24 Search Results for "Isaac, Antoine"

Document
DOI: 10.4230/LIPIcs.SWAT.2026.39
Faster Approximate Linear Matroid Intersection

Authors: Tatsuya Terao

Published in: LIPIcs, Volume 370, 20th Scandinavian Symposium on Algorithm Theory (SWAT 2026)

Abstract
We consider a fast approximation algorithm for the linear matroid intersection problem. In this problem, we are given two r × n matrices M₁ and M₂, and the objective is to find a largest set of columns that are linearly independent in both M₁ and M₂. We design a (1 - ε)-approximation algorithm with time complexity Õ_{ε}(nnz(M₁) + nnz(M₂) + r_{*}^{ω}), where nnz(M_i) denotes the number of nonzero entries in M_i for i = 1, 2, r_{*} denotes the maximum size of a common independent set, and ω < 2.372 denotes the matrix multiplication exponent. Our approximation algorithm is faster than the exact algorithm by Harvey [FOCS'06 & SICOMP'09] and Cheung-Kwok-Lau [STOC'12 & JACM'13], which runs in Õ(nnz(M₁) + nnz(M₂) + n r_{*}^{ω - 1}) time. We also develop a fast (1 - ε)-approximation algorithm for the weighted version of the linear matroid intersection problem. In fact, we design a (1 - ε)-approximation algorithm for weighted linear matroid intersection with time complexity Õ_{ε}(nnz(M₁) + nnz(M₂) + r_{*}^{ω}). Our algorithm improves upon the (1 - ε)-approximation algorithm by Huang-Kakimura-Kamiyama [SODA'16 & Math. Program.'19], which runs in Õ_{ε}(nnz(M₁) + nnz(M₂) + nr_{*}^{ω - 1}) time. To obtain these results, we combine Quanrud’s adaptive sparsification framework [ICALP'24] with a simple yet effective method for efficiently checking whether a given vector lies in the linear span of a subset of vectors, which is of independent interest.
Cite as

Tatsuya Terao. Faster Approximate Linear Matroid Intersection. In 20th Scandinavian Symposium on Algorithm Theory (SWAT 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 370, pp. 39:1-39:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{terao:LIPIcs.SWAT.2026.39,
  author =	{Terao, Tatsuya},
  title =	{{Faster Approximate Linear Matroid Intersection}},
  booktitle =	{20th Scandinavian Symposium on Algorithm Theory (SWAT 2026)},
  pages =	{39:1--39:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-421-5},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{370},
  editor =	{Fraigniaud, Pierre},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SWAT.2026.39},
  URN =		{urn:nbn:de:0030-drops-260756},
  doi =		{10.4230/LIPIcs.SWAT.2026.39},
  annote =	{Keywords: Linear matroid intersection, fast approximation algorithm}
}
Document
DOI: 10.4230/OASIcs.NINeS.2026.13
In-Kernel Aggregation and Broadcast Acceleration for Distributed Communication

Authors: Jianchang Su, Yifan Zhang, and Wei Zhang

Published in: OASIcs, Volume 139, 1st New Ideas in Networked Systems (NINeS 2026)

Abstract
Broadcasting and aggregation dominate the communication overhead in distributed systems, from machine learning training to data analytics. Current acceleration approaches require specialized hardware (RDMA) or dedicated resources (DPDK), limiting their deployment in commodity clouds. However, we present a counter-intuitive alternative: rather than bypassing the kernel, we move operations into it using eBPF. While this imposes severe constraints including no floating-point, limited memory, and stateless execution, we show these restrictions paradoxically drive innovative protocol designs that yield unexpected benefits. We introduce AggBox, which implements broadcast and aggregation operations entirely within eBPF’s constrained environment. Our key innovations include stateless group acknowledgments for reliability, edge quantization for floating-point aggregation using only integer arithmetic, and tail-call chains that create virtual memory beyond eBPF’s 512-byte stack limit. These designs emerge from and exploit the constraints rather than fighting them. AggBox achieves remarkable performance on commodity hardware: 84.5% reduction in broadcast latency, 43× speedup for MapReduce workloads, and 56.1% faster ML gradient aggregation, all without specialized NICs or dedicated cores. Beyond performance, our work demonstrates that constrained environments can drive fundamental innovation in protocol design, offering insights for future resource-limited and verified systems.
Cite as

Jianchang Su, Yifan Zhang, and Wei Zhang. In-Kernel Aggregation and Broadcast Acceleration for Distributed Communication. In 1st New Ideas in Networked Systems (NINeS 2026). Open Access Series in Informatics (OASIcs), Volume 139, pp. 13:1-13:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{su_et_al:OASIcs.NINeS.2026.13,
  author =	{Su, Jianchang and Zhang, Yifan and Zhang, Wei},
  title =	{{In-Kernel Aggregation and Broadcast Acceleration for Distributed Communication}},
  booktitle =	{1st New Ideas in Networked Systems (NINeS 2026)},
  pages =	{13:1--13:23},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-414-7},
  ISSN =	{2190-6807},
  year =	{2026},
  volume =	{139},
  editor =	{Argyraki, Katerina and Panda, Aurojit},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.NINeS.2026.13},
  URN =		{urn:nbn:de:0030-drops-255981},
  doi =		{10.4230/OASIcs.NINeS.2026.13},
  annote =	{Keywords: eBPF, distributed communication, broadcast, aggregation, in-kernel processing, XDP}
}
Document
DOI: 10.4230/OASIcs.NINeS.2026.19
Simulate Before Sending: Rethinking Transport in Datacenter Networks

Authors: Dan Straussman, Isaac Keslassy, Alexander Shpiner, and Liran Liss

Published in: OASIcs, Volume 139, 1st New Ideas in Networked Systems (NINeS 2026)

Abstract
Existing transport protocols in commodity datacenter networks struggle to provide low collective completion times (CCTs) to AI training collectives, as packet losses and retransmissions significantly degrade performance. We propose dcSim, an efficient transport that achieves low CCTs and practically lossless performance with commodity switches. In dcSim, each packet first employs a small simulation probe to traverse the network and explore congestion along a candidate path. Only packets whose simulation probes succeed are then transmitted, expecting to succeed as well. Evaluations confirm that dcSim achieves faster CCTs than existing schemes, with small queues and virtually zero packet loss. Finally, dcSim also excels in adverse conditions, including oversubscribed topologies.
Cite as

Dan Straussman, Isaac Keslassy, Alexander Shpiner, and Liran Liss. Simulate Before Sending: Rethinking Transport in Datacenter Networks. In 1st New Ideas in Networked Systems (NINeS 2026). Open Access Series in Informatics (OASIcs), Volume 139, pp. 19:1-19:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{straussman_et_al:OASIcs.NINeS.2026.19,
  author =	{Straussman, Dan and Keslassy, Isaac and Shpiner, Alexander and Liss, Liran},
  title =	{{Simulate Before Sending: Rethinking Transport in Datacenter Networks}},
  booktitle =	{1st New Ideas in Networked Systems (NINeS 2026)},
  pages =	{19:1--19:22},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-414-7},
  ISSN =	{2190-6807},
  year =	{2026},
  volume =	{139},
  editor =	{Argyraki, Katerina and Panda, Aurojit},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.NINeS.2026.19},
  URN =		{urn:nbn:de:0030-drops-256044},
  doi =		{10.4230/OASIcs.NINeS.2026.19},
  annote =	{Keywords: Datacenter networks, transport protocols, AI training, lossless networks}
}
Document
DOI: 10.4230/LIPIcs.STACS.2026.10
A Polynomial Bound on the Pathwidth of Graphs Edge-Coverable by k Shortest Paths

Authors: Julien Baste, Lucas De Meyer, Ugo Giocanti, Etienne Objois, and Timothé Picavet

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

Abstract
Dumas, Foucaud, Perez and Todinca [SIAM J. Disc. Math., 2024] recently proved that every graph whose edge set can be covered by k shortest paths has pathwidth at most 3^k. In this paper, we improve this upper bound on the pathwidth to a polynomial bound; namely, we show that every graph whose edge set can be covered by k shortest paths has pathwidth O(k⁴), answering a question from the same paper. Moreover, we also prove that when k ≤ 3, every such graph has pathwidth at most k (and this bound is tight). Eventually, we show that even though there exist graphs with arbitrary large treewidth whose vertex set can be covered by 2 isometric trees, every graph whose set of edges can be covered by 2 isometric trees has treewidth at most 2.
Cite as

Julien Baste, Lucas De Meyer, Ugo Giocanti, Etienne Objois, and Timothé Picavet. A Polynomial Bound on the Pathwidth of Graphs Edge-Coverable by k Shortest Paths. In 43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 364, pp. 10:1-10:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{baste_et_al:LIPIcs.STACS.2026.10,
  author =	{Baste, Julien and De Meyer, Lucas and Giocanti, Ugo and Objois, Etienne and Picavet, Timoth\'{e}},
  title =	{{A Polynomial Bound on the Pathwidth of Graphs Edge-Coverable by k Shortest Paths}},
  booktitle =	{43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026)},
  pages =	{10:1--10:17},
  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.2026.10},
  URN =		{urn:nbn:de:0030-drops-254999},
  doi =		{10.4230/LIPIcs.STACS.2026.10},
  annote =	{Keywords: Structural Graph Theory, Coverings, Metrics, Pathwidth, Treewdidth, Parameterized Algorithms, Layerings}
}
Document
DOI: 10.4230/LIPIcs.ISAAC.2025.10
New Algorithmic Directions in Optimal Transport and Applications for Product Spaces

Authors: Salman Beigi, Omid Etesami, Mohammad Mahmoody, and Amir Najafi

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

Abstract
We consider the problem of optimal transport between two high-dimensional distributions μ,ν in ℝⁿ from a new algorithmic perspective, in which we are given a sample x ∼ μ and we have to find a close y ∼ ν while running in poly(n) time, where n is the size/dimension of x,y. In other words, we are interested in making the running time bounded in dimension of the spaces rather than bounded in the total size of the representations of the two distributions. Our main result is a general algorithmic transport result between any product distribution μ and an arbitrary distribution ν of total cost Δ + δ under 𝓁_p^p cost; here Δ is the cost of the so-called Knothe–Rosenblatt transport from μ to ν, while δ is a computational error that goes to zero for larger running time in the transport algorithm. For this result, we need ν to be "sequentially samplable" with a "bounded average sampling cost" which is a novel but natural notion of independent interest. In addition, we prove the following. - We prove an algorithmic version of the celebrated Talagrand’s inequality for transporting the standard Gaussian distribution Φⁿ to an arbitrary ν under the Euclidean-squared cost. When ν is Φⁿ conditioned on a set S of measure ε, we show how to implement the needed sequential sampler for ν in expected time poly(n/ε), using membership oracle access to S. Hence, we obtain an algorithmic transport that maps Φⁿ to Φⁿ|S in time poly(n/ε) and expected Euclidean-squared distance O(log 1/ε), which is optimal for a general set S of measure ε. - As corollary, we find the first computational concentration (Etesami et al. SODA 2020) result for the Gaussian measure under the Euclidean distance with a dimension-independent transportation cost, resolving a question of Etesami et al. More precisely, for any set S of Gaussian measure ε, we map most of Φⁿ samples to S with Euclidean distance O(√{log 1/ε}) in time poly(n/ε).
Cite as

Salman Beigi, Omid Etesami, Mohammad Mahmoody, and Amir Najafi. New Algorithmic Directions in Optimal Transport and Applications for Product Spaces. In 36th International Symposium on Algorithms and Computation (ISAAC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 359, pp. 10:1-10:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{beigi_et_al:LIPIcs.ISAAC.2025.10,
  author =	{Beigi, Salman and Etesami, Omid and Mahmoody, Mohammad and Najafi, Amir},
  title =	{{New Algorithmic Directions in Optimal Transport and Applications for Product Spaces}},
  booktitle =	{36th International Symposium on Algorithms and Computation (ISAAC 2025)},
  pages =	{10:1--10:21},
  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.2025.10},
  URN =		{urn:nbn:de:0030-drops-249187},
  doi =		{10.4230/LIPIcs.ISAAC.2025.10},
  annote =	{Keywords: Optimal transport, Randomized algorithms, Concentration bounds}
}
Document
DOI: 10.4230/LIPIcs.AFT.2025.7
Mechanism Design for Automated Market Makers

Authors: T-H. Hubert Chan, Ke Wu, and Elaine Shi

Published in: LIPIcs, Volume 354, 7th Conference on Advances in Financial Technologies (AFT 2025)

Abstract
Blockchains have popularized automated market makers (AMMs), applications that run on a blockchain, maintain a pool of crypto-assets, and execute trades with users governed by some pricing function. AMMs have also introduced a significant challenge known as the Miner Extractable Value (MEV). Specifically, miners who control the contents and sequencing of transactions in a block can extract value by front-running and back-running users' transactions, creating arbitrage opportunities that guarantee them risk-free returns. MEV not only harms ordinary users, but more critically, encourages miners to auction off favorable transaction placements to users and arbitragers. This has fostered a more centralized off-chain eco-system, departing from the decentralized equilibrium originally envisioned for the blockchain infrastructure layer. In this paper, we consider how to design AMM mechanisms that eliminate MEV opportunities. Specifically, we propose a new AMM mechanism that processes all transactions contained within a block according to some pre-defined rules, ensuring that some constant potential function is maintained after processing the batch. We show that our new mechanism satisfies two tiers of guarantees. First, for legacy blockchains where each block is proposed by a single (possibly rotating) miner, we prove that our mechanism satisfies arbitrage resilience, i.e., a miner cannot gain risk-free profit. Second, for blockchains where the block proposal process is decentralized and offers sequencing-fairness, we prove a strictly stronger notion called strategy proofness - roughly speaking, we guarantee that any individual user’s best response is to follow the honest strategy. Our results complement prior works on MEV resilience in the following senses. First, prior works have shown impossibilities to address MEV entirely at the consensus level. Our work demonstrates a new paradigm of mechanism design at the application (i.e., smart contract) layer to ensure provable guarantees of strategy proofness. Second, many works have attempted to augment the underlying consensus protocol with extra properties such as sequencing fairness. While most previous works heuristically argued why these extra properties help to mitigate MEV, our work demonstrates in a mathematically formal manner how to leverage such consensus-level properties to aid the design of strategy-proof mechanisms.
Cite as

T-H. Hubert Chan, Ke Wu, and Elaine Shi. Mechanism Design for Automated Market Makers. In 7th Conference on Advances in Financial Technologies (AFT 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 354, pp. 7:1-7:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{chan_et_al:LIPIcs.AFT.2025.7,
  author =	{Chan, T-H. Hubert and Wu, Ke and Shi, Elaine},
  title =	{{Mechanism Design for Automated Market Makers}},
  booktitle =	{7th Conference on Advances in Financial Technologies (AFT 2025)},
  pages =	{7:1--7:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-400-0},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{354},
  editor =	{Avarikioti, Zeta and Christin, Nicolas},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.AFT.2025.7},
  URN =		{urn:nbn:de:0030-drops-247265},
  doi =		{10.4230/LIPIcs.AFT.2025.7},
  annote =	{Keywords: Mechanism design, game theory, strategy proof, blockchain}
}
Document
APPROX
DOI: 10.4230/LIPIcs.APPROX/RANDOM.2025.10
Improved Approximation Guarantees for Advertisement Placement

Authors: Waldo Gálvez, Roberto Oliva, and Victor Verdugo

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

Abstract
The advertisement placement problem involves selecting and scheduling ads within a timeline that has capacity constraints to maximize profit. Each task is characterized by its height, width, and profit, and must be fully scheduled across multiple time slots. This problem models practical scenarios such as internet advertising and energy management, and it also generalizes classical combinatorial optimization problems like the knapsack and bin packing problems. We present a simple (2+ε)-approximation algorithm for any ε > 0, which improves upon the state-of-the-art 3+ε factor established by Freund and Naor twenty years ago. Our approach combines rounding techniques with dynamic programming and an efficient extension of list scheduling. Furthermore, we enhance this method with linear programming techniques to provide an almost optimal (1+ε)-approximation algorithm under resource augmentation, which allows for a slight increase in time slot capacities.
Cite as

Waldo Gálvez, Roberto Oliva, and Victor Verdugo. Improved Approximation Guarantees for Advertisement Placement. In Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 353, pp. 10:1-10:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{galvez_et_al:LIPIcs.APPROX/RANDOM.2025.10,
  author =	{G\'{a}lvez, Waldo and Oliva, Roberto and Verdugo, Victor},
  title =	{{Improved Approximation Guarantees for Advertisement Placement}},
  booktitle =	{Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025)},
  pages =	{10:1--10:16},
  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.2025.10},
  URN =		{urn:nbn:de:0030-drops-243762},
  doi =		{10.4230/LIPIcs.APPROX/RANDOM.2025.10},
  annote =	{Keywords: Advertisement Placement, Two-dimensional Packing, Geometric Knapsack, Resource Allocation}
}
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.
Cite as

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.2025.9
Linear Time Subsequence and Supersequence Regex Matching

Authors: Antoine Amarilli, Florin Manea, Tina Ringleb, and Markus L. Schmid

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

Abstract
It is well-known that checking whether a given string w matches a given regular expression r can be done in quadratic time O(|w|⋅ |r|) and that this cannot be improved to a truly subquadratic running time of O((|w|⋅ |r|)^{1-ε}) assuming the strong exponential time hypothesis (SETH). We study a different matching paradigm where we ask instead whether w has a subsequence that matches r, and show that regex matching in this sense can be solved in linear time O(|w| + |r|). Further, the same holds if we ask for a supersequence. We show that the quantitative variants where we want to compute a longest or shortest subsequence or supersequence of w that matches r can be solved in O(|w|⋅ |r|), i. e., asymptotically no worse than classical regex matching; and we show that O(|w| + |r|) is conditionally not possible for these problems. We also investigate these questions with respect to other natural string relations like the infix, prefix, left-extension or extension relation instead of the subsequence and supersequence relation. We further study the complexity of the universal problem where we ask if all subsequences (or supersequences, infixes, prefixes, left-extensions or extensions) of an input string satisfy a given regular expression.
Cite as

Antoine Amarilli, Florin Manea, Tina Ringleb, and Markus L. Schmid. Linear Time Subsequence and Supersequence Regex Matching. In 50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 345, pp. 9:1-9:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{amarilli_et_al:LIPIcs.MFCS.2025.9,
  author =	{Amarilli, Antoine and Manea, Florin and Ringleb, Tina and Schmid, Markus L.},
  title =	{{Linear Time Subsequence and Supersequence Regex Matching}},
  booktitle =	{50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025)},
  pages =	{9:1--9:19},
  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.2025.9},
  URN =		{urn:nbn:de:0030-drops-241162},
  doi =		{10.4230/LIPIcs.MFCS.2025.9},
  annote =	{Keywords: subsequence, supersequence, regular language, regular expression, automata}
}
Document
DOI: 10.4230/LIPIcs.DNA.31.4
Differentiable Programming of Indexed Chemical Reaction Networks and Reaction-Diffusion Systems

Authors: Inhoo Lee, Salvador Buse, and Erik Winfree

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

Abstract
Many molecular systems are best understood in terms of prototypical species and reactions. The central dogma and related biochemistry are rife with examples: gene i is transcribed into RNA i, which is translated into protein i; kinase n phosphorylates substrate m; protein p dimerizes with protein q. Engineered nucleic acid systems also often have this form: oligonucleotide i hybridizes to complementary oligonucleotide j; signal strand n displaces the output of seesaw gate m; hairpin p triggers the opening of target q. When there are many variants of a small number of prototypes, it can be conceptually cleaner and computationally more efficient to represent the full system in terms of indexed species (e.g. for dimerization, M_p, D_pq) and indexed reactions (M_p + M_q → D_pq). Here, we formalize the Indexed Chemical Reaction Network (ICRN) model and describe a Python software package designed to simulate such systems in the well-mixed and reaction-diffusion settings, using a differentiable programming framework originally developed for large-scale neural network models, taking advantage of GPU acceleration when available. Notably, this framework makes it straightforward to train the models’ initial conditions and rate constants to optimize a target behavior, such as matching experimental data, performing a computation, or exhibiting spatial pattern formation. The natural map of indexed chemical reaction networks onto neural network formalisms provides a tangible yet general perspective for translating concepts and techniques from the theory and practice of neural computation into the design of biomolecular systems.
Cite as

Inhoo Lee, Salvador Buse, and Erik Winfree. Differentiable Programming of Indexed Chemical Reaction Networks and Reaction-Diffusion Systems. In 31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 4:1-4:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{lee_et_al:LIPIcs.DNA.31.4,
  author =	{Lee, Inhoo and Buse, Salvador and Winfree, Erik},
  title =	{{Differentiable Programming of Indexed Chemical Reaction Networks and Reaction-Diffusion Systems}},
  booktitle =	{31st International Conference on DNA Computing and Molecular Programming (DNA 31)},
  pages =	{4:1--4:23},
  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.31.4},
  URN =		{urn:nbn:de:0030-drops-238534},
  doi =		{10.4230/LIPIcs.DNA.31.4},
  annote =	{Keywords: Differentiable Programming, Chemical Reaction Networks, Reaction-Diffusion Systems}
}
Document
DOI: 10.4230/LIPIcs.WABI.2025.6
Fast Pseudoalignment Queries on Compressed Colored de Bruijn Graphs

Authors: Alessio Campanelli, Giulio Ermanno Pibiri, and Rob Patro

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

Abstract
Motivation. Indexes for the colored de Bruijn graph (c-dBG) play a crucial role in computational biology by facilitating complex tasks such as read mapping and assembly. These indexes map k-mers (substrings of length k) appearing in a large collection of reference strings to the set of identifiers of the strings where they appear. These sets, colloquially referred to as color sets, tend to occupy large quantities of memory, especially for large pangenomes. Our previous work thus focused on leveraging the repetitiveness of the color sets to improve the space effectiveness of the resulting index. As a matter of fact, repetition-aware indexes can be up to one order of magnitude smaller on large pangenomes compared to indexes that do not exploit such repetitiveness. Such improved space effectiveness, on the other hand, imposes an overhead at query time when performing tasks such as pseudoalignment that require the collection and processing of multiple related color sets. Methods. In this paper, we show how to avoid this overhead. We devise novel query algorithms tailored for the specific repetition-aware representations adopted by the Fulgor index, a state-of-the-art c-dBG index, to significantly improve its pseudoalignment efficiency and without consuming additional space. Results. Our results indicate that with increasing redundancy in the pangenomes, the compression factor provided by the Fulgor index increases, while the relative query time actually reduces. For example, while the space of the Fulgor index improves by 2.5× with repetition-aware compression and its query time improves by 1.6× on a collection of 5,000 Salmonella Enterica genomes, these factors become (6.1×,2.8×) and (11.2×,3.2×) for 50,000 and 150,000 genomes respectively. For an even larger collection of 300,000 genomes, we obtained an index that is 22.3× smaller and 2.2× faster.
Cite as

Alessio Campanelli, Giulio Ermanno Pibiri, and Rob Patro. Fast Pseudoalignment Queries on Compressed Colored de Bruijn Graphs. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 6:1-6:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{campanelli_et_al:LIPIcs.WABI.2025.6,
  author =	{Campanelli, Alessio and Pibiri, Giulio Ermanno and Patro, Rob},
  title =	{{Fast Pseudoalignment Queries on Compressed Colored de Bruijn Graphs}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{6:1--6:21},
  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.2025.6},
  URN =		{urn:nbn:de:0030-drops-239327},
  doi =		{10.4230/LIPIcs.WABI.2025.6},
  annote =	{Keywords: Colored de Bruijn graphs, Pseudoalignment, Repetition-aware compression}
}
Document
DOI: 10.4230/LIPIcs.SEA.2025.25
Blocked Bloom Filters with Choices

Authors: Johanna Elena Schmitz, Jens Zentgraf, and Sven Rahmann

Published in: LIPIcs, Volume 338, 23rd International Symposium on Experimental Algorithms (SEA 2025)

Abstract
Probabilistic filters are approximate set membership data structures that represent a set of keys in small space, and answer set membership queries without false negative answers, but with a certain allowed false positive probability. Such filters are widely used in database systems, networks, storage systems and in biological sequence analysis because of their fast query times and low space requirements. Starting with Bloom filters in the 1970s, many filter data structures have been developed, each with its own advantages and disadvantages, e.g., Blocked Bloom filters, Cuckoo filters, XOR filters, Ribbon filters, and more. We introduce Blocked Bloom filters with choices that work similarly to Blocked Bloom filters, except that for each key there are two (or more) alternative choices of blocks where the key’s information may be stored. When inserting a key, we select the block using a cost function which takes into account the current load and the additional number of bits to be set in the candidate blocks. The result is a filter that partially inherits the advantages of a Blocked Bloom filter, such as the ability to insert keys rapidly online or the ability to slightly overload the filter with only a small penalty to the false positive rate. At the same time, it avoids the major disadvantage of a Blocked Bloom filter, namely the larger space consumption. Our new data structure uses less space at the same false positive rate, or has a lower false positive rate at the same space consumption as a Blocked Bloom filter. We discuss the methodology, cost functions for block selection, engineered implementation, a detailed performance evaluation and use cases in bioinformatics of Blocked Bloom filters with choices, showing that they can be of practical value. The implementation of the evaluated filters and the workflows used are provided via Gitlab at https://gitlab.com/rahmannlab/blowchoc-filters.
Cite as

Johanna Elena Schmitz, Jens Zentgraf, and Sven Rahmann. Blocked Bloom Filters with Choices. In 23rd International Symposium on Experimental Algorithms (SEA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 338, pp. 25:1-25:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{schmitz_et_al:LIPIcs.SEA.2025.25,
  author =	{Schmitz, Johanna Elena and Zentgraf, Jens and Rahmann, Sven},
  title =	{{Blocked Bloom Filters with Choices}},
  booktitle =	{23rd International Symposium on Experimental Algorithms (SEA 2025)},
  pages =	{25:1--25:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-375-1},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{338},
  editor =	{Mutzel, Petra and Prezza, Nicola},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2025.25},
  URN =		{urn:nbn:de:0030-drops-232631},
  doi =		{10.4230/LIPIcs.SEA.2025.25},
  annote =	{Keywords: Probabilistic filter, Bloom filter, power of two choices}
}
Document
Track B: Automata, Logic, Semantics, and Theory of Programming
DOI: 10.4230/LIPIcs.ICALP.2025.144
Probabilistic and Causal Satisfiability: Constraining the Model

Authors: Markus Bläser, Julian Dörfler, Maciej Liśkiewicz, and Benito van der Zander

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

Abstract
We study the complexity of satisfiability problems in probabilistic and causal reasoning. Given random variables X₁, X₂,… over finite domains, the basic terms are probabilities of propositional formulas over atomic events X_i = x_i, such as ℙ(X₁ = x₁) or ℙ(X₁ = x₁ ∨ X₂ = x₂). The basic terms can be combined using addition (yielding linear terms) or multiplication (polynomial terms). The probabilistic satisfiability problem asks whether a joint probability distribution satisfies a Boolean combination of (in)equalities over such terms. Fagin et al. [Fagin et al., 1990] showed that for basic and linear terms, this problem is NP-complete, making it no harder than Boolean satisfiability, while Mossé et al. [Mossé et al., 2022] proved that for polynomial terms, it is complete for the existential theory of the reals. Pearl’s Causal Hierarchy (PCH) extends the probabilistic setting with interventional and counterfactual reasoning, enriching the expressiveness of the languages. However, Mossé et al. [Mossé et al., 2022] found that the complexity of satisfiability remains unchanged. Van der Zander et al. [van der Zander et al., 2023] showed that introducing a marginalization operator to languages induces a significant increase in complexity. We extend this line of work by adding two new dimensions to the problem by constraining the models. First, we fix the graph structure of the underlying structural causal model, motivated by settings like Pearl’s do-calculus, and give a nearly complete landscape across different arithmetics and PCH levels. Second, we study small models. While earlier work showed that satisfiable instances admit polynomial-size models, this is no longer guaranteed with compact marginalization. We characterize the complexities of satisfiability under small-model constraints across different settings.
Cite as

Markus Bläser, Julian Dörfler, Maciej Liśkiewicz, and Benito van der Zander. Probabilistic and Causal Satisfiability: Constraining the Model. In 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 334, pp. 144:1-144:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{blaser_et_al:LIPIcs.ICALP.2025.144,
  author =	{Bl\"{a}ser, Markus and D\"{o}rfler, Julian and Li\'{s}kiewicz, Maciej and van der Zander, Benito},
  title =	{{Probabilistic and Causal Satisfiability: Constraining the Model}},
  booktitle =	{52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)},
  pages =	{144:1--144:20},
  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.2025.144},
  URN =		{urn:nbn:de:0030-drops-235214},
  doi =		{10.4230/LIPIcs.ICALP.2025.144},
  annote =	{Keywords: Existential theory of the real numbers, Computational complexity, Probabilistic logic, Structural Causal Models}
}
Document
Track B: Automata, Logic, Semantics, and Theory of Programming
DOI: 10.4230/LIPIcs.ICALP.2025.141
The Trichotomy of Regular Property Testing

Authors: Gabriel Bathie, Nathanaël Fijalkow, and Corto Mascle

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

Abstract
Property testing is concerned with the design of algorithms making a sublinear number of queries to distinguish whether the input satisfies a given property or is far from having this property. A seminal paper of Alon, Krivelevich, Newman, and Szegedy in 2001 introduced property testing of formal languages: the goal is to determine whether an input word belongs to a given language, or is far from any word in that language. They constructed the first property testing algorithm for the class of all regular languages. This opened a line of work with improved complexity results and applications to streaming algorithms. In this work, we show a trichotomy result: the class of regular languages can be divided into three classes, each associated with an optimal query complexity. Our analysis yields effective characterizations for all three classes using so-called minimal blocking sequences, reasoning directly and combinatorially on automata.
Cite as

Gabriel Bathie, Nathanaël Fijalkow, and Corto Mascle. The Trichotomy of Regular Property Testing. In 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 334, pp. 141:1-141:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{bathie_et_al:LIPIcs.ICALP.2025.141,
  author =	{Bathie, Gabriel and Fijalkow, Nathana\"{e}l and Mascle, Corto},
  title =	{{The Trichotomy of Regular Property Testing}},
  booktitle =	{52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)},
  pages =	{141:1--141:21},
  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.2025.141},
  URN =		{urn:nbn:de:0030-drops-235186},
  doi =		{10.4230/LIPIcs.ICALP.2025.141},
  annote =	{Keywords: property testing, regular languages}
}
Document
DOI: 10.4230/LIPIcs.SoCG.2025.31
A Linear Time Algorithm for the Maximum Overlap of Two Convex Polygons Under Translation

Authors: Timothy M. Chan and Isaac M. Hair

Published in: LIPIcs, Volume 332, 41st International Symposium on Computational Geometry (SoCG 2025)

Abstract
Given two convex polygons P and Q with n and m edges, the maximum overlap problem is to find a translation of P that maximizes the area of its intersection with Q. We give the first randomized algorithm for this problem with linear running time. Our result improves the previous two-and-a-half-decades-old algorithm by de Berg, Cheong, Devillers, van Kreveld, and Teillaud (1998), which ran in O((n+m)log(n+m)) time, as well as multiple recent algorithms given for special cases of the problem.
Cite as

Timothy M. Chan and Isaac M. Hair. A Linear Time Algorithm for the Maximum Overlap of Two Convex Polygons Under Translation. In 41st International Symposium on Computational Geometry (SoCG 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 332, pp. 31:1-31:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{chan_et_al:LIPIcs.SoCG.2025.31,
  author =	{Chan, Timothy M. and Hair, Isaac M.},
  title =	{{A Linear Time Algorithm for the Maximum Overlap of Two Convex Polygons Under Translation}},
  booktitle =	{41st International Symposium on Computational Geometry (SoCG 2025)},
  pages =	{31:1--31:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-370-6},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{332},
  editor =	{Aichholzer, Oswin and Wang, Haitao},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SoCG.2025.31},
  URN =		{urn:nbn:de:0030-drops-231832},
  doi =		{10.4230/LIPIcs.SoCG.2025.31},
  annote =	{Keywords: Convex polygons, shape matching, prune-and-search, parametric search}
}
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