30 Search Results for "Cooper, Martin C."

Document
DOI: 10.4230/LIPIcs.STACS.2026.15
The Complexity of Resilience for Digraph Queries

Authors: Manuel Bodirsky and Žaneta Semanišinová

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

Abstract
We prove a complexity dichotomy for the resilience problem for unions of conjunctive digraph queries (i.e., for existential positive sentences over the signature {R} of directed graphs). Specifically, for every union μ of conjunctive digraph queries, the following problem is in P or NP-complete: given a directed multigraph G and a natural number u, can we remove u edges from G so that G ⊧ ¬ μ? In fact, we verify a more general dichotomy conjecture from [Bodirsky et al., 2024] for all resilience problems in the special case of directed graphs, and show that for such unions of queries μ there exists a countably infinite (`dual') valued structure Δ_μ which either primitively positively constructs 1-in-3-3-SAT, and hence the resilience problem for μ is NP-complete by general principles, or has a pseudo cyclic canonical fractional polymorphism, and the resilience problem for μ is in P.
Cite as

Manuel Bodirsky and Žaneta Semanišinová. The Complexity of Resilience for Digraph Queries. In 43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 364, pp. 15:1-15:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{bodirsky_et_al:LIPIcs.STACS.2026.15,
  author =	{Bodirsky, Manuel and Semani\v{s}inov\'{a}, \v{Z}aneta},
  title =	{{The Complexity of Resilience for Digraph Queries}},
  booktitle =	{43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026)},
  pages =	{15:1--15:20},
  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.2026.15},
  URN =		{urn:nbn:de:0030-drops-255045},
  doi =		{10.4230/LIPIcs.STACS.2026.15},
  annote =	{Keywords: valued constraints, unions of conjunctive queries, resilience, computational complexity, pp-constructions}
}
Document
DOI: 10.4230/LIPIcs.STACS.2026.59
When Is Local Search Both Effective and Efficient?

Authors: Artem Kaznatcheev and Sofia Vazquez Alferez

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

Abstract
Combinatorial optimization problems implicitly define fitness landscapes that combine the numeric structure of the "fitness" function to be maximized with the combinatorial structure of which assignments are "adjacent". Local search starts at an assignment in this landscape and successively moves assignments until no further improvement is possible among the adjacent assignments. Classic analyses of local search algorithms have focused more on the question of effectiveness ("did we find a good solution?") and often implicitly assumed that there are no doubts about their efficiency ("did we find it quickly?"). But there are many reasons to doubt the efficiency of local search. Even if we focus on fitness landscapes on the hypercube that are single peaked on every subcube (known as semismooth fitness landscapes, completely unimodal pseudo-Boolean functions, or acyclic unique sink orientations) where effectiveness is obvious, many local search algorithms are known to be inefficient. Since fitness landscapes are unwieldy exponentially large objects, we focus on their polynomial-sized representations by instances of valued constraint satisfaction problems (VCSP). We define a "direction" for valued constraints such that directed VCSPs generate semismooth fitness landscapes. We call directed VCSPs oriented if they do not have any pair of variables with arcs in both directions. Since recognizing if a VCSP-instance is directed or oriented is coNP-complete, we generalized oriented VCSPs as conditionally-smooth fitness landscapes where the structural property of "conditionally-smooth" is recognizable in polynomial time for a VCSP-instance. We prove that many popular local search algorithms like random ascent, simulated annealing, history-based rules, jumping rules, and the Kernighan-Lin heuristic are very efficient on conditionally-smooth landscapes. But conditionally-smooth landscapes are still expressive enough so that other well-regarded local search algorithms like steepest ascent and random facet require a super-polynomial number of steps to find the fitness peak.
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Artem Kaznatcheev and Sofia Vazquez Alferez. When Is Local Search Both Effective and Efficient?. In 43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 364, pp. 59:1-59:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{kaznatcheev_et_al:LIPIcs.STACS.2026.59,
  author =	{Kaznatcheev, Artem and Vazquez Alferez, Sofia},
  title =	{{When Is Local Search Both Effective and Efficient?}},
  booktitle =	{43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026)},
  pages =	{59:1--59:19},
  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.2026.59},
  URN =		{urn:nbn:de:0030-drops-255480},
  doi =		{10.4230/LIPIcs.STACS.2026.59},
  annote =	{Keywords: valued constraint satisfaction problem, local search, algorithm analysis, constraint graphs, pseudo-Boolean functions, parameterized complexity}
}
Document
Invited Talk
DOI: 10.4230/LIPIcs.IPEC.2025.1
A Brief History of Parameterized Algorithms for Block-Structured Integer Programs (Invited Talk)

Authors: Martin Koutecký

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

Abstract
Integer Programming (IP) is a fundamental but computationally hard problem. Still, certain efficiently solvable subclasses have been identified over time, most notably totally unimodular IPs in the 1950s, and fixed-dimension IPs in the 1980s. Starting around the year 2000, a stream of research has identified block-structured IPs as yet another tractable subclass. In this paper, we give a brief and incomplete review of this history, with a focus on several of the author’s contributions.
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Martin Koutecký. A Brief History of Parameterized Algorithms for Block-Structured Integer Programs (Invited Talk). In 20th International Symposium on Parameterized and Exact Computation (IPEC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 358, pp. 1:1-1:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{koutecky:LIPIcs.IPEC.2025.1,
  author =	{Kouteck\'{y}, Martin},
  title =	{{A Brief History of Parameterized Algorithms for Block-Structured Integer Programs}},
  booktitle =	{20th International Symposium on Parameterized and Exact Computation (IPEC 2025)},
  pages =	{1:1--1:20},
  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.2025.1},
  URN =		{urn:nbn:de:0030-drops-251338},
  doi =		{10.4230/LIPIcs.IPEC.2025.1},
  annote =	{Keywords: Integer Programming, Parameterized Algorithm, Graver Basis, Treedepth, n-fold, tree-fold, 2-stage stochastic, multistage stochastic, Mixed-Integer Programming}
}
Document
DOI: 10.4230/LIPIcs.FSTTCS.2025.21
Overlay Network Construction: Improved Overall and Node-Wise Message Complexity

Authors: Yi-Jun Chang, Yanyu Chen, and Gopinath Mishra

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

Abstract
We consider the problem of constructing distributed overlay networks, where nodes in a reconfigurable system can create or sever connections with nodes whose identifiers they know. Initially, each node knows only its own and its neighbors' identifiers, forming a local channel, while the evolving structure is termed the global channel. The goal is to reconfigure any connected graph into a desired topology, such as a bounded-degree expander graph or a well-formed tree (WFT) with a constant maximum degree and logarithmic diameter, minimizing the total number of rounds and message complexity. This problem mirrors real-world peer-to-peer network construction, where creating robust and efficient systems is desired. We study the overlay reconstruction problem in a network of n nodes in two models: GOSSIP-reply and HYBRID. In the GOSSIP-reply model, each node can send a message and receive a corresponding reply message in one round. In the HYBRID model, a node can send O(1) messages to each neighbor in the local channel and a total of O(log n) messages in the global channel. In both models, we propose protocols for WFT construction with O (n log n) message complexities using messages of O(log n) bits. In the GOSSIP-reply model, our protocol takes O(log n) rounds while in the HYBRID model, our protocol takes O(log² n) rounds. Both protocols use O (n log² n) bits of communication. We obtain improved bounds over prior work: GOSSIP-reply: A recent result by Dufoulon et al. (ITCS 2024) achieved O(log⁵ n) round complexity and O (n log⁵ n) message complexity using messages of at least Ω(log² n) bits in GOSSIP-reply. With messages of size O(log n), our protocol achieves an optimal round complexity of O(log n) and an improved message complexity of O(n log n). HYBRID: Götte et al. (Distributed Computing 2023) showed an optimal O(log n)-round algorithm with O(log² n) global messages per round which incurs a message complexity of Ω(m), where m is the number of edges in the initial topology. At the cost of increasing the round complexity to O(log² n) while using only O(log n) messages globally, our protocol achieves a message complexity that is independent of m. Our approach ensures that the total number of messages for node v, with degree deg(v) in the initial topology, is bounded by O(deg(v) + log n), while the algorithm of Götte et al. requires O(deg(v) + (log⁴ n)/(log log n)) messages per node.
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Yi-Jun Chang, Yanyu Chen, and Gopinath Mishra. Overlay Network Construction: Improved Overall and Node-Wise Message Complexity. 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. 21:1-21:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{chang_et_al:LIPIcs.FSTTCS.2025.21,
  author =	{Chang, Yi-Jun and Chen, Yanyu and Mishra, Gopinath},
  title =	{{Overlay Network Construction: Improved Overall and Node-Wise Message Complexity}},
  booktitle =	{45th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2025)},
  pages =	{21:1--21:21},
  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.2025.21},
  URN =		{urn:nbn:de:0030-drops-251025},
  doi =		{10.4230/LIPIcs.FSTTCS.2025.21},
  annote =	{Keywords: Distributed algorithms, Overlay networks, Expander graphs}
}
Document
DOI: 10.4230/LIPIcs.GD.2025.21
On Geometric Bipartite Graphs with Asymptotically Smallest Zarankiewicz Numbers

Authors: Parinya Chalermsook, Ly Orgo, and Minoo Zarsav

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

Abstract
This paper considers the Zarankiewicz problem in bipartite graphs with low-dimensional geometric representation (i.e., low Ferrers dimension). Let Z(n;k) be the maximum number of edges in a bipartite graph with n nodes and is free of a k-by-k biclique. Note that Z(n;k) ∈ Ω(nk) for all "natural" graph classes. Our first result reveals a separation between bipartite graphs of Ferrers dimension three and four: while we show that Z(n;k) ≤ 9n(k-1) for graphs of Ferrers dimension three, Z(n;k) ∈ Ω(n k ⋅ (log n)/(log log n)) for Ferrers dimension four graphs (Chan & Har-Peled, 2023) (Chazelle, 1990). To complement this, we derive a tight upper bound of 2n(k-1) for chordal bipartite graphs and 54n(k-1) for grid intersection graphs (GIG), a prominent graph class residing in four Ferrers dimensions and capturing planar bipartite graphs as well as bipartite intersection graphs of rectangles. Previously, the best-known bound for GIG was Z(n;k) ∈ O(2^{O(k)} n), implied by the results of Fox & Pach (2006) and Mustafa & Pach (2016). Our results advance and offer new insights into the interplay between Ferrers dimensions and extremal combinatorics.
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Parinya Chalermsook, Ly Orgo, and Minoo Zarsav. On Geometric Bipartite Graphs with Asymptotically Smallest Zarankiewicz Numbers. In 33rd International Symposium on Graph Drawing and Network Visualization (GD 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 357, pp. 21:1-21:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{chalermsook_et_al:LIPIcs.GD.2025.21,
  author =	{Chalermsook, Parinya and Orgo, Ly and Zarsav, Minoo},
  title =	{{On Geometric Bipartite Graphs with Asymptotically Smallest Zarankiewicz Numbers}},
  booktitle =	{33rd International Symposium on Graph Drawing and Network Visualization (GD 2025)},
  pages =	{21:1--21:24},
  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.2025.21},
  URN =		{urn:nbn:de:0030-drops-250074},
  doi =		{10.4230/LIPIcs.GD.2025.21},
  annote =	{Keywords: Bipartite graph classes, extremal graph theory, geometric intersection graphs, Zarankiewicz problem, bicliques}
}
Document
APPROX
DOI: 10.4230/LIPIcs.APPROX/RANDOM.2025.19
On the Constant-Factor Approximability of Minimum Cost Constraint Satisfaction Problems

Authors: Ian DeHaan, Neng Huang, and Euiwoong Lee

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

Abstract
We study minimum cost constraint satisfaction problems (MinCostCSP) through the algebraic lens. We show that for any constraint language Γ which has the dual discriminator operation as a polymorphism, there exists a |D|-approximation algorithm for MinCostCSP(Γ) where D is the domain. Complementing our algorithmic result, we show that any constraint language Γ where MinCostCSP(Γ) admits a constant-factor approximation must have a near-unanimity (NU) polymorphism unless P = NP, extending a similar result by Dalmau et al. on MinCSPs. These results imply a dichotomy of constant-factor approximability for constraint languages that contain all permutation relations (a natural generalization for Boolean CSPs that allow variable negation): either MinCostCSP(Γ) has an NU polymorphism and is |D|-approximable, or it does not have any NU polymorphism and is NP-hard to approximate within any constant factor. Finally, we present a constraint language which has a majority polymorphism, but is nonetheless NP-hard to approximate within any constant factor assuming the Unique Games Conjecture, showing that the condition of having an NU polymorphism is in general not sufficient unless UGC fails.
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Ian DeHaan, Neng Huang, and Euiwoong Lee. On the Constant-Factor Approximability of Minimum Cost Constraint Satisfaction Problems. In Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 353, pp. 19:1-19:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{dehaan_et_al:LIPIcs.APPROX/RANDOM.2025.19,
  author =	{DeHaan, Ian and Huang, Neng and Lee, Euiwoong},
  title =	{{On the Constant-Factor Approximability of Minimum Cost Constraint Satisfaction Problems}},
  booktitle =	{Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025)},
  pages =	{19:1--19:24},
  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.2025.19},
  URN =		{urn:nbn:de:0030-drops-243851},
  doi =		{10.4230/LIPIcs.APPROX/RANDOM.2025.19},
  annote =	{Keywords: Constraint satisfaction problems, approximation algorithms, polymorphisms}
}
Document
DOI: 10.4230/LIPIcs.MFCS.2025.24
Temporal Valued Constraint Satisfaction Problems

Authors: Manuel Bodirsky, Édouard Bonnet, and Žaneta Semanišinová

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

Abstract
We study the computational complexity of the valued constraint satisfaction problem (VCSP) for every valued structure over ℚ that is preserved by all order-preserving bijections. Such VCSPs will be called temporal, in analogy to the (classical) constraint satisfaction problem: a relational structure is preserved by all order-preserving bijections if and only if all its relations have a first-order definition in (ℚ; <), and the CSPs for such structures are called temporal CSPs. Many optimization problems that have been studied intensively in the literature can be phrased as a temporal VCSP. We prove that a temporal VCSP is in P, or NP-complete. Our analysis uses the concept of fractional polymorphisms. This is the first dichotomy result for VCSPs over infinite domains which is complete in the sense that it treats all valued structures that contain a given automorphism group.
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Manuel Bodirsky, Édouard Bonnet, and Žaneta Semanišinová. Temporal Valued Constraint Satisfaction Problems. In 50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 345, pp. 24:1-24:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{bodirsky_et_al:LIPIcs.MFCS.2025.24,
  author =	{Bodirsky, Manuel and Bonnet, \'{E}douard and Semani\v{s}inov\'{a}, \v{Z}aneta},
  title =	{{Temporal Valued Constraint Satisfaction Problems}},
  booktitle =	{50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025)},
  pages =	{24:1--24:19},
  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.2025.24},
  URN =		{urn:nbn:de:0030-drops-241311},
  doi =		{10.4230/LIPIcs.MFCS.2025.24},
  annote =	{Keywords: Constraint Satisfaction Problems, valued CSPs, temporal CSPs, fractional polymorphisms, complexity dichotomy, min CSPs}
}
Document
DOI: 10.4230/LIPIcs.CONCUR.2025.12
The Non-Cooperative Rational Synthesis Problem for SPEs and ω-Regular Objectives

Authors: Véronique Bruyère, Jean-François Raskin, Alexis Reynouard, and Marie Van Den Bogaard

Published in: LIPIcs, Volume 348, 36th International Conference on Concurrency Theory (CONCUR 2025)

Abstract
This paper studies the rational synthesis problem for multi-player games played on graphs when rational players are following subgame perfect equilibria. In these games, one player, the system, declares his strategy upfront, and the other players, composing the environment, then rationally respond by playing strategies forming a subgame perfect equilibrium. We study the complexity of the rational synthesis problem when the players have ω-regular objectives encoded as parity objectives. Our algorithm is based on an encoding into a three-player game with imperfect information, showing that the problem is in 2ExpTime. When the number of environment players is fixed, the problem is in ExpTime and is NP- and coNP-hard. Moreover, for a fixed number of players and reachability objectives, we get a polynomial algorithm.
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Véronique Bruyère, Jean-François Raskin, Alexis Reynouard, and Marie Van Den Bogaard. The Non-Cooperative Rational Synthesis Problem for SPEs and ω-Regular Objectives. In 36th International Conference on Concurrency Theory (CONCUR 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 348, pp. 12:1-12:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{bruyere_et_al:LIPIcs.CONCUR.2025.12,
  author =	{Bruy\`{e}re, V\'{e}ronique and Raskin, Jean-Fran\c{c}ois and Reynouard, Alexis and Van Den Bogaard, Marie},
  title =	{{The Non-Cooperative Rational Synthesis Problem for SPEs and \omega-Regular Objectives}},
  booktitle =	{36th International Conference on Concurrency Theory (CONCUR 2025)},
  pages =	{12:1--12:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-389-8},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{348},
  editor =	{Bouyer, Patricia and van de Pol, Jaco},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CONCUR.2025.12},
  URN =		{urn:nbn:de:0030-drops-239622},
  doi =		{10.4230/LIPIcs.CONCUR.2025.12},
  annote =	{Keywords: non-zero-sum games, subgame perfect equilibria, rational synthesis}
}
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.2025.11
Mutational Signature Refitting on Sparse Pan-Cancer Data

Authors: Gal Gilad, Teresa M. Przytycka, and Roded Sharan

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

Abstract
Mutational processes shape cancer genomes, leaving characteristic marks that are termed signatures. The level of activity of each such process, or its signature exposure, provides important information on the disease, improving patient stratification and the prediction of drug response. Thus, there is growing interest in developing refitting methods that decipher those exposures. Previous work in this domain was unsupervised in nature, employing algebraic decomposition and probabilistic inference methods. Here we provide a supervised approach to the problem of signature refitting and show its superiority over current methods. Our method, SuRe, leverages a neural network model to capture correlations between signature exposures in real data. We show that SuRe outperforms previous methods on sparse mutation data from tumor type specific data sets, as well as pan-cancer data sets, with an increasing advantage as the data become sparser. We further demonstrate its utility in clinical settings.
Cite as

Gal Gilad, Teresa M. Przytycka, and Roded Sharan. Mutational Signature Refitting on Sparse Pan-Cancer Data. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 11:1-11:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{gilad_et_al:LIPIcs.WABI.2025.11,
  author =	{Gilad, Gal and Przytycka, Teresa M. and Sharan, Roded},
  title =	{{Mutational Signature Refitting on Sparse Pan-Cancer Data}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{11:1--11:23},
  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.2025.11},
  URN =		{urn:nbn:de:0030-drops-239374},
  doi =		{10.4230/LIPIcs.WABI.2025.11},
  annote =	{Keywords: mutational signatures, signature refitting, cancer genomics, genomic data analysis, somatic mutations}
}
Document
DOI: 10.4230/LIPIcs.CP.2025.18
Greed Is Slow on Sparse Graphs of Oriented Valued Constraints

Authors: Artem Kaznatcheev and Sofia Vazquez Alferez

Published in: LIPIcs, Volume 340, 31st International Conference on Principles and Practice of Constraint Programming (CP 2025)

Abstract
Greedy local search is especially popular for solving valued constraint satisfaction problems (VCSPs). Since any method will be slow for some VCSPs, we ask: what is the simplest VCSP on which greedy local search is slow? We construct a VCSP on 6n Boolean variables for which greedy local search takes 7(2ⁿ - 1) steps to find the unique peak. Our VCSP is simple in two ways. First, it is very sparse: its constraint graph has pathwidth 2 and maximum degree 3. This is the simplest VCSP on which some local search could be slow. Second, it is "oriented" – there is an ordering on the variables such that later variables are conditionally-independent of earlier ones. Being oriented allows many non-greedy local search methods to find the unique peak in a quadratic number of steps. Thus, we conclude that - among local search methods - greed is particularly slow.
Cite as

Artem Kaznatcheev and Sofia Vazquez Alferez. Greed Is Slow on Sparse Graphs of Oriented Valued Constraints. In 31st International Conference on Principles and Practice of Constraint Programming (CP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 340, pp. 18:1-18:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{kaznatcheev_et_al:LIPIcs.CP.2025.18,
  author =	{Kaznatcheev, Artem and Vazquez Alferez, Sofia},
  title =	{{Greed Is Slow on Sparse Graphs of Oriented Valued Constraints}},
  booktitle =	{31st International Conference on Principles and Practice of Constraint Programming (CP 2025)},
  pages =	{18:1--18:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-380-5},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{340},
  editor =	{de la Banda, Maria Garcia},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CP.2025.18},
  URN =		{urn:nbn:de:0030-drops-238793},
  doi =		{10.4230/LIPIcs.CP.2025.18},
  annote =	{Keywords: valued constraint satisfaction problem, local search, algorithm analysis, constraint graphs}
}
Document
Track A: Algorithms, Complexity and Games
DOI: 10.4230/LIPIcs.ICALP.2025.34
On the Degree Automatability of Sum-Of-Squares Proofs

Authors: Alex Bortolotti, Monaldo Mastrolilli, and Luis Felipe Vargas

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

Abstract
The Sum-of-Squares (SoS) hierarchy, also known as Lasserre hierarchy, has emerged as a promising tool in optimization. However, it remains unclear whether fixed-degree SoS proofs can be automated [O'Donnell (2017)]. Indeed, there are examples of polynomial systems with bounded coefficients that admit low-degree SoS proofs, but these proofs necessarily involve numbers with an exponential number of bits, implying that low-degree SoS proofs cannot always be found efficiently. A sufficient condition derived from the Nullstellensatz proof system [Raghavendra and Weitz (2017)] identifies cases where bit complexity issues can be circumvented. One of the main problems left open by Raghavendra and Weitz is proving any result for refutations, as their condition applies only to polynomial systems with a large set of solutions. In this work, we broaden the class of polynomial systems for which degree-d SoS proofs can be automated. To achieve this, we develop a new criterion and we demonstrate how our criterion applies to polynomial systems beyond the scope of Raghavendra and Weitz’s result. In particular, we establish a separation for instances arising from Constraint Satisfaction Problems (CSPs). Moreover, our result extends to refutations, establishing that polynomial-time refutation is possible for broad classes of polynomial time solvable constraint problems, highlighting a first advancement in this area.
Cite as

Alex Bortolotti, Monaldo Mastrolilli, and Luis Felipe Vargas. On the Degree Automatability of Sum-Of-Squares Proofs. In 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 334, pp. 34:1-34:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{bortolotti_et_al:LIPIcs.ICALP.2025.34,
  author =	{Bortolotti, Alex and Mastrolilli, Monaldo and Vargas, Luis Felipe},
  title =	{{On the Degree Automatability of Sum-Of-Squares Proofs}},
  booktitle =	{52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)},
  pages =	{34:1--34:19},
  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.2025.34},
  URN =		{urn:nbn:de:0030-drops-234110},
  doi =		{10.4230/LIPIcs.ICALP.2025.34},
  annote =	{Keywords: Sum of squares, Polynomial calculus, Polynomial ideal membership, Polymorphisms, Gr\"{o}bner basis theory, Constraint satisfaction problems, Proof complexity}
}
Document
DOI: 10.4230/LIPIcs.ECOOP.2025.13
FuzzFlesh: Randomised Testing of Decompilers via Control Flow Graph-Based Program Generation

Authors: Amber Gorzynski and Alastair F. Donaldson

Published in: LIPIcs, Volume 333, 39th European Conference on Object-Oriented Programming (ECOOP 2025)

Abstract
Decompilation is the process of translating compiled code into high-level code. Control flow recovery is a challenging part of the process. "Misdecompilations" can occur, whereby the decompiled code does not accurately represent the semantics of the compiled code, despite it being syntactically valid. This is problematic because it can mislead users who are trying to reason about the program. We present CFG-based program generation: a novel approach to randomised testing that aims to improve the control flow recovery of decompilers. CFG-based program generation involves randomly generating control flow graphs (CFGs) and paths through each graph. Inspired by prior work in the domain of GPU computing, (CFG, path) pairs are "fleshed" into test programs. Each program is decompiled and recompiled. The test oracle verifies whether the actual runtime path through the graph matches the expected path. Any difference in the execution paths after recompilation indicates a possible misdecompilation. A key benefit of this approach is that it is largely independent of the source and target languages in question because it is focused on control flow. The approach is therefore applicable to numerous decompilation settings. The trade-off resulting from the focus on control flow is that misdecompilation bugs that do not relate to control flow (e.g. bugs that involve specific arithmetic operations) are out of scope. We have implemented this approach in FuzzFlesh, an open-source randomised testing tool. FuzzFlesh can be easily configured to target a variety of low-level languages and decompiler toolchains because most of the CFG and path generation process is language-independent. At present, FuzzFlesh supports testing decompilation of Java bytecode, .NET assembly and x86 machine code. In addition to program generation, FuzzFlesh also includes an automated test-case reducer that operates on the CFG rather than the low-level program, which means that it can be applied to any of the target languages. We present a large experimental campaign applying FuzzFlesh to a variety of decompilers, leading to the discovery of 12 previously-unknown bugs across two language formats, six of which have been fixed. We present experiments comparing our generic FuzzFlesh tool to two state-of-the-art decompiler testing tools targeted at specific languages. As expected, the coverage our generic FuzzFlesh tool achieves on a given decompiler is lower than the coverage achieved by a tool specifically designed for the input format of that decompiler. However, due to its focus on control flow, FuzzFlesh is able to cover sections of control flow recovery code that the targeted tools cannot reach, and identify control flow related bugs that the targeted tools miss.
Cite as

Amber Gorzynski and Alastair F. Donaldson. FuzzFlesh: Randomised Testing of Decompilers via Control Flow Graph-Based Program Generation. In 39th European Conference on Object-Oriented Programming (ECOOP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 333, pp. 13:1-13:26, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{gorzynski_et_al:LIPIcs.ECOOP.2025.13,
  author =	{Gorzynski, Amber and Donaldson, Alastair F.},
  title =	{{FuzzFlesh: Randomised Testing of Decompilers via Control Flow Graph-Based Program Generation}},
  booktitle =	{39th European Conference on Object-Oriented Programming (ECOOP 2025)},
  pages =	{13:1--13:26},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-373-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{333},
  editor =	{Aldrich, Jonathan and Silva, Alexandra},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECOOP.2025.13},
  URN =		{urn:nbn:de:0030-drops-233062},
  doi =		{10.4230/LIPIcs.ECOOP.2025.13},
  annote =	{Keywords: Decompiler, Reverse Engineering, Control Flow, Software Testing, Fuzzing}
}
Document
DOI: 10.4230/LIPIcs.ECOOP.2025.4
Ensuring Convergence and Invariants Without Coordination

Authors: Dina Borrego, Nuno Preguiça, Elisa Gonzalez Boix, and Carla Ferreira

Published in: LIPIcs, Volume 333, 39th European Conference on Object-Oriented Programming (ECOOP 2025)

Abstract
The CAP theorem demonstrates a trade-off between consistency and availability (and, by extension, latency) in systems where network partitions are unavoidable, such as in cloud computing and local-first software. While adopting weak consistency can preserve availability, it may result in inconsistencies that compromise application correctness. Replicated data types provide a principled, coordination-free approach to guarantee convergence but do not consider application invariants. Existing methods for maintaining invariants in replicated systems either rely on coordination - undermining the benefits of weak consistency - or suffer from limited applicability. This paper introduces the No-Op framework, a generic approach for enforcing consistency without coordination while guaranteeing both convergence and invariant preservation. The core idea of the No-Op approach is to resolve conflicts among concurrent operations by prioritising one operation over the other according to programmer-defined conflict resolution policies. This prioritisation transforms the less-preferred operation into a no-side-effect operation, ensuring conflict-free execution. We formalise the model underlying the No-Op framework and introduce a replication protocol built upon it, accompanied by a formal proof of correctness for both the framework and the protocol. Furthermore, we demonstrate the framework’s applicability by showcasing the design of widely used replicated data types and the preservation of a wide range of application invariants.
Cite as

Dina Borrego, Nuno Preguiça, Elisa Gonzalez Boix, and Carla Ferreira. Ensuring Convergence and Invariants Without Coordination. In 39th European Conference on Object-Oriented Programming (ECOOP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 333, pp. 4:1-4:29, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{borrego_et_al:LIPIcs.ECOOP.2025.4,
  author =	{Borrego, Dina and Pregui\c{c}a, Nuno and Gonzalez Boix, Elisa and Ferreira, Carla},
  title =	{{Ensuring Convergence and Invariants Without Coordination}},
  booktitle =	{39th European Conference on Object-Oriented Programming (ECOOP 2025)},
  pages =	{4:1--4:29},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-373-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{333},
  editor =	{Aldrich, Jonathan and Silva, Alexandra},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECOOP.2025.4},
  URN =		{urn:nbn:de:0030-drops-232978},
  doi =		{10.4230/LIPIcs.ECOOP.2025.4},
  annote =	{Keywords: distributed systems, conflict resolution, RDTs, invariant preservation}
}
Document
DOI: 10.4230/LIPIcs.ECOOP.2025.25
Reusing Highly Optimized IR in Dynamic Compilation

Authors: Andrej Pečimúth, David Leopoldseder, and Petr Tůma

Published in: LIPIcs, Volume 333, 39th European Conference on Object-Oriented Programming (ECOOP 2025)

Abstract
Virtual machines (VMs) with dynamic compilers typically specialize compiled code to the state of the running VM instance and thus cannot reuse the code between multiple runs of the same application. The JIT compiler must recompile the same methods for each run of the application separately, which can prolong the application’s warmup time. We propose a technique to reduce compilation time by reusing a highly optimized intermediate representation (IR). We achieve this by tracing compiler-interface calls during compilation. The validity of the specializations in the IR is verified during a replay stage, and the replay also facilitates the relocation of runtime object references. The IR is stored on a compilation server, which can compile it to machine code and provide the code to local or remote VM instances. We implemented a compilation server with IR caching for GraalVM, a high-performance production-grade Java Virtual Machine (JVM). We present an evaluation based on four industry-standard benchmark suites. In each suite, our approach reduces compilation time by 23.6% to 36.8% and warmup time by 13.1% to 21.2% on average while preserving peak application performance.
Cite as

Andrej Pečimúth, David Leopoldseder, and Petr Tůma. Reusing Highly Optimized IR in Dynamic Compilation. In 39th European Conference on Object-Oriented Programming (ECOOP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 333, pp. 25:1-25:25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{pecimuth_et_al:LIPIcs.ECOOP.2025.25,
  author =	{Pe\v{c}im\'{u}th, Andrej and Leopoldseder, David and T\r{u}ma, Petr},
  title =	{{Reusing Highly Optimized IR in Dynamic Compilation}},
  booktitle =	{39th European Conference on Object-Oriented Programming (ECOOP 2025)},
  pages =	{25:1--25:25},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-373-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{333},
  editor =	{Aldrich, Jonathan and Silva, Alexandra},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECOOP.2025.25},
  URN =		{urn:nbn:de:0030-drops-233176},
  doi =		{10.4230/LIPIcs.ECOOP.2025.25},
  annote =	{Keywords: code reuse, compilation time, warmup, remote compilation, dynamic compilation, virtual machines}
}
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