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Documents authored by Bals, Ben

Document
DOI: 10.4230/LIPIcs.ESA.2025.53
When Is String Reconstruction Using de Bruijn Graphs Hard?

Authors: Ben Bals, Sebastiaan van Krieken, Solon P. Pissis, Leen Stougie, and Hilde Verbeek

Published in: LIPIcs, Volume 351, 33rd Annual European Symposium on Algorithms (ESA 2025)

Abstract
The reduction of the fragment assembly problem to (variations of) the classical Eulerian trail problem [Pevzner et al., PNAS 2001] has led to remarkable progress in genome assembly. This reduction employs the notion of de Bruijn graph G = (V,E) of order k over an alphabet Σ. A single Eulerian trail in G represents a candidate genome reconstruction. Bernardini et al. have also introduced the complementary idea in data privacy [ALENEX 2020] based on z-anonymity. Let S be a private string that we would like to release, preventing, however, its full reconstruction. For a privacy threshold z > 0, we compute the largest k for which there exist at least z Eulerian trails in the order-k de Bruijn graph of S, and release a string S' obtained via a random Eulerian trail. The pressing question is: How hard is it to reconstruct a best string from a de Bruijn graph given a function that models domain knowledge? Such a function maps every length-k string to an interval of positions where it may occur in the reconstructed string. By the above reduction to de Bruijn graphs, the latter function translates into a function c mapping every edge to an interval where it may occur in an Eulerian trail. This gives rise to the following basic problem on graphs: Given an instance (G,c), can we efficiently compute an Eulerian trail respecting c? Hannenhalli et al. [CABIOS 1996] formalized this problem and showed that it is NP-complete. Ben-Dor et al. [J. Comput. Biol. 2002] showed that it is NP-complete, even on de Bruin graphs with |Σ| = 4. In this work, we settle the lower-bound side of this problem by showing that finding a c-respecting Eulerian trail in de Bruijn graphs over alphabets of size 2 is NP-complete. We then shift our focus to parametrization aiming to capture the quality of our domain knowledge in the complexity. Ben-Dor et al. developed an algorithm to solve the problem on de Bruijn graphs in 𝒪(m⋅w^{1.5} 4^w) time, where m = |E| and w is the maximum interval length over all edges in E. Bumpus and Meeks [Algorithmica 2023] later rediscovered the same algorithm on temporal graphs, which highlights the relevance of this problem in other contexts. Our central contribution is showing how combinatorial insights lead to exponential-time improvements over the state-of-the-art algorithm. In particular, for the important class of de Bruijn graphs, we develop an algorithm parametrized by w (log w+1) /(k-1): for a de Bruijn graph of order k, it runs in 𝒪(mw⋅2^{w(log(w)+1)/(k-1)}) time. Our result improves on the state of the art by roughly an exponent of (log(w)+1)/(k-1). The existing algorithms have a natural interpretation for string reconstruction: when for each length-k string, we know a small range of positions it must lie in, string reconstruction can be solved in linear time. Our improved algorithm shows that it is enough when the range of positions is small relative to k. We then generalize both the existing and our novel FPT algorithm by allowing the cost at every position of an interval to vary. In this optimization version, our hardness result translates into inapproximability and the FPT algorithms work with a slight extension. Surprisingly, even in this more general setting, we extend the FPT algorithms to count and enumerate the min-cost Eulerian trails. The counting result has direct applications in the data privacy framework of Bernardini et al.
Cite as

Ben Bals, Sebastiaan van Krieken, Solon P. Pissis, Leen Stougie, and Hilde Verbeek. When Is String Reconstruction Using de Bruijn Graphs Hard?. In 33rd Annual European Symposium on Algorithms (ESA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 351, pp. 53:1-53:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{bals_et_al:LIPIcs.ESA.2025.53,
  author =	{Bals, Ben and van Krieken, Sebastiaan and Pissis, Solon P. and Stougie, Leen and Verbeek, Hilde},
  title =	{{When Is String Reconstruction Using de Bruijn Graphs Hard?}},
  booktitle =	{33rd Annual European Symposium on Algorithms (ESA 2025)},
  pages =	{53:1--53:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-395-9},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{351},
  editor =	{Benoit, Anne and Kaplan, Haim and Wild, Sebastian and Herman, Grzegorz},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2025.53},
  URN =		{urn:nbn:de:0030-drops-245215},
  doi =		{10.4230/LIPIcs.ESA.2025.53},
  annote =	{Keywords: string algorithm, graph algorithm, de Bruijn graph, Eulerian trail}
}
Document
DOI: 10.4230/LIPIcs.ESA.2024.11
How to Reduce Temporal Cliques to Find Sparse Spanners

Authors: Sebastian Angrick, Ben Bals, Tobias Friedrich, Hans Gawendowicz, Niko Hastrich, Nicolas Klodt, Pascal Lenzner, Jonas Schmidt, George Skretas, and Armin Wells

Published in: LIPIcs, Volume 308, 32nd Annual European Symposium on Algorithms (ESA 2024)

Abstract
Many real-world networks, such as transportation or trade networks, are dynamic in the sense that the edge-set may change over time, but these changes are known in advance. This behavior is captured by the temporal graphs model, which has recently become a trending topic in theoretical computer science. A core open problem in the field is to prove the existence of linear-size temporal spanners in temporal cliques, i.e., sparse subgraphs of complete temporal graphs that ensure all-pairs reachability via temporal paths. So far, the best known result is the existence of temporal spanners with 𝒪(nlog n) many edges. We present significant progress towards proving whether linear-size temporal spanners exist in all temporal cliques. We adapt techniques used in previous works and heavily expand and generalize them. This allows us to show that the existence of a linear spanner in cliques and bi-cliques is equivalent and using this, we provide a simpler and more intuitive proof of the 𝒪(nlog n) bound by giving an efficient algorithm for finding linearithmic spanners. Moreover, we use our novel and efficiently computable approach to show that a large class of temporal cliques, called edge-pivotable graphs, admit linear-size temporal spanners. To contrast this, we investigate other classes of temporal cliques that do not belong to the class of edge-pivotable graphs. We introduce two such graph classes and we develop novel algorithmic techniques for establishing the existence of linear temporal spanners in these graph classes as well.
Cite as

Sebastian Angrick, Ben Bals, Tobias Friedrich, Hans Gawendowicz, Niko Hastrich, Nicolas Klodt, Pascal Lenzner, Jonas Schmidt, George Skretas, and Armin Wells. How to Reduce Temporal Cliques to Find Sparse Spanners. In 32nd Annual European Symposium on Algorithms (ESA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 308, pp. 11:1-11:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{angrick_et_al:LIPIcs.ESA.2024.11,
  author =	{Angrick, Sebastian and Bals, Ben and Friedrich, Tobias and Gawendowicz, Hans and Hastrich, Niko and Klodt, Nicolas and Lenzner, Pascal and Schmidt, Jonas and Skretas, George and Wells, Armin},
  title =	{{How to Reduce Temporal Cliques to Find Sparse Spanners}},
  booktitle =	{32nd Annual European Symposium on Algorithms (ESA 2024)},
  pages =	{11:1--11:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-338-6},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{308},
  editor =	{Chan, Timothy and Fischer, Johannes and Iacono, John and Herman, Grzegorz},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2024.11},
  URN =		{urn:nbn:de:0030-drops-210822},
  doi =		{10.4230/LIPIcs.ESA.2024.11},
  annote =	{Keywords: Temporal Graphs, temporal Clique, temporal Spanner, Reachability, Graph Connectivity, Graph Sparsification}
}
Document
DOI: 10.4230/LIPIcs.SEA.2023.10
Solving Directed Feedback Vertex Set by Iterative Reduction to Vertex Cover

Authors: Sebastian Angrick, Ben Bals, Katrin Casel, Sarel Cohen, Tobias Friedrich, Niko Hastrich, Theresa Hradilak, Davis Issac, Otto Kißig, Jonas Schmidt, and Leo Wendt

Published in: LIPIcs, Volume 265, 21st International Symposium on Experimental Algorithms (SEA 2023)

Abstract
In the Directed Feedback Vertex Set (DFVS) problem, one is given a directed graph G = (V,E) and wants to find a minimum cardinality set S ⊆ V such that G-S is acyclic. DFVS is a fundamental problem in computer science and finds applications in areas such as deadlock detection. The problem was the subject of the 2022 PACE coding challenge. We develop a novel exact algorithm for the problem that is tailored to perform well on instances that are mostly bi-directed. For such instances, we adapt techniques from the well-researched vertex cover problem. Our core idea is an iterative reduction to vertex cover. To this end, we also develop a new reduction rule that reduces the number of not bi-directed edges. With the resulting algorithm, we were able to win third place in the exact track of the PACE challenge. We perform computational experiments and compare the running time to other exact algorithms, in particular to the winning algorithm in PACE. Our experiments show that we outpace the other algorithms on instances that have a low density of uni-directed edges.
Cite as

Sebastian Angrick, Ben Bals, Katrin Casel, Sarel Cohen, Tobias Friedrich, Niko Hastrich, Theresa Hradilak, Davis Issac, Otto Kißig, Jonas Schmidt, and Leo Wendt. Solving Directed Feedback Vertex Set by Iterative Reduction to Vertex Cover. In 21st International Symposium on Experimental Algorithms (SEA 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 265, pp. 10:1-10:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{angrick_et_al:LIPIcs.SEA.2023.10,
  author =	{Angrick, Sebastian and Bals, Ben and Casel, Katrin and Cohen, Sarel and Friedrich, Tobias and Hastrich, Niko and Hradilak, Theresa and Issac, Davis and Ki{\ss}ig, Otto and Schmidt, Jonas and Wendt, Leo},
  title =	{{Solving Directed Feedback Vertex Set by Iterative Reduction to Vertex Cover}},
  booktitle =	{21st International Symposium on Experimental Algorithms (SEA 2023)},
  pages =	{10:1--10:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-279-2},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{265},
  editor =	{Georgiadis, Loukas},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2023.10},
  URN =		{urn:nbn:de:0030-drops-183602},
  doi =		{10.4230/LIPIcs.SEA.2023.10},
  annote =	{Keywords: directed feedback vertex set, vertex cover, reduction rules}
}
Document
PACE Solver Description
DOI: 10.4230/LIPIcs.IPEC.2022.28
PACE Solver Description: Mount Doom - An Exact Solver for Directed Feedback Vertex Set

Authors: Sebastian Angrick, Ben Bals, Katrin Casel, Sarel Cohen, Tobias Friedrich, Niko Hastrich, Theresa Hradilak, Davis Issac, Otto Kißig, Jonas Schmidt, and Leo Wendt

Published in: LIPIcs, Volume 249, 17th International Symposium on Parameterized and Exact Computation (IPEC 2022)

Abstract
In this document we describe the techniques we used and implemented for our submission to the Parameterized Algorithms and Computational Experiments Challenge (PACE) 2022. The given problem is Directed Feedback Vertex Set (DFVS), where one is given a directed graph G = (V,E) and wants to find a minimum S ⊆ V such that G-S is acyclic. We approach this problem by first exhaustively applying a set of reduction rules. In order to find a minimum DFVS on the remaining instance, we create and solve a series of Vertex Cover instances.
Cite as

Sebastian Angrick, Ben Bals, Katrin Casel, Sarel Cohen, Tobias Friedrich, Niko Hastrich, Theresa Hradilak, Davis Issac, Otto Kißig, Jonas Schmidt, and Leo Wendt. PACE Solver Description: Mount Doom - An Exact Solver for Directed Feedback Vertex Set. In 17th International Symposium on Parameterized and Exact Computation (IPEC 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 249, pp. 28:1-28:4, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{angrick_et_al:LIPIcs.IPEC.2022.28,
  author =	{Angrick, Sebastian and Bals, Ben and Casel, Katrin and Cohen, Sarel and Friedrich, Tobias and Hastrich, Niko and Hradilak, Theresa and Issac, Davis and Ki{\ss}ig, Otto and Schmidt, Jonas and Wendt, Leo},
  title =	{{PACE Solver Description: Mount Doom - An Exact Solver for Directed Feedback Vertex Set}},
  booktitle =	{17th International Symposium on Parameterized and Exact Computation (IPEC 2022)},
  pages =	{28:1--28:4},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-260-0},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{249},
  editor =	{Dell, Holger and Nederlof, Jesper},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.IPEC.2022.28},
  URN =		{urn:nbn:de:0030-drops-173847},
  doi =		{10.4230/LIPIcs.IPEC.2022.28},
  annote =	{Keywords: directed feedback vertex set, vertex cover, reduction rules}
}
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