14 Search Results for "Tsur, Dekel"

Document
DOI: 10.4230/LIPIcs.IPEC.2025.3
Parameterized Maximum Node-Disjoint Paths

Authors: Michael Lampis and Manolis Vasilakis

Published in: LIPIcs, Volume 358, 20th International Symposium on Parameterized and Exact Computation (IPEC 2025)

Abstract
We revisit the Maximum Node-Disjoint Paths problem, the natural optimization version of the famous Node-Disjoint Paths problem, where we are given an undirected graph G, k (demand) pairs of vertices (s_i, t_i), and an integer 𝓁, and are asked whether there exist at least 𝓁 vertex-disjoint paths in G whose endpoints are given pairs. This problem has been intensely studied from both the approximation and parameterized complexity point of view and is notably known to be intractable by standard structural parameters, such as tree-depth, as well as the combined parameter 𝓁 plus pathwidth. We present several results improving and clarifying this state of the art, with an emphasis towards FPT approximation. Our main positive contribution is to show that the problem’s intractability can be overcome using approximation: We show that for several of the structural parameters for which the problem is hard, most notably tree-depth, the problem admits an efficient FPT approximation scheme, returning a (1-ε)-approximate solution in time f(td,ε)n^𝒪(1). We manage to obtain these results by comprehensively mapping out the structural parameters for which the problem is FPT if 𝓁 is also a parameter, hence showing that understanding 𝓁 as a parameter is key to the problem’s approximability. This, in turn, is a problem we are able to solve via a surprisingly simple color-coding algorithm, which relies on identifying an insightful problem-specific variant of the natural parameter, namely the number of vertices used in the solution. The results above are quite encouraging, as they indicate that in some situations where the problem does not admit an FPT algorithm, it is still solvable almost to optimality in FPT time. A natural question is whether the FPT approximation algorithm we devised for tree-depth can be extended to pathwidth. We resolve this negatively, showing that under the Parameterized Inapproximability Hypothesis no FPT approximation scheme for this parameter is possible, even in time f(pw,ε)n^g(ε). We thus precisely determine the parameter border where the problem transitions from "hard but approximable" to "inapproximable". Lastly, we strengthen existing lower bounds by replacing W[1]-hardness by XNLP-completeness for parameter pathwidth, and improving the n^o(√{td}) ETH-based lower bound for tree-depth to (the optimal) n^o(td).
Cite as

Michael Lampis and Manolis Vasilakis. Parameterized Maximum Node-Disjoint Paths. In 20th International Symposium on Parameterized and Exact Computation (IPEC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 358, pp. 3:1-3:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{lampis_et_al:LIPIcs.IPEC.2025.3,
  author =	{Lampis, Michael and Vasilakis, Manolis},
  title =	{{Parameterized Maximum Node-Disjoint Paths}},
  booktitle =	{20th International Symposium on Parameterized and Exact Computation (IPEC 2025)},
  pages =	{3:1--3:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-407-9},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{358},
  editor =	{Agrawal, Akanksha and van Leeuwen, Erik Jan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.IPEC.2025.3},
  URN =		{urn:nbn:de:0030-drops-251357},
  doi =		{10.4230/LIPIcs.IPEC.2025.3},
  annote =	{Keywords: ETH, Maximum Node-Disjoint Paths, Parameterized Complexity, PIH}
}
Document
DOI: 10.4230/LIPIcs.IPEC.2025.32
The PACE 2025 Parameterized Algorithms and Computational Experiments Challenge: Dominating Set and Hitting Set

Authors: Mario Grobler and Sebastian Siebertz

Published in: LIPIcs, Volume 358, 20th International Symposium on Parameterized and Exact Computation (IPEC 2025)

Abstract
The 10th iteration of the of the Parameterized Algorithms and Computational Experiments challenge (PACE) 2025 was devoted to engineer algorithms solving the Dominating Set problem as well as the Hitting Set problem. In contrast to the last iterations, these problems are (under standard assumptions) not fixed-parameter tractable (fpt) in general. However, restricting the structure of the input (e.g. to planar graphs or degenerate graphs for Dominating Set, or to set systems with sets of bounded size for Hitting Set) renders these problems fpt. Following the spirit of the last iterations of the PACE challenge, there is an exact track and a heuristic track for each problem; each track coming with a benchmark set of 100 public instances and 100 private instances. Overall, the PACE 2025 had 71 participants from 25 teams, 13 countries, and 3 continents. In this report, we briefly describe the setup of the challenge, the selection of benchmark instances, as well as the ranking of the participating teams. We also briefly outline the approaches used in the submitted solvers.
Cite as

Mario Grobler and Sebastian Siebertz. The PACE 2025 Parameterized Algorithms and Computational Experiments Challenge: Dominating Set and Hitting Set. In 20th International Symposium on Parameterized and Exact Computation (IPEC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 358, pp. 32:1-32:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{grobler_et_al:LIPIcs.IPEC.2025.32,
  author =	{Grobler, Mario and Siebertz, Sebastian},
  title =	{{The PACE 2025 Parameterized Algorithms and Computational Experiments Challenge: Dominating Set and Hitting Set}},
  booktitle =	{20th International Symposium on Parameterized and Exact Computation (IPEC 2025)},
  pages =	{32:1--32:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-407-9},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{358},
  editor =	{Agrawal, Akanksha and van Leeuwen, Erik Jan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.IPEC.2025.32},
  URN =		{urn:nbn:de:0030-drops-251644},
  doi =		{10.4230/LIPIcs.IPEC.2025.32},
  annote =	{Keywords: PACE 2025 Report, Dominating Set, Hitting Set, Algorithm Engineering, FPT, Heuristics}
}
Document
DOI: 10.4230/LIPIcs.FSTTCS.2025.39
Improved Approximation for Pathwidth One Vertex Deletion and Parameterized Complexity of Its Variants

Authors: Satyabrata Jana, Soumen Mandal, Ashutosh Rai, and Saket Saurabh

Published in: LIPIcs, Volume 360, 45th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2025)

Abstract
The pathwidth of a graph is a measure of how path-like the graph is. The Pathwidth One Vertex Deletion (POVD) problem asks whether, given an undirected graph G and an integer k, one can delete at most k vertices from G so that the remaining graph has pathwidth at most one. This is a natural variation of the classical Feedback vertex Set (FVS) problem, where the deletion of at most k vertices results in a graph of treewidth at most one. In this work, we investigate POVD in the realm of approximation algorithms. We first design a 3-approximation algorithm for POVD running in polynomial time. Then, using this constant factor approximation algorithm, we obtain a randomized parameterized approximation algorithm for POVD running in time 𝒪^*((h_β)^k), that improves the fastest existing running times for approximation ratios in the range (1.76147,3). Here the constant h_β depends on the approximation factor β alone and has value 2^{(3-β)}, which lies in the range (1,2.3596), when β ∈ (1.76147,3). Taking inspiration from two extensively studied problems, namely Connected FVS and Independent FVS, we investigate two variations of the POVD problem from the perspective of parameterized algorithms. These variations are the connected variant, called Connected pathwidth One Vertex Deletion (CPOVD) and the independent variant, called Independent Pathwidth One Vertex Deletion (IPOVD). While in CPOVD the subgraph G[S] induced by the vertices to be deleted needs to be connected, in IPOVD it needs to be independent. Specifically, we show the following results. - CPOVD can be solved in {𝒪}^*(14^k) time and admits no polynomial kernel unless NP ⊆ {co-NP/poly}. - IPOVD can be solved in {𝒪}^*(7^k) time, and admits a kernel of size 𝒪(k³).
Cite as

Satyabrata Jana, Soumen Mandal, Ashutosh Rai, and Saket Saurabh. Improved Approximation for Pathwidth One Vertex Deletion and Parameterized Complexity of Its Variants. In 45th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 360, pp. 39:1-39:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{jana_et_al:LIPIcs.FSTTCS.2025.39,
  author =	{Jana, Satyabrata and Mandal, Soumen and Rai, Ashutosh and Saurabh, Saket},
  title =	{{Improved Approximation for Pathwidth One Vertex Deletion and Parameterized Complexity of Its Variants}},
  booktitle =	{45th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2025)},
  pages =	{39:1--39:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-406-2},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{360},
  editor =	{Aiswarya, C. and Mehta, Ruta and Roy, Subhajit},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FSTTCS.2025.39},
  URN =		{urn:nbn:de:0030-drops-251192},
  doi =		{10.4230/LIPIcs.FSTTCS.2025.39},
  annote =	{Keywords: Pathwidth, Parameterized complexity, Approximation, Kernelization}
}
Document
DOI: 10.4230/LIPIcs.ISAAC.2025.48
Quadratic Kernel for Cliques or Trees Vertex Deletion

Authors: Soh Kumabe

Published in: LIPIcs, Volume 359, 36th International Symposium on Algorithms and Computation (ISAAC 2025)

Abstract
We consider Cliques or Trees Vertex Deletion, which is a hybrid of two fundamental parameterized problems: Cluster Vertex Deletion and Feedback Vertex Set. In this problem, we are given an undirected graph G and an integer k, and asked to find a vertex subset X of size at most k such that each connected component of G-X is either a clique or a tree. Jacob et al. (ISAAC, 2024) provided a kernel of O(k⁵) vertices for this problem, which was recently improved to O(k⁴) by Tsur (IPL, 2025). Our main result is a kernel of O(k²) vertices. This result closes the gap between the kernelization result for Feedback Vertex Set, which corresponds to the case where each connected component of G-X must be a tree. Although both cluster vertex deletion number and feedback vertex set number are well-studied structural parameters, little attention has been given to parameters that generalize both of them. In fact, the lowest common well-known generalization of them is clique-width, which is a highly general parameter. To fill the gap here, we initiate the study of the cliques or trees vertex deletion number as a structural parameter. We prove that Longest Cycle, which is a fundamental problem that does not admit o(n^k)-time algorithm unless ETH fails when k is the clique-width, becomes fixed-parameter tractable when parameterized by the cliques or trees vertex deletion number.
Cite as

Soh Kumabe. Quadratic Kernel for Cliques or Trees Vertex Deletion. In 36th International Symposium on Algorithms and Computation (ISAAC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 359, pp. 48:1-48:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{kumabe:LIPIcs.ISAAC.2025.48,
  author =	{Kumabe, Soh},
  title =	{{Quadratic Kernel for Cliques or Trees Vertex Deletion}},
  booktitle =	{36th International Symposium on Algorithms and Computation (ISAAC 2025)},
  pages =	{48:1--48:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-408-6},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{359},
  editor =	{Chen, Ho-Lin and Hon, Wing-Kai and Tsai, Meng-Tsung},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ISAAC.2025.48},
  URN =		{urn:nbn:de:0030-drops-249568},
  doi =		{10.4230/LIPIcs.ISAAC.2025.48},
  annote =	{Keywords: Fixed-Parameter Tractability, Kernelization, Deletion to Scattered Graph Classes, Cluster Vertex Deletion, Feedback Vertex Set}
}
Document
DOI: 10.4230/LIPIcs.ESA.2025.7
Graph Modification of Bounded Size to Minor-Closed Classes as Fast as Vertex Deletion

Authors: Laure Morelle, Ignasi Sau, and Dimitrios M. Thilikos

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

Abstract
A replacement action is a function ℒ that maps each graph H to a collection of graphs of size at most |V(H)|. Given a graph class ℋ, we consider a general family of graph modification problems, called ℒ-Replacement to ℋ, where the input is a graph G and the question is whether it is possible to replace some induced subgraph H₁ of G on at most k vertices by a graph H₂ in ℒ(H₁) so that the resulting graph belongs to ℋ. ℒ-Replacement to ℋ can simulate many graph modification problems including vertex deletion, edge deletion/addition/edition/contraction, vertex identification, subgraph complementation, independent set deletion, (induced) matching deletion/contraction, etc. We present two algorithms. The first one solves ℒ-Replacement to ℋ in time 2^poly(k) ⋅ |V(G)|² for every minor-closed graph class ℋ, where poly is a polynomial whose degree depends on ℋ, under a mild technical condition on ℒ. This generalizes the results of Morelle, Sau, Stamoulis, and Thilikos [ICALP 2020, ICALP 2023] for the particular case of Vertex Deletion to ℋ within the same running time. Our second algorithm is an improvement of the first one when ℋ is the class of graphs embeddable in a surface of Euler genus at most g and runs in time 2^𝒪(k⁹) ⋅ |V(G)|², where the 𝒪(⋅) notation depends on g. To the best of our knowledge, these are the first parameterized algorithms with a reasonable parametric dependence for such a general family of graph modification problems to minor-closed classes.
Cite as

Laure Morelle, Ignasi Sau, and Dimitrios M. Thilikos. Graph Modification of Bounded Size to Minor-Closed Classes as Fast as Vertex Deletion. In 33rd Annual European Symposium on Algorithms (ESA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 351, pp. 7:1-7:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{morelle_et_al:LIPIcs.ESA.2025.7,
  author =	{Morelle, Laure and Sau, Ignasi and Thilikos, Dimitrios M.},
  title =	{{Graph Modification of Bounded Size to Minor-Closed Classes as Fast as Vertex Deletion}},
  booktitle =	{33rd Annual European Symposium on Algorithms (ESA 2025)},
  pages =	{7:1--7:18},
  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.2025.7},
  URN =		{urn:nbn:de:0030-drops-244751},
  doi =		{10.4230/LIPIcs.ESA.2025.7},
  annote =	{Keywords: Graph modification problems, Parameterized complexity, Graph minors, Flat Wall theorem, Irrelevant vertex technique, Algorithmic meta-theorem, Parametric dependence, Dynamic programming}
}
Document
DOI: 10.4230/LIPIcs.MFCS.2025.90
Elimination Distance to Dominated Clusters

Authors: Nicole Schirrmacher, Sebastian Siebertz, and Alexandre Vigny

Published in: LIPIcs, Volume 345, 50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025)

Abstract
In the Dominated Cluster Deletion problem, we are given an undirected graph G and integers k and d and the question is to decide whether there exists a set of at most k vertices whose removal results in a graph in which each connected component has a dominating set of size at most d. In the Elimination Distance to Dominated Clusters problem, we are again given an undirected graph G and integers k and d and the question is to decide whether we can recursively delete vertices up to depth k such that each remaining connected component has a dominating set of size at most d. Bentert et al. [Bentert et al., MFCS 2024] recently provided an almost complete classification of the parameterized complexity of Dominated Cluster Deletion with respect to the parameters k, d, c, and Δ, where c and Δ are the degeneracy, and the maximum degree of the input graph, respectively. In particular, they provided a non-uniform algorithm with running time f(k,d)⋅ n^{𝒪(d)}. They left as an open problem whether the problem is fixed-parameter tractable with respect to the parameter k + d + c. We provide a uniform algorithm running in time f(k,d)⋅ n^{𝒪(d)} for both Dominated Cluster Deletion and Elimination Distance to Dominated Clusters. We furthermore show that both problems are FPT when parameterized by k+d+𝓁, where 𝓁 is the semi-ladder index of the input graph, a parameter that is upper bounded and may be much smaller than the degeneracy c, positively answering the open question of Bentert et al. We further complete the picture by providing an almost full classification for the parameterized complexity and kernelization complexity of Elimination Distance to Dominated Clusters. The one difficult base case that remains open is whether Treedepth (the case d = 0) is NP-hard on graphs of bounded maximum degree.
Cite as

Nicole Schirrmacher, Sebastian Siebertz, and Alexandre Vigny. Elimination Distance to Dominated Clusters. In 50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 345, pp. 90:1-90:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{schirrmacher_et_al:LIPIcs.MFCS.2025.90,
  author =	{Schirrmacher, Nicole and Siebertz, Sebastian and Vigny, Alexandre},
  title =	{{Elimination Distance to Dominated Clusters}},
  booktitle =	{50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025)},
  pages =	{90:1--90:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-388-1},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{345},
  editor =	{Gawrychowski, Pawe{\l} and Mazowiecki, Filip and Skrzypczak, Micha{\l}},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2025.90},
  URN =		{urn:nbn:de:0030-drops-241978},
  doi =		{10.4230/LIPIcs.MFCS.2025.90},
  annote =	{Keywords: Graph theory, Fixed-parameter algorithms, Dominated cluster, Elimination distance}
}
Document
DOI: 10.4230/LIPIcs.WABI.2025.22
Design of Worst-Case-Optimal Spaced Seeds

Authors: Jens Zentgraf and Sven Rahmann

Published in: LIPIcs, Volume 344, 25th International Conference on Algorithms for Bioinformatics (WABI 2025)

Abstract
Read mapping (and alignment) is a fundamental problem in biological sequence analysis. For speed and computational efficiency, many popular read mappers tolerate only a few differences between the read and the corresponding part of the reference genome, which leads to reference bias: Reads with too many differences are not guaranteed to be mapped correctly or at all, because to even consider a genomic position, a sufficiently long exact match (seed) must exist. While pangenomes and their graph-based representations provide one way to avoid reference bias by enlarging the reference, we explore an orthogonal approach and consider stronger substitution-tolerant primitives, namely spaced seeds or gapped k-mers. Given two integers k ≤ w, one considers k selected positions, described by a mask, from each length-w window in a sequence. In the existing literature, masks with certain probabilistic guarantees have been designed for small values of k. Here, for the first time, we take a combinatorial approach from a worst-case perspective. For any mask, using integer linear programs, we find least favorable distributions of sequence changes in two different senses: (1) minimizing the number of unchanged windows; (2) minimizing the number of positions covered by unchanged windows. Then, among all masks or all symmetric masks of a given shape (k,w), we find the set of best masks that maximize these minima. As a result, we obtain robust masks, even for large numbers of changes. We illustrate the properties of these masks by constructing a challenging set of reads that contain many approximately equidistributed substitutions (but no indels) that many existing tools cannot map, even though they are in principle easily mappable (apart from the large number of changes) because they originate from selected non-repetitive regions of the human reference genome. We observe that the majority of these reads can be mapped with a simple alignment-free approach using chosen spaced masks, where seeding approaches based on contiguous k-mers fail.
Cite as

Jens Zentgraf and Sven Rahmann. Design of Worst-Case-Optimal Spaced Seeds. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 22:1-22:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{zentgraf_et_al:LIPIcs.WABI.2025.22,
  author =	{Zentgraf, Jens and Rahmann, Sven},
  title =	{{Design of Worst-Case-Optimal Spaced Seeds}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{22:1--22:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-386-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{344},
  editor =	{Brejov\'{a}, Bro\v{n}a and Patro, Rob},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2025.22},
  URN =		{urn:nbn:de:0030-drops-239488},
  doi =		{10.4230/LIPIcs.WABI.2025.22},
  annote =	{Keywords: Spaced seed, Gapped k-mer, Integer linear program (ILP), Worst-case design, Reference bias}
}
Document
DOI: 10.4230/LIPIcs.WABI.2025.13
Spark: Sparsified Hierarchical Energy Minimization of RNA Pseudoknots

Authors: Mateo Gray, Sebastian Will, and Hosna Jabbari

Published in: LIPIcs, Volume 344, 25th International Conference on Algorithms for Bioinformatics (WABI 2025)

Abstract
Motivation. Determining RNA structure is essential for understanding RNA function and interaction networks. Although experimental techniques yield high‑accuracy structures, they are costly and time‑consuming; thus, computational approaches - especially minimum‑free‑energy (MFE) prediction algorithms - are indispensable. Accurately predicting pseudoknots, however, remains challenging because their inclusion usually leads to prohibitive computational complexity. Recent work demonstrated that sparsification can improve the efficiency of complex pseudoknot prediction algorithms such as Knotty. This finding suggests similar gains are possible for already efficient algorithms like HFold, which targets a complementary class of hierarchically constrained pseudoknots. Results. We introduce Spark, an exact, fully sparsified algorithm for predicting pseudoknotted RNA structures. Like its non‑sparsified predecessor HFold, Spark searches for the minimum‑energy structure under the HotKots 2.0 energy model, a pseudoknot extension of the Turner model. Because the sparsification is non‑heuristic, Spark preserves the asymptotic time‑ and space‑complexity guarantees of HFold while greatly reducing the constant factors. We benchmarked the performance of Spark against HFold and, as a pseudoknot‑free baseline, RNAfold. Compared with HFold, Spark substantially lowers both run time and memory usage, while achieving run‑time figures close to those of RNAfold. Across all tested sequence lengths, Spark used the least memory and consistently ran faster than HFold. Conclusion. By extending non‑heuristic sparsification to hierarchical pseudoknot prediction, Spark delivers an exceptionally fast and memory‑efficient tool accurate prediction of pseudoknotted RNA structures, enabling routine analysis of long sequences. The algorithm broadens the practical scope of computational RNA biology and provides a solid foundation for future advances in structure‑based functional annotation. Availability. Spark’s implementation and detailed results are available at https://github.com/TheCOBRALab/Spark.
Cite as

Mateo Gray, Sebastian Will, and Hosna Jabbari. Spark: Sparsified Hierarchical Energy Minimization of RNA Pseudoknots. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 13:1-13:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{gray_et_al:LIPIcs.WABI.2025.13,
  author =	{Gray, Mateo and Will, Sebastian and Jabbari, Hosna},
  title =	{{Spark: Sparsified Hierarchical Energy Minimization of RNA Pseudoknots}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{13:1--13:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-386-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{344},
  editor =	{Brejov\'{a}, Bro\v{n}a and Patro, Rob},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2025.13},
  URN =		{urn:nbn:de:0030-drops-239383},
  doi =		{10.4230/LIPIcs.WABI.2025.13},
  annote =	{Keywords: RNA, MFE, Secondary Structure Prediction, Pseudoknot, Sparsification, Space Complexity, Time Complexity}
}
Document
Research
DOI: 10.4230/OASIcs.Grossi.12
Encoding Data Structures for Range Queries on Arrays

Authors: Seungbum Jo and Srinivasa Rao Satti

Published in: OASIcs, Volume 132, From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday (2025)

Abstract
Efficiently processing range queries on arrays is a fundamental problem in computer science, with applications spanning diverse domains such as database management, computational biology, and geographic information systems. A range query retrieves information about a specific segment of an array, such as the sum, minimum, maximum, or median of elements within a given range. The challenge lies in designing data structures that allow such queries to be answered quickly, often in constant or logarithmic time, while keeping space overhead (and preprocessing time) small. Encoding data structures for range queries has emerged as a pivotal area of research due to the increasing demand for high-performance systems handling massive datasets. These structures consider the data together with the queries and aim to store only as much information about the data as is needed to answer the queries. The data structure does not need to access the original data to answer the queries. Encoding-based solutions often leverage techniques from succinct data structures, bit manipulation, and combinatorial optimization to achieve both space and time efficiency. By encoding the array in a manner that preserves critical information, these methods strike a balance between query time and space usage. In this survey article, we explore the landscape of encoding data structures for range queries on arrays, providing a comprehensive overview of some important results on space-efficient encodings for various types of range query.
Cite as

Seungbum Jo and Srinivasa Rao Satti. Encoding Data Structures for Range Queries on Arrays. In From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday. Open Access Series in Informatics (OASIcs), Volume 132, pp. 12:1-12:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{jo_et_al:OASIcs.Grossi.12,
  author =	{Jo, Seungbum and Satti, Srinivasa Rao},
  title =	{{Encoding Data Structures for Range Queries on Arrays}},
  booktitle =	{From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday},
  pages =	{12:1--12:12},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-391-1},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{132},
  editor =	{Conte, Alessio and Marino, Andrea and Rosone, Giovanna and Vitter, Jeffrey Scott},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.Grossi.12},
  URN =		{urn:nbn:de:0030-drops-238116},
  doi =		{10.4230/OASIcs.Grossi.12},
  annote =	{Keywords: range queries, RMQ, Cartesian tree, top-k queries, range median, range mode}
}
Document
DOI: 10.4230/OASIcs.Manzini.9
Search Schemes for Approximate Pattern Matching: An Overview

Authors: Lore Depuydt, Jan Fostier, Simon Gottlieb, Gregory Kucherov, Knut Reinert, and Luca Renders

Published in: OASIcs, Volume 131, The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday (2025)

Abstract
We provide a brief survey of results on solving the approximate pattern matching problem using search schemes, as introduced by Kucherov et al. (2016). We demonstrate that search schemes constitute a flexible and versatile tool that enable the specification of various search strategies, including several known filtering methods. We present approaches for designing efficient search schemes and for implementing them effectively. Finally, we conclude with experimental results comparing multiple search schemes on DNA sequencing data using the Columba software by Renders et al. (2021).
Cite as

Lore Depuydt, Jan Fostier, Simon Gottlieb, Gregory Kucherov, Knut Reinert, and Luca Renders. Search Schemes for Approximate Pattern Matching: An Overview. In The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday. Open Access Series in Informatics (OASIcs), Volume 131, pp. 9:1-9:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{depuydt_et_al:OASIcs.Manzini.9,
  author =	{Depuydt, Lore and Fostier, Jan and Gottlieb, Simon and Kucherov, Gregory and Reinert, Knut and Renders, Luca},
  title =	{{Search Schemes for Approximate Pattern Matching: An Overview}},
  booktitle =	{The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday},
  pages =	{9:1--9:16},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-390-4},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{131},
  editor =	{Ferragina, Paolo and Gagie, Travis and Navarro, Gonzalo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.Manzini.9},
  URN =		{urn:nbn:de:0030-drops-239172},
  doi =		{10.4230/OASIcs.Manzini.9},
  annote =	{Keywords: FM-index, bidirectional index, approximate pattern matching, search scheme}
}
Document
Track A: Algorithms, Complexity and Games
DOI: 10.4230/LIPIcs.ICALP.2025.82
(Almost-)Optimal FPT Algorithm and Kernel for T-Cycle on Planar Graphs

Authors: Harmender Gahlawat, Abhishek Rathod, and Meirav Zehavi

Published in: LIPIcs, Volume 334, 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)

Abstract
Research of cycles through specific vertices is a central topic in graph theory. In this context, we focus on a well-studied computational problem, T-Cycle: given an undirected n-vertex graph G and a set of k vertices T ⊆ V(G) termed terminals, the objective is to determine whether G contains a simple cycle C through all the terminals. Our contribution is twofold: (i) We provide a 2^{O(√klog k)}⋅ n-time fixed-parameter deterministic algorithm for T-Cycle on planar graphs; (ii) We provide a k^{O(1)}⋅ n-time deterministic kernelization algorithm for T-Cycle on planar graphs where the produced instance is of size klog^{O(1)}k. Both of our algorithms are optimal in terms of both k and n up to (poly)logarithmic factors in k under the ETH. In fact, our algorithms are the first subexponential-time fixed-parameter algorithm for T-Cycle on planar graphs, as well as the first polynomial kernel for T-Cycle on planar graphs. This substantially improves upon/expands the known literature on the parameterized complexity of the problem.
Cite as

Harmender Gahlawat, Abhishek Rathod, and Meirav Zehavi. (Almost-)Optimal FPT Algorithm and Kernel for T-Cycle on Planar Graphs. In 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 334, pp. 82:1-82:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{gahlawat_et_al:LIPIcs.ICALP.2025.82,
  author =	{Gahlawat, Harmender and Rathod, Abhishek and Zehavi, Meirav},
  title =	{{(Almost-)Optimal FPT Algorithm and Kernel for T-Cycle on Planar Graphs}},
  booktitle =	{52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)},
  pages =	{82:1--82:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-372-0},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{334},
  editor =	{Censor-Hillel, Keren and Grandoni, Fabrizio and Ouaknine, Jo\"{e}l and Puppis, Gabriele},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2025.82},
  URN =		{urn:nbn:de:0030-drops-234593},
  doi =		{10.4230/LIPIcs.ICALP.2025.82},
  annote =	{Keywords: FPT Algorithms, Kernelization, T-Cycle, Subexponential Algorithmms}
}
Document
Track A: Algorithms, Complexity and Games
DOI: 10.4230/LIPIcs.ICALP.2025.39
Sampling with a Black Box: Faster Parameterized Approximation Algorithms for Vertex Deletion Problems

Authors: Barış Can Esmer and Ariel Kulik

Published in: LIPIcs, Volume 334, 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)

Abstract
In this paper, we present Sampling with a Black Box, a unified framework for the design of parameterized approximation algorithms for vertex deletion problems (e.g., Vertex Cover, Feedback Vertex Set, etc.). The framework relies on two components: - A Sampling Step. A polynomial-time randomized algorithm that, given a graph G, returns a random vertex v such that the optimum of G⧵ {v} is smaller by 1 than the optimum of G, with some prescribed probability q. We show that such algorithms exist for multiple vertex deletion problems. - A Black Box algorithm which is either an exact parameterized algorithm, a polynomial-time approximation algorithm, or a parameterized-approximation algorithm. The framework combines these two components together. The sampling step is applied iteratively to remove vertices from the input graph, and then the solution is extended using the black box algorithm. The process is repeated sufficiently many times so that the target approximation ratio is attained with a constant probability. We use the technique to derive parameterized approximation algorithms for several vertex deletion problems, including Feedback Vertex Set, d-Hitting Set and 𝓁-Path Vertex Cover. In particular, for every approximation ratio 1 < β < 2, we attain a parameterized β-approximation for Feedback Vertex Set, which is faster than the parameterized β-approximation of [Jana, Lokshtanov, Mandal, Rai and Saurabh, MFCS 23']. Furthermore, our algorithms are always faster than the algorithms attained using Fidelity Preserving Transformations [Fellows, Kulik, Rosamond, and Shachnai, JCSS 18'].
Cite as

Barış Can Esmer and Ariel Kulik. Sampling with a Black Box: Faster Parameterized Approximation Algorithms for Vertex Deletion Problems. In 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 334, pp. 39:1-39:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{canesmer_et_al:LIPIcs.ICALP.2025.39,
  author =	{Can Esmer, Bar{\i}\c{s} and Kulik, Ariel},
  title =	{{Sampling with a Black Box: Faster Parameterized Approximation Algorithms for Vertex Deletion Problems}},
  booktitle =	{52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)},
  pages =	{39:1--39:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-372-0},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{334},
  editor =	{Censor-Hillel, Keren and Grandoni, Fabrizio and Ouaknine, Jo\"{e}l and Puppis, Gabriele},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2025.39},
  URN =		{urn:nbn:de:0030-drops-234165},
  doi =		{10.4230/LIPIcs.ICALP.2025.39},
  annote =	{Keywords: Parameterized Approximation Algorithms, Random Sampling}
}
Document
DOI: 10.4230/LIPIcs.STACS.2025.64
Cluster Editing on Cographs and Related Classes

Authors: Manuel Lafond, Alitzel López Sánchez, and Weidong Luo

Published in: LIPIcs, Volume 327, 42nd International Symposium on Theoretical Aspects of Computer Science (STACS 2025)

Abstract
In the Cluster Editing problem, sometimes known as (unweighted) Correlation Clustering, we must insert and delete a minimum number of edges to achieve a graph in which every connected component is a clique. Owing to its applications in computational biology, social network analysis, machine learning, and others, this problem has been widely studied for decades and is still undergoing active research. There exist several parameterized algorithms for general graphs, but little is known about the complexity of the problem on specific classes of graphs. Among the few important results in this direction, if only deletions are allowed, the problem can be solved in polynomial time on cographs, which are the P₄-free graphs. However, the complexity of the broader editing problem on cographs is still open. We show that even on a very restricted subclass of cographs, the problem is NP-hard, W[1]-hard when parameterized by the number p of desired clusters, and that time n^o(p/log p) is forbidden under the ETH. This shows that the editing variant is substantially harder than the deletion-only case, and that hardness holds for the many superclasses of cographs (including graphs of clique-width at most 2, perfect graphs, circle graphs, permutation graphs). On the other hand, we provide an almost tight upper bound of time n^O(p), which is a consequence of a more general n^O(cw⋅p) time algorithm, where cw is the clique-width. Given that forbidding P₄s maintains NP-hardness, we look at {P₄, C₄}-free graphs, also known as trivially perfect graphs, and provide a cubic-time algorithm for this class.
Cite as

Manuel Lafond, Alitzel López Sánchez, and Weidong Luo. Cluster Editing on Cographs and Related Classes. In 42nd International Symposium on Theoretical Aspects of Computer Science (STACS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 327, pp. 64:1-64:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{lafond_et_al:LIPIcs.STACS.2025.64,
  author =	{Lafond, Manuel and L\'{o}pez S\'{a}nchez, Alitzel and Luo, Weidong},
  title =	{{Cluster Editing on Cographs and Related Classes}},
  booktitle =	{42nd International Symposium on Theoretical Aspects of Computer Science (STACS 2025)},
  pages =	{64:1--64:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-365-2},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{327},
  editor =	{Beyersdorff, Olaf and Pilipczuk, Micha{\l} and Pimentel, Elaine and Thắng, Nguy\~{ê}n Kim},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.STACS.2025.64},
  URN =		{urn:nbn:de:0030-drops-228895},
  doi =		{10.4230/LIPIcs.STACS.2025.64},
  annote =	{Keywords: Cluster editing, cographs, parameterized algorithms, clique-width, trivially perfect graphs}
}
Document
DOI: 10.4230/LIPIcs.CPM.2016.17
On Almost Monge All Scores Matrices

Authors: Amir Carmel, Dekel Tsur, and Michal Ziv-Ukelson

Published in: LIPIcs, Volume 54, 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)

Abstract
The all scores matrix of a grid graph is a matrix containing the optimal scores of paths from every vertex on the first row of the graph to every vertex on the last row. This matrix is commonly used to solve diverse string comparison problems. All scores matrices have the Monge property, and this was exploited by previous works that used all scores matrices for solving various problems. In this paper, we study an extension of grid graphs that contain an additional set of edges, called bridges. Our main result is to show several properties of the all scores matrices of such graphs. We also give an O(r(nm + n2)) time algorithm for constructing the all scores matrix of an m × n grid graph with r bridges.
Cite as

Amir Carmel, Dekel Tsur, and Michal Ziv-Ukelson. On Almost Monge All Scores Matrices. In 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 54, pp. 17:1-17:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)

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@InProceedings{carmel_et_al:LIPIcs.CPM.2016.17,
  author =	{Carmel, Amir and Tsur, Dekel and Ziv-Ukelson, Michal},
  title =	{{On Almost Monge All Scores Matrices}},
  booktitle =	{27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)},
  pages =	{17:1--17:12},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-012-5},
  ISSN =	{1868-8969},
  year =	{2016},
  volume =	{54},
  editor =	{Grossi, Roberto and Lewenstein, Moshe},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2016.17},
  URN =		{urn:nbn:de:0030-drops-60770},
  doi =		{10.4230/LIPIcs.CPM.2016.17},
  annote =	{Keywords: Sequence alignment, longest common subsequences, DIST matrices, Monge matrices, all path score computations.}
}
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