21 Search Results for "Harvey, Paul"

Document
DOI: 10.4230/LIPIcs.SEA.2026.20
QuadRank: Engineering a High Throughput Rank

Authors: Ragnar Groot Koerkamp

Published in: LIPIcs, Volume 371, 24th International Symposium on Experimental Algorithms (SEA 2026)

Abstract
Motivation. Given a text, a query rank(q, c) counts the number of occurrences of character c among the first q characters of the text. Space-efficient methods to answer these rank queries form an important building block in many succinct data structures. For example, the FM-index [Ferragina and Manzini, 2000] is a widely used data structure that uses rank queries to locate all occurrences of a pattern in a text. In bioinformatics applications, the goal is usually to process large inputs as fast as possible. Thus, data structures should have high throughput when used with many threads. Contributions. We first survey existing results on rank data structures. For the σ = 2 binary alphabet, we then develop BiRank, which has 3.28% space overhead. BiRank merges the central ideas of two recent papers: (1) we interleave (inline) offsets in each cache line of the underlying bit vector [Laws et al., 2024], reducing cache misses, and (2) these offsets are to the middle of each block so that only half of each needs popcounting [Gottlieb and Reinert, 2025]. In QuadRank (14.4% overhead), we extend these techniques to the σ = 4 (DNA) alphabet. Both data structures typically require only a single cache miss per query, making them highly suitable for high-throughput and memory-bound settings. To enable efficient batch-processing, we support prefetching the cache lines required to answer upcoming queries. Results. BiRank and QuadRank are around 1.5× and 2× faster than similar-overhead methods that do not use interleaving. Prefetching gives an additional 2× speedup, at which point the dual-channel DDR4 RAM bandwidth becomes a hard limit on the total throughput. With prefetching, both methods outperform all other methods apart from SPIDER [Laws et al., 2024] by 2×. When using QuadRank with prefetching in a toy count-only FM-index, QuadFm, this results in a smaller size and up to 4× speedup over Genedex, a state-of-the-art batching FM-index implementation. Conclusion. Optimizing data structures for high throughput, by minimizing cache misses and branch-misses and adding support for prefetching, can result in significant speedups when benchmarks are adjusted accordingly.
Cite as

Ragnar Groot Koerkamp. QuadRank: Engineering a High Throughput Rank. In 24th International Symposium on Experimental Algorithms (SEA 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 371, pp. 20:1-20:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{grootkoerkamp:LIPIcs.SEA.2026.20,
  author =	{Groot Koerkamp, Ragnar},
  title =	{{QuadRank: Engineering a High Throughput Rank}},
  booktitle =	{24th International Symposium on Experimental Algorithms (SEA 2026)},
  pages =	{20:1--20:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-422-2},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{371},
  editor =	{Aum\"{u}ller, Martin and Finocchi, Irene},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2026.20},
  URN =		{urn:nbn:de:0030-drops-260248},
  doi =		{10.4230/LIPIcs.SEA.2026.20},
  annote =	{Keywords: Rank, Succinct Data Structures, Cache Performance, Prefetching}
}
Document
DOI: 10.4230/LIPIcs.CPM.2026.14
Hardness Results on Characteristics for Elastic-Degenerate Strings

Authors: Dominik Köppl and Jannik Olbrich

Published in: LIPIcs, Volume 369, 37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026)

Abstract
Generalizations of plain strings have been proposed as a compact way to represent a collection of nearly identical sequences or to express uncertainty at specific text positions by enumerating all possibilities. While a plain string stores a character at each of its positions, generalizations consider a set of characters (indeterminate strings), a set of strings of equal length (generalized degenerate strings, or shortly GD strings), or a set of strings of arbitrary lengths (elastic-degenerate strings, or shortly ED strings). These generalizations are of importance to compactly represent such type of data, and find applications in bioinformatics for representing and maintaining a set of genetic sequences of the same taxonomy or a multiple sequence alignment. To be of use, attention has been drawn to answering various query types such as pattern matching or measuring similarity of ED strings by generalizing techniques known to plain strings. However, for some types of queries, it has been shown that a generalization of a polynomial-time solvable query on classic strings becomes NP-hard on ED strings, e.g. [Russo et al., 2022]. In that light, we wonder about other types of queries that are of particular interest to bioinformatics: unique substrings, absent words, anti-powers, longest previous factors, and Lempel-Ziv-like compression schemes. While we obtain a polynomial time algorithm for a variation of longest previous factors, we show that all other problems are NP-hard to compute, some of them even under the restriction that the input can be modeled as an indeterminate or GD string.
Cite as

Dominik Köppl and Jannik Olbrich. Hardness Results on Characteristics for Elastic-Degenerate Strings. In 37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 369, pp. 14:1-14:25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{koppl_et_al:LIPIcs.CPM.2026.14,
  author =	{K\"{o}ppl, Dominik and Olbrich, Jannik},
  title =	{{Hardness Results on Characteristics for Elastic-Degenerate Strings}},
  booktitle =	{37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026)},
  pages =	{14:1--14:25},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-420-8},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{369},
  editor =	{Bille, Philip and Prezza, Nicola},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2026.14},
  URN =		{urn:nbn:de:0030-drops-259409},
  doi =		{10.4230/LIPIcs.CPM.2026.14},
  annote =	{Keywords: Elastic-degenerate strings, NP-hardness, longest common factor, minimal unique substring, minimal absent word, anti-power, longest previous factor}
}
Document
DOI: 10.4230/LIPIcs.SoCG.2026.37
A Free Lunch: Manifolds of Positive Reach Can Be Smoothed Without Decreasing the Reach

Authors: Hana Dal Poz Kouřimská, André Lieutier, and Mathijs Wintraecken

Published in: LIPIcs, Volume 367, 42nd International Symposium on Computational Geometry (SoCG 2026)

Abstract
Assumptions on the reach are crucial for ensuring the correctness of many geometric and topological algorithms, including triangulation, manifold reconstruction and learning, homotopy reconstruction, and methods for estimating curvature or reach. However, these assumptions are often coupled with the requirement that the manifold be smooth, typically at least C². In this paper, we prove that any manifold with positive reach can be approximated arbitrarily well by a C^∞ manifold without significantly reducing the reach. More precisely, given a manifold with reach R, we construct a manifold that is ε-close to it in the C¹ sense (both the manifold and its tangent spaces are close), and has reach at least R-ε. The proof employs techniques from differential topology - partitions of unity and smoothing using convolution kernels. This result implies that nearly all theorems established for C² or manifolds with a certain reach naturally extend to manifolds with the same reach, even if they are not C², for free!
Cite as

Hana Dal Poz Kouřimská, André Lieutier, and Mathijs Wintraecken. A Free Lunch: Manifolds of Positive Reach Can Be Smoothed Without Decreasing the Reach. In 42nd International Symposium on Computational Geometry (SoCG 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 367, pp. 37:1-37:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{dalpozkourimska_et_al:LIPIcs.SoCG.2026.37,
  author =	{Dal Poz Kou\v{r}imsk\'{a}, Hana and Lieutier, Andr\'{e} and Wintraecken, Mathijs},
  title =	{{A Free Lunch: Manifolds of Positive Reach Can Be Smoothed Without Decreasing the Reach}},
  booktitle =	{42nd International Symposium on Computational Geometry (SoCG 2026)},
  pages =	{37:1--37:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-418-5},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{367},
  editor =	{Ahn, Hee-Kap and Hoffmann, Michael and Nayyeri, Amir},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SoCG.2026.37},
  URN =		{urn:nbn:de:0030-drops-258434},
  doi =		{10.4230/LIPIcs.SoCG.2026.37},
  annote =	{Keywords: Reach, Manifolds, Smoothing, Differentiability, Differential topology}
}
Document
Invited Talk
DOI: 10.4230/LIPIcs.ICDT.2026.3
Building Relational Circuits (Invited Talk)

Authors: Florent Capelli

Published in: LIPIcs, Volume 365, 29th International Conference on Database Theory (ICDT 2026)

Abstract
We review two algorithms which allow to build a factorized representation of the answers set of join queries. In a nutshell, the representation builds a circuit representing the answers set of a join query by starting from atomic relations and iteratively combine them by either constructing the Cartesian product or the disjoint union of previously computed relations. The first one can be seen as the trace of the celebrated Yannakakis algorithm, building the answer set from the inputs to the output of the circuit while the second adopts a top-down approach which can be seen as a generalization of the exhaustive DPLL algorithm, originally designed to solve the #SAT problem.
Cite as

Florent Capelli. Building Relational Circuits (Invited Talk). In 29th International Conference on Database Theory (ICDT 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 365, pp. 3:1-3:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{capelli:LIPIcs.ICDT.2026.3,
  author =	{Capelli, Florent},
  title =	{{Building Relational Circuits}},
  booktitle =	{29th International Conference on Database Theory (ICDT 2026)},
  pages =	{3:1--3:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-413-0},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{365},
  editor =	{ten Cate, Balder and Funk, Maurice},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICDT.2026.3},
  URN =		{urn:nbn:de:0030-drops-256172},
  doi =		{10.4230/LIPIcs.ICDT.2026.3},
  annote =	{Keywords: Conjunctive queries, factorized databases, knowledge compilation}
}
Document
DOI: 10.4230/LIPIcs.ITCS.2026.99
AC⁰[p]-Frege Cannot Efficiently Prove That Constant-Depth Algebraic Circuit Lower Bounds Are Hard

Authors: Jiaqi Lu, Rahul Santhanam, and Iddo Tzameret

Published in: LIPIcs, Volume 362, 17th Innovations in Theoretical Computer Science Conference (ITCS 2026)

Abstract
We study whether lower bounds against constant-depth algebraic circuits computing the Permanent over finite fields (Limaye-Srinivasan-Tavenas [J. ACM, 2025] and Forbes [CCC'24]) are hard to prove in certain proof systems. We focus on a DNF formula that expresses that such lower bounds are hard for constant-depth algebraic proofs. Using an adaptation of the diagonalization framework of Santhanam and Tzameret (SIAM J. Comput., 2025), we show unconditionally that this family of DNF formulas does not admit polynomial-size propositional AC⁰[p]-Frege proofs, infinitely often. This rules out the possibility that the DNF family is easy, and establishes that its status is either that of a hard tautology for AC⁰[p]-Frege or else unprovable (i.e., not a tautology). While it remains open whether the DNFs in question are tautologies, we provide evidence in this direction. In particular, under the plausible assumption that certain (weak) properties of multilinear algebra - specifically, those involving tensor rank - do not admit short constant-depth algebraic proofs, the DNFs are tautologies. We also observe that several weaker variants of the DNF formula are provably tautologies, and we show that the question of whether the DNFs are tautologies connects to conjectures of Razborov (ICALP'96) and Krajíček (J. Symb. Log., 2004). Additionally, our result has the following special features: ii) Existential depth amplification: the DNF formula considered is parameterised by a constant depth d bounding the depth of the algebraic proofs. We show that there exists some fixed depth d such that if there are no small depth-d algebraic proofs of certain circuit lower bounds for the Permanent, then there are no such small algebraic proofs in any constant depth. iii) Necessity: We show that our result is a necessary step towards establishing lower bounds against constant-depth algebraic proofs, and more generally against any sufficiently strong proof system. In particular, showing there are no short proofs for our DNF formulas, obtained by replacing "constant-depth algebraic circuits" with any "reasonable" algebraic circuit class C, is necessary in order to prove any super-polynomial lower bounds against algebraic proofs operating with circuits from C.
Cite as

Jiaqi Lu, Rahul Santhanam, and Iddo Tzameret. AC⁰[p]-Frege Cannot Efficiently Prove That Constant-Depth Algebraic Circuit Lower Bounds Are Hard. In 17th Innovations in Theoretical Computer Science Conference (ITCS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 362, pp. 99:1-99:25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{lu_et_al:LIPIcs.ITCS.2026.99,
  author =	{Lu, Jiaqi and Santhanam, Rahul and Tzameret, Iddo},
  title =	{{AC⁰\lbrackp\rbrack-Frege Cannot Efficiently Prove That Constant-Depth Algebraic Circuit Lower Bounds Are Hard}},
  booktitle =	{17th Innovations in Theoretical Computer Science Conference (ITCS 2026)},
  pages =	{99:1--99:25},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-410-9},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{362},
  editor =	{Saraf, Shubhangi},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITCS.2026.99},
  URN =		{urn:nbn:de:0030-drops-253865},
  doi =		{10.4230/LIPIcs.ITCS.2026.99},
  annote =	{Keywords: Complexity, Lower bounds, Proof complexity, AC⁰\lbrackp\rbrack-Frege, Diagonalisation, Algebraic complexity}
}
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.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.2025.55
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/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
RANDOM
DOI: 10.4230/LIPIcs.APPROX/RANDOM.2025.60
Sink-Free Orientations: A Local Sampler with Applications

Authors: Konrad Anand, Graham Freifeld, Heng Guo, Chunyang Wang, and Jiaheng Wang

Published in: LIPIcs, Volume 353, Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025)

Abstract
For sink-free orientations in graphs of minimum degree at least 3, we show that there is a deterministic approximate counting algorithm that runs in time O((n^33/ε^32)log(n/ε)), a near-linear time sampling algorithm, and a randomised approximate counting algorithm that runs in time O((n/ε)²log(n/ε)), where n denotes the number of vertices of the input graph and 0 < ε < 1 is the desired accuracy. All three algorithms are based on a local implementation of the sink popping method (Cohn, Pemantle, and Propp, 2002) under the partial rejection sampling framework (Guo, Jerrum, and Liu, 2019).
Cite as

Konrad Anand, Graham Freifeld, Heng Guo, Chunyang Wang, and Jiaheng Wang. Sink-Free Orientations: A Local Sampler with Applications. In Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 353, pp. 60:1-60:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{anand_et_al:LIPIcs.APPROX/RANDOM.2025.60,
  author =	{Anand, Konrad and Freifeld, Graham and Guo, Heng and Wang, Chunyang and Wang, Jiaheng},
  title =	{{Sink-Free Orientations: A Local Sampler with Applications}},
  booktitle =	{Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025)},
  pages =	{60:1--60:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-397-3},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{353},
  editor =	{Ene, Alina and Chattopadhyay, Eshan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.APPROX/RANDOM.2025.60},
  URN =		{urn:nbn:de:0030-drops-244267},
  doi =		{10.4230/LIPIcs.APPROX/RANDOM.2025.60},
  annote =	{Keywords: Sink-free orientations, local sampling, deterministic counting}
}
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.
Cite as

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
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}
}
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