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PACE Solver Description

**Published in:** LIPIcs, Volume 214, 16th International Symposium on Parameterized and Exact Computation (IPEC 2021)

We describe PACA-JAVA, an algorithm for solving the cluster editing problem submitted for the exact track of the Parameterized Algorithms and Computational Experiments challenge (PACE) in 2021. The algorithm solves the cluster editing problem by applying data-reduction rules, performing a layout heuristic, local search, iterative ILP verification, and branch-and-bound. We implemented the algorithm in the scope of a student project at the University of Bremen.

Jona Dirks, Mario Grobler, Roman Rabinovich, Yannik Schnaubelt, Sebastian Siebertz, and Maximilian Sonneborn. PACE Solver Description: PACA-JAVA. In 16th International Symposium on Parameterized and Exact Computation (IPEC 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 214, pp. 30:1-30:4, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

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@InProceedings{dirks_et_al:LIPIcs.IPEC.2021.30, author = {Dirks, Jona and Grobler, Mario and Rabinovich, Roman and Schnaubelt, Yannik and Siebertz, Sebastian and Sonneborn, Maximilian}, title = {{PACE Solver Description: PACA-JAVA}}, booktitle = {16th International Symposium on Parameterized and Exact Computation (IPEC 2021)}, pages = {30:1--30:4}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-216-7}, ISSN = {1868-8969}, year = {2021}, volume = {214}, editor = {Golovach, Petr A. and Zehavi, Meirav}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.IPEC.2021.30}, URN = {urn:nbn:de:0030-drops-154138}, doi = {10.4230/LIPIcs.IPEC.2021.30}, annote = {Keywords: Cluster editing, parameterized complexity, PACE 2021} }

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

The notions of bounded expansion [Nešetřil and Ossona de Mendez, 2008] and nowhere denseness [Nešetřil and Ossona de Mendez, 2011], introduced by Nešetřil and Ossona de Mendez as structural measures for undirected graphs, have been applied very successfully in algorithmic graph theory. We study the corresponding notions of directed bounded expansion and nowhere crownfulness on directed graphs, introduced by Kreutzer and Tazari [Kreutzer and Tazari, 2012]. The classes of directed graphs having those properties are very general classes of sparse directed graphs, as they include, on one hand, all classes of directed graphs whose underlying undirected class has bounded expansion, such as planar, bounded-genus, and H-minor-free graphs, and on the other hand, they also contain classes whose underlying undirected class is not even nowhere dense. We show that many of the algorithmic tools that were developed for undirected bounded expansion classes can, with some care, also be applied in their directed counterparts, and thereby we highlight a rich algorithmic structure theory of directed bounded expansion and nowhere crownful classes.

Stephan Kreutzer, Irene Muzi, Patrice Ossona de Mendez, Roman Rabinovich, and Sebastian Siebertz. Algorithmic Properties of Sparse Digraphs. In 36th International Symposium on Theoretical Aspects of Computer Science (STACS 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 126, pp. 46:1-46:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)

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@InProceedings{kreutzer_et_al:LIPIcs.STACS.2019.46, author = {Kreutzer, Stephan and Muzi, Irene and Ossona de Mendez, Patrice and Rabinovich, Roman and Siebertz, Sebastian}, title = {{Algorithmic Properties of Sparse Digraphs}}, booktitle = {36th International Symposium on Theoretical Aspects of Computer Science (STACS 2019)}, pages = {46:1--46:20}, 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-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.STACS.2019.46}, URN = {urn:nbn:de:0030-drops-102859}, doi = {10.4230/LIPIcs.STACS.2019.46}, annote = {Keywords: Directed graphs, graph algorithms, parameterized complexity, approximation} }

Document

**Published in:** LIPIcs, Volume 103, 17th International Symposium on Experimental Algorithms (SEA 2018)

The notions of bounded expansion and nowhere denseness not only offer robust and general definitions of uniform sparseness of graphs, they also describe the tractability boundary for several important algorithmic questions. In this paper we study two structural properties of these graph classes that are of particular importance in this context, namely the property of having bounded generalized coloring numbers and the property of being uniformly quasi-wide. We provide experimental evaluations of several algorithms that approximate these parameters on real-world graphs. On the theoretical side, we provide a new algorithm for uniform quasi-wideness with polynomial size guarantees in graph classes of bounded expansion and show a lower bound indicating that the guarantees of this algorithm are close to optimal in graph classes with fixed excluded minor.

Wojciech Nadara, Marcin Pilipczuk, Roman Rabinovich, Felix Reidl, and Sebastian Siebertz. Empirical Evaluation of Approximation Algorithms for Generalized Graph Coloring and Uniform Quasi-Wideness. In 17th International Symposium on Experimental Algorithms (SEA 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 103, pp. 14:1-14:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@InProceedings{nadara_et_al:LIPIcs.SEA.2018.14, author = {Nadara, Wojciech and Pilipczuk, Marcin and Rabinovich, Roman and Reidl, Felix and Siebertz, Sebastian}, title = {{Empirical Evaluation of Approximation Algorithms for Generalized Graph Coloring and Uniform Quasi-Wideness}}, booktitle = {17th International Symposium on Experimental Algorithms (SEA 2018)}, pages = {14:1--14:16}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-070-5}, ISSN = {1868-8969}, year = {2018}, volume = {103}, editor = {D'Angelo, Gianlorenzo}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2018.14}, URN = {urn:nbn:de:0030-drops-89493}, doi = {10.4230/LIPIcs.SEA.2018.14}, annote = {Keywords: Empirical Evaluation of Algorithms, Sparse Graph Classes, Generalized Coloring Numbers, Uniform Quasi-Wideness} }

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**Published in:** LIPIcs, Volume 80, 44th International Colloquium on Automata, Languages, and Programming (ICALP 2017)

We prove that whenever G is a graph from a nowhere dense graph class C, and A is a subset of vertices of G, then the number of subsets of A that are realized as intersections of A with r-neighborhoods of vertices of G is at most f(r,eps)|A|^(1+eps), where r is any positive integer, eps is any positive real, and f is a function that depends only on the class C. This yields a characterization of nowhere dense classes of graphs in terms of neighborhood complexity, which answers a question posed by [Reidl et al., CoRR, 2016]. As an algorithmic application of the above result, we show that for every fixed integer r, the parameterized Distance-r Dominating Set problem admits an almost linear kernel on any nowhere dense graph class. This proves a conjecture posed by [Drange et al., STACS 2016], and shows that the limit of parameterized tractability of Distance-r Dominating Set on subgraph-closed graph classes lies exactly on the boundary between nowhere denseness and somewhere denseness.

Kord Eickmeyer, Archontia C. Giannopoulou, Stephan Kreutzer, O-joung Kwon, Michal Pilipczuk, Roman Rabinovich, and Sebastian Siebertz. Neighborhood Complexity and Kernelization for Nowhere Dense Classes of Graphs. In 44th International Colloquium on Automata, Languages, and Programming (ICALP 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 80, pp. 63:1-63:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)

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@InProceedings{eickmeyer_et_al:LIPIcs.ICALP.2017.63, author = {Eickmeyer, Kord and Giannopoulou, Archontia C. and Kreutzer, Stephan and Kwon, O-joung and Pilipczuk, Michal and Rabinovich, Roman and Siebertz, Sebastian}, title = {{Neighborhood Complexity and Kernelization for Nowhere Dense Classes of Graphs}}, booktitle = {44th International Colloquium on Automata, Languages, and Programming (ICALP 2017)}, pages = {63:1--63:14}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-041-5}, ISSN = {1868-8969}, year = {2017}, volume = {80}, editor = {Chatzigiannakis, Ioannis and Indyk, Piotr and Kuhn, Fabian and Muscholl, Anca}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2017.63}, URN = {urn:nbn:de:0030-drops-74288}, doi = {10.4230/LIPIcs.ICALP.2017.63}, annote = {Keywords: Graph Structure Theory, Nowhere Dense Graphs, Parameterized Complexity, Kernelization, Dominating Set} }

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**Published in:** LIPIcs, Volume 66, 34th Symposium on Theoretical Aspects of Computer Science (STACS 2017)

Bounded expansion and nowhere dense graph classes, introduced by Nesetril and Ossona de Mendez, form a large variety of classes of uniformly sparse graphs which includes the class of planar graphs, actually all classes with excluded minors, and also bounded degree graphs. Since their initial definition it was shown that these graph classes can be defined in many equivalent ways: by generalised colouring numbers, neighbourhood complexity, sparse neighbourhood covers, a game known as the splitter game, and many more.
We study the corresponding concepts for directed graphs. We show that the densities of bounded depth directed minors and bounded depth topological minors relate in a similar way as in the undirected case. We provide a characterisation of bounded expansion classes by a directed version of the generalised colouring numbers. As an application we show how to construct sparse directed neighbourhood covers and how to approximate directed distance-r dominating sets on classes of bounded expansion. On the other hand, we show that linear neighbourhood complexity does not characterise directed classes of bounded expansion.

Stephan Kreutzer, Roman Rabinovich, Sebastian Siebertz, and Grischa Weberstädt. Structural Properties and Constant Factor-Approximation of Strong Distance-r Dominating Sets in Sparse Directed Graphs. In 34th Symposium on Theoretical Aspects of Computer Science (STACS 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 66, pp. 48:1-48:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)

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@InProceedings{kreutzer_et_al:LIPIcs.STACS.2017.48, author = {Kreutzer, Stephan and Rabinovich, Roman and Siebertz, Sebastian and Weberst\"{a}dt, Grischa}, title = {{Structural Properties and Constant Factor-Approximation of Strong Distance-r Dominating Sets in Sparse Directed Graphs}}, booktitle = {34th Symposium on Theoretical Aspects of Computer Science (STACS 2017)}, pages = {48:1--48:15}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-028-6}, ISSN = {1868-8969}, year = {2017}, volume = {66}, editor = {Vollmer, Heribert and Vall\'{e}e, Brigitte}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.STACS.2017.48}, URN = {urn:nbn:de:0030-drops-69868}, doi = {10.4230/LIPIcs.STACS.2017.48}, annote = {Keywords: Directed Graph Structure Theory, Bounded Expansion, Generalised Colouring Numbers, Splitter Game, Approximation Algorithms, Dominating Set} }

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**Published in:** LIPIcs, Volume 58, 41st International Symposium on Mathematical Foundations of Computer Science (MFCS 2016)

We study the version of the k-disjoint paths problem where k demand pairs (s_1,t_1), ..., (s_k,t_k) are specified in the input and the paths in the solution are allowed to intersect, but such that no vertex is on more than c paths. We show that on directed acyclic graphs the problem is solvable in time n^{O(d)} if we allow congestion k-d for k paths. Furthermore, we show that, under a suitable complexity theoretic assumption, the problem cannot be solved in time f(k)n^{o(d*log(d))} for any computable function f.

Saeed Akhoondian Amiri, Stephan Kreutzer, Dániel Marx, and Roman Rabinovich. Routing with Congestion in Acyclic Digraphs. In 41st International Symposium on Mathematical Foundations of Computer Science (MFCS 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 58, pp. 7:1-7:11, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)

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@InProceedings{amiri_et_al:LIPIcs.MFCS.2016.7, author = {Amiri, Saeed Akhoondian and Kreutzer, Stephan and Marx, D\'{a}niel and Rabinovich, Roman}, title = {{Routing with Congestion in Acyclic Digraphs}}, booktitle = {41st International Symposium on Mathematical Foundations of Computer Science (MFCS 2016)}, pages = {7:1--7:11}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-016-3}, ISSN = {1868-8969}, year = {2016}, volume = {58}, editor = {Faliszewski, Piotr and Muscholl, Anca and Niedermeier, Rolf}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2016.7}, URN = {urn:nbn:de:0030-drops-64244}, doi = {10.4230/LIPIcs.MFCS.2016.7}, annote = {Keywords: algorithms, disjoint paths, congestion, acyclic digraphs, XP, W\lbrack1\rbrack-hard} }

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**Published in:** LIPIcs, Volume 58, 41st International Symposium on Mathematical Foundations of Computer Science (MFCS 2016)

The generalised colouring numbers adm_r(G), col_r(G), and wcol_r(G) were introduced by Kierstead and Yang as generalisations of the usual colouring number, also known as the degeneracy of a graph, and have since then found important applications in the theory of bounded expansion and nowhere dense classes of graphs, introduced by Nesetril and Ossona de Mendez. In this paper, we study the relation of the colouring numbers with two other measures that characterise nowhere dense classes of graphs, namely with uniform quasi-wideness, studied first by Dawar et al. in the context of preservation theorems for first-order logic, and with the splitter game, introduced by Grohe et al. We show that every graph excluding a fixed topological minor admits a universal order, that is, one order witnessing that the colouring numbers are small for every value of r. Finally, we use our construction of such orders to give a new proof of a result of Eickmeyer and Kawarabayashi, showing that the model-checking problem for successor-invariant first-order formulas is fixed parameter tractable on classes of graphs with excluded topological minors.

Stephan Kreutzer, Michal Pilipczuk, Roman Rabinovich, and Sebastian Siebertz. The Generalised Colouring Numbers on Classes of Bounded Expansion. In 41st International Symposium on Mathematical Foundations of Computer Science (MFCS 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 58, pp. 85:1-85:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)

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@InProceedings{kreutzer_et_al:LIPIcs.MFCS.2016.85, author = {Kreutzer, Stephan and Pilipczuk, Michal and Rabinovich, Roman and Siebertz, Sebastian}, title = {{The Generalised Colouring Numbers on Classes of Bounded Expansion}}, booktitle = {41st International Symposium on Mathematical Foundations of Computer Science (MFCS 2016)}, pages = {85:1--85:13}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-016-3}, ISSN = {1868-8969}, year = {2016}, volume = {58}, editor = {Faliszewski, Piotr and Muscholl, Anca and Niedermeier, Rolf}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2016.85}, URN = {urn:nbn:de:0030-drops-64937}, doi = {10.4230/LIPIcs.MFCS.2016.85}, annote = {Keywords: graph structure theory, nowhere dense graphs, generalised colouring numbers, splitter game, first-order model-checking} }

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**Published in:** LIPIcs, Volume 30, 32nd International Symposium on Theoretical Aspects of Computer Science (STACS 2015)

In cops and robber games a number of cops tries to capture a robber in
a graph. A variant of these games on undirected graphs characterises tree width by the least number of cops needed to win. We consider cops and robber games on digraphs and width measures (such as DAG-width, directed tree width or D-width) corresponding to them. All of them generalise tree width and the game characterising it.
For the DAG-width game we prove that the problem to decide the minimal
number of cops required to capture the robber (which is the same as deciding DAG-width), is PSPACE-complete, in contrast to most other similar games. We also show that the cop-monotonicity cost for directed tree width games cannot be bounded by any function. As a consequence, D-width is not bounded in directed tree width, refuting a conjecture by Safari.
A large number of directed width measures generalising tree width has been proposed in the literature. However, only very little was known about the relation between them, in particular about whether classes of digraphs of bounded width in one measure have bounded width in another. In this paper we establish an almost complete order among the most prominent width measures with respect to mutual boundedness.

Saeed Akhoondian Amiri, Lukasz Kaiser, Stephan Kreutzer, Roman Rabinovich, and Sebastian Siebertz. Graph Searching Games and Width Measures for Directed Graphs. In 32nd International Symposium on Theoretical Aspects of Computer Science (STACS 2015). Leibniz International Proceedings in Informatics (LIPIcs), Volume 30, pp. 34-47, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2015)

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@InProceedings{akhoondianamiri_et_al:LIPIcs.STACS.2015.34, author = {Akhoondian Amiri, Saeed and Kaiser, Lukasz and Kreutzer, Stephan and Rabinovich, Roman and Siebertz, Sebastian}, title = {{Graph Searching Games and Width Measures for Directed Graphs}}, booktitle = {32nd International Symposium on Theoretical Aspects of Computer Science (STACS 2015)}, pages = {34--47}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-939897-78-1}, ISSN = {1868-8969}, year = {2015}, volume = {30}, editor = {Mayr, Ernst W. and Ollinger, Nicolas}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.STACS.2015.34}, URN = {urn:nbn:de:0030-drops-49020}, doi = {10.4230/LIPIcs.STACS.2015.34}, annote = {Keywords: cops and robber games, directed graphs, DAG-width} }

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