19 Search Results for "Kobayashi, Yasuaki"

Document
DOI: 10.4230/LIPIcs.WABI.2024.21
McDag: Indexing Maximal Common Subsequences in Practice

Authors: Giovanni Buzzega, Alessio Conte, Roberto Grossi, and Giulia Punzi

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

Abstract
Analyzing and comparing sequences of symbols is among the most fundamental problems in computer science, possibly even more so in bioinformatics. Maximal Common Subsequences (MCSs), i.e., inclusion-maximal sequences of non-contiguous symbols common to two or more strings, have only recently received attention in this area, despite being a basic notion and a natural generalization of more common tools like Longest Common Substrings/Subsequences. In this paper we simplify and engineer recent advancements on MCSs into a practical tool called McDag, the first publicly available tool that can index MCSs of real genomic data. We demonstrate that our tool can index sequences exceeding 10,000 base pairs within minutes, utilizing only 4-7% more than the minimum required nodes, while also extracting relevant insights.
Cite as

Giovanni Buzzega, Alessio Conte, Roberto Grossi, and Giulia Punzi. McDag: Indexing Maximal Common Subsequences in Practice. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 21:1-21:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{buzzega_et_al:LIPIcs.WABI.2024.21,
  author =	{Buzzega, Giovanni and Conte, Alessio and Grossi, Roberto and Punzi, Giulia},
  title =	{{McDag: Indexing Maximal Common Subsequences in Practice}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{21:1--21:18},
  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.2024.21},
  URN =		{urn:nbn:de:0030-drops-206650},
  doi =		{10.4230/LIPIcs.WABI.2024.21},
  annote =	{Keywords: Index data structure, DAG, Common subsequence, Inclusion-wise maximality, LCS}
}
Document
DOI: 10.4230/LIPIcs.MFCS.2024.16
Tractability of Packing Vertex-Disjoint A-Paths Under Length Constraints

Authors: Susobhan Bandopadhyay, Aritra Banik, Diptapriyo Majumdar, and Abhishek Sahu

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

Abstract
Given an undirected graph G and a set A ⊆ V(G), an A-path is a path in G that starts and ends at two distinct vertices of A with intermediate vertices in V(G)⧵A. An A-path is called an (A,𝓁)-path if the length of the path is exactly 𝓁. In the (A, 𝓁)-Path Packing problem (ALPP), we seek to determine whether there exist k vertex-disjoint (A, 𝓁)-paths in G or not. The problem is already known to be fixed-parmeter tractable when parameterized by k+𝓁 via color coding while it remains Para-NP-hard when parameterized by k (Hamiltonian Path) or 𝓁 (P₃-Partition) alone. Therefore, a logical direction to pursue this problem is to examine it in relation to structural parameters. Belmonte et al. initiated a study along these lines and proved that ALPP parameterized by pw+|A| is W[1]-hard where pw is the pathwidth of G. In this paper, we strengthen their result and prove that it is unlikely that ALPP is fixed-parameter tractable even with respect to a bigger parameter (|A|+dtp) where dtp denotes the distance between G and a path graph (distance to path). We use a randomized reduction to achieve the mentioned result. Toward this, we prove a lemma similar to the influential "isolation lemma": Given a set system (X,ℱ) if the elements of X are assigned a weight uniformly at random from a set of values fairly large, then each subset in ℱ will have a unique weight with high probability. We believe that this result will be useful beyond the scope of this paper. ALPP being hard even for structural parameters like distance to path+|A| rules out the possibility of any FPT algorithms for many well-known other structural parameters, including FVS+|A| and treewidth+|A|. There is a straightforward FPT algorithm for ALPP parameterized by vc, the vertex cover number of the input graph. Following this, we consider the parameters CVD(cluster vertex deletion)+|A| and CVD+|𝓁| and show the problem to be FPT with respect to these parameters. Note that CVD is incomparable to the treewidth of a graph and has been in vogue recently.
Cite as

Susobhan Bandopadhyay, Aritra Banik, Diptapriyo Majumdar, and Abhishek Sahu. Tractability of Packing Vertex-Disjoint A-Paths Under Length Constraints. In 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 306, pp. 16:1-16:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{bandopadhyay_et_al:LIPIcs.MFCS.2024.16,
  author =	{Bandopadhyay, Susobhan and Banik, Aritra and Majumdar, Diptapriyo and Sahu, Abhishek},
  title =	{{Tractability of Packing Vertex-Disjoint A-Paths Under Length Constraints}},
  booktitle =	{49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)},
  pages =	{16:1--16:18},
  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.2024.16},
  URN =		{urn:nbn:de:0030-drops-205725},
  doi =		{10.4230/LIPIcs.MFCS.2024.16},
  annote =	{Keywords: Parameterized complexity, (A,𝓁)-Path Packing, Kernelization, Randomized-Exponential Time Hypothesis, Graph Classes}
}
Document
DOI: 10.4230/LIPIcs.MFCS.2024.29
Equitable Connected Partition and Structural Parameters Revisited: N-Fold Beats Lenstra

Authors: Václav Blažej, Dušan Knop, Jan Pokorný, and Šimon Schierreich

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

Abstract
In the Equitable Connected Partition (ECP for short) problem, we are given a graph G = (V,E) together with an integer p ∈ ℕ, and our goal is to find a partition of V into p parts such that each part induces a connected sub-graph of G and the size of each two parts differs by at most 1. On the one hand, the problem is known to be NP-hard in general and W[1]-hard with respect to the path-width, the feedback-vertex set, and the number of parts p combined. On the other hand, fixed-parameter algorithms are known for parameters the vertex-integrity and the max leaf number. In this work, we systematically study ECP with respect to various structural restrictions of the underlying graph and provide a clear dichotomy of its parameterised complexity. Specifically, we show that the problem is in FPT when parameterized by the modular-width and the distance to clique. Next, we prove W[1]-hardness with respect to the distance to cluster, the 4-path vertex cover number, the distance to disjoint paths, and the feedback-edge set, and NP-hardness for constant shrub-depth graphs. Our hardness results are complemented by matching algorithmic upper-bounds: we give an XP algorithm for parameterisation by the tree-width and the distance to cluster. We also give an improved FPT algorithm for parameterisation by the vertex integrity and the first explicit FPT algorithm for the 3-path vertex cover number. The main ingredient of these algorithms is a formulation of ECP as N-fold IP, which clearly indicates that such formulations may, in certain scenarios, significantly outperform existing algorithms based on the famous algorithm of Lenstra.
Cite as

Václav Blažej, Dušan Knop, Jan Pokorný, and Šimon Schierreich. Equitable Connected Partition and Structural Parameters Revisited: N-Fold Beats Lenstra. In 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 306, pp. 29:1-29:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{blazej_et_al:LIPIcs.MFCS.2024.29,
  author =	{Bla\v{z}ej, V\'{a}clav and Knop, Du\v{s}an and Pokorn\'{y}, Jan and Schierreich, \v{S}imon},
  title =	{{Equitable Connected Partition and Structural Parameters Revisited: N-Fold Beats Lenstra}},
  booktitle =	{49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)},
  pages =	{29:1--29:16},
  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.2024.29},
  URN =		{urn:nbn:de:0030-drops-205857},
  doi =		{10.4230/LIPIcs.MFCS.2024.29},
  annote =	{Keywords: Equitable Connected Partition, structural parameters, fixed-parameter tractability, N-fold integer programming, tree-width, shrub-depth, modular-width}
}
Document
DOI: 10.4230/LIPIcs.MFCS.2024.45
Nearly-Tight Bounds for Flow Sparsifiers in Quasi-Bipartite Graphs

Authors: Syamantak Das, Nikhil Kumar, and Daniel Vaz

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

Abstract
Flow sparsification is a classic graph compression technique which, given a capacitated graph G on k terminals, aims to construct another capacitated graph H, called a flow sparsifier, that preserves, either exactly or approximately, every multicommodity flow between terminals (ideally, with size as a small function of k). Cut sparsifiers are a restricted variant of flow sparsifiers which are only required to preserve maximum flows between bipartitions of the terminal set. It is known that exact cut sparsifiers require 2^Ω(k) many vertices [Krauthgamer and Rika, SODA 2013], with the hard instances being quasi-bipartite graphs, where there are no edges between non-terminals. On the other hand, it has been shown recently that exact (or even (1+ε)-approximate) flow sparsifiers on networks with just 6 terminals require unbounded size [Krauthgamer and Mosenzon, SODA 2023, Chen and Tan, SODA 2024]. In this paper, we construct exact flow sparsifiers of size 3^k³ and exact cut sparsifiers of size 2^k² for quasi-bipartite graphs. In particular, the flow sparsifiers are contraction-based, that is, they are obtained from the input graph by (vertex) contraction operations. Our main contribution is a new technique to construct sparsifiers that exploits connections to polyhedral geometry, and that can be generalized to graphs with a small separator that separates the graph into small components. We also give an improved reduction theorem for graphs of bounded treewidth [Andoni et al., SODA 2011], implying a flow sparsifier of size O(k⋅w) and quality O((log w)/log log w), where w is the treewidth.
Cite as

Syamantak Das, Nikhil Kumar, and Daniel Vaz. Nearly-Tight Bounds for Flow Sparsifiers in Quasi-Bipartite Graphs. In 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 306, pp. 45:1-45:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{das_et_al:LIPIcs.MFCS.2024.45,
  author =	{Das, Syamantak and Kumar, Nikhil and Vaz, Daniel},
  title =	{{Nearly-Tight Bounds for Flow Sparsifiers in Quasi-Bipartite Graphs}},
  booktitle =	{49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)},
  pages =	{45:1--45:17},
  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.2024.45},
  URN =		{urn:nbn:de:0030-drops-206018},
  doi =		{10.4230/LIPIcs.MFCS.2024.45},
  annote =	{Keywords: Graph Sparsification, Cut Sparsifiers, Flow Sparsifiers, Quasi-bipartite Graphs, Bounded Treewidth}
}
Document
DOI: 10.4230/LIPIcs.MFCS.2024.52
Structural Parameters for Dense Temporal Graphs

Authors: Jessica Enright, Samuel D. Hand, Laura Larios-Jones, and Kitty Meeks

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

Abstract
Temporal graphs provide a useful model for many real-world networks. Unfortunately, the majority of algorithmic problems we might consider on such graphs are intractable. There has been recent progress in defining structural parameters which describe tractable cases by simultaneously restricting the underlying structure and the times at which edges appear in the graph. These all rely on the temporal graph being sparse in some sense. We introduce temporal analogues of three increasingly restrictive static graph parameters - cliquewidth, modular-width and neighbourhood diversity - which take small values for highly structured temporal graphs, even if a large number of edges are active at each timestep. The computational problems solvable efficiently when the temporal cliquewidth of the input graph is bounded form a subset of those solvable efficiently when the temporal modular-width is bounded, which is in turn a subset of problems efficiently solvable when the temporal neighbourhood diversity is bounded. By considering specific temporal graph problems, we demonstrate that (up to standard complexity theoretic assumptions) these inclusions are strict.
Cite as

Jessica Enright, Samuel D. Hand, Laura Larios-Jones, and Kitty Meeks. Structural Parameters for Dense Temporal Graphs. In 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 306, pp. 52:1-52:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{enright_et_al:LIPIcs.MFCS.2024.52,
  author =	{Enright, Jessica and Hand, Samuel D. and Larios-Jones, Laura and Meeks, Kitty},
  title =	{{Structural Parameters for Dense Temporal Graphs}},
  booktitle =	{49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)},
  pages =	{52:1--52:15},
  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.2024.52},
  URN =		{urn:nbn:de:0030-drops-206082},
  doi =		{10.4230/LIPIcs.MFCS.2024.52},
  annote =	{Keywords: Graph algorithms, Parameterized Algorithms, Temporal Graphs}
}
Document
DOI: 10.4230/LIPIcs.MFCS.2024.58
Parameterized Vertex Integrity Revisited

Authors: Tesshu Hanaka, Michael Lampis, Manolis Vasilakis, and Kanae Yoshiwatari

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

Abstract
Vertex integrity is a graph parameter that measures the connectivity of a graph. Informally, its meaning is that a graph has small vertex integrity if it has a small separator whose removal disconnects the graph into connected components which are themselves also small. Graphs with low vertex integrity are very structured; this renders many hard problems tractable and has recently attracted interest in this notion from the parameterized complexity community. In this paper we revisit the NP-complete problem of computing the vertex integrity of a given graph from the point of view of structural parameterizations. We present a number of new results, which also answer some recently posed open questions from the literature. Specifically, we show that unweighted vertex integrity is W[1]-hard parameterized by treedepth; we show that the problem remains W[1]-hard if we parameterize by feedback edge set size (via a reduction from a Bin Packing variant which may be of independent interest); and complementing this we show that the problem is FPT by max-leaf number. Furthermore, for weighted vertex integrity, we show that the problem admits a single-exponential FPT algorithm parameterized by vertex cover or by modular width, the latter result improving upon a previous algorithm which required weights to be polynomially bounded.
Cite as

Tesshu Hanaka, Michael Lampis, Manolis Vasilakis, and Kanae Yoshiwatari. Parameterized Vertex Integrity Revisited. In 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 306, pp. 58:1-58:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{hanaka_et_al:LIPIcs.MFCS.2024.58,
  author =	{Hanaka, Tesshu and Lampis, Michael and Vasilakis, Manolis and Yoshiwatari, Kanae},
  title =	{{Parameterized Vertex Integrity Revisited}},
  booktitle =	{49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)},
  pages =	{58:1--58:14},
  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.2024.58},
  URN =		{urn:nbn:de:0030-drops-206141},
  doi =		{10.4230/LIPIcs.MFCS.2024.58},
  annote =	{Keywords: Parameterized Complexity, Treedepth, Vertex Integrity}
}
Document
Track A: Algorithms, Complexity and Games
DOI: 10.4230/LIPIcs.ICALP.2024.29
A Tight Monte-Carlo Algorithm for Steiner Tree Parameterized by Clique-Width

Authors: Narek Bojikian and Stefan Kratsch

Published in: LIPIcs, Volume 297, 51st International Colloquium on Automata, Languages, and Programming (ICALP 2024)

Abstract
Given a graph G = (V,E), a set T ⊆ V, and an integer b, the Steiner Tree problem asks whether G has a connected subgraph H with at most b vertices that spans all of T. This work presents a 3^k⋅ n^𝒪(1) time one-sided Monte-Carlo algorithm for solving Steiner Tree when additionally a clique-expression of width k is provided. Known lower bounds for less expressive parameters imply that this dependence on the clique-width of G is optimal assuming the Strong Exponential-Time Hypothesis (SETH). Indeed our work establishes that the parameter dependence of Steiner Tree is the same for any graph parameter between cutwidth and clique-width, assuming SETH. Our work contributes to the program of determining the exact parameterized complexity of fundamental hard problems relative to structural graph parameters such as treewidth, which was initiated by Lokshtanov et al. [SODA 2011 & TALG 2018] and which by now has seen a plethora of results. Since the cut-and-count framework of Cygan et al. [FOCS 2011 & TALG 2022], connectivity problems have played a key role in this program as they pose many challenges for developing tight upper and lower bounds. Recently, Hegerfeld and Kratsch [ESA 2023] gave the first application of the cut-and-count technique to problems parameterized by clique-width and obtained tight bounds for Connected Dominating Set and Connected Vertex Cover, leaving open the complexity of other benchmark connectivity problems such as Steiner Tree and Feedback Vertex Set. Our algorithm for Steiner Tree does not follow the cut-and-count technique and instead works with the connectivity patterns of partial solutions. As a first technical contribution we identify a special family of so-called complete patterns that has strong (existential) representation properties, and using these at least one solution will be preserved. Furthermore, there is a family of 3^k basis patterns that (parity) represents the complete patterns, i.e., it has the same number of solutions modulo two. Our main technical contribution, a new technique called "isolating a representative," allows us to leverage both forms of representation (existential and parity). Both complete patterns and isolation of a representative will likely be applicable to other (connectivity) problems.
Cite as

Narek Bojikian and Stefan Kratsch. A Tight Monte-Carlo Algorithm for Steiner Tree Parameterized by Clique-Width. In 51st International Colloquium on Automata, Languages, and Programming (ICALP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 297, pp. 29:1-29:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{bojikian_et_al:LIPIcs.ICALP.2024.29,
  author =	{Bojikian, Narek and Kratsch, Stefan},
  title =	{{A Tight Monte-Carlo Algorithm for Steiner Tree Parameterized by Clique-Width}},
  booktitle =	{51st International Colloquium on Automata, Languages, and Programming (ICALP 2024)},
  pages =	{29:1--29:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-322-5},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{297},
  editor =	{Bringmann, Karl and Grohe, Martin and Puppis, Gabriele and Svensson, Ola},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2024.29},
  URN =		{urn:nbn:de:0030-drops-201728},
  doi =		{10.4230/LIPIcs.ICALP.2024.29},
  annote =	{Keywords: Parameterized complexity, Steiner tree, clique-width}
}
Document
Track A: Algorithms, Complexity and Games
DOI: 10.4230/LIPIcs.ICALP.2024.61
Parameterized Algorithms for Steiner Forest in Bounded Width Graphs

Authors: Andreas Emil Feldmann and Michael Lampis

Published in: LIPIcs, Volume 297, 51st International Colloquium on Automata, Languages, and Programming (ICALP 2024)

Abstract
In this paper we reassess the parameterized complexity and approximability of the well-studied Steiner Forest problem in several graph classes of bounded width. The problem takes an edge-weighted graph and pairs of vertices as input, and the aim is to find a minimum cost subgraph in which each given vertex pair lies in the same connected component. It is known that this problem is APX-hard in general, and NP-hard on graphs of treewidth 3, treedepth 4, and feedback vertex set size 2. However, Bateni, Hajiaghayi and Marx [JACM, 2011] gave an approximation scheme with a runtime of n^O(k²/ε) on graphs of treewidth k. Our main result is a much faster efficient parameterized approximation scheme (EPAS) with a runtime of 2^O(k²/ε log k/ε)⋅n^O(1). If k instead is the vertex cover number of the input graph, we show how to compute the optimum solution in 2^O(k log k)⋅n^O(1) time, and we also prove that this runtime dependence on k is asymptotically best possible, under ETH. Furthermore, if k is the size of a feedback edge set, then we obtain a faster 2^O(k)⋅n^O(1) time algorithm, which again cannot be improved under ETH.
Cite as

Andreas Emil Feldmann and Michael Lampis. Parameterized Algorithms for Steiner Forest in Bounded Width Graphs. In 51st International Colloquium on Automata, Languages, and Programming (ICALP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 297, pp. 61:1-61:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{feldmann_et_al:LIPIcs.ICALP.2024.61,
  author =	{Feldmann, Andreas Emil and Lampis, Michael},
  title =	{{Parameterized Algorithms for Steiner Forest in Bounded Width Graphs}},
  booktitle =	{51st International Colloquium on Automata, Languages, and Programming (ICALP 2024)},
  pages =	{61:1--61:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-322-5},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{297},
  editor =	{Bringmann, Karl and Grohe, Martin and Puppis, Gabriele and Svensson, Ola},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2024.61},
  URN =		{urn:nbn:de:0030-drops-202048},
  doi =		{10.4230/LIPIcs.ICALP.2024.61},
  annote =	{Keywords: Steiner Forest, Approximation Algorithms, FPT algorithms}
}
Document
DOI: 10.4230/LIPIcs.CPM.2024.27
Finding Diverse Strings and Longest Common Subsequences in a Graph

Authors: Yuto Shida, Giulia Punzi, Yasuaki Kobayashi, Takeaki Uno, and Hiroki Arimura

Published in: LIPIcs, Volume 296, 35th Annual Symposium on Combinatorial Pattern Matching (CPM 2024)

Abstract
In this paper, we study for the first time the Diverse Longest Common Subsequences (LCSs) problem under Hamming distance. Given a set of a constant number of input strings, the problem asks to decide if there exists some subset X of K longest common subsequences whose diversity is no less than a specified threshold Δ, where we consider two types of diversities of a set X of strings of equal length: the Sum diversity and the Min diversity defined as the sum and the minimum of the pairwise Hamming distance between any two strings in X, respectively. We analyze the computational complexity of the respective problems with Sum- and Min-diversity measures, called the Max-Sum and Max-Min Diverse LCSs, respectively, considering both approximation algorithms and parameterized complexity. Our results are summarized as follows. When K is bounded, both problems are polynomial time solvable. In contrast, when K is unbounded, both problems become NP-hard, while Max-Sum Diverse LCSs problem admits a PTAS. Furthermore, we analyze the parameterized complexity of both problems with combinations of parameters K and r, where r is the length of the candidate strings to be selected. Importantly, all positive results above are proven in a more general setting, where an input is an edge-labeled directed acyclic graph (DAG) that succinctly represents a set of strings of the same length. Negative results are proven in the setting where an input is explicitly given as a set of strings. The latter results are equipped with an encoding such a set as the longest common subsequences of a specific input string set.
Cite as

Yuto Shida, Giulia Punzi, Yasuaki Kobayashi, Takeaki Uno, and Hiroki Arimura. Finding Diverse Strings and Longest Common Subsequences in a Graph. In 35th Annual Symposium on Combinatorial Pattern Matching (CPM 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 296, pp. 27:1-27:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{shida_et_al:LIPIcs.CPM.2024.27,
  author =	{Shida, Yuto and Punzi, Giulia and Kobayashi, Yasuaki and Uno, Takeaki and Arimura, Hiroki},
  title =	{{Finding Diverse Strings and Longest Common Subsequences in a Graph}},
  booktitle =	{35th Annual Symposium on Combinatorial Pattern Matching (CPM 2024)},
  pages =	{27:1--27:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-326-3},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{296},
  editor =	{Inenaga, Shunsuke and Puglisi, Simon J.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2024.27},
  URN =		{urn:nbn:de:0030-drops-201370},
  doi =		{10.4230/LIPIcs.CPM.2024.27},
  annote =	{Keywords: Sequence analysis, longest common subsequence, Hamming distance, dispersion, approximation algorithms, parameterized complexity}
}
Document
DOI: 10.4230/LIPIcs.MFCS.2023.58
Polynomial-Delay Enumeration of Large Maximal Common Independent Sets in Two Matroids

Authors: Yasuaki Kobayashi, Kazuhiro Kurita, and Kunihiro Wasa

Published in: LIPIcs, Volume 272, 48th International Symposium on Mathematical Foundations of Computer Science (MFCS 2023)

Abstract
Finding a maximum cardinality common independent set in two matroids (also known as Matroid Intersection) is a classical combinatorial optimization problem, which generalizes several well-known problems, such as finding a maximum bipartite matching, a maximum colorful forest, and an arborescence in directed graphs. Enumerating all maximal common independent sets in two (or more) matroids is a classical enumeration problem. In this paper, we address an "intersection" of these problems: Given two matroids and a threshold τ, the goal is to enumerate all maximal common independent sets in the matroids with cardinality at least τ. We show that this problem can be solved in polynomial delay and polynomial space. We also discuss how to enumerate all maximal common independent sets of two matroids in non-increasing order of their cardinalities.
Cite as

Yasuaki Kobayashi, Kazuhiro Kurita, and Kunihiro Wasa. Polynomial-Delay Enumeration of Large Maximal Common Independent Sets in Two Matroids. In 48th International Symposium on Mathematical Foundations of Computer Science (MFCS 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 272, pp. 58:1-58:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{kobayashi_et_al:LIPIcs.MFCS.2023.58,
  author =	{Kobayashi, Yasuaki and Kurita, Kazuhiro and Wasa, Kunihiro},
  title =	{{Polynomial-Delay Enumeration of Large Maximal Common Independent Sets in Two Matroids}},
  booktitle =	{48th International Symposium on Mathematical Foundations of Computer Science (MFCS 2023)},
  pages =	{58:1--58:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-292-1},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{272},
  editor =	{Leroux, J\'{e}r\^{o}me and Lombardy, Sylvain and Peleg, David},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2023.58},
  URN =		{urn:nbn:de:0030-drops-185921},
  doi =		{10.4230/LIPIcs.MFCS.2023.58},
  annote =	{Keywords: Polynomial-delay enumeration, Ranked Enumeration, Matroid intersection, Reverse search}
}
Document
DOI: 10.4230/LIPIcs.ESA.2022.61
Algorithmic Meta-Theorems for Combinatorial Reconfiguration Revisited

Authors: Tatsuya Gima, Takehiro Ito, Yasuaki Kobayashi, and Yota Otachi

Published in: LIPIcs, Volume 244, 30th Annual European Symposium on Algorithms (ESA 2022)

Abstract
Given a graph and two vertex sets satisfying a certain feasibility condition, a reconfiguration problem asks whether we can reach one vertex set from the other by repeating prescribed modification steps while maintaining feasibility. In this setting, Mouawad et al. [IPEC 2014] presented an algorithmic meta-theorem for reconfiguration problems that says if the feasibility can be expressed in monadic second-order logic (MSO), then the problem is fixed-parameter tractable parameterized by treewidth + 𝓁, where 𝓁 is the number of steps allowed to reach the target set. On the other hand, it is shown by Wrochna [J. Comput. Syst. Sci. 2018] that if 𝓁 is not part of the parameter, then the problem is PSPACE-complete even on graphs of bounded bandwidth. In this paper, we present the first algorithmic meta-theorems for the case where 𝓁 is not part of the parameter, using some structural graph parameters incomparable with bandwidth. We show that if the feasibility is defined in MSO, then the reconfiguration problem under the so-called token jumping rule is fixed-parameter tractable parameterized by neighborhood diversity. We also show that the problem is fixed-parameter tractable parameterized by treedepth + k, where k is the size of sets being transformed. We finally complement the positive result for treedepth by showing that the problem is PSPACE-complete on forests of depth 3.
Cite as

Tatsuya Gima, Takehiro Ito, Yasuaki Kobayashi, and Yota Otachi. Algorithmic Meta-Theorems for Combinatorial Reconfiguration Revisited. In 30th Annual European Symposium on Algorithms (ESA 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 244, pp. 61:1-61:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{gima_et_al:LIPIcs.ESA.2022.61,
  author =	{Gima, Tatsuya and Ito, Takehiro and Kobayashi, Yasuaki and Otachi, Yota},
  title =	{{Algorithmic Meta-Theorems for Combinatorial Reconfiguration Revisited}},
  booktitle =	{30th Annual European Symposium on Algorithms (ESA 2022)},
  pages =	{61:1--61:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-247-1},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{244},
  editor =	{Chechik, Shiri and Navarro, Gonzalo and Rotenberg, Eva 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.2022.61},
  URN =		{urn:nbn:de:0030-drops-169991},
  doi =		{10.4230/LIPIcs.ESA.2022.61},
  annote =	{Keywords: Combinatorial reconfiguration, monadic second-order logic, fixed-parameter tractability, treedepth, neighborhood diversity}
}
Document
DOI: 10.4230/LIPIcs.MFCS.2022.6
Parameterized Complexity of Non-Separating and Non-Disconnecting Paths and Sets

Authors: Ankit Abhinav, Susobhan Bandopadhyay, Aritra Banik, Yasuaki Kobayashi, Shunsuke Nagano, Yota Otachi, and Saket Saurabh

Published in: LIPIcs, Volume 241, 47th International Symposium on Mathematical Foundations of Computer Science (MFCS 2022)

Abstract
For a connected graph G = (V, E) and s, t ∈ V, a non-separating s-t path is a path P between s and t such that the set of vertices of P does not separate G, that is, G - V(P) is connected. An s-t path P is non-disconnecting if G - E(P) is connected. The problems of finding shortest non-separating and non-disconnecting paths are both known to be NP-hard. In this paper, we consider the problems from the viewpoint of parameterized complexity. We show that the problem of finding a non-separating s-t path of length at most k is W[1]-hard parameterized by k, while the non-disconnecting counterpart is fixed-parameter tractable (FPT) parameterized by k. We also consider the shortest non-separating path problem on several classes of graphs and show that this problem is NP-hard even on bipartite graphs, split graphs, and planar graphs. As for positive results, the shortest non-separating path problem is FPT parameterized by k on planar graphs and on unit disk graphs (where no s, t is given). Further, we give a polynomial-time algorithm on chordal graphs if k is the distance of the shortest path between s and t.
Cite as

Ankit Abhinav, Susobhan Bandopadhyay, Aritra Banik, Yasuaki Kobayashi, Shunsuke Nagano, Yota Otachi, and Saket Saurabh. Parameterized Complexity of Non-Separating and Non-Disconnecting Paths and Sets. In 47th International Symposium on Mathematical Foundations of Computer Science (MFCS 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 241, pp. 6:1-6:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{abhinav_et_al:LIPIcs.MFCS.2022.6,
  author =	{Abhinav, Ankit and Bandopadhyay, Susobhan and Banik, Aritra and Kobayashi, Yasuaki and Nagano, Shunsuke and Otachi, Yota and Saurabh, Saket},
  title =	{{Parameterized Complexity of Non-Separating and Non-Disconnecting Paths and Sets}},
  booktitle =	{47th International Symposium on Mathematical Foundations of Computer Science (MFCS 2022)},
  pages =	{6:1--6:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-256-3},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{241},
  editor =	{Szeider, Stefan and Ganian, Robert and Silva, Alexandra},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2022.6},
  URN =		{urn:nbn:de:0030-drops-168041},
  doi =		{10.4230/LIPIcs.MFCS.2022.6},
  annote =	{Keywords: Non-separating path, Parameterized complexity}
}
Document
DOI: 10.4230/LIPIcs.MFCS.2022.58
Independent Set Reconfiguration on Directed Graphs

Authors: Takehiro Ito, Yuni Iwamasa, Yasuaki Kobayashi, Yu Nakahata, Yota Otachi, Masahiro Takahashi, and Kunihiro Wasa

Published in: LIPIcs, Volume 241, 47th International Symposium on Mathematical Foundations of Computer Science (MFCS 2022)

Abstract
Directed Token Sliding asks, given a directed graph and two sets of pairwise nonadjacent vertices, whether one can reach from one set to the other by repeatedly applying a local operation that exchanges a vertex in the current set with one of its out-neighbors, while keeping the nonadjacency. It can be seen as a reconfiguration process where a token is placed on each vertex in the current set, and the local operation slides a token along an arc respecting its direction. Previously, such a problem was extensively studied on undirected graphs, where the edges have no directions and thus the local operation is symmetric. Directed Token Sliding is a generalization of its undirected variant since an undirected edge can be simulated by two arcs of opposite directions. In this paper, we initiate the algorithmic study of Directed Token Sliding. We first observe that the problem is PSPACE-complete even if we forbid parallel arcs in opposite directions and that the problem on directed acyclic graphs is NP-complete and W[1]-hard parameterized by the size of the sets in consideration. We then show our main result: a linear-time algorithm for the problem on directed graphs whose underlying undirected graphs are trees, which are called polytrees. Such a result is also known for the undirected variant of the problem on trees [Demaine et al. TCS 2015], but the techniques used here are quite different because of the asymmetric nature of the directed problem. We present a characterization of yes-instances based on the existence of a certain set of directed paths, and then derive simple equivalent conditions from it by some observations, which yield an efficient algorithm. For the polytree case, we also present a quadratic-time algorithm that outputs, if the input is a yes-instance, one of the shortest reconfiguration sequences.
Cite as

Takehiro Ito, Yuni Iwamasa, Yasuaki Kobayashi, Yu Nakahata, Yota Otachi, Masahiro Takahashi, and Kunihiro Wasa. Independent Set Reconfiguration on Directed Graphs. In 47th International Symposium on Mathematical Foundations of Computer Science (MFCS 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 241, pp. 58:1-58:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{ito_et_al:LIPIcs.MFCS.2022.58,
  author =	{Ito, Takehiro and Iwamasa, Yuni and Kobayashi, Yasuaki and Nakahata, Yu and Otachi, Yota and Takahashi, Masahiro and Wasa, Kunihiro},
  title =	{{Independent Set Reconfiguration on Directed Graphs}},
  booktitle =	{47th International Symposium on Mathematical Foundations of Computer Science (MFCS 2022)},
  pages =	{58:1--58:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-256-3},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{241},
  editor =	{Szeider, Stefan and Ganian, Robert and Silva, Alexandra},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2022.58},
  URN =		{urn:nbn:de:0030-drops-168567},
  doi =		{10.4230/LIPIcs.MFCS.2022.58},
  annote =	{Keywords: Combinatorial reconfiguration, token sliding, directed graph, independent set, graph algorithm}
}
Document
DOI: 10.4230/LIPIcs.IPEC.2020.21
Parameterized Complexity of Graph Burning

Authors: Yasuaki Kobayashi and Yota Otachi

Published in: LIPIcs, Volume 180, 15th International Symposium on Parameterized and Exact Computation (IPEC 2020)

Abstract
Graph Burning asks, given a graph G = (V,E) and an integer k, whether there exists (b₀,… ,b_{k-1}) ∈ V^{k} such that every vertex in G has distance at most i from some b_i. This problem is known to be NP-complete even on connected caterpillars of maximum degree 3. We study the parameterized complexity of this problem and answer all questions arose by Kare and Reddy [IWOCA 2019] about parameterized complexity of the problem. We show that the problem is W[2]-complete parameterized by k and that it does not admit a polynomial kernel parameterized by vertex cover number unless NP ⊆ coNP/poly. We also show that the problem is fixed-parameter tractable parameterized by clique-width plus the maximum diameter among all connected components. This implies the fixed-parameter tractability parameterized by modular-width, by treedepth, and by distance to cographs. Although the parameterization by distance to split graphs cannot be handled with the clique-width argument, we show that this is also tractable by a reduction to a generalized problem with a smaller solution size.
Cite as

Yasuaki Kobayashi and Yota Otachi. Parameterized Complexity of Graph Burning. In 15th International Symposium on Parameterized and Exact Computation (IPEC 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 180, pp. 21:1-21:10, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@InProceedings{kobayashi_et_al:LIPIcs.IPEC.2020.21,
  author =	{Kobayashi, Yasuaki and Otachi, Yota},
  title =	{{Parameterized Complexity of Graph Burning}},
  booktitle =	{15th International Symposium on Parameterized and Exact Computation (IPEC 2020)},
  pages =	{21:1--21:10},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-172-6},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{180},
  editor =	{Cao, Yixin and Pilipczuk, Marcin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.IPEC.2020.21},
  URN =		{urn:nbn:de:0030-drops-133241},
  doi =		{10.4230/LIPIcs.IPEC.2020.21},
  annote =	{Keywords: Graph burning, parameterized complexity, fixed-parameter tractability}
}
Document
DOI: 10.4230/LIPIcs.MFCS.2020.60
Efficient Enumerations for Minimal Multicuts and Multiway Cuts

Authors: Kazuhiro Kurita and Yasuaki Kobayashi

Published in: LIPIcs, Volume 170, 45th International Symposium on Mathematical Foundations of Computer Science (MFCS 2020)

Abstract
Let G = (V, E) be an undirected graph and let B ⊆ V × V be a set of terminal pairs. A node/edge multicut is a subset of vertices/edges of G whose removal destroys all the paths between every terminal pair in B. The problem of computing a minimum node/edge multicut is NP-hard and extensively studied from several viewpoints. In this paper, we study the problem of enumerating all minimal node multicuts. We give an incremental polynomial delay enumeration algorithm for minimal node multicuts, which extends an enumeration algorithm due to Khachiyan et al. (Algorithmica, 2008) for minimal edge multicuts. Important special cases of node/edge multicuts are node/edge multiway cuts, where the set of terminal pairs contains every pair of vertices in some subset T ⊆ V, that is, B = T × T. We improve the running time bound for this special case: We devise a polynomial delay and exponential space enumeration algorithm for minimal node multiway cuts and a polynomial delay and space enumeration algorithm for minimal edge multiway cuts.
Cite as

Kazuhiro Kurita and Yasuaki Kobayashi. Efficient Enumerations for Minimal Multicuts and Multiway Cuts. In 45th International Symposium on Mathematical Foundations of Computer Science (MFCS 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 170, pp. 60:1-60:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@InProceedings{kurita_et_al:LIPIcs.MFCS.2020.60,
  author =	{Kurita, Kazuhiro and Kobayashi, Yasuaki},
  title =	{{Efficient Enumerations for Minimal Multicuts and Multiway Cuts}},
  booktitle =	{45th International Symposium on Mathematical Foundations of Computer Science (MFCS 2020)},
  pages =	{60:1--60:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-159-7},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{170},
  editor =	{Esparza, Javier and Kr\'{a}l', Daniel},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2020.60},
  URN =		{urn:nbn:de:0030-drops-127272},
  doi =		{10.4230/LIPIcs.MFCS.2020.60},
  annote =	{Keywords: Multicuts, Multiway cuts, Enumeration algorithms}
}
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