree Diet: Reducing the Treewidth to Unlock FPT Algorithms in RNA Bioinformatics

Authors: Bertrand Marchand, Yann Ponty, and Laurent Bulteau

Published in: LIPIcs, Volume 201, 21st International Workshop on Algorithms in Bioinformatics (WABI 2021)

Abstract
Hard graph problems are ubiquitous in Bioinformatics, inspiring the design of specialized Fixed-Parameter Tractable algorithms, many of which rely on a combination of tree-decomposition and dynamic programming. The time/space complexities of such approaches hinge critically on low values for the treewidth tw of the input graph. In order to extend their scope of applicability, we introduce the Tree-Diet problem, i.e. the removal of a minimal set of edges such that a given tree-decomposition can be slimmed down to a prescribed treewidth tw'. Our rationale is that the time gained thanks to a smaller treewidth in a parameterized algorithm compensates the extra post-processing needed to take deleted edges into account. Our core result is an FPT dynamic programming algorithm for Tree-Diet, using 2^{O(tw)}n time and space. We complement this result with parameterized complexity lower-bounds for stronger variants (e.g., NP-hardness when tw' or tw-tw' is constant). We propose a prototype implementation for our approach which we apply on difficult instances of selected RNA-based problems: RNA design, sequence-structure alignment, and search of pseudoknotted RNAs in genomes, revealing very encouraging results. This work paves the way for a wider adoption of tree-decomposition-based algorithms in Bioinformatics.
Cite as

Bertrand Marchand, Yann Ponty, and Laurent Bulteau. Tree Diet: Reducing the Treewidth to Unlock FPT Algorithms in RNA Bioinformatics. In 21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 201, pp. 7:1-7:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

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@InProceedings{marchand_et_al:LIPIcs.WABI.2021.7,
  author =	{Marchand, Bertrand and Ponty, Yann and Bulteau, Laurent},
  title =	{{Tree Diet: Reducing the Treewidth to Unlock FPT Algorithms in RNA Bioinformatics}},
  booktitle =	{21st International Workshop on Algorithms in Bioinformatics (WABI 2021)},
  pages =	{7:1--7:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-200-6},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{201},
  editor =	{Carbone, Alessandra and El-Kebir, Mohammed},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2021.7},
  URN =		{urn:nbn:de:0030-drops-143604},
  doi =		{10.4230/LIPIcs.WABI.2021.7},
  annote =	{Keywords: RNA, treewidth, FPT algorithms, RNA design, structure-sequence alignment}
}
Document
DOI: 10.4230/LIPIcs.IPEC.2018.2
A Complexity Dichotomy for Hitting Small Planar Minors Parameterized by Treewidth

Authors: Julien Baste, Ignasi Sau, and Dimitrios M. Thilikos

Published in: LIPIcs, Volume 115, 13th International Symposium on Parameterized and Exact Computation (IPEC 2018)

Abstract
For a fixed graph H, we are interested in the parameterized complexity of the following problem, called {H}-M-Deletion, parameterized by the treewidth tw of the input graph: given an n-vertex graph G and an integer k, decide whether there exists S subseteq V(G) with |S| <= k such that G setminus S does not contain H as a minor. In previous work [IPEC, 2017] we proved that if H is planar and connected, then the problem cannot be solved in time 2^{o(tw)} * n^{O(1)} under the ETH, and can be solved in time 2^{O(tw * log tw)} * n^{O(1)}. In this article we manage to classify the optimal asymptotic complexity of {H}-M-Deletion when H is a connected planar graph on at most 5 vertices. Out of the 29 possibilities (discarding the trivial case H = K_1), we prove that 9 of them are solvable in time 2^{Theta (tw)} * n^{O(1)}, and that the other 20 ones are solvable in time 2^{Theta (tw * log tw)} * n^{O(1)}. Namely, we prove that K_4 and the diamond are the only graphs on at most 4 vertices for which the problem is solvable in time 2^{Theta (tw * log tw)} * n^{O(1)}, and that the chair and the banner are the only graphs on 5 vertices for which the problem is solvable in time 2^{Theta (tw)} * n^{O(1)}. For the version of the problem where H is forbidden as a topological minor, the case H = K_{1,4} can be solved in time 2^{Theta (tw)} * n^{O(1)}. This exhibits, to the best of our knowledge, the first difference between the computational complexity of both problems.
Cite as

Julien Baste, Ignasi Sau, and Dimitrios M. Thilikos. A Complexity Dichotomy for Hitting Small Planar Minors Parameterized by Treewidth. In 13th International Symposium on Parameterized and Exact Computation (IPEC 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 115, pp. 2:1-2:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)

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@InProceedings{baste_et_al:LIPIcs.IPEC.2018.2,
  author =	{Baste, Julien and Sau, Ignasi and Thilikos, Dimitrios M.},
  title =	{{A Complexity Dichotomy for Hitting Small Planar Minors Parameterized by Treewidth}},
  booktitle =	{13th International Symposium on Parameterized and Exact Computation (IPEC 2018)},
  pages =	{2:1--2:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-084-2},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{115},
  editor =	{Paul, Christophe and Pilipczuk, Michal},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.IPEC.2018.2},
  URN =		{urn:nbn:de:0030-drops-102033},
  doi =		{10.4230/LIPIcs.IPEC.2018.2},
  annote =	{Keywords: parameterized complexity, graph minors, treewidth, hitting minors, topological minors, dynamic programming, Exponential Time Hypothesis}
}
Document
DOI: 10.4230/LIPIcs.IPEC.2017.3
Parameterized Complexity of Finding a Spanning Tree with Minimum Reload Cost Diameter

Authors: Julien Baste, Didem Gözüpek, Christophe Paul, Ignasi Sau, Mordechai Shalom, and Dimitrios M. Thilikos

Published in: LIPIcs, Volume 89, 12th International Symposium on Parameterized and Exact Computation (IPEC 2017)

Abstract
We study the minimum diameter spanning tree problem under the reload cost model (DIAMETER-TREE for short) introduced by Wirth and Steffan (2001). In this problem, given an undirected edge-colored graph G, reload costs on a path arise at a node where the path uses consecutive edges of different colors. The objective is to find a spanning tree of G of minimum diameter with respect to the reload costs. We initiate a systematic study of the parameterized complexity of the DIAMETER-TREE problem by considering the following parameters: the cost of a solution, and the treewidth and the maximum degree Delta of the input graph. We prove that DIAMETER-TREE is para-np-hard for any combination of two of these three parameters, and that it is FPT parameterized by the three of them. We also prove that the problem can be solved in polynomial time on cactus graphs. This result is somehow surprising since we prove DIAMETER-TREE to be NP-hard on graphs of treewidth two, which is best possible as the problem can be trivially solved on forests. When the reload costs satisfy the triangle inequality, Wirth and Steffan (2001) proved that the problem can be solved in polynomial time on graphs with Delta=3, and Galbiati (2008) proved that it is NP-hard if Delta=4. Our results show, in particular, that without the requirement of the triangle inequality, the problem is NP-hard if Delta=3, which is also best possible. Finally, in the case where the reload costs are polynomially bounded by the size of the input graph, we prove that DIAMETER-TREE is in XP and W[1]-hard parameterized by the treewidth plus Delta.
Cite as

Julien Baste, Didem Gözüpek, Christophe Paul, Ignasi Sau, Mordechai Shalom, and Dimitrios M. Thilikos. Parameterized Complexity of Finding a Spanning Tree with Minimum Reload Cost Diameter. In 12th International Symposium on Parameterized and Exact Computation (IPEC 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 89, pp. 3:1-3:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@InProceedings{baste_et_al:LIPIcs.IPEC.2017.3,
  author =	{Baste, Julien and G\"{o}z\"{u}pek, Didem and Paul, Christophe and Sau, Ignasi and Shalom, Mordechai and Thilikos, Dimitrios M.},
  title =	{{Parameterized Complexity of Finding a Spanning Tree with Minimum Reload Cost Diameter}},
  booktitle =	{12th International Symposium on Parameterized and Exact Computation (IPEC 2017)},
  pages =	{3:1--3:12},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-051-4},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{89},
  editor =	{Lokshtanov, Daniel and Nishimura, Naomi},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.IPEC.2017.3},
  URN =		{urn:nbn:de:0030-drops-85545},
  doi =		{10.4230/LIPIcs.IPEC.2017.3},
  annote =	{Keywords: reload cost problems, minimum diameter spanning tree, parameterized complexity, FPT algorithm, treewidth, dynamic programming}
}
Document
DOI: 10.4230/LIPIcs.IPEC.2017.4
Optimal Algorithms for Hitting (Topological) Minors on Graphs of Bounded Treewidth

Authors: Julien Baste, Ignasi Sau, and Dimitrios M. Thilikos

Published in: LIPIcs, Volume 89, 12th International Symposium on Parameterized and Exact Computation (IPEC 2017)

Abstract
For a fixed collection of graphs F, the F-M-DELETION problem consists in, given a graph G and an integer k, decide whether there exists a subset S of V(G) of size at most k such that G-S does not contain any of the graphs in F as a minor. We are interested in the parameterized complexity of F-M-DELETION when the parameter is the treewidth of G, denoted by tw. Our objective is to determine, for a fixed F}, the smallest function f_F such that F-M-DELETION can be solved in time f_F(tw)n^{O(1)} on n-vertex graphs. Using and enhancing the machinery of boundaried graphs and small sets of representatives introduced by Bodlaender et al. [J ACM, 2016], we prove that when all the graphs in F are connected and at least one of them is planar, then f_F(w) = 2^{O(wlog w)}. When F is a singleton containing a clique, a cycle, or a path on i vertices, we prove the following asymptotically tight bounds: - f_{K_4}(w) = 2^{Theta(wlog w)}. - f_{C_i}(w) = 2^{Theta(w)} for every i<5, and f_{C_i}(w) = 2^{Theta(wlog w)} for every i>4. - f_{P_i}(w) = 2^{Theta(w)} for every i<5, and f_{P_i}(w) = 2^{Theta(wlog w)} for every i>5. The lower bounds hold unless the Exponential Time Hypothesis fails, and the superexponential ones are inspired by a reduction of Marcin Pilipczuk [Discrete Appl Math, 2016]. The single-exponential algorithms use, in particular, the rank-based approach introduced by Bodlaender et al. [Inform Comput, 2015]. We also consider the version of the problem where the graphs in F are forbidden as topological minors, and prove essentially the same set of results holds.
Cite as

Julien Baste, Ignasi Sau, and Dimitrios M. Thilikos. Optimal Algorithms for Hitting (Topological) Minors on Graphs of Bounded Treewidth. In 12th International Symposium on Parameterized and Exact Computation (IPEC 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 89, pp. 4:1-4:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@InProceedings{baste_et_al:LIPIcs.IPEC.2017.4,
  author =	{Baste, Julien and Sau, Ignasi and Thilikos, Dimitrios M.},
  title =	{{Optimal Algorithms for Hitting (Topological) Minors on Graphs of Bounded Treewidth}},
  booktitle =	{12th International Symposium on Parameterized and Exact Computation (IPEC 2017)},
  pages =	{4:1--4:12},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-051-4},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{89},
  editor =	{Lokshtanov, Daniel and Nishimura, Naomi},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.IPEC.2017.4},
  URN =		{urn:nbn:de:0030-drops-85556},
  doi =		{10.4230/LIPIcs.IPEC.2017.4},
  annote =	{Keywords: parameterized complexity, graph minors, treewidth, hitting minors, topological minors, dynamic programming, Exponential Time Hypothesis}
}
Document
DOI: 10.4230/LIPIcs.IPEC.2017.5
Contraction-Bidimensionality of Geometric Intersection Graphs

Authors: Julien Baste and Dimitrios M. Thilikos

Published in: LIPIcs, Volume 89, 12th International Symposium on Parameterized and Exact Computation (IPEC 2017)

Abstract
Given a graph G, we define bcg(G) as the minimum k for which G can be contracted to the uniformly triangulated grid Gamma_k. A graph class G has the SQGC property if every graph G in G has treewidth O(bcg(G)c) for some 1 <= c < 2. The SQGC property is important for algorithm design as it defines the applicability horizon of a series of meta-algorithmic results, in the framework of bidimensionality theory, related to fast parameterized algorithms, kernelization, and approximation schemes. These results apply to a wide family of problems, namely problems that are contraction-bidimensional. Our main combinatorial result reveals a general family of graph classes that satisfy the SQGC property and includes bounded-degree string graphs. This considerably extends the applicability of bidimensionality theory for several intersection graph classes of 2-dimensional geometrical objects.
Cite as

Julien Baste and Dimitrios M. Thilikos. Contraction-Bidimensionality of Geometric Intersection Graphs. In 12th International Symposium on Parameterized and Exact Computation (IPEC 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 89, pp. 5:1-5:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@InProceedings{baste_et_al:LIPIcs.IPEC.2017.5,
  author =	{Baste, Julien and Thilikos, Dimitrios M.},
  title =	{{Contraction-Bidimensionality of Geometric Intersection Graphs}},
  booktitle =	{12th International Symposium on Parameterized and Exact Computation (IPEC 2017)},
  pages =	{5:1--5:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-051-4},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{89},
  editor =	{Lokshtanov, Daniel and Nishimura, Naomi},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.IPEC.2017.5},
  URN =		{urn:nbn:de:0030-drops-85487},
  doi =		{10.4230/LIPIcs.IPEC.2017.5},
  annote =	{Keywords: Grid exlusion theorem, Bidimensionality, Geometric intersection graphs, String Graphs}
}
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