41 Search Results for "Cook, William R."

Document
DOI: 10.4230/LIPIcs.STACS.2026.25
Homomorphism Indistinguishability, Multiplicity Automata Equivalence, and Polynomial Identity Testing

Authors: Marek Černý and Tim Seppelt

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

Abstract
Two graphs G and H are homomorphism indistinguishable over a graph class ℱ if they admit the same number of homomorphisms from every graph F ∈ ℱ. Many graph isomorphism relaxations such as (quantum) isomorphism and cospectrality can be characterised as homomorphism indistinguishability over specific graph classes. Thereby, the problems HomInd(ℱ) of deciding homomorphism indistinguishability over ℱ subsume diverse graph isomorphism relaxations whose complexities range from logspace to undecidable. Establishing the first general result on the complexity of HomInd(ℱ), Seppelt (MFCS 2024) showed that HomInd(ℱ) is in randomised polynomial time for every graph class ℱ of bounded treewidth that can be defined in counting monadic second-order logic CMSO₂. We show that this algorithm is conditionally optimal, i.e. it cannot be derandomised unless polynomial identity testing is in P. For CMSO₂-definable graph classes ℱ of bounded pathwidth, we improve the previous complexity upper bound for HomInd(ℱ) from P to C_ = L and show that this is tight. Secondarily, we establish a connection between homomorphism indistinguishability and multiplicity automata equivalence which allows us to pinpoint the complexity of the latter problem as C_ = L-complete.
Cite as

Marek Černý and Tim Seppelt. Homomorphism Indistinguishability, Multiplicity Automata Equivalence, and Polynomial Identity Testing. In 43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 364, pp. 25:1-25:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{cerny_et_al:LIPIcs.STACS.2026.25,
  author =	{\v{C}ern\'{y}, Marek and Seppelt, Tim},
  title =	{{Homomorphism Indistinguishability, Multiplicity Automata Equivalence, and Polynomial Identity Testing}},
  booktitle =	{43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026)},
  pages =	{25:1--25:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-412-3},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{364},
  editor =	{Mahajan, Meena and Manea, Florin and McIver, Annabelle and Thắng, Nguy\~{ê}n Kim},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.STACS.2026.25},
  URN =		{urn:nbn:de:0030-drops-255144},
  doi =		{10.4230/LIPIcs.STACS.2026.25},
  annote =	{Keywords: treewidth, Courcelle’s theorem, logspace, multiplicity automata, polynomial identity testing}
}
Document
DOI: 10.4230/LIPIcs.STACS.2026.41
On the Complexity of Computing Strahler Numbers

Authors: Moses Ganardi and Markus Lohrey

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

Abstract
It is shown that the problem of computing the Strahler number of a binary tree given as a term is complete for the circuit complexity class uniform NC¹. For several variants, where the binary tree is given by a pointer structure or in a succinct form by a directed acyclic graph or a tree straight-line program, the complexity of computing the Strahler number is determined as well. The problem, whether a given context-free grammar in Chomsky normal form produces a derivation tree (resp., an acyclic derivation tree), whose Strahler number is at least a given number k is shown to be P-complete (resp., PSPACE-complete).
Cite as

Moses Ganardi and Markus Lohrey. On the Complexity of Computing Strahler Numbers. In 43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 364, pp. 41:1-41:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{ganardi_et_al:LIPIcs.STACS.2026.41,
  author =	{Ganardi, Moses and Lohrey, Markus},
  title =	{{On the Complexity of Computing Strahler Numbers}},
  booktitle =	{43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026)},
  pages =	{41:1--41:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-412-3},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{364},
  editor =	{Mahajan, Meena and Manea, Florin and McIver, Annabelle and Thắng, Nguy\~{ê}n Kim},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.STACS.2026.41},
  URN =		{urn:nbn:de:0030-drops-255301},
  doi =		{10.4230/LIPIcs.STACS.2026.41},
  annote =	{Keywords: Strahler number, circuit complexity classes, context-free grammars}
}
Document
DOI: 10.4230/LIPIcs.ITCS.2026.43
Efficient Catalytic Graph Algorithms

Authors: James Cook and Edward Pyne

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

Abstract
We give fast, simple, and implementable catalytic logspace algorithms for two fundamental graph problems. First, a randomized catalytic algorithm for s → t connectivity running in Õ(nm) time, and a deterministic catalytic algorithm for the same running in Õ(n³ m) time. The former algorithm is the first algorithmic use of randomization in CL. The algorithm uses one register per vertex and repeatedly "pushes" values along the edges in the graph. Second, a deterministic catalytic algorithm for simulating random walks which in Õ(m T² / ε) time estimates the probability a T-step random walk ends at a given vertex within ε additive error. The algorithm uses one register for each vertex and increments it at each visit to ensure repeated visits follow different outgoing edges. Prior catalytic algorithms for both problems did not have explicit runtime bounds beyond being polynomial in n.
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James Cook and Edward Pyne. Efficient Catalytic Graph Algorithms. In 17th Innovations in Theoretical Computer Science Conference (ITCS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 362, pp. 43:1-43:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{cook_et_al:LIPIcs.ITCS.2026.43,
  author =	{Cook, James and Pyne, Edward},
  title =	{{Efficient Catalytic Graph Algorithms}},
  booktitle =	{17th Innovations in Theoretical Computer Science Conference (ITCS 2026)},
  pages =	{43:1--43:22},
  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.2026.43},
  URN =		{urn:nbn:de:0030-drops-253305},
  doi =		{10.4230/LIPIcs.ITCS.2026.43},
  annote =	{Keywords: catalytic computing, graph algorithms, catalytic logspace}
}
Document
DOI: 10.4230/LIPIcs.ITCS.2026.8
Intersection Theorems: A Potential Approach to Proof Complexity Lower Bounds

Authors: Yaroslav Alekseev and Nikita Gaevoy

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

Abstract
Recently, Göös et al. [Göös et al., 2024] showed that Res ⋏ uSA = RevRes in the following sense: if a formula φ has refutations of size at most s and width/degree at most w in both Res and uSA, then there is a refutation for φ of size at most poly(s ⋅ 2^w) in RevRes. Their proof relies on the TFNP characterization of the aforementioned proof systems. In our work, we give a direct and simplified proof of this result, simultaneously achieving better bounds: we show that if for a formula φ there are refutations of size at most s in both Res and uSA, then there is a refutation of φ of size at most poly(s) in RevRes. This potentially allows us to "lift" size lower bounds from RevRes to Res for the formulas for which there are upper bounds in uSA. This kind of lifting was not possible before because of the exponential blow-up in size from the width. Similarly, we improve the bounds in another intersection theorem from [Göös et al., 2024] by giving a direct proof of Res ⋏ uNS = RevResT. Finally, we generalize those intersection theorems to some proof systems for which we currently do not have a TFNP characterization. For example, we show that Res(⊕) ⋏ u-wRes(⊕) = RevRes(⊕), which effectively allows us to reduce the problem of proving Pigeonhole Principle lower bounds in Res(⊕) to proving Pigeonhole Principle lower bounds in RevRes(⊕), a potentially weaker proof system.
Cite as

Yaroslav Alekseev and Nikita Gaevoy. Intersection Theorems: A Potential Approach to Proof Complexity Lower Bounds. In 17th Innovations in Theoretical Computer Science Conference (ITCS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 362, pp. 8:1-8:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{alekseev_et_al:LIPIcs.ITCS.2026.8,
  author =	{Alekseev, Yaroslav and Gaevoy, Nikita},
  title =	{{Intersection Theorems: A Potential Approach to Proof Complexity Lower Bounds}},
  booktitle =	{17th Innovations in Theoretical Computer Science Conference (ITCS 2026)},
  pages =	{8:1--8:18},
  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.2026.8},
  URN =		{urn:nbn:de:0030-drops-252953},
  doi =		{10.4230/LIPIcs.ITCS.2026.8},
  annote =	{Keywords: proof complexity, intersection theorems}
}
Document
DOI: 10.4230/LIPIcs.ITCS.2026.60
Total Search Problems in ZPP

Authors: Noah Fleming, Stefan Grosser, Siddhartha Jain, Jiawei Li, Hanlin Ren, Morgan Shirley, and Weiqiang Yuan

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

Abstract
We initiate a systematic study of TFZPP, the class of total NP search problems solvable by polynomial time randomized algorithms. TFZPP contains a variety of important search problems such as Bertrand-Chebyshev (finding a prime between N and 2N), refuter problems for many circuit lower bounds, and Lossy-Code. The Lossy-Code problem has found prominence due to its fundamental connections to derandomization, catalytic computing, and the metamathematics of complexity theory, among other areas. While TFZPP collapses to FP under standard derandomization assumptions in the white-box setting, we are able to separate TFZPP from the major TFNP subclasses in the black-box setting. In fact, we are able to separate it from every uniform TFNP class assuming that NP is not in quasi-polynomial time. To do so, we extend the connection between proof complexity and black-box TFNP to randomized proof systems and randomized reductions. Next, we turn to developing a taxonomy of TFZPP problems. We highlight a problem called Nephew, originating from an infinity axiom in set theory. We show that Nephew is in PWPP∩ TFZPP and conjecture that it is not reducible to Lossy-Code. Intriguingly, except for some artificial examples, most other black-box TFZPP problems that we are aware of reduce to Lossy-Code: - We define a problem called Empty-Child capturing finding a leaf in a rooted (binary) tree, and show that this problem is equivalent to Lossy-Code. We also show that a variant of Empty-Child with "heights" is complete for the intersection of SOPL and Lossy-Code. - We strengthen Lossy-Code with several combinatorial inequalities such as the AM-GM inequality. Somewhat surprisingly, we show the resulting new problems are still reducible to Lossy-Code. A technical highlight of this result is that they are proved by formalizations in bounded arithmetic, specifically in Jeřábek’s theory APC₁ (JSL 2007). - Finally, we show that the Dense-Linear-Ordering problem reduces to Lossy-Code.
Cite as

Noah Fleming, Stefan Grosser, Siddhartha Jain, Jiawei Li, Hanlin Ren, Morgan Shirley, and Weiqiang Yuan. Total Search Problems in ZPP. In 17th Innovations in Theoretical Computer Science Conference (ITCS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 362, pp. 60:1-60:26, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{fleming_et_al:LIPIcs.ITCS.2026.60,
  author =	{Fleming, Noah and Grosser, Stefan and Jain, Siddhartha and Li, Jiawei and Ren, Hanlin and Shirley, Morgan and Yuan, Weiqiang},
  title =	{{Total Search Problems in ZPP}},
  booktitle =	{17th Innovations in Theoretical Computer Science Conference (ITCS 2026)},
  pages =	{60:1--60:26},
  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.2026.60},
  URN =		{urn:nbn:de:0030-drops-253473},
  doi =		{10.4230/LIPIcs.ITCS.2026.60},
  annote =	{Keywords: TFNP, lossy code, randomized proof systems, query complexity}
}
Document
DOI: 10.4230/LIPIcs.ITCS.2026.3
Linear Matroid Intersection Is in Catalytic Logspace

Authors: Aryan Agarwala, Yaroslav Alekseev, and Antoine Vinciguerra

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

Abstract
Linear matroid intersection is an important problem in combinatorial optimization. Given two linear matroids over the same ground set, the linear matroid intersection problem asks you to find a common independent set of maximum size. The deep interest in linear matroid intersection is due to the fact that it generalises many classical problems in theoretical computer science, such as bipartite matching, edge disjoint spanning trees, rainbow spanning tree, and many more. We study this problem in the model of catalytic computation: space-bounded machines are granted access to catalytic space, which is additional working memory that is full with arbitrary data that must be preserved at the end of its computation. Although linear matroid intersection has had a polynomial time algorithm for over 50 years, it remains an important open problem to show that linear matroid intersection belongs to any well studied subclass of {P}. We address this problem for the class catalytic logspace (CL) with a polynomial time bound (CLP). Recently, Agarwala and Mertz (2025) showed that bipartite maximum matching can be computed in the class CLP ⊆ {P}. This was the first subclass of {P} shown to contain bipartite matching, and additionally the first problem outside TC¹ shown to be contained in CL. We significantly improve the result of Agarwala and Mertz by showing that linear matroid intersection can be computed in CLP.
Cite as

Aryan Agarwala, Yaroslav Alekseev, and Antoine Vinciguerra. Linear Matroid Intersection Is in Catalytic Logspace. In 17th Innovations in Theoretical Computer Science Conference (ITCS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 362, pp. 3:1-3:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{agarwala_et_al:LIPIcs.ITCS.2026.3,
  author =	{Agarwala, Aryan and Alekseev, Yaroslav and Vinciguerra, Antoine},
  title =	{{Linear Matroid Intersection Is in Catalytic Logspace}},
  booktitle =	{17th Innovations in Theoretical Computer Science Conference (ITCS 2026)},
  pages =	{3:1--3:23},
  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.2026.3},
  URN =		{urn:nbn:de:0030-drops-252908},
  doi =		{10.4230/LIPIcs.ITCS.2026.3},
  annote =	{Keywords: Catalytic Computing, Computational Complexity, Matroid Theory, Algorithms}
}
Document
PACE Solver Description
DOI: 10.4230/LIPIcs.IPEC.2025.37
PACE Solver Description: Minimum Hitting Set Computation via Core-Guided MaxSAT Solving

Authors: André Schidler

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

Abstract
This paper describes our hybrid MaxSAT and mixed integer programming approach for finding minimum hitting sets as submitted to the 2025 PACE challenge. We also discuss hitting set specific challenges, lower bounds, preprocessing and design choices.
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André Schidler. PACE Solver Description: Minimum Hitting Set Computation via Core-Guided MaxSAT Solving. In 20th International Symposium on Parameterized and Exact Computation (IPEC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 358, pp. 37:1-37:4, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{schidler:LIPIcs.IPEC.2025.37,
  author =	{Schidler, Andr\'{e}},
  title =	{{PACE Solver Description: Minimum Hitting Set Computation via Core-Guided MaxSAT Solving}},
  booktitle =	{20th International Symposium on Parameterized and Exact Computation (IPEC 2025)},
  pages =	{37:1--37:4},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-407-9},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{358},
  editor =	{Agrawal, Akanksha and van Leeuwen, Erik Jan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.IPEC.2025.37},
  URN =		{urn:nbn:de:0030-drops-251692},
  doi =		{10.4230/LIPIcs.IPEC.2025.37},
  annote =	{Keywords: hitting set, maxsat, core-guided}
}
Document
DOI: 10.4230/LIPIcs.ISAAC.2025.15
Parameterized Complexity of Directed Traveling Salesman Problem

Authors: Václav Blažej, Andreas Emil Feldmann, Foivos Fioravantes, Paweł Rzążewski, and Ondřej Suchý

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

Abstract
The Directed Traveling Salesman Problem (DTSP) is a variant of the classical Traveling Salesman Problem in which the edges in the graph are directed and a vertex and edge can be visited multiple times. The goal is to find a directed closed walk of minimum length (or total weight) that visits every vertex of the given graph at least once. In a yet more general version, Directed Waypoint Routing Problem (DWRP), some vertices are marked as terminals and we are only required to visit all terminals. Furthermore, each edge has its capacity bounding the number of times this edge can be used by a solution. While both problems (and many other variants of TSP) were extensively investigated, mostly from the approximation point of view, there are surprisingly few results concerning the parameterized complexity. Our starting point is the result of Marx et al. [APPROX/RANDOM 2016] who proved that DTSP is W[1]-hard parameterized by distance to pathwidth 3. In this paper we aim to initiate the systematic complexity study of variants of Directed Traveling Salesman Problem with respect to various, mostly structural, parameters. We show that DWRP is FPT parameterized by the solution size, the feedback edge number and the vertex integrity of the underlying undirected graph. Furthermore, the problem is XP parameterized by treewidth. On the complexity side, we show that the problem is W[1]-hard parameterized by the distance to constant treedepth.
Cite as

Václav Blažej, Andreas Emil Feldmann, Foivos Fioravantes, Paweł Rzążewski, and Ondřej Suchý. Parameterized Complexity of Directed Traveling Salesman Problem. In 36th International Symposium on Algorithms and Computation (ISAAC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 359, pp. 15:1-15:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{blazej_et_al:LIPIcs.ISAAC.2025.15,
  author =	{Bla\v{z}ej, V\'{a}clav and Feldmann, Andreas Emil and Fioravantes, Foivos and Rz\k{a}\.{z}ewski, Pawe{\l} and Such\'{y}, Ond\v{r}ej},
  title =	{{Parameterized Complexity of Directed Traveling Salesman Problem}},
  booktitle =	{36th International Symposium on Algorithms and Computation (ISAAC 2025)},
  pages =	{15:1--15:18},
  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.2025.15},
  URN =		{urn:nbn:de:0030-drops-249231},
  doi =		{10.4230/LIPIcs.ISAAC.2025.15},
  annote =	{Keywords: Directed TSP, parameterized complexity, vertex integrity, treedepth}
}
Document
DOI: 10.4230/LIPIcs.ESA.2025.34
On the Approximability of Train Routing and the Min-Max Disjoint Paths Problem

Authors: Umang Bhaskar, Katharina Eickhoff, Lennart Kauther, Jannik Matuschke, Britta Peis, and Laura Vargas Koch

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

Abstract
In train routing, the headway is the minimum distance that must be maintained between successive trains for safety and robustness. We introduce a model for train routing that requires a fixed headway to be maintained between trains, and study the problem of minimizing the makespan, i.e., the arrival time of the last train, in a single-source single-sink network. For this problem, we first show that there exists an optimal solution where trains move in convoys - that is, the optimal paths for any two trains are either the same or are arc-disjoint. Via this insight, we are able to reduce the approximability of our train routing problem to that of the min-max disjoint paths problem, which asks for a collection of disjoint paths where the maximum length of any path in the collection is as small as possible. While min-max disjoint paths inherits a strong inapproximability result on directed acyclic graphs from the multi-level bottleneck assignment problem, we show that a natural greedy composition approach yields a logarithmic approximation in the number of disjoint paths for series-parallel graphs. We also present an alternative analysis of this approach that yields a guarantee depending on how often the decomposition tree of the series-parallel graph alternates between series and parallel compositions on any root-leaf path.
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Umang Bhaskar, Katharina Eickhoff, Lennart Kauther, Jannik Matuschke, Britta Peis, and Laura Vargas Koch. On the Approximability of Train Routing and the Min-Max Disjoint Paths Problem. In 33rd Annual European Symposium on Algorithms (ESA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 351, pp. 34:1-34:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{bhaskar_et_al:LIPIcs.ESA.2025.34,
  author =	{Bhaskar, Umang and Eickhoff, Katharina and Kauther, Lennart and Matuschke, Jannik and Peis, Britta and Vargas Koch, Laura},
  title =	{{On the Approximability of Train Routing and the Min-Max Disjoint Paths Problem}},
  booktitle =	{33rd Annual European Symposium on Algorithms (ESA 2025)},
  pages =	{34:1--34:15},
  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.2025.34},
  URN =		{urn:nbn:de:0030-drops-245029},
  doi =		{10.4230/LIPIcs.ESA.2025.34},
  annote =	{Keywords: Train Routing, Scheduling, Approximation Algorithms, Flows over Time, Min-Max Disjoint Paths}
}
Document
DOI: 10.4230/LIPIcs.TQC.2025.11
Quantum Catalytic Space

Authors: Harry Buhrman, Marten Folkertsma, Ian Mertz, Florian Speelman, Sergii Strelchuk, Sathyawageeswar Subramanian, and Quinten Tupker

Published in: LIPIcs, Volume 350, 20th Conference on the Theory of Quantum Computation, Communication and Cryptography (TQC 2025)

Abstract
Space complexity is a key field of study in theoretical computer science. In the quantum setting there are clear motivations to understand the power of space-restricted computation, as qubits are an especially precious and limited resource. Recently, a new branch of space-bounded complexity called catalytic computing has shown that reusing space is a very powerful computational resource, especially for subroutines that incur little to no space overhead. While quantum catalysis in an information theoretic context, and the power of "dirty" qubits for quantum computation, has been studied over the years, these models are generally not suitable for use in quantum space-bounded algorithms, as they either rely on specific catalytic states or destroy the memory being borrowed. We define the notion of catalytic computing in the quantum setting and show a number of initial results about the model. First, we show that quantum catalytic logspace can always be computed quantumly in polynomial time; the classical analogue of this is the largest open question in catalytic computing. This also allows quantum catalytic space to be defined in an equivalent way with respect to circuits instead of Turing machines. We also prove that quantum catalytic logspace can simulate log-depth threshold circuits, a class which is known to contain (and believed to strictly contain) quantum logspace, thus showcasing the power of quantum catalytic space. Finally we show that both unitary quantum catalytic logspace and classical catalytic logspace can be simulated in the one-clean qubit model.
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Harry Buhrman, Marten Folkertsma, Ian Mertz, Florian Speelman, Sergii Strelchuk, Sathyawageeswar Subramanian, and Quinten Tupker. Quantum Catalytic Space. In 20th Conference on the Theory of Quantum Computation, Communication and Cryptography (TQC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 350, pp. 11:1-11:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{buhrman_et_al:LIPIcs.TQC.2025.11,
  author =	{Buhrman, Harry and Folkertsma, Marten and Mertz, Ian and Speelman, Florian and Strelchuk, Sergii and Subramanian, Sathyawageeswar and Tupker, Quinten},
  title =	{{Quantum Catalytic Space}},
  booktitle =	{20th Conference on the Theory of Quantum Computation, Communication and Cryptography (TQC 2025)},
  pages =	{11:1--11:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-392-8},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{350},
  editor =	{Fefferman, Bill},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.TQC.2025.11},
  URN =		{urn:nbn:de:0030-drops-240606},
  doi =		{10.4230/LIPIcs.TQC.2025.11},
  annote =	{Keywords: quantum computing, quantum complexity, space-bounded algorithms, catalytic computation, one clean qubit}
}
Document
DOI: 10.4230/LIPIcs.MFCS.2025.6
Catalytic Computing and Register Programs Beyond Log-Depth

Authors: Yaroslav Alekseev, Yuval Filmus, Ian Mertz, Alexander Smal, and Antoine Vinciguerra

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

Abstract
In a seminal work, Buhrman et al. (STOC 2014) defined the class CSPACE(s,c) of problems solvable in space s with an additional catalytic tape of size c, which is a tape whose initial content must be restored at the end of the computation. They showed that uniform TC¹ circuits are computable in catalytic logspace, i.e., CL = CSPACE(O(log{n}), 2^{O(log{n})}), thus giving strong evidence that catalytic space gives L strict additional power. Their study focuses on an arithmetic model called register programs, which has been a focal point in development since then. Understanding CL remains a major open problem, as TC¹ remains the most powerful containment to date. In this work, we study the power of catalytic space and register programs to compute circuits of larger depth. Using register programs, we show that for every ε > 0, SAC² ⊆ CSPACE (O((log²n)/(log log n)), 2^{O(log^{1+ε} n)}) . On the other hand, we know that SAC² ⊆ TC² ⊆ CSPACE(O(log²{n}) , 2^{O(log{n})}). Our result thus shows an O(log log n) factor improvement on the free space needed to compute SAC², at the expense of a nearly-polynomial-sized catalytic tape. We also exhibit non-trivial register programs for matrix powering, which is a further step towards showing NC² ⊆ CL.
Cite as

Yaroslav Alekseev, Yuval Filmus, Ian Mertz, Alexander Smal, and Antoine Vinciguerra. Catalytic Computing and Register Programs Beyond Log-Depth. In 50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 345, pp. 6:1-6:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{alekseev_et_al:LIPIcs.MFCS.2025.6,
  author =	{Alekseev, Yaroslav and Filmus, Yuval and Mertz, Ian and Smal, Alexander and Vinciguerra, Antoine},
  title =	{{Catalytic Computing and Register Programs Beyond Log-Depth}},
  booktitle =	{50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025)},
  pages =	{6:1--6:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-388-1},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{345},
  editor =	{Gawrychowski, Pawe{\l} and Mazowiecki, Filip and Skrzypczak, Micha{\l}},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2025.6},
  URN =		{urn:nbn:de:0030-drops-241136},
  doi =		{10.4230/LIPIcs.MFCS.2025.6},
  annote =	{Keywords: catalytic computing, circuit classes, polynomial method}
}
Document
DOI: 10.4230/LIPIcs.DNA.31.2
A Coupled Reconfiguration Mechanism That Enables Powerful, Pseudoknot-Robust DNA Strand Displacement Devices with 2-Stranded Inputs

Authors: Hope Amber Johnson and Anne Condon

Published in: LIPIcs, Volume 347, 31st International Conference on DNA Computing and Molecular Programming (DNA 31) (2025)

Abstract
DNA strand displacement, a collective name for certain behaviors of short strands of DNA, has been used to build many interesting molecular devices over the past few decades. Among those devices are general implementation schemes for Chemical Reaction Networks, suggesting a place in an abstraction hierarchy for complex molecular programming. However, the possibilities of DNA strand displacement are far from fully explored. On a theoretical level, most DNA strand displacement systems are built out of a few simple motifs, with the space of possible motifs otherwise unexplored. On a practical level, the desire for general, large-scale DNA strand displacement systems is not fulfilled. Those systems that are scalable are not general, and those that are general don't scale up well. We have recently been exploring the space of possibilities for DNA strand displacement systems where all input complexes are made out of at most two strands of DNA. As a test case, we've had an open question of whether such systems can implement general Chemical Reaction Networks, in a way that has a certain set of other desirable properties - reversible, systematic, O(1) toeholds, bimolecular reactions, and correct according to CRN bisimulation - that the state-of-the-art implementations with more than 2-stranded inputs have. Until now we've had a few results that have all but one of those desirable properties, including one based on a novel mechanism we called coupled reconfiguration, but that depended on the physically questionable assumption that pseudoknots cannot occur. We wondered whether the same type of mechanism could be done in a pseudoknot-robust way. In this work we show that in fact, coupled reconfiguration can be done in a pseudoknot-robust way, and this mechanism can implement general Chemical Reaction Networks with all inputs being single strands of DNA. Going further, the same motifs used in this mechanism can implement stacks and surface-based bimolecular reactions. Those have been previously studied as part of polymer extensions of the Chemical Reaction Network model, and on an abstract model level, the resulting extensions are Turing-complete in ways the base Chemical Reaction Network model is not. Our mechanisms are significantly different from previously tested DNA strand displacement systems, which raises questions about their ability to be implemented experimentally, but we have some reasons to believe the challenges are solvable. So we present the pseudoknot-robust coupled reconfiguration mechanism and its use for general Chemical Reaction Network implementations; we present the extensions of the mechanism to stack and surface reactions; and we discuss the possible obstacles and solutions to experimental implementation, as well as the theoretical implications of this mechanism.
Cite as

Hope Amber Johnson and Anne Condon. A Coupled Reconfiguration Mechanism That Enables Powerful, Pseudoknot-Robust DNA Strand Displacement Devices with 2-Stranded Inputs. In 31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 2:1-2:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{johnson_et_al:LIPIcs.DNA.31.2,
  author =	{Johnson, Hope Amber and Condon, Anne},
  title =	{{A Coupled Reconfiguration Mechanism That Enables Powerful, Pseudoknot-Robust DNA Strand Displacement Devices with 2-Stranded Inputs}},
  booktitle =	{31st International Conference on DNA Computing and Molecular Programming (DNA 31)},
  pages =	{2:1--2:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-399-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{347},
  editor =	{Schaeffer, Josie and Zhang, Fei},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.31.2},
  URN =		{urn:nbn:de:0030-drops-238514},
  doi =		{10.4230/LIPIcs.DNA.31.2},
  annote =	{Keywords: Molecular programming, DNA strand displacement, Chemical Reaction Networks}
}
Document
DOI: 10.4230/LIPIcs.DNA.31.9
Synchronous Versus Asynchronous Tile-Based Self-Assembly

Authors: Florent Becker, Phillip Drake, Matthew J. Patitz, and Trent A. Rogers

Published in: LIPIcs, Volume 347, 31st International Conference on DNA Computing and Molecular Programming (DNA 31) (2025)

Abstract
In this paper we study the relationship between mathematical models of tile-based self-assembly which differ in terms of the synchronicity of tile additions. In the standard abstract Tile Assembly Model (aTAM), each step of assembly consists of a single tile being added to an assembly. At any given time, each location on the perimeter of an assembly to which a tile can legally bind is called a frontier location, and for each step of assembly one frontier location is randomly selected and a tile is added. In the Synchronous Tile Assembly Model (syncTAM), at each step of assembly every frontier location simultaneously receives a tile. Our results show that while directed, non-cooperative syncTAM systems are capable of universal computation (while directed, non-cooperative aTAM systems are known not to be), and they are capable of building shapes that can't be built within the aTAM, the non-cooperative aTAM is also capable of building shapes that can't be built within the syncTAM even cooperatively. We show a variety of results that demonstrate the similarities and differences between these two models.
Cite as

Florent Becker, Phillip Drake, Matthew J. Patitz, and Trent A. Rogers. Synchronous Versus Asynchronous Tile-Based Self-Assembly. In 31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 9:1-9:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{becker_et_al:LIPIcs.DNA.31.9,
  author =	{Becker, Florent and Drake, Phillip and Patitz, Matthew J. and Rogers, Trent A.},
  title =	{{Synchronous Versus Asynchronous Tile-Based Self-Assembly}},
  booktitle =	{31st International Conference on DNA Computing and Molecular Programming (DNA 31)},
  pages =	{9:1--9:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-399-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{347},
  editor =	{Schaeffer, Josie and Zhang, Fei},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.31.9},
  URN =		{urn:nbn:de:0030-drops-238580},
  doi =		{10.4230/LIPIcs.DNA.31.9},
  annote =	{Keywords: self-assembly, noncooperative self-assembly, models of computation, tile assembly systems}
}
Document
DOI: 10.4230/LIPIcs.WABI.2025.10
DiVerG: Scalable Distance Index for Validation of Paired-End Alignments in Sequence Graphs

Authors: Ali Ghaffaari, Alexander Schönhuth, and Tobias Marschall

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

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

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

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@InProceedings{ghaffaari_et_al:LIPIcs.WABI.2025.10,
  author =	{Ghaffaari, Ali and Sch\"{o}nhuth, Alexander and Marschall, Tobias},
  title =	{{DiVerG: Scalable Distance Index for Validation of Paired-End Alignments in Sequence Graphs}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{10:1--10:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-386-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{344},
  editor =	{Brejov\'{a}, Bro\v{n}a and Patro, Rob},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2025.10},
  URN =		{urn:nbn:de:0030-drops-239369},
  doi =		{10.4230/LIPIcs.WABI.2025.10},
  annote =	{Keywords: Sequence graph, distance index, read mapping, sparse matrix}
}
Document
DOI: 10.4230/LIPIcs.WABI.2025.14
Human Readable Compression of GFA Paths Using Grammar-Based Code

Authors: Peter Heringer and Daniel Doerr

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

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

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@InProceedings{heringer_et_al:LIPIcs.WABI.2025.14,
  author =	{Heringer, Peter and Doerr, Daniel},
  title =	{{Human Readable Compression of GFA Paths Using Grammar-Based Code}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{14:1--14:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-386-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{344},
  editor =	{Brejov\'{a}, Bro\v{n}a and Patro, Rob},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2025.14},
  URN =		{urn:nbn:de:0030-drops-239395},
  doi =		{10.4230/LIPIcs.WABI.2025.14},
  annote =	{Keywords: pangenomics, pangenome graphs, compression, grammar-based code, byte pair encoding}
}
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