24 Search Results for "Harvey, Daniel J."

Document
DOI: 10.4230/LIPIcs.STACS.2026.33
Higher Hardness Results for the Reconfiguration of Odd Matchings

Authors: Joseph Dorfer

Published in: LIPIcs, Volume 364, 43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026)

Abstract
We study the reconfiguration of odd matchings of combinatorial graphs. Odd matchings are matchings that cover all but one vertex of a graph. A reconfiguration step, or flip, is an operation that matches the isolated vertex and, consequently, isolates another vertex. The flip graph of odd matchings is a graph that has all odd matchings of a graph as vertices and an edge between two vertices if their corresponding matchings can be transformed into one another via a single flip. We show that computing the diameter of the flip graph of odd matchings is Π₂^p-hard. This complements a recent result by Wulf [FOCS25] that it is Π₂^p-hard to compute the diameter of the flip graph of perfect matchings where a flip swaps matching edges along a single cycle of unbounded size. Further, we show that computing the radius of the flip graph of odd matchings is Σ₃^p-hard. The respective decision problems for the diameter and the radius are also complete in the respective level of the polynomial hierarchy. This shows that computing the radius of the flip graph of odd matchings is provably harder than computing its diameter, unless the polynomial hierarchy collapses. Finally, we reduce set cover to the problem of finding shortest flip sequences. As a consequence, we show APX-hardness and that the problem cannot be approximated by a sublogarithmic factor. By doing so, we answer a question asked by Aichholzer, Brenner, Dorfer, Hoang, Perz, Rieck, and Verciani [GD25].
Cite as

Joseph Dorfer. Higher Hardness Results for the Reconfiguration of Odd Matchings. In 43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 364, pp. 33:1-33:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{dorfer:LIPIcs.STACS.2026.33,
  author =	{Dorfer, Joseph},
  title =	{{Higher Hardness Results for the Reconfiguration of Odd Matchings}},
  booktitle =	{43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026)},
  pages =	{33:1--33:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-412-3},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{364},
  editor =	{Mahajan, Meena and Manea, Florin and McIver, Annabelle 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.2026.33},
  URN =		{urn:nbn:de:0030-drops-255222},
  doi =		{10.4230/LIPIcs.STACS.2026.33},
  annote =	{Keywords: Graph Reconfiguration Problems, Flip Graphs, Polynomial Hierarchy, APX-hardness}
}
Document
DOI: 10.4230/LIPIcs.FSTTCS.2025.31
Token Sliding Independent Set Reconfiguration on Block Graphs

Authors: Mathew C. Francis and Veena Prabhakaran

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

Abstract
Let S be an independent set of a simple undirected graph G. Suppose that each vertex of S has a token placed on it. The tokens are allowed to be moved, one at a time, by sliding along the edges of G while maintaining the property that after each move, the vertices having tokens always form an independent set of G. We would like to determine whether the tokens can be eventually brought to stay on the vertices of another independent set S' of G in this manner. In other words, we would like to decide if we can transform S into S' through a sequence of steps, each of which involves substituting a vertex in the current independent set with one of its neighbours to obtain another independent set. This problem of determining if one independent set of a graph "is reachable" from another independent set of it is known to be PSPACE-hard even for split graphs, planar graphs, and graphs of bounded treewidth. Polynomial time algorithms have been obtained for certain graph classes like trees, interval graphs, claw-free graphs, and bipartite permutation graphs. We present a polynomial time algorithm for the problem on block graphs, which are the graphs in which every maximal 2-connected subgraph is a clique. Our algorithm is the first generalization of the known polynomial time algorithm for trees to a larger class of graphs.
Cite as

Mathew C. Francis and Veena Prabhakaran. Token Sliding Independent Set Reconfiguration on Block Graphs. 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. 31:1-31:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{francis_et_al:LIPIcs.FSTTCS.2025.31,
  author =	{Francis, Mathew C. and Prabhakaran, Veena},
  title =	{{Token Sliding Independent Set Reconfiguration on Block Graphs}},
  booktitle =	{45th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2025)},
  pages =	{31:1--31:19},
  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.2025.31},
  URN =		{urn:nbn:de:0030-drops-251120},
  doi =		{10.4230/LIPIcs.FSTTCS.2025.31},
  annote =	{Keywords: Token sliding independent set reconfiguration, block graphs, polynomial time algorithm}
}
Document
DOI: 10.4230/LIPIcs.ISAAC.2025.39
Reachability of Independent Sets and Vertex Covers Under Extended Reconfiguration Rules

Authors: Shuichi Hirahara, Naoto Ohsaka, Tatsuhiro Suga, Akira Suzuki, Yuma Tamura, and Xiao Zhou

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

Abstract
In reconfiguration problems, we are given two feasible solutions to a graph problem and asked whether one can be transformed into the other via a sequence of feasible intermediate solutions under a given reconfiguration rule. While earlier work focused on modifying a single element at a time, recent studies have started examining how different rules impact computational complexity. Motivated by recent progress, we study Independent Set Reconfiguration (ISR) and Vertex Cover Reconfiguration (VCR) under the k-Token Jumping (k-TJ) and k-Token Sliding (k-TS) models. In k-TJ, up to k vertices may be replaced, while k-TS additionally requires a perfect matching between removed and added vertices. It is known that the complexity of ISR crucially depends on k, ranging from PSPACE-complete and NP-complete to polynomial-time solvable. In this paper, we further explore the gradient of computational complexity of the problems. We first show that ISR under k-TJ with k = |I| - μ remains NP-hard when μ is any fixed positive integer and the input graph is restricted to graphs of maximum degree 3 or planar graphs of maximum degree 4, where |I| is the size of feasible solutions. In addition, we prove that the problem belongs to NP not only for μ = O(1) but also for μ = O(log |I|). In contrast, we show that VCR under k-TJ is in XP when parameterized by μ = |S| - k, where |S| is the size of feasible solutions. Furthermore, we establish the PSPACE-completeness of ISR and VCR under both k-TJ and k-TS on several graph classes, for fixed k as well as superconstant k relative to the size of feasible solutions.
Cite as

Shuichi Hirahara, Naoto Ohsaka, Tatsuhiro Suga, Akira Suzuki, Yuma Tamura, and Xiao Zhou. Reachability of Independent Sets and Vertex Covers Under Extended Reconfiguration Rules. In 36th International Symposium on Algorithms and Computation (ISAAC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 359, pp. 39:1-39:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{hirahara_et_al:LIPIcs.ISAAC.2025.39,
  author =	{Hirahara, Shuichi and Ohsaka, Naoto and Suga, Tatsuhiro and Suzuki, Akira and Tamura, Yuma and Zhou, Xiao},
  title =	{{Reachability of Independent Sets and Vertex Covers Under Extended Reconfiguration Rules}},
  booktitle =	{36th International Symposium on Algorithms and Computation (ISAAC 2025)},
  pages =	{39:1--39:20},
  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.2025.39},
  URN =		{urn:nbn:de:0030-drops-249474},
  doi =		{10.4230/LIPIcs.ISAAC.2025.39},
  annote =	{Keywords: combinatorial reconfiguration, extended reconfiguration rule, independent set reconfiguration, vertex cover reconfiguration, PSPACE-completeness, NP-completeness}
}
Document
DOI: 10.4230/LIPIcs.ISAAC.2025.3
Circle-Segment Intersection Queries in Connected Geometric Graphs

Authors: Peyman Afshani, Yannick Bosch, and Sabine Storandt

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

Abstract
In this paper, we study the problem of efficiently reporting all intersections between a given set of line segments in the plane and a query circle, focusing on the case where the segments form the edges of a connected geometric graph. While previous data structures for circle-segment intersection queries on general segment sets incur high space or query time costs, we exploit the connectivity of the input to obtain significantly improved performance. In fact, we propose a new circle-segment intersection data structure that can be constructed in 𝒪((n + C) log³ n) time and space on connected graphs with n edges and C edge crossings. It answers intersection queries in 𝒪(k log³ n) time, where k denotes the output size. Our method relies on the construction of efficient circle-graph intersection oracles as well as a novel linear-time algorithm to partition the edges of the graph into balanced, connected components, which might be of independent interest. In a proof-of-concept experimental study on real-world road networks, we show that our novel data structure also performs well in practice. Even on networks with millions of edges, the construction time is within minutes and queries are answered in a few milliseconds.
Cite as

Peyman Afshani, Yannick Bosch, and Sabine Storandt. Circle-Segment Intersection Queries in Connected Geometric Graphs. In 36th International Symposium on Algorithms and Computation (ISAAC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 359, pp. 3:1-3:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{afshani_et_al:LIPIcs.ISAAC.2025.3,
  author =	{Afshani, Peyman and Bosch, Yannick and Storandt, Sabine},
  title =	{{Circle-Segment Intersection Queries in Connected Geometric Graphs}},
  booktitle =	{36th International Symposium on Algorithms and Computation (ISAAC 2025)},
  pages =	{3:1--3:16},
  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.2025.3},
  URN =		{urn:nbn:de:0030-drops-249114},
  doi =		{10.4230/LIPIcs.ISAAC.2025.3},
  annote =	{Keywords: Intersection data structure, Graph partitioning, Dobkin-Kirkpatrick hierarchy}
}
Document
DOI: 10.4230/LIPIcs.GD.2025.32
Planar Stories of Graph Drawings: Algorithms and Experiments

Authors: Carla Binucci, Sabine Cornelsen, Walter Didimo, Seok-Hee Hong, Eleni Katsanou, Maurizio Patrignani, Antonios Symvonis, and Samuel Wolf

Published in: LIPIcs, Volume 357, 33rd International Symposium on Graph Drawing and Network Visualization (GD 2025)

Abstract
We address the problem of computing a dynamic visualization of a geometric graph G as a sequence of frames. Each frame shows only a portion of the graph but their union covers G entirely. The two main requirements of our dynamic visualization are: (i) guaranteeing drawing stability, so to preserve the user’s mental map; (ii) keeping the visual complexity of each frame low. To satisfy the first requirement, we never change the position of the vertices. Regarding the second requirement, we avoid edge crossings in each frame. More precisely, in the first frame we visualize a suitable subset of non-crossing edges; in each subsequent frame, exactly one new edge enters the visualization and all the edges that cross with it are deleted. We call such a sequence of frames a planar story of G. Our goal is to find a planar story whose minimum number of edges contemporarily displayed is maximized (i.e., a planar story that maximizes the minimum frame size). Besides studying our model from a theoretical point of view, we also design and experimentally compare different algorithms, both exact techniques and heuristics. These algorithms provide an array of alternative trade-offs between efficiency and effectiveness, also depending on the structure of the input graph.
Cite as

Carla Binucci, Sabine Cornelsen, Walter Didimo, Seok-Hee Hong, Eleni Katsanou, Maurizio Patrignani, Antonios Symvonis, and Samuel Wolf. Planar Stories of Graph Drawings: Algorithms and Experiments. In 33rd International Symposium on Graph Drawing and Network Visualization (GD 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 357, pp. 32:1-32:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{binucci_et_al:LIPIcs.GD.2025.32,
  author =	{Binucci, Carla and Cornelsen, Sabine and Didimo, Walter and Hong, Seok-Hee and Katsanou, Eleni and Patrignani, Maurizio and Symvonis, Antonios and Wolf, Samuel},
  title =	{{Planar Stories of Graph Drawings: Algorithms and Experiments}},
  booktitle =	{33rd International Symposium on Graph Drawing and Network Visualization (GD 2025)},
  pages =	{32:1--32:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-403-1},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{357},
  editor =	{Dujmovi\'{c}, Vida and Montecchiani, Fabrizio},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.GD.2025.32},
  URN =		{urn:nbn:de:0030-drops-250182},
  doi =		{10.4230/LIPIcs.GD.2025.32},
  annote =	{Keywords: Graph Drawing, Dynamic Graphs, Graph Stories, Heuristics, ILP}
}
Document
DOI: 10.4230/LIPIcs.ESA.2025.14
Testing Sumsets Is Hard

Authors: Xi Chen, Shivam Nadimpalli, Tim Randolph, Rocco A. Servedio, and Or Zamir

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

Abstract
A subset S of the Boolean hypercube 𝔽₂ⁿ is a sumset if S = {a + b : a, b ∈ A} for some A ⊆ 𝔽₂ⁿ. Sumsets are central objects of study in additive combinatorics, where they play a role in several of the field’s most important results. We prove a lower bound of Ω(2^{n/2}) for the number of queries needed to test whether a Boolean function f:𝔽₂ⁿ → {0,1} is the indicator function of a sumset, ruling out an efficient testing algorithm for sumsets. Our lower bound for testing sumsets follows from sharp bounds on the related problem of shift testing, which may be of independent interest. We also give a near-optimal {2^{n/2} ⋅ poly(n)}-query algorithm for a smoothed analysis formulation of the sumset refutation problem. Finally, we include a simple proof that the number of different sumsets in 𝔽₂ⁿ is 2^{(1±o(1))2^{n-1}}.
Cite as

Xi Chen, Shivam Nadimpalli, Tim Randolph, Rocco A. Servedio, and Or Zamir. Testing Sumsets Is Hard. In 33rd Annual European Symposium on Algorithms (ESA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 351, pp. 14:1-14:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{chen_et_al:LIPIcs.ESA.2025.14,
  author =	{Chen, Xi and Nadimpalli, Shivam and Randolph, Tim and Servedio, Rocco A. and Zamir, Or},
  title =	{{Testing Sumsets Is Hard}},
  booktitle =	{33rd Annual European Symposium on Algorithms (ESA 2025)},
  pages =	{14:1--14:16},
  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.2025.14},
  URN =		{urn:nbn:de:0030-drops-244822},
  doi =		{10.4230/LIPIcs.ESA.2025.14},
  annote =	{Keywords: Sumsets, additive combinatorics, property testing, Boolean functions}
}
Document
DOI: 10.4230/LIPIcs.ESA.2025.55
Safe Sequences via Dominators in DAGs for Path-Covering Problems

Authors: Francisco Sena, Romeo Rizzi, and Alexandru I. Tomescu

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

Abstract
A path-covering problem on a directed acyclic graph (DAG) requires finding a set of source-to-sink paths that cover all the nodes, all the arcs, or subsets thereof, and additionally they are optimal with respect to some function. In this paper we study safe sequences of nodes or arcs, namely sequences that appear in some path of every path cover of a DAG. We show that safe sequences admit a simple characterization via cutnodes. Moreover, we establish a connection between maximal safe sequences and leaf-to-root paths in the source- and sink-dominator trees of the DAG, which may be of independent interest in the extensive literature on dominators. With dominator trees, safe sequences admit an O(n)-size representation and a linear-time output-sensitive enumeration algorithm running in time O(m + o), where n and m are the number of nodes and arcs, respectively, and o is the total length of the maximal safe sequences. We then apply maximal safe sequences to simplify Integer Linear Programs (ILPs) for two path-covering problems, LeastSquares and MinPathError, which are at the core of RNA transcript assembly problems from bioinformatics. On various datasets, maximal safe sequences can be computed in under 0.1 seconds per graph, on average, and ILP solvers whose search space is reduced in this manner exhibit significant speed-ups. For example on graphs with a large width, average speed-ups are in the range 50-250× for MinPathError and in the range 80-350× for LeastSquares. Optimizing ILPs using safe sequences can thus become a fast building block of practical RNA transcript assembly tools, and more generally, of path-covering problems.
Cite as

Francisco Sena, Romeo Rizzi, and Alexandru I. Tomescu. Safe Sequences via Dominators in DAGs for Path-Covering Problems. In 33rd Annual European Symposium on Algorithms (ESA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 351, pp. 55:1-55:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{sena_et_al:LIPIcs.ESA.2025.55,
  author =	{Sena, Francisco and Rizzi, Romeo and Tomescu, Alexandru I.},
  title =	{{Safe Sequences via Dominators in DAGs for Path-Covering Problems}},
  booktitle =	{33rd Annual European Symposium on Algorithms (ESA 2025)},
  pages =	{55:1--55:17},
  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.2025.55},
  URN =		{urn:nbn:de:0030-drops-245230},
  doi =		{10.4230/LIPIcs.ESA.2025.55},
  annote =	{Keywords: directed acyclic graph, path cover, dominator tree, integer linear programming, least squares, minimum path error}
}
Document
DOI: 10.4230/LIPIcs.ESA.2025.29
The Tape Reconfiguration Problem and Its Consequences for Dominating Set Reconfiguration

Authors: Nicolas Bousquet, Quentin Deschamps, Arnaud Mary, Amer E. Mouawad, and Théo Pierron

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

Abstract
A dominating set of a graph G = (V,E) is a set of vertices D ⊆ V whose closed neighborhood is V, i.e., N[D] = V. We view a dominating set as a collection of tokens placed on the vertices of D. In the token sliding variant of the Dominating Set Reconfiguration problem (TS-DSR), we seek to transform a source dominating set into a target dominating set in G by sliding tokens along edges, and while maintaining a dominating set all along the transformation. TS-DSR is known to be PSPACE-complete even restricted to graphs of pathwidth w, for some non-explicit constant w and to be XL-complete parameterized by the size k of the solution. The first contribution of this article consists in using a novel approach to provide the first explicit constant for which the TS-DSR problem is PSPACE-complete, a question that was left open in the literature. From a parameterized complexity perspective, the token jumping variant of DSR, i.e., where tokens can jump to arbitrary vertices, is known to be FPT when parameterized by the size of the dominating sets on nowhere dense classes of graphs. But, in contrast, no non-trivial result was known about TS-DSR. We prove that DSR is actually much harder in the sliding model since it is XL-complete when restricted to bounded pathwidth graphs and even when parameterized by k plus the feedback vertex set number of the graph. This gives, for the first time, a difference of behavior between the complexity under token sliding and token jumping for some problem on graphs of bounded treewidth. All our results are obtained using a brand new method, based on the hardness of the so-called Tape Reconfiguration problem, a problem we believe to be of independent interest. We complement these hardness results with a positive result showing that DSR (parameterized by k) in the sliding model is FPT on planar graphs, also answering an open problem from the literature.
Cite as

Nicolas Bousquet, Quentin Deschamps, Arnaud Mary, Amer E. Mouawad, and Théo Pierron. The Tape Reconfiguration Problem and Its Consequences for Dominating Set Reconfiguration. In 33rd Annual European Symposium on Algorithms (ESA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 351, pp. 29:1-29:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{bousquet_et_al:LIPIcs.ESA.2025.29,
  author =	{Bousquet, Nicolas and Deschamps, Quentin and Mary, Arnaud and Mouawad, Amer E. and Pierron, Th\'{e}o},
  title =	{{The Tape Reconfiguration Problem and Its Consequences for Dominating Set Reconfiguration}},
  booktitle =	{33rd Annual European Symposium on Algorithms (ESA 2025)},
  pages =	{29:1--29:15},
  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.2025.29},
  URN =		{urn:nbn:de:0030-drops-244974},
  doi =		{10.4230/LIPIcs.ESA.2025.29},
  annote =	{Keywords: combinatorial reconfiguration, parameterized complexity, structural graph parameters, treewidth, dominating set}
}
Document
DOI: 10.4230/LIPIcs.ESA.2025.36
Efficient Contractions of Dynamic Graphs - With Applications

Authors: Monika Henzinger, Evangelos Kosinas, Robin Münk, and Harald Räcke

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

Abstract
A non-trivial minimum cut (NMC) sparsifier is a multigraph Ĝ that preserves all non-trivial minimum cuts of a given undirected graph G. We introduce a flexible data structure for fully dynamic graphs that can efficiently provide an NMC sparsifier upon request at any point during the sequence of updates. We employ simple dynamic forest data structures to achieve a fast from-scratch construction of the sparsifier at query time. Based on the strength of the adversary and desired type of time bounds, the data structure comes with different guarantees. Specifically, let G be a fully dynamic simple graph with n vertices and minimum degree δ. Then our data structure supports an insertion/deletion of an edge to/from G in n^o(1) worst-case time. Furthermore, upon request, it can return w.h.p. an NMC sparsifier of G that has O(n/δ) vertices and O(n) edges, in Ô(n) time. The probabilistic guarantees hold against an adaptive adversary. Alternatively, the update and query times can be improved to Õ(1) and Õ(n) respectively, if amortized-time guarantees are sufficient, or if the adversary is oblivious. Throughout the paper, we use Õ to hide polylogarithmic factors and Ô to hide subpolynomial (i.e., n^o(1)) factors. We discuss two applications of our new data structure. First, it can be used to efficiently report a cactus representation of all minimum cuts of a fully dynamic simple graph. Building this cactus for the NMC sparsifier instead of the original graph allows for a construction time that is sublinear in the number of edges. Against an adaptive adversary, we can with high probability output the cactus representation in worst-case Ô(n) time. Second, our data structure allows us to efficiently compute the maximal k-edge-connected subgraphs of undirected simple graphs, by repeatedly applying a minimum cut algorithm on the NMC sparsifier. Specifically, we can compute with high probability the maximal k-edge-connected subgraphs of a simple graph with n vertices and m edges in Õ(m+n²/k) time. This improves the best known time bounds for k = Ω(n^{1/8}) and naturally extends to the case of fully dynamic graphs.
Cite as

Monika Henzinger, Evangelos Kosinas, Robin Münk, and Harald Räcke. Efficient Contractions of Dynamic Graphs - With Applications. In 33rd Annual European Symposium on Algorithms (ESA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 351, pp. 36:1-36:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{henzinger_et_al:LIPIcs.ESA.2025.36,
  author =	{Henzinger, Monika and Kosinas, Evangelos and M\"{u}nk, Robin and R\"{a}cke, Harald},
  title =	{{Efficient Contractions of Dynamic Graphs - With Applications}},
  booktitle =	{33rd Annual European Symposium on Algorithms (ESA 2025)},
  pages =	{36:1--36:14},
  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.2025.36},
  URN =		{urn:nbn:de:0030-drops-245047},
  doi =		{10.4230/LIPIcs.ESA.2025.36},
  annote =	{Keywords: Graph Algorithms, Cut Sparsifiers, Dynamic Algorithms}
}
Document
DOI: 10.4230/OASIcs.SpaceCHI.2025.32
Virtual Reality Prototyping Environment for Concurrent Design, Training and Rover Operations

Authors: Pinar Dogru, Hanjo Schnellbächer, Tarek Can Battikh, and Kristina Remić

Published in: OASIcs, Volume 130, Advancing Human-Computer Interaction for Space Exploration (SpaceCHI 2025)

Abstract
As part of the CASIMAR (Collaborative Astronaut Supporting Interregional Moon Analog Rover) project, initiated by the BVSR e.V. (Bundesverband Studentischer Raumfahrt), the TUDSaT (TU Darmstadt Space Technology e.V.) team is developing a Virtual Reality (VR) prototype environment to support the interdisciplinary design process of lunar exploration technologies. Given the complexity of collaboration among eight organizations, this tool aims to streamline design integration and enhance mission planning. The primary objective is to create a comprehensive 3D model of the rover, complete with predefined procedures and activities, to simulate astronaut-robot interaction. By leveraging VR technology, astronauts can familiarize themselves with the rover and its EVA (Extravehicular Activity) tools before actual deployment, improving operational safety and efficiency. Beyond training applications, this virtual environment serves as a critical platform for designing, testing, and benchmarking rover functionalities and EVA procedures. Ultimately, our work contributes to optimizing human-robotic interaction, ensuring that lunar exploration missions are both effective and well-prepared before reaching the Moon.
Cite as

Pinar Dogru, Hanjo Schnellbächer, Tarek Can Battikh, and Kristina Remić. Virtual Reality Prototyping Environment for Concurrent Design, Training and Rover Operations. In Advancing Human-Computer Interaction for Space Exploration (SpaceCHI 2025). Open Access Series in Informatics (OASIcs), Volume 130, pp. 32:1-32:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{dogru_et_al:OASIcs.SpaceCHI.2025.32,
  author =	{Dogru, Pinar and Schnellb\"{a}cher, Hanjo and Battikh, Tarek Can and Remi\'{c}, Kristina},
  title =	{{Virtual Reality Prototyping Environment for Concurrent Design, Training and Rover Operations}},
  booktitle =	{Advancing Human-Computer Interaction for Space Exploration (SpaceCHI 2025)},
  pages =	{32:1--32:13},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-384-3},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{130},
  editor =	{Bensch, Leonie and Nilsson, Tommy and Nisser, Martin and Pataranutaporn, Pat and Schmidt, Albrecht and Sumini, Valentina},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.SpaceCHI.2025.32},
  URN =		{urn:nbn:de:0030-drops-240226},
  doi =		{10.4230/OASIcs.SpaceCHI.2025.32},
  annote =	{Keywords: virtual reality (VR), digital twin, human-robot-interaction (HRI), LUNA analog facility, rover, extravehicular activities (EVA), gamification, simulation, user-centered design (UCD), concurrent engineering (CE), space system engineering}
}
Document
DOI: 10.4230/LIPIcs.WADS.2025.6
Vantage Point Selection Algorithms for Bottleneck Capacity Estimation

Authors: Vikrant Ashvinkumar, Rezaul Chowdhury, Jie Gao, Mayank Goswami, Joseph S. B. Mitchell, and Valentin Polishchuk

Published in: LIPIcs, Volume 349, 19th International Symposium on Algorithms and Data Structures (WADS 2025)

Abstract
Motivated by the problem of estimating bottleneck capacities on the Internet, we formulate and study the problem of vantage point selection. We are given a graph G = (V, E) whose edges E have unknown capacity values that are to be discovered. Probes from a vantage point, i.e, a vertex v ∈ V, along shortest paths from v to all other vertices, reveal bottleneck edge capacities along each path. Our goal is to select k vantage points from V that reveal the maximum number of bottleneck edge capacities. We consider both a non-adaptive setting where all k vantage points are selected before any bottleneck capacity is revealed, and an adaptive setting where each vantage point selection instantly reveals bottleneck capacities along all shortest paths starting from that point. In the non-adaptive setting, by considering a relaxed model where edge capacities are drawn from a random permutation (which still leaves the problem of maximizing the expected number of revealed edges NP-hard), we are able to give a 1-1/e approximate algorithm. In the adaptive setting we work with the least permissive model where edge capacities are arbitrarily fixed but unknown. We compare with the best solution for the particular input instance (i.e. by enumerating all choices of k tuples), and provide both lower bounds on instance optimal approximation algorithms and upper bounds for trees and planar graphs.
Cite as

Vikrant Ashvinkumar, Rezaul Chowdhury, Jie Gao, Mayank Goswami, Joseph S. B. Mitchell, and Valentin Polishchuk. Vantage Point Selection Algorithms for Bottleneck Capacity Estimation. In 19th International Symposium on Algorithms and Data Structures (WADS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 349, pp. 6:1-6:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{ashvinkumar_et_al:LIPIcs.WADS.2025.6,
  author =	{Ashvinkumar, Vikrant and Chowdhury, Rezaul and Gao, Jie and Goswami, Mayank and Mitchell, Joseph S. B. and Polishchuk, Valentin},
  title =	{{Vantage Point Selection Algorithms for Bottleneck Capacity Estimation}},
  booktitle =	{19th International Symposium on Algorithms and Data Structures (WADS 2025)},
  pages =	{6:1--6:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-398-0},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{349},
  editor =	{Morin, Pat and Oh, Eunjin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WADS.2025.6},
  URN =		{urn:nbn:de:0030-drops-242376},
  doi =		{10.4230/LIPIcs.WADS.2025.6},
  annote =	{Keywords: Bottleneck capacity, Approximation algorithms, Instance optimality}
}
Document
DOI: 10.4230/LIPIcs.WABI.2025.20
A k-mer-Based Estimator of the Substitution Rate Between Repetitive Sequences

Authors: Haonan Wu, Antonio Blanca, and Paul Medvedev

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

Abstract
K-mer-based analysis of genomic data is ubiquitous, but the presence of repetitive k-mers continues to pose problems for the accuracy of many methods. For example, the Mash tool (Ondov et al. 2016) can accurately estimate the substitution rate between two low-repetitive sequences from their k-mer sketches; however, it is inaccurate on repetitive sequences such as the centromere of a human chromosome. Follow-up work by Blanca et al. (2021) has attempted to model how mutations affect k-mer sets based on strong assumptions that the sequence is non-repetitive and that mutations do not create spurious k-mer matches. However, the theoretical foundations for extending an estimator like Mash to work in the presence of repeat sequences have been lacking. In this work, we relax the non-repetitive assumption and propose a novel estimator for the mutation rate. We derive theoretical bounds on our estimator’s bias. Our experiments show that it remains accurate for repetitive genomic sequences, such as the alpha satellite higher order repeats in centromeres. We demonstrate our estimator’s robustness across diverse datasets and various ranges of the substitution rate and k-mer size. Finally, we show how sketching can be used to avoid dealing with large k-mer sets while retaining accuracy. Our software is available at https://github.com/medvedevgroup/Repeat-Aware_Substitution_Rate_Estimator.
Cite as

Haonan Wu, Antonio Blanca, and Paul Medvedev. A k-mer-Based Estimator of the Substitution Rate Between Repetitive Sequences. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 20:1-20:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{wu_et_al:LIPIcs.WABI.2025.20,
  author =	{Wu, Haonan and Blanca, Antonio and Medvedev, Paul},
  title =	{{A k-mer-Based Estimator of the Substitution Rate Between Repetitive Sequences}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{20:1--20:20},
  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.2025.20},
  URN =		{urn:nbn:de:0030-drops-239465},
  doi =		{10.4230/LIPIcs.WABI.2025.20},
  annote =	{Keywords: k-mers, sketching, mutation rates}
}
Document
DOI: 10.4230/LIPIcs.WABI.2025.10
DiVerG: Scalable Distance Index for Validation of Paired-End Alignments in Sequence Graphs

Authors: Ali Ghaffaari, Alexander Schönhuth, and Tobias Marschall

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

Abstract
Determining the distance between two loci within a genomic region is a recurrent operation in various tasks in computational genomics. A notable example of this task arises in paired-end read mapping as a form of validation of distances between multiple alignments. While straightforward for a single genome, graph-based reference structures render the operation considerably more involved. Given the sheer number of such queries in a typical read mapping experiment, an efficient algorithm for answering distance queries is crucial. In this paper, we introduce DiVerG, a compact data structure as well as a fast and scalable algorithm, for constructing distance indexes for general sequence graphs on multi-core CPU and many-core GPU architectures. DiVerG is based on PairG [Jain et al., 2019], but overcomes the limitations of PairG by exploiting the extensive potential for improvements in terms of scalability and space efficiency. As a consequence, DiVerG can process substantially larger datasets, such as whole human genomes, which are unmanageable by PairG. DiVerG offers faster index construction time and consistently faster query time with gains proportional to the size of the underlying compact data structure. We demonstrate that our method performs favorably on multiple real datasets at various scales. DiVerG achieves superior performance over PairG; e.g. resulting to 2.5-4x speed-up in query time, 44-340x smaller index size, and 3-50x faster construction time for the genome graph of the MHC region, as a particularly variable region of the human genome. The implementation is available at: https://github.com/cartoonist/diverg
Cite as

Ali Ghaffaari, Alexander Schönhuth, and Tobias Marschall. DiVerG: Scalable Distance Index for Validation of Paired-End Alignments in Sequence Graphs. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 10:1-10:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{ghaffaari_et_al:LIPIcs.WABI.2025.10,
  author =	{Ghaffaari, Ali and Sch\"{o}nhuth, Alexander and Marschall, Tobias},
  title =	{{DiVerG: Scalable Distance Index for Validation of Paired-End Alignments in Sequence Graphs}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{10:1--10:24},
  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.2025.10},
  URN =		{urn:nbn:de:0030-drops-239369},
  doi =		{10.4230/LIPIcs.WABI.2025.10},
  annote =	{Keywords: Sequence graph, distance index, read mapping, sparse matrix}
}
Document
DOI: 10.4230/LIPIcs.WABI.2025.14
Human Readable Compression of GFA Paths Using Grammar-Based Code

Authors: Peter Heringer and Daniel Doerr

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

Abstract
Pangenome graphs offer a compact and comprehensive representation of genomic diversity, improving tasks such as variant calling, genotyping, and other downstream analyses. Although the underlying graph structures scale sublinearly with the number of haplotypes, the widely used GFA file format suffers from rapidly growing file sizes due to the explicit and repetitive encoding of haplotype paths. In this work, we introduce an extension to the GFA format that enables efficient grammar-based compression of haplotype paths while retaining human readability. In addition, grammar-based encoding provides an efficient in-memory data structure that does not require decompression, but conversely improves the runtime of many computational tasks that involve haplotype comparisons. We present sqz, a method that makes use of the proposed format extension to encode haplotype paths using byte pair encoding, a grammar-based compression scheme. We evaluate sqz on recent human pangenome graphs from Heumos et al. and the Human Pangenome Reference Consortium (HPRC), comparing it to existing compressors bgzip, gbz, and sequitur. sqz scales sublinearly with the number of haplotypes in a pangenome graph and consistently achieves higher compression ratios than sequitur and up to 5 times better compression than bgzip in HPRC graphs and up to 10 times in the graph from Heumos et al.. When combined with bgzip, sqz matches or excels the compression ratio of gbz across all our datasets. These results demonstrate the potential of our proposed extension of the GFA format in reducing haplotype path redundancy and improving storage efficiency for pangenome graphs.
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Peter Heringer and Daniel Doerr. Human Readable Compression of GFA Paths Using Grammar-Based Code. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 14:1-14:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{heringer_et_al:LIPIcs.WABI.2025.14,
  author =	{Heringer, Peter and Doerr, Daniel},
  title =	{{Human Readable Compression of GFA Paths Using Grammar-Based Code}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{14:1--14:19},
  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.2025.14},
  URN =		{urn:nbn:de:0030-drops-239395},
  doi =		{10.4230/LIPIcs.WABI.2025.14},
  annote =	{Keywords: pangenomics, pangenome graphs, compression, grammar-based code, byte pair encoding}
}
Document
Track A: Algorithms, Complexity and Games
DOI: 10.4230/LIPIcs.ICALP.2025.18
q-Partitioning Valuations: Exploring the Space Between Subadditive and Fractionally Subadditive Valuations

Authors: Kiril Bangachev and S. Matthew Weinberg

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

Abstract
For a set M of m elements, we define a decreasing chain of classes of normalized monotone-increasing valuation functions from 2^M to ℝ_{≥ 0}, parameterized by an integer q ∈ [2,m]. For a given q, we refer to the class as q-partitioning. A valuation function is subadditive if and only if it is 2-partitioning, and fractionally subadditive if and only if it is m-partitioning. Thus, our chain establishes an interpolation between subadditive and fractionally subadditive valuations. We show that this interpolation is smooth (q-partitioning valuations are "nearly" (q-1)-partitioning in a precise sense, Theorem 6), interpretable (the definition arises by analyzing the core of a cost-sharing game, à la the Bondareva-Shapley Theorem for fractionally subadditive valuations, Section 3.1), and non-trivial (the class of q-partitioning valuations is distinct for all q, Proposition 3). For domains where provable separations exist between subadditive and fractionally subadditive, we interpolate the stronger guarantees achievable for fractionally subadditive valuations to all q ∈ {2,…, m}. Two highlights are the following: 1) An Ω ((log log q)/(log log m))-competitive posted price mechanism for q-partitioning valuations. Note that this matches asymptotically the state-of-the-art for both subadditive (q = 2) [Paul Dütting et al., 2020], and fractionally subadditive (q = m) [Feldman et al., 2015]. 2) Two upper-tail concentration inequalities on 1-Lipschitz, q-partitioning valuations over independent items. One extends the state-of-the-art for q = m to q < m, the other improves the state-of-the-art for q = 2 for q > 2. Our concentration inequalities imply several corollaries that interpolate between subadditive and fractionally subadditive, for example: 𝔼[v(S)] ≤ (1 + 1/log q)Median[v(S)] + O(log q). To prove this, we develop a new isoperimetric inequality using Talagrand’s method of control by q points, which may be of independent interest. We also discuss other probabilistic inequalities and game-theoretic applications of q-partitioning valuations, and connections to subadditive MPH-k valuations [Tomer Ezra et al., 2019].
Cite as

Kiril Bangachev and S. Matthew Weinberg. q-Partitioning Valuations: Exploring the Space Between Subadditive and Fractionally Subadditive Valuations. In 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 334, pp. 18:1-18:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{bangachev_et_al:LIPIcs.ICALP.2025.18,
  author =	{Bangachev, Kiril and Weinberg, S. Matthew},
  title =	{{q-Partitioning Valuations: Exploring the Space Between Subadditive and Fractionally Subadditive Valuations}},
  booktitle =	{52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)},
  pages =	{18:1--18:20},
  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.2025.18},
  URN =		{urn:nbn:de:0030-drops-233956},
  doi =		{10.4230/LIPIcs.ICALP.2025.18},
  annote =	{Keywords: Subadditive Functions, Fractionally Subadditive Functions, Posted Price Mechanisms, Concentration Inequalities}
}
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