12 Search Results for "Sikora, Florian"

Artifact
Software
DOI: 10.4230/artifacts.22474
Unit 2-interval graph checker

Authors: Abdallah Saffidine

Abstract
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Abdallah Saffidine. Unit 2-interval graph checker (Software, Source Code). Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@misc{dagstuhl-artifact-22474,
   title = {{Unit 2-interval graph checker}}, 
   author = {Saffidine, Abdallah},
   note = {Software, swhId: \href{https://archive.softwareheritage.org/swh:1:dir:3d7b6495d1f70618a537cd23c94530c23c030215;origin=https://github.com/AbdallahS/unit-graphs;visit=swh:1:snp:84b7b457760a919cc007e2290179e1fc6fe861e3;anchor=swh:1:rev:516ab210d2ff334ac34348619bc42d252824cac4}{\texttt{swh:1:dir:3d7b6495d1f70618a537cd23c94530c23c030215}} (visited on 2024-11-28)},
   url = {https://github.com/AbdallahS/unit-graphs},
   doi = {10.4230/artifacts.22474},
}
Document
DOI: 10.4230/LIPIcs.WABI.2024.5
Memoization on Shared Subtrees Accelerates Computations on Genealogical Forests

Authors: Lukas Hübner and Alexandros Stamatakis

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

Abstract
The field of population genetics attempts to advance our understanding of evolutionary processes. It has applications, for example, in medical research, wildlife conservation, and - in conjunction with recent advances in ancient DNA sequencing technology - studying human migration patterns over the past few thousand years. The basic toolbox of population genetics includes genealogical trees, which describe the shared evolutionary history among individuals of the same species. They are calculated on the basis of genetic variations. However, in recombining organisms, a single tree is insufficient to describe the evolutionary history of the whole genome. Instead, a collection of correlated trees can be used, where each describes the evolutionary history of a consecutive region of the genome. The current corresponding state of-the-art data structure, tree sequences, compresses these genealogical trees via edit operations when moving from one tree to the next along the genome instead of storing the full, often redundant, description for each tree. We propose a new data structure, genealogical forests, which compresses the set of genealogical trees into a DAG. In this DAG identical subtrees that are shared across the input trees are encoded only once, thereby allowing for straight-forward memoization of intermediate results. Additionally, we provide a C++ implementation of our proposed data structure, called gfkit, which is 2.1 to 11.2 (median 4.0) times faster than the state-of-the-art tool on empirical and simulated datasets at computing important population genetics statistics such as the Allele Frequency Spectrum, Patterson’s f, the Fixation Index, Tajima’s D, pairwise Lowest Common Ancestors, and others. On Lowest Common Ancestor queries with more than two samples as input, gfkit scales asymptotically better than the state-of-the-art, and is thus up to 990 times faster. In conclusion, our proposed data structure compresses genealogical trees by storing shared subtrees only once, thereby enabling straight-forward memoization of intermediate results, yielding a substantial runtime reduction and a potentially more intuitive data representation over the state-of-the-art. Our improvements will boost the development of novel analyses and models in the field of population genetics and increases scalability to ever-growing genomic datasets.
Cite as

Lukas Hübner and Alexandros Stamatakis. Memoization on Shared Subtrees Accelerates Computations on Genealogical Forests. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 5:1-5:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{hubner_et_al:LIPIcs.WABI.2024.5,
  author =	{H\"{u}bner, Lukas and Stamatakis, Alexandros},
  title =	{{Memoization on Shared Subtrees Accelerates Computations on Genealogical Forests}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{5:1--5:22},
  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.2024.5},
  URN =		{urn:nbn:de:0030-drops-206499},
  doi =		{10.4230/LIPIcs.WABI.2024.5},
  annote =	{Keywords: bioinformatics, population genetics, algorithms}
}
Document
DOI: 10.4230/LIPIcs.WABI.2024.19
RNA Inverse Folding Can Be Solved in Linear Time for Structures Without Isolated Stacks or Base Pairs

Authors: Théo Boury, Laurent Bulteau, and Yann Ponty

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

Abstract
Inverse folding is a classic instance of negative RNA design which consists in finding a sequence that uniquely folds into a target secondary structure with respect to energy minimization. A breakthrough result of Bonnet et al. shows that, even in simple base pairs-based (BP) models, the decision version of a mildly constrained version of inverse folding is NP-hard. In this work, we show that inverse folding can be solved in linear time for a large collection of targets, including every structure that contains no isolated BP and no isolated stack (or, equivalently, when all helices consist of 3^{+} base pairs). For structures featuring shorter helices, our linear algorithm is no longer guaranteed to produce a solution, but still does so for a large proportion of instances. Our approach introduces a notion of modulo m-separability, generalizing a property pioneered by Hales et al. Separability is a sufficient condition for the existence of a solution to the inverse folding problem. We show that, for any input secondary structure of length n, a modulo m-separated sequence can be produced in time 𝒪(n 2^m) anytime such a sequence exists. Meanwhile, we show that any structure consisting of 3^{+} base pairs is either trivially non-designable, or always admits a modulo-2 separated solution (m = 2). Solution sequences can thus be produced in linear time, and even be uniformly generated within the set of modulo-2 separable sequences.
Cite as

Théo Boury, Laurent Bulteau, and Yann Ponty. RNA Inverse Folding Can Be Solved in Linear Time for Structures Without Isolated Stacks or Base Pairs. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 19:1-19:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{boury_et_al:LIPIcs.WABI.2024.19,
  author =	{Boury, Th\'{e}o and Bulteau, Laurent and Ponty, Yann},
  title =	{{RNA Inverse Folding Can Be Solved in Linear Time for Structures Without Isolated Stacks or Base Pairs}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{19:1--19:23},
  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.2024.19},
  URN =		{urn:nbn:de:0030-drops-206632},
  doi =		{10.4230/LIPIcs.WABI.2024.19},
  annote =	{Keywords: RNA structure, String Design, Parameterized Complexity, Uniform Sampling}
}
Document
DOI: 10.4230/LIPIcs.MFCS.2024.12
Generalizing Roberts' Characterization of Unit Interval Graphs

Authors: Virginia Ardévol Martínez, Romeo Rizzi, Abdallah Saffidine, Florian Sikora, and Stéphane Vialette

Published in: LIPIcs, Volume 306, 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)

Abstract
For any natural number d, a graph G is a (disjoint) d-interval graph if it is the intersection graph of (disjoint) d-intervals, the union of d (disjoint) intervals on the real line. Two important subclasses of d-interval graphs are unit and balanced d-interval graphs (where every interval has unit length or all the intervals associated to a same vertex have the same length, respectively). A celebrated result by Roberts gives a simple characterization of unit interval graphs being exactly claw-free interval graphs. Here, we study the generalization of this characterization for d-interval graphs. In particular, we prove that for any d ⩾ 2, if G is a K_{1,2d+1}-free interval graph, then G is a unit d-interval graph. However, somehow surprisingly, under the same assumptions, G is not always a disjoint unit d-interval graph. This implies that the class of disjoint unit d-interval graphs is strictly included in the class of unit d-interval graphs. Finally, we study the relationships between the classes obtained under disjoint and non-disjoint d-intervals in the balanced case and show that the classes of disjoint balanced 2-intervals and balanced 2-intervals coincide, but this is no longer true for d > 2.
Cite as

Virginia Ardévol Martínez, Romeo Rizzi, Abdallah Saffidine, Florian Sikora, and Stéphane Vialette. Generalizing Roberts' Characterization of Unit Interval Graphs. In 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 306, pp. 12:1-12:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{ardevolmartinez_et_al:LIPIcs.MFCS.2024.12,
  author =	{Ard\'{e}vol Mart{\'\i}nez, Virginia and Rizzi, Romeo and Saffidine, Abdallah and Sikora, Florian and Vialette, St\'{e}phane},
  title =	{{Generalizing Roberts' Characterization of Unit Interval Graphs}},
  booktitle =	{49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)},
  pages =	{12:1--12:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-335-5},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{306},
  editor =	{Kr\'{a}lovi\v{c}, Rastislav and Ku\v{c}era, Anton{\'\i}n},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2024.12},
  URN =		{urn:nbn:de:0030-drops-205687},
  doi =		{10.4230/LIPIcs.MFCS.2024.12},
  annote =	{Keywords: Interval graphs, Multiple Interval Graphs, Unit Interval Graphs, Characterization}
}
Document
DOI: 10.4230/LIPIcs.ISAAC.2023.8
Recognizing Unit Multiple Intervals Is Hard

Authors: Virginia Ardévol Martínez, Romeo Rizzi, Florian Sikora, and Stéphane Vialette

Published in: LIPIcs, Volume 283, 34th International Symposium on Algorithms and Computation (ISAAC 2023)

Abstract
Multiple interval graphs are a well-known generalization of interval graphs introduced in the 1970s to deal with situations arising naturally in scheduling and allocation. A d-interval is the union of d intervals on the real line, and a graph is a d-interval graph if it is the intersection graph of d-intervals. In particular, it is a unit d-interval graph if it admits a d-interval representation where every interval has unit length. Whereas it has been known for a long time that recognizing 2-interval graphs and other related classes such as 2-track interval graphs is NP-complete, the complexity of recognizing unit 2-interval graphs remains open. Here, we settle this question by proving that the recognition of unit 2-interval graphs is also NP-complete. Our proof technique uses a completely different approach from the other hardness results of recognizing related classes. Furthermore, we extend the result for unit d-interval graphs for any d ⩾ 2, which does not follow directly in graph recognition problems -as an example, it took almost 20 years to close the gap between d = 2 and d > 2 for the recognition of d-track interval graphs. Our result has several implications, including that recognizing (x, …, x) d-interval graphs and depth r unit 2-interval graphs is NP-complete for every x ⩾ 11 and every r ⩾ 4.
Cite as

Virginia Ardévol Martínez, Romeo Rizzi, Florian Sikora, and Stéphane Vialette. Recognizing Unit Multiple Intervals Is Hard. In 34th International Symposium on Algorithms and Computation (ISAAC 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 283, pp. 8:1-8:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{ardevolmartinez_et_al:LIPIcs.ISAAC.2023.8,
  author =	{Ard\'{e}vol Mart{\'\i}nez, Virginia and Rizzi, Romeo and Sikora, Florian and Vialette, St\'{e}phane},
  title =	{{Recognizing Unit Multiple Intervals Is Hard}},
  booktitle =	{34th International Symposium on Algorithms and Computation (ISAAC 2023)},
  pages =	{8:1--8:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-289-1},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{283},
  editor =	{Iwata, Satoru and Kakimura, Naonori},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ISAAC.2023.8},
  URN =		{urn:nbn:de:0030-drops-193102},
  doi =		{10.4230/LIPIcs.ISAAC.2023.8},
  annote =	{Keywords: Interval graphs, unit multiple interval graphs, recognition, NP-hardness}
}
Document
DOI: 10.4230/LIPIcs.CPM.2021.14
The Longest Run Subsequence Problem: Further Complexity Results

Authors: Riccardo Dondi and Florian Sikora

Published in: LIPIcs, Volume 191, 32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021)

Abstract
Longest Run Subsequence is a problem introduced recently in the context of the scaffolding phase of genome assembly (Schrinner et al., WABI 2020). The problem asks for a maximum length subsequence of a given string that contains at most one run for each symbol (a run is a maximum substring of consecutive identical symbols). The problem has been shown to be NP-hard and to be fixed-parameter tractable when the parameter is the size of the alphabet on which the input string is defined. In this paper we further investigate the complexity of the problem and we show that it is fixed-parameter tractable when it is parameterized by the number of runs in a solution, a smaller parameter. Moreover, we investigate the kernelization complexity of Longest Run Subsequence and we prove that it does not admit a polynomial kernel when parameterized by the size of the alphabet or by the number of runs. Finally, we consider the restriction of Longest Run Subsequence when each symbol has at most two occurrences in the input string and we show that it is APX-hard.
Cite as

Riccardo Dondi and Florian Sikora. The Longest Run Subsequence Problem: Further Complexity Results. In 32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 191, pp. 14:1-14:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

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@InProceedings{dondi_et_al:LIPIcs.CPM.2021.14,
  author =	{Dondi, Riccardo and Sikora, Florian},
  title =	{{The Longest Run Subsequence Problem: Further Complexity Results}},
  booktitle =	{32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021)},
  pages =	{14:1--14:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-186-3},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{191},
  editor =	{Gawrychowski, Pawe{\l} and Starikovskaya, Tatiana},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2021.14},
  URN =		{urn:nbn:de:0030-drops-139652},
  doi =		{10.4230/LIPIcs.CPM.2021.14},
  annote =	{Keywords: Parameterized complexity, Kernelization, Approximation Hardness, Longest Subsequence}
}
Document
DOI: 10.4230/LIPIcs.STACS.2020.58
Grundy Coloring & Friends, Half-Graphs, Bicliques

Authors: Pierre Aboulker, Édouard Bonnet, Eun Jung Kim, and Florian Sikora

Published in: LIPIcs, Volume 154, 37th International Symposium on Theoretical Aspects of Computer Science (STACS 2020)

Abstract
The first-fit coloring is a heuristic that assigns to each vertex, arriving in a specified order σ, the smallest available color. The problem Grundy Coloring asks how many colors are needed for the most adversarial vertex ordering σ, i.e., the maximum number of colors that the first-fit coloring requires over all possible vertex orderings. Since its inception by Grundy in 1939, Grundy Coloring has been examined for its structural and algorithmic aspects. A brute-force f(k)n^{2^{k-1}}-time algorithm for Grundy Coloring on general graphs is not difficult to obtain, where k is the number of colors required by the most adversarial vertex ordering. It was asked several times whether the dependency on k in the exponent of n can be avoided or reduced, and its answer seemed elusive until now. We prove that Grundy Coloring is W[1]-hard and the brute-force algorithm is essentially optimal under the Exponential Time Hypothesis, thus settling this question by the negative. The key ingredient in our W[1]-hardness proof is to use so-called half-graphs as a building block to transmit a color from one vertex to another. Leveraging the half-graphs, we also prove that b-Chromatic Core is W[1]-hard, whose parameterized complexity was posed as an open question by Panolan et al. [JCSS '17]. A natural follow-up question is, how the parameterized complexity changes in the absence of (large) half-graphs. We establish fixed-parameter tractability on K_{t,t}-free graphs for b-Chromatic Core and Partial Grundy Coloring, making a step toward answering this question. The key combinatorial lemma underlying the tractability result might be of independent interest.
Cite as

Pierre Aboulker, Édouard Bonnet, Eun Jung Kim, and Florian Sikora. Grundy Coloring & Friends, Half-Graphs, Bicliques. In 37th International Symposium on Theoretical Aspects of Computer Science (STACS 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 154, pp. 58:1-58:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@InProceedings{aboulker_et_al:LIPIcs.STACS.2020.58,
  author =	{Aboulker, Pierre and Bonnet, \'{E}douard and Kim, Eun Jung and Sikora, Florian},
  title =	{{Grundy Coloring \& Friends, Half-Graphs, Bicliques}},
  booktitle =	{37th International Symposium on Theoretical Aspects of Computer Science (STACS 2020)},
  pages =	{58:1--58:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-140-5},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{154},
  editor =	{Paul, Christophe and Bl\"{a}ser, Markus},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.STACS.2020.58},
  URN =		{urn:nbn:de:0030-drops-119190},
  doi =		{10.4230/LIPIcs.STACS.2020.58},
  annote =	{Keywords: Grundy coloring, parameterized complexity, ETH lower bounds, K\underline\{t,t\}-free graphs, half-graphs}
}
Document
DOI: 10.4230/LIPIcs.STACS.2019.13
Token Sliding on Split Graphs

Authors: Rémy Belmonte, Eun Jung Kim, Michael Lampis, Valia Mitsou, Yota Otachi, and Florian Sikora

Published in: LIPIcs, Volume 126, 36th International Symposium on Theoretical Aspects of Computer Science (STACS 2019)

Abstract
We consider the complexity of the Independent Set Reconfiguration problem under the Token Sliding rule. In this problem we are given two independent sets of a graph and are asked if we can transform one to the other by repeatedly exchanging a vertex that is currently in the set with one of its neighbors, while maintaining the set independent. Our main result is to show that this problem is PSPACE-complete on split graphs (and hence also on chordal graphs), thus resolving an open problem in this area. We then go on to consider the c-Colorable Reconfiguration problem under the same rule, where the constraint is now to maintain the set c-colorable at all times. As one may expect, a simple modification of our reduction shows that this more general problem is PSPACE-complete for all fixed c >= 1 on chordal graphs. Somewhat surprisingly, we show that the same cannot be said for split graphs: we give a polynomial time (n^{O(c)}) algorithm for all fixed values of c, except c=1, for which the problem is PSPACE-complete. We complement our algorithm with a lower bound showing that c-Colorable Reconfiguration is W[2]-hard on split graphs parameterized by c and the length of the solution, as well as a tight ETH-based lower bound for both parameters.
Cite as

Rémy Belmonte, Eun Jung Kim, Michael Lampis, Valia Mitsou, Yota Otachi, and Florian Sikora. Token Sliding on Split Graphs. In 36th International Symposium on Theoretical Aspects of Computer Science (STACS 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 126, pp. 13:1-13:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)

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@InProceedings{belmonte_et_al:LIPIcs.STACS.2019.13,
  author =	{Belmonte, R\'{e}my and Kim, Eun Jung and Lampis, Michael and Mitsou, Valia and Otachi, Yota and Sikora, Florian},
  title =	{{Token Sliding on Split Graphs}},
  booktitle =	{36th International Symposium on Theoretical Aspects of Computer Science (STACS 2019)},
  pages =	{13:1--13:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-100-9},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{126},
  editor =	{Niedermeier, Rolf and Paul, Christophe},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.STACS.2019.13},
  URN =		{urn:nbn:de:0030-drops-102529},
  doi =		{10.4230/LIPIcs.STACS.2019.13},
  annote =	{Keywords: reconfiguration, independent set, split graph}
}
Document
DOI: 10.4230/LIPIcs.IPEC.2018.26
The PACE 2018 Parameterized Algorithms and Computational Experiments Challenge: The Third Iteration

Authors: Édouard Bonnet and Florian Sikora

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

Abstract
The Program Committee of the Third Parameterized Algorithms and Computational Experiments challenge (PACE 2018) reports on the third iteration of the PACE challenge. This year, all three tracks were dedicated to solve the Steiner Tree problem, in which, given an edge-weighted graph and a subset of its vertices called terminals, one has to find a minimum-weight subgraph which spans all the terminals. In Track A, the number of terminals was limited. In Track B, a tree-decomposition of the graph was provided in the input, and the treewidth was limited. Finally, Track C welcomed heuristics. Over 80 participants on 40 teams from 16 countries submitted their implementations to the competition.
Cite as

Édouard Bonnet and Florian Sikora. The PACE 2018 Parameterized Algorithms and Computational Experiments Challenge: The Third Iteration. In 13th International Symposium on Parameterized and Exact Computation (IPEC 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 115, pp. 26:1-26:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)

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@InProceedings{bonnet_et_al:LIPIcs.IPEC.2018.26,
  author =	{Bonnet, \'{E}douard and Sikora, Florian},
  title =	{{The PACE 2018 Parameterized Algorithms and Computational Experiments Challenge: The Third Iteration}},
  booktitle =	{13th International Symposium on Parameterized and Exact Computation (IPEC 2018)},
  pages =	{26:1--26:15},
  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.dagstuhl.de/entities/document/10.4230/LIPIcs.IPEC.2018.26},
  URN =		{urn:nbn:de:0030-drops-102275},
  doi =		{10.4230/LIPIcs.IPEC.2018.26},
  annote =	{Keywords: Steiner tree problem, contest, implementation challenge, FPT}
}
Document
DOI: 10.4230/LIPIcs.SoCG.2018.12
QPTAS and Subexponential Algorithm for Maximum Clique on Disk Graphs

Authors: Édouard Bonnet, Panos Giannopoulos, Eun Jung Kim, Pawel Rzazewski, and Florian Sikora

Published in: LIPIcs, Volume 99, 34th International Symposium on Computational Geometry (SoCG 2018)

Abstract
A (unit) disk graph is the intersection graph of closed (unit) disks in the plane. Almost three decades ago, an elegant polynomial-time algorithm was found for Maximum Clique on unit disk graphs [Clark, Colbourn, Johnson; Discrete Mathematics '90]. Since then, it has been an intriguing open question whether or not tractability can be extended to general disk graphs. We show the rather surprising structural result that a disjoint union of cycles is the complement of a disk graph if and only if at most one of those cycles is of odd length. From that, we derive the first QPTAS and subexponential algorithm running in time 2^{O~(n^{2/3})} for Maximum Clique on disk graphs. In stark contrast, Maximum Clique on intersection graphs of filled ellipses or filled triangles is unlikely to have such algorithms, even when the ellipses are close to unit disks. Indeed, we show that there is a constant ratio of approximation which cannot be attained even in time 2^{n^{1-epsilon}}, unless the Exponential Time Hypothesis fails.
Cite as

Édouard Bonnet, Panos Giannopoulos, Eun Jung Kim, Pawel Rzazewski, and Florian Sikora. QPTAS and Subexponential Algorithm for Maximum Clique on Disk Graphs. In 34th International Symposium on Computational Geometry (SoCG 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 99, pp. 12:1-12:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@InProceedings{bonnet_et_al:LIPIcs.SoCG.2018.12,
  author =	{Bonnet, \'{E}douard and Giannopoulos, Panos and Kim, Eun Jung and Rzazewski, Pawel and Sikora, Florian},
  title =	{{QPTAS and Subexponential Algorithm for Maximum Clique on Disk Graphs}},
  booktitle =	{34th International Symposium on Computational Geometry (SoCG 2018)},
  pages =	{12:1--12:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-066-8},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{99},
  editor =	{Speckmann, Bettina and T\'{o}th, Csaba D.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SoCG.2018.12},
  URN =		{urn:nbn:de:0030-drops-87259},
  doi =		{10.4230/LIPIcs.SoCG.2018.12},
  annote =	{Keywords: disk graph, maximum clique, computational complexity}
}
Document
DOI: 10.4230/LIPIcs.SWAT.2018.24
Parameterized Orientable Deletion

Authors: Tesshu Hanaka, Ioannis Katsikarelis, Michael Lampis, Yota Otachi, and Florian Sikora

Published in: LIPIcs, Volume 101, 16th Scandinavian Symposium and Workshops on Algorithm Theory (SWAT 2018)

Abstract
A graph is d-orientable if its edges can be oriented so that the maximum in-degree of the resulting digraph is at most d. d-orientability is a well-studied concept with close connections to fundamental graph-theoretic notions and applications as a load balancing problem. In this paper we consider the d-Orientable Deletion problem: given a graph G=(V,E), delete the minimum number of vertices to make G d-orientable. We contribute a number of results that improve the state of the art on this problem. Specifically: - We show that the problem is W[2]-hard and log n-inapproximable with respect to k, the number of deleted vertices. This closes the gap in the problem's approximability. - We completely characterize the parameterized complexity of the problem on chordal graphs: it is FPT parameterized by d+k, but W-hard for each of the parameters d,k separately. - We show that, under the SETH, for all d,epsilon, the problem does not admit a (d+2-epsilon)^{tw}, algorithm where tw is the graph's treewidth, resolving as a special case an open problem on the complexity of PseudoForest Deletion. - We show that the problem is W-hard parameterized by the input graph's clique-width. Complementing this, we provide an algorithm running in time d^{O(d * cw)}, showing that the problem is FPT by d+cw, and improving the previously best know algorithm for this case.
Cite as

Tesshu Hanaka, Ioannis Katsikarelis, Michael Lampis, Yota Otachi, and Florian Sikora. Parameterized Orientable Deletion. In 16th Scandinavian Symposium and Workshops on Algorithm Theory (SWAT 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 101, pp. 24:1-24:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

Copy BibTex To Clipboard

@InProceedings{hanaka_et_al:LIPIcs.SWAT.2018.24,
  author =	{Hanaka, Tesshu and Katsikarelis, Ioannis and Lampis, Michael and Otachi, Yota and Sikora, Florian},
  title =	{{Parameterized Orientable Deletion}},
  booktitle =	{16th Scandinavian Symposium and Workshops on Algorithm Theory (SWAT 2018)},
  pages =	{24:1--24:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-068-2},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{101},
  editor =	{Eppstein, David},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SWAT.2018.24},
  URN =		{urn:nbn:de:0030-drops-88506},
  doi =		{10.4230/LIPIcs.SWAT.2018.24},
  annote =	{Keywords: Graph orientations, FPT algorithms, Treewidth, SETH}
}
Document
DOI: 10.4230/LIPIcs.IPEC.2015.319
The Graph Motif Problem Parameterized by the Structure of the Input Graph

Authors: Édouard Bonnet and Florian Sikora

Published in: LIPIcs, Volume 43, 10th International Symposium on Parameterized and Exact Computation (IPEC 2015)

Abstract
The Graph Motif problem was introduced in 2006 in the context of biological networks. It consists of deciding whether or not a multiset of colors occurs in a connected subgraph of a vertex-colored graph. Graph Motif has been analyzed from the standpoint of parameterized complexity. The main parameters which came into consideration were the size of the multiset and the number of colors. Though, in the many applications of Graph Motif, the input graph originates from real-life and has structure. Motivated by this prosaic observation, we systematically study its complexity relatively to graph structural parameters. For a wide range of parameters, we give new or improved FPT algorithms, or show that the problem remains intractable. Interestingly, we establish that Graph Motif is W[1]-hard (while in W[P]) for parameter max leaf number, which is, to the best of our knowledge, the first problem to behave this way.
Cite as

Édouard Bonnet and Florian Sikora. The Graph Motif Problem Parameterized by the Structure of the Input Graph. In 10th International Symposium on Parameterized and Exact Computation (IPEC 2015). Leibniz International Proceedings in Informatics (LIPIcs), Volume 43, pp. 319-330, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2015)

Copy BibTex To Clipboard

@InProceedings{bonnet_et_al:LIPIcs.IPEC.2015.319,
  author =	{Bonnet, \'{E}douard and Sikora, Florian},
  title =	{{The Graph Motif Problem Parameterized by the Structure of the Input Graph}},
  booktitle =	{10th International Symposium on Parameterized and Exact Computation (IPEC 2015)},
  pages =	{319--330},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-939897-92-7},
  ISSN =	{1868-8969},
  year =	{2015},
  volume =	{43},
  editor =	{Husfeldt, Thore and Kanj, Iyad},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.IPEC.2015.319},
  URN =		{urn:nbn:de:0030-drops-55937},
  doi =		{10.4230/LIPIcs.IPEC.2015.319},
  annote =	{Keywords: Parameterized Complexity, Structural Parameters, Graph Motif, Computational Biology}
}
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