17 Search Results for "Harvey, Paul"


Document
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
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
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
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
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
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
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
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
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
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
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
Track A: Algorithms, Complexity and Games
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}
}
Document
Track A: Algorithms, Complexity and Games
Fourier Analysis of Iterative Algorithms

Authors: Chris Jones and Lucas Pesenti

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


Abstract
We study a general class of nonlinear iterative algorithms which includes power iteration, belief propagation and approximate message passing, and many forms of gradient descent. When the input is a random matrix with i.i.d. entries, we use Boolean Fourier analysis to analyze these algorithms as low-degree polynomials in the entries of the input matrix. Each symmetrized Fourier character represents all monomials with a certain shape as specified by a small graph, which we call a Fourier diagram. We prove fundamental asymptotic properties of the Fourier diagrams: over the randomness of the input, all diagrams with cycles are negligible; the tree-shaped diagrams form a basis of asymptotically independent Gaussian vectors; and, when restricted to the trees, iterative algorithms exactly follow an idealized Gaussian dynamic. We use this to prove a state evolution formula, giving a "complete" asymptotic description of the algorithm’s trajectory. The restriction to tree-shaped monomials mirrors the assumption of the cavity method, a 40-year-old non-rigorous technique in statistical physics which has served as one of the most important techniques in the field. We demonstrate how to implement cavity method derivations by 1) restricting the iteration to its tree approximation, and 2) observing that heuristic cavity method-type arguments hold rigorously on the simplified iteration. Our proofs use combinatorial arguments similar to the trace method from random matrix theory. Finally, we push the diagram analysis to a number of iterations that scales with the dimension n of the input matrix, proving that the tree approximation still holds for a simple variant of power iteration all the way up to n^{Ω(1)} iterations.

Cite as

Chris Jones and Lucas Pesenti. Fourier Analysis of Iterative Algorithms. In 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 334, pp. 102:1-102:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)


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@InProceedings{jones_et_al:LIPIcs.ICALP.2025.102,
  author =	{Jones, Chris and Pesenti, Lucas},
  title =	{{Fourier Analysis of Iterative Algorithms}},
  booktitle =	{52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)},
  pages =	{102:1--102:21},
  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.2025.102},
  URN =		{urn:nbn:de:0030-drops-234791},
  doi =		{10.4230/LIPIcs.ICALP.2025.102},
  annote =	{Keywords: Iterative Algorithms, Message-passing Algorithms, Random Matrix Theory}
}
Document
Track A: Algorithms, Complexity and Games
Asymptotically Optimal Inapproximability of Maxmin k-Cut Reconfiguration

Authors: Shuichi Hirahara and Naoto Ohsaka

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


Abstract
k-Coloring Reconfiguration is one of the most well-studied reconfiguration problems, which asks to transform a given proper k-coloring of a graph to another by repeatedly recoloring a single vertex. Its approximate version, Maxmin k-Cut Reconfiguration, is defined as an optimization problem of maximizing the minimum fraction of bichromatic edges during the transformation between (not necessarily proper) k-colorings. In this paper, we demonstrate that the optimal approximation factor of this problem is 1 - Θ(1/k) for every k ≥ 2. Specifically, we prove the PSPACE-hardness of approximating the objective value within a factor of 1 - ε/k for some universal constant ε > 0, whereas we develop a deterministic polynomial-time algorithm that achieves the approximation factor of 1 - 2/k. To prove the hardness result, we propose a new probabilistic verifier that tests a "striped" pattern. Our approximation algorithm is based on a random transformation that passes through a random k-coloring.

Cite as

Shuichi Hirahara and Naoto Ohsaka. Asymptotically Optimal Inapproximability of Maxmin k-Cut Reconfiguration. In 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 334, pp. 96:1-96:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)


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@InProceedings{hirahara_et_al:LIPIcs.ICALP.2025.96,
  author =	{Hirahara, Shuichi and Ohsaka, Naoto},
  title =	{{Asymptotically Optimal Inapproximability of Maxmin k-Cut Reconfiguration}},
  booktitle =	{52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)},
  pages =	{96:1--96:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-372-0},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{334},
  editor =	{Censor-Hillel, Keren and Grandoni, Fabrizio and Ouaknine, Jo\"{e}l and Puppis, Gabriele},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2025.96},
  URN =		{urn:nbn:de:0030-drops-234733},
  doi =		{10.4230/LIPIcs.ICALP.2025.96},
  annote =	{Keywords: reconfiguration problems, graph coloring, hardness of approximation}
}
Document
Track A: Algorithms, Complexity and Games
Yet Another Simple Proof of the PCRP Theorem

Authors: Naoto Ohsaka

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


Abstract
The Probabilistically Checkable Reconfiguration Proof (PCRP) theorem, proven by Hirahara and Ohsaka (STOC 2024) [Hirahara and Ohsaka, 2024] and Karthik C. S. and Manurangsi [{Karthik {C. S.}} and Manurangsi, 2023], provides a new PCP-type characterization of PSPACE: A language L is in PSPACE if and only if there exists a probabilistic verifier 𝒱 and a pair of polynomial-time computable proofs π^ini, π^end such that the following hold for every input x: - If x ∈ L, then π^ini(x) can be transformed into π^end(x) by repeatedly flipping a single bit of the proof at a time, while making 𝒱(x) to accept every intermediate proof with probability 1. - If x ∉ L, then any such transformation induces a proof that is rejected by 𝒱(x) with probability more than 1/2. The PCRP theorem finds many applications in PSPACE-hardness of approximation for reconfiguration problems. In this paper, we present an alternative proof of the PCRP theorem that is "simpler" than those of Hirahara and Ohsaka [Hirahara and Ohsaka, 2024] and Karthik C. S. and Manurangsi [Karthik C. S. and Manurangsi, 2023]. Our PCRP system is obtained by combining simple robustization and composition steps in a modular fashion, which renders its analysis more intuitive. The crux of implementing the robustization step is an error-correcting code that enjoys both list decodability and reconfigurability, the latter of which enables to reconfigure between a pair of codewords, while avoiding getting too close to any other codewords.

Cite as

Naoto Ohsaka. Yet Another Simple Proof of the PCRP Theorem. In 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 334, pp. 122:1-122:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)


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@InProceedings{ohsaka:LIPIcs.ICALP.2025.122,
  author =	{Ohsaka, Naoto},
  title =	{{Yet Another Simple Proof of the PCRP Theorem}},
  booktitle =	{52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)},
  pages =	{122:1--122:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-372-0},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{334},
  editor =	{Censor-Hillel, Keren and Grandoni, Fabrizio and Ouaknine, Jo\"{e}l and Puppis, Gabriele},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2025.122},
  URN =		{urn:nbn:de:0030-drops-234995},
  doi =		{10.4230/LIPIcs.ICALP.2025.122},
  annote =	{Keywords: reconfiguration problems, hardness of approximation, probabilistic proof systems}
}
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