69 Search Results for "Simpson, Alex"


Volume

LIPIcs, Volume 216

30th EACSL Annual Conference on Computer Science Logic (CSL 2022)

CSL 2022, February 14-19, 2022, Göttingen, Germany (Virtual Conference)

Editors: Florin Manea and Alex Simpson

Document
A Convenient Fibration for Dependently-Typed Probability Theory

Authors: Danel Ahman, Ohad Kammar, and Rasmus Ejlers Møgelberg

Published in: LIPIcs, Volume 380, 41st Annual Symposium on Logic in Computer Science (LICS 2026)


Abstract
We describe semantic structures relevant for interpreting dependent types for statistical and probabilistic modelling. Our development extends the theory of quasi-Borel spaces (qbses) of Staton et. al, which support simply-typed, higher-order probability theory with continuous distributions. It is well-known that qbses can interpret a dependent-type theory supporting dependent function-spaces through the codomain fibration. We define an equivalent split fibration based on the family fibration, which we call quasi-Borel families (qbfs), characterise its structure, equip it with fibred monads of measures and probability, and use them to develop dependently-typed probability theory. We characterise the structure of the qbf fibration that is relevant for dependently-typed probability theory in elementary form. Our characterisations include: context extension, dependent pairs, dependent functions, extensional identity types, fibred products and coproducts, subspaces, a universe of propositions, and straightforward internalisation and externalisation principles for discrete spaces. We use these concepts to define fibred distribution and probability monads, the semantic structure needed to interpret probability distributions under a dependent context. We show that this structure satisfies a fibred version of Kock’s synthetic measure theory. We also use these concepts to develop a qbs counterpart to Kolmogorov’s conditional expectation. Our main result is a version of the conditional expectation that, under standard regularity assumptions, is measurable in both the random variables we are conditioning, and the observation map we are conditioning by.

Cite as

Danel Ahman, Ohad Kammar, and Rasmus Ejlers Møgelberg. A Convenient Fibration for Dependently-Typed Probability Theory. In 41st Annual Symposium on Logic in Computer Science (LICS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 380, pp. 4:1-4:27, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)


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@InProceedings{ahman_et_al:LIPIcs.LICS.2026.4,
  author =	{Ahman, Danel and Kammar, Ohad and M{\o}gelberg, Rasmus Ejlers},
  title =	{{A Convenient Fibration for Dependently-Typed Probability Theory}},
  booktitle =	{41st Annual Symposium on Logic in Computer Science (LICS 2026)},
  pages =	{4:1--4:27},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-434-5},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{380},
  editor =	{Faggian, Claudia and Katoen, Joost-Pieter},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.LICS.2026.4},
  URN =		{urn:nbn:de:0030-drops-267915},
  doi =		{10.4230/LIPIcs.LICS.2026.4},
  annote =	{Keywords: probability theory, quasi-Borel space, Grothendieck fibration, fibred monad, conditional expectation, measure theory, random variables, dependent types, quasitopos, probabilistic programming, denotational semantics, synthetic measure theory}
}
Document
SwiftQueue: Optimizing Low-Latency Applications with Swift Packet Queuing

Authors: Siddhant Ray, Xi Jiang, Jack Luo, Nick Feamster, and Junchen Jiang

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


Abstract
Low Latency, Low Loss, and Scalable Throughput (L4S), as an emerging router-queue management technique, has seen steady deployment in the industry. An L4S-enabled router assigns each packet to the queue based on the packet header marking. Currently, L4S employs per-flow queue selection, i.e., all packets of a flow are marked the same way and thus use the same queues, even though each packet is marked separately. However, this may hurt tail latency and latency-sensitive applications because transient congestion and queue buildups may only affect a fraction of packets in a flow. We present SwiftQueue, a new L4S queue-selection strategy in which a sender uses a novel per-packet latency predictor to pinpoint which packets likely have latency spikes or drops. The insight is that many packet-level latency variations result from complex interactions among recent packets at shared router queues. Yet, these intricate packet-level latency patterns are hard to learn efficiently by traditional models. Instead, SwiftQueue uses a custom Transformer, which is well-studied for its expressiveness on sequential patterns, to predict the next packet’s latency based on the latencies of recently received ACKs. Based on the predicted latency of each outgoing packet, SwiftQueue’s sender dynamically marks the L4S packet header to assign packets to potentially different queues, even within the same flow. Using real network traces, we show that SwiftQueue is 45-65% more accurate in predicting latency and its variations than state-of-art methods. Based on its latency prediction, SwiftQueue reduces the tail latency for L4S-enabled flows by 36-45%, compared with the existing L4S queue-selection method.

Cite as

Siddhant Ray, Xi Jiang, Jack Luo, Nick Feamster, and Junchen Jiang. SwiftQueue: Optimizing Low-Latency Applications with Swift Packet Queuing. In 1st New Ideas in Networked Systems (NINeS 2026). Open Access Series in Informatics (OASIcs), Volume 139, pp. 24:1-24:29, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)


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@InProceedings{ray_et_al:OASIcs.NINeS.2026.24,
  author =	{Ray, Siddhant and Jiang, Xi and Luo, Jack and Feamster, Nick and Jiang, Junchen},
  title =	{{SwiftQueue: Optimizing Low-Latency Applications with Swift Packet Queuing}},
  booktitle =	{1st New Ideas in Networked Systems (NINeS 2026)},
  pages =	{24:1--24:29},
  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.2026.24},
  URN =		{urn:nbn:de:0030-drops-256093},
  doi =		{10.4230/OASIcs.NINeS.2026.24},
  annote =	{Keywords: Latency prediction, L4S Queue Management}
}
Document
Accio: Rethinking OS-Architecture Co-Design for Next-Gen I/O

Authors: Amirmohammad Nazari, Rajit Manohar, and Robert Soulé

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


Abstract
In this paper, we propose a novel software/hardware design to improve I/O performance while maintaining existing POSIX-standard APIs. Our approach stands in contrast to existing kernel-bypass strategies that improve performance at the expense of abandoning familiar programming abstractions. Our key insight is that navigating the performance-functionality trade-off requires changes to the processor; it cannot be done without support of the CPU micro-architecture. Our design, called Accio, includes: dedicated hardware for interrupt management, a hardware assist for thread scheduling, tables in hardware that manage I/O state, and modifications to the operating system to support the new hardware. Our evaluation demonstrates that Accio saturates the bus bandwidth, reduces CPU usage by up to 66% compared to state-of-the-art kernel-bypass systems, and reduces latency to 1/12th of that of the Linux kernel, matching that of kernel-bypass systems.

Cite as

Amirmohammad Nazari, Rajit Manohar, and Robert Soulé. Accio: Rethinking OS-Architecture Co-Design for Next-Gen I/O. In 1st New Ideas in Networked Systems (NINeS 2026). Open Access Series in Informatics (OASIcs), Volume 139, pp. 21:1-21:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)


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@InProceedings{nazari_et_al:OASIcs.NINeS.2026.21,
  author =	{Nazari, Amirmohammad and Manohar, Rajit and Soul\'{e}, Robert},
  title =	{{Accio: Rethinking OS-Architecture Co-Design for Next-Gen I/O}},
  booktitle =	{1st New Ideas in Networked Systems (NINeS 2026)},
  pages =	{21:1--21:24},
  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.2026.21},
  URN =		{urn:nbn:de:0030-drops-256063},
  doi =		{10.4230/OASIcs.NINeS.2026.21},
  annote =	{Keywords: Networks, Operating Systems, I/O Optimization}
}
Document
Useful Call-by-Value: A Semantic Interpretation via Quantitative Types

Authors: Pablo Barenbaum, Delia Kesner, and Mariana Milicich

Published in: LIPIcs, Volume 363, 34th EACSL Annual Conference on Computer Science Logic (CSL 2026)


Abstract
Useful evaluation is an optimised evaluation mechanism for functional programming languages. It relies on representing terms with sharing and imposing a restricted notion of useful substitutions, that intuitively disallows copying subterms that do not contribute to the progress of the computation. In particular, useful call-by-value evaluation optimises the standard call-by-value strategy by preserving its original semantics. This preservation result has been shown by means of syntactical rewriting techniques, difficult to adapt to alternative variants of the calculi at play. In this work, we present the first semantic model of useful call-by-value evaluation through the non-idempotent intersection type system 𝒰. Our first contribution is a characterisation of termination for useful call-by-value evaluation via system 𝒰. That is, a term is typable in system 𝒰 if and only if it terminates in the useful call-by-value strategy. As a second contribution, we show that system 𝒰 provides a quantitative interpretation for useful call-by-value evaluation, offering exact step-count information for program evaluation. Our third contribution is that termination in call-by-value and useful call-by-value are equivalent. This ensures in particular that call-by-value, which is (potentially) erasing, and useful call-by-value, which is non-erasing, are observationally equivalent. Even though the specification of the operational semantics of useful evaluation is highly complex, system 𝒰 is notably simple. As far as we know, system 𝒰 is one of the scarce quantitative type systems capturing exactly the substitution step-count for variables and abstractions in an open call-by-value strategy.

Cite as

Pablo Barenbaum, Delia Kesner, and Mariana Milicich. Useful Call-by-Value: A Semantic Interpretation via Quantitative Types. In 34th EACSL Annual Conference on Computer Science Logic (CSL 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 363, pp. 47:1-47:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)


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@InProceedings{barenbaum_et_al:LIPIcs.CSL.2026.47,
  author =	{Barenbaum, Pablo and Kesner, Delia and Milicich, Mariana},
  title =	{{Useful Call-by-Value: A Semantic Interpretation via Quantitative Types}},
  booktitle =	{34th EACSL Annual Conference on Computer Science Logic (CSL 2026)},
  pages =	{47:1--47:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-411-6},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{363},
  editor =	{Guerrini, Stefano and K\"{o}nig, Barbara},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CSL.2026.47},
  URN =		{urn:nbn:de:0030-drops-254721},
  doi =		{10.4230/LIPIcs.CSL.2026.47},
  annote =	{Keywords: Lambda calculus, Evaluation strategies, Call-by-Value, Useful Evaluation, Intersection types, Quantitative models}
}
Document
Cyclic Proof Theory of Generalised Inductive Definitions

Authors: Gianluca Curzi and Lukas Melgaard

Published in: LIPIcs, Volume 363, 34th EACSL Annual Conference on Computer Science Logic (CSL 2026)


Abstract
We study cyclic proof systems for μPA, an extension of Peano arithmetic by generalised inductive definitions that is arithmetically equivalent to the (impredicative) subsystem of second-order arithmetic Π^1_2-CA₀ by Möllerfeld. The main result of this paper is that cyclic and inductive μPA have the same proof-theoretic strength. First, we translate cyclic proofs into an annotated variant based on Sprenger and Dam’s systems for first-order μ-calculus, whose stronger validity condition allows for a simpler proof of soundness. We then formalise this argument within Π^1_2-CA₀, leveraging Möllerfeld’s conservativity properties. To this end, we build on prior work by Curzi and Das on the reverse mathematics of the Knaster-Tarski theorem. As a byproduct of our proof methods we show that, despite the stronger validity condition, annotated and "plain" cyclic proofs for μPA prove the same theorems. This work represents a further step in the non-wellfounded proof-theoretic analysis of theories of arithmetic via impredicative fragments of second-order arithmetic, an approach initiated by Simpson’s Cyclic Arithmetic, and continued by Das and Melgaard in the context of arithmetical inductive definitions.

Cite as

Gianluca Curzi and Lukas Melgaard. Cyclic Proof Theory of Generalised Inductive Definitions. In 34th EACSL Annual Conference on Computer Science Logic (CSL 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 363, pp. 15:1-15:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)


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@InProceedings{curzi_et_al:LIPIcs.CSL.2026.15,
  author =	{Curzi, Gianluca and Melgaard, Lukas},
  title =	{{Cyclic Proof Theory of Generalised Inductive Definitions}},
  booktitle =	{34th EACSL Annual Conference on Computer Science Logic (CSL 2026)},
  pages =	{15:1--15:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-411-6},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{363},
  editor =	{Guerrini, Stefano and K\"{o}nig, Barbara},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CSL.2026.15},
  URN =		{urn:nbn:de:0030-drops-254399},
  doi =		{10.4230/LIPIcs.CSL.2026.15},
  annote =	{Keywords: cyclic proofs, positive inductive definitions, arithmetic, fixed points, proof theory, reset proof systems}
}
Document
Invited Talk
Automata and Algebras for Probability and Nondeterminism (Invited Talk)

Authors: Ana Sokolova

Published in: LIPIcs, Volume 363, 34th EACSL Annual Conference on Computer Science Logic (CSL 2026)


Abstract
Probabilistic models of computation have been studied for over three decades now, from foundational, logical, coalgebraic, categorical, as well as more practical verification-motivated point of view. In my work, and in this talk, we focus on the foundational, semantics side of probabilistic automata and transition systems, and in particular the relevant monads, and their algebras. The interplay of probability and non-determinism has been particularly challenging from a semantics point of view for some decades, as it does not just yield a monad. There are by now well-studied solutions to this and several monads for probability and non-determinism: some enriching the structure with convexity to obtain a monad, albeit a non-commutative one, others deliberately simplifying it, by imposing commutativity. It is well known that monads have two faces: a computational one - we think here of the powerset monad modelling non-determinism, or the probability distribution monad modelling probabilistic choices, and a universal-algebraic one - where we think of the algebraic presentation of the monads, like semilattices for the powerset monad and (variants of) convex algebras for (variants of) the probability distribution monad. Combining non-determinism and probability yields other combined monads, among which probably the most studied is the convex-subsets-of-distributions monad. This monad is presented by so-called convex semilattices, algebraic structures that are both a semilattice and a convex algebra, with suitable distributivity connecting the operations. From a semantics point of view, the algebraic presentations give us a nice way to define (and sometimes compute) language (aka trace) equivalence of the corresponding automata. Moreover, the presentations are useful for axiomatizations of language equivalence. From an algebraic point of view, these algebras are interesting and many questions about them are still open. We will discuss language semantics, its axiomatization, as well as some obtained and open algebraic problems for convex algebras and convex semilattices - and their computational consequences. In particular, we have a full characterization of congruences of (variants of) convex algebras, which for example yields decidability of distribution semantics; other results on congruences, e.g. a result on a congruence being finitely generated as a subalgebra, surprisingly accellerated the proof of completeness of infinite trace semanitcs, etc. We will review some existing results: all congruences are described and fp = fg for convex algebras, termination is a black hole, useful functors are proper on convex algebras, cancellativity of convex semi-lattices; as well as mention ongoing work on: mid-point-cancellativity, subalgebras, and homomorphisms for convex semi-lattices, as well as topological convex semilattices. This talk is based on previous joint works with Filippo Bonchi, Alexandra Silva, Valeria Vignudelli, and Harald Woracek, as well as on ongoing work and discussions with Matteo Mio, Alex Simpson, and Harald Woracek.

Cite as

Ana Sokolova. Automata and Algebras for Probability and Nondeterminism (Invited Talk). In 34th EACSL Annual Conference on Computer Science Logic (CSL 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 363, p. 5:1, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)


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@InProceedings{sokolova:LIPIcs.CSL.2026.5,
  author =	{Sokolova, Ana},
  title =	{{Automata and Algebras for Probability and Nondeterminism}},
  booktitle =	{34th EACSL Annual Conference on Computer Science Logic (CSL 2026)},
  pages =	{5:1--5:1},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-411-6},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{363},
  editor =	{Guerrini, Stefano and K\"{o}nig, Barbara},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CSL.2026.5},
  URN =		{urn:nbn:de:0030-drops-254295},
  doi =		{10.4230/LIPIcs.CSL.2026.5},
  annote =	{Keywords: probabilistic transition systems and automata, Labelled Markov processes, Markov decision processes, convex algebras, convex semilattices, coalgebraic semantics}
}
Document
A Modular Framework for Proof-Search via Formalised Modal Completeness in HOL Light

Authors: Antonella Bilotta, Marco Maggesi, and Cosimo Perini Brogi

Published in: LIPIcs, Volume 363, 34th EACSL Annual Conference on Computer Science Logic (CSL 2026)


Abstract
We extend the existing HOL Light Library for Modal Systems (HOLMS) to support a modular implementation of modal reasoning within the HOL Light proof assistant. We deeply embed axiomatic calculi and relational semantics for seven normal modal logics (K, T, B, K4, S4, S5, GL) and formalise modal adequacy theorems for these systems. We then leverage those formalisations to implement a mechanism for automated reasoning via proof-search in the associated labelled sequent calculi, which we shallowly embed in HOL Light’s goal-stack mechanism. This way, we equip the general-purpose proof assistant with (semi)decision procedures for these logics that, in case of failure to construct a proof for the input formula, return a certified countermodel within the appropriate class for the logic under consideration. On the methodological side, we propose a precise measure of the modularity of our approach by systematically adopting Christopher Strachey’s distinction between ad hoc and parametric polymorphism throughout the library.

Cite as

Antonella Bilotta, Marco Maggesi, and Cosimo Perini Brogi. A Modular Framework for Proof-Search via Formalised Modal Completeness in HOL Light. In 34th EACSL Annual Conference on Computer Science Logic (CSL 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 363, pp. 18:1-18:29, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)


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@InProceedings{bilotta_et_al:LIPIcs.CSL.2026.18,
  author =	{Bilotta, Antonella and Maggesi, Marco and Perini Brogi, Cosimo},
  title =	{{A Modular Framework for Proof-Search via Formalised Modal Completeness in HOL Light}},
  booktitle =	{34th EACSL Annual Conference on Computer Science Logic (CSL 2026)},
  pages =	{18:1--18:29},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-411-6},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{363},
  editor =	{Guerrini, Stefano and K\"{o}nig, Barbara},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CSL.2026.18},
  URN =		{urn:nbn:de:0030-drops-254427},
  doi =		{10.4230/LIPIcs.CSL.2026.18},
  annote =	{Keywords: Modal logic, HOL Light, Labelled sequent calculi, Logical verification, Interactive theorem proving, Automated proof-search}
}
Document
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.

Cite as

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
Just Verification of Mutual Exclusion Algorithms

Authors: Rob van Glabbeek, Bas Luttik, and Myrthe S. C. Spronck

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


Abstract
We verify the correctness of a variety of mutual exclusion algorithms through model checking. We look at algorithms where communication is via shared read/write registers, where those registers can be atomic or non-atomic. For the verification of liveness properties, it is necessary to assume a completeness criterion to eliminate spurious counterexamples. We use justness as completeness criterion. Justness depends on a concurrency relation; we consider several such relations, modelling different assumptions on the working of the shared registers. We present executions demonstrating the violation of correctness properties by several algorithms, and in some cases suggest improvements.

Cite as

Rob van Glabbeek, Bas Luttik, and Myrthe S. C. Spronck. Just Verification of Mutual Exclusion Algorithms. In 36th International Conference on Concurrency Theory (CONCUR 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 348, pp. 17:1-17:25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)


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@InProceedings{vanglabbeek_et_al:LIPIcs.CONCUR.2025.17,
  author =	{van Glabbeek, Rob and Luttik, Bas and Spronck, Myrthe S. C.},
  title =	{{Just Verification of Mutual Exclusion Algorithms}},
  booktitle =	{36th International Conference on Concurrency Theory (CONCUR 2025)},
  pages =	{17:1--17:25},
  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.2025.17},
  URN =		{urn:nbn:de:0030-drops-239670},
  doi =		{10.4230/LIPIcs.CONCUR.2025.17},
  annote =	{Keywords: Mutual exclusion, safe registers, regular registers, overlapping reads and writes, atomicity, safety, liveness, starvation freedom, justness, model checking, mCRL2}
}
Document
DiVerG: Scalable Distance Index for Validation of Paired-End Alignments in Sequence Graphs

Authors: Ali Ghaffaari, Alexander Schönhuth, and Tobias Marschall

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


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

Cite as

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


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

Authors: Quentin Aristote

Published in: LIPIcs, Volume 342, 11th Conference on Algebra and Coalgebra in Computer Science (CALCO 2025)


Abstract
We give a new proof of a result from well quasi-order theory on the computability of bases for upwards-closed sets of words. This new proof is based on Angluin’s L* algorithm, that learns an automaton from a minimally adequate teacher. This relates in particular two results from the 1980s: Angluin’s L* algorithm, and a result from Valk and Jantzen on the computability of bases for upwards-closed sets of tuples of integers. Along the way, we describe an algorithm for learning quasi-ordered automata from a minimally adequate teacher, and extend a generalization of Valk and Jantzen’s result, encompassing both words and integers, to finitely generated monoids.

Cite as

Quentin Aristote. Active Learning of Upward-Closed Sets of Words ((Co)algebraic pearl). In 11th Conference on Algebra and Coalgebra in Computer Science (CALCO 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 342, pp. 16:1-16:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)


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@InProceedings{aristote:LIPIcs.CALCO.2025.16,
  author =	{Aristote, Quentin},
  title =	{{Active Learning of Upward-Closed Sets of Words}},
  booktitle =	{11th Conference on Algebra and Coalgebra in Computer Science (CALCO 2025)},
  pages =	{16:1--16:12},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-383-6},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{342},
  editor =	{C\^{i}rstea, Corina and Knapp, Alexander},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CALCO.2025.16},
  URN =		{urn:nbn:de:0030-drops-235751},
  doi =		{10.4230/LIPIcs.CALCO.2025.16},
  annote =	{Keywords: active learning, well quasi-orders, Valk-Jantzen lemma, piecewise-testable languages, monoids}
}
Document
Invited Talk
Computation First: Rebuilding Constructivism with Effects (Invited Talk)

Authors: Liron Cohen

Published in: LIPIcs, Volume 337, 10th International Conference on Formal Structures for Computation and Deduction (FSCD 2025)


Abstract
Constructive logic and type theory have traditionally been grounded in pure, effect-free model of computation. This paper argues that such a restriction is not a foundational necessity but a historical artifact, and it advocates for a broader perspective of effectful constructivism, where computational effects, such as state, non-determinism, and exceptions, are directly and internally embedded in the logical and computational foundations. We begin by surveying examples where effects reshape logical principles, and then outline three approaches to effectful constructivism, focusing on realizability models: Monadic Combinatory Algebras, which extend classical partial combinatory algebras with effectful computation; Evidenced Frames, a flexible semantic structure capable of uniformly capturing a wide range of effects; and Effectful Higher-Order Logic (EffHOL), a syntactic approach that directly translates logical propositions into specifications for effectful programs. We further illustrate how concrete type theories can internalize effects, via the family of type theories TT^□_C. Together, these works demonstrate that effectful constructivism is not merely possible but a natural and robust extension of traditional frameworks.

Cite as

Liron Cohen. Computation First: Rebuilding Constructivism with Effects (Invited Talk). In 10th International Conference on Formal Structures for Computation and Deduction (FSCD 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 337, pp. 1:1-1:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)


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@InProceedings{cohen:LIPIcs.FSCD.2025.1,
  author =	{Cohen, Liron},
  title =	{{Computation First: Rebuilding Constructivism with Effects}},
  booktitle =	{10th International Conference on Formal Structures for Computation and Deduction (FSCD 2025)},
  pages =	{1:1--1:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-374-4},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{337},
  editor =	{Fern\'{a}ndez, Maribel},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FSCD.2025.1},
  URN =		{urn:nbn:de:0030-drops-236167},
  doi =		{10.4230/LIPIcs.FSCD.2025.1},
  annote =	{Keywords: Effectful constructivism, realizability, type theory, monadic combinatory algebras, evidenced frame}
}
Document
The Cost of Skeletal Call-By-Need, Smoothly

Authors: Beniamino Accattoli, Francesco Magliocca, Loïc Peyrot, and Claudio Sacerdoti Coen

Published in: LIPIcs, Volume 337, 10th International Conference on Formal Structures for Computation and Deduction (FSCD 2025)


Abstract
Skeletal call-by-need is an optimization of call-by-need evaluation also known as "fully lazy sharing": when the duplication of a value has to take place, it is first split into "skeleton", which is then duplicated, and "flesh" which is instead kept shared. Here, we provide two cost analyses of skeletal call-by-need. Firstly, we provide a family of terms showing that skeletal call-by-need can be asymptotically exponentially faster than call-by-need in both time and space; it is the first such evidence, to our knowledge. Secondly, we prove that skeletal call-by-need can be implemented efficiently, that is, with bi-linear overhead. This result is obtained by providing a new smooth presentation of ideas by Shivers and Wand for the reconstruction of skeletons, which is then smoothly plugged into the study of an abstract machine following the distillation technique by Accattoli et al.

Cite as

Beniamino Accattoli, Francesco Magliocca, Loïc Peyrot, and Claudio Sacerdoti Coen. The Cost of Skeletal Call-By-Need, Smoothly. In 10th International Conference on Formal Structures for Computation and Deduction (FSCD 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 337, pp. 5:1-5:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)


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@InProceedings{accattoli_et_al:LIPIcs.FSCD.2025.5,
  author =	{Accattoli, Beniamino and Magliocca, Francesco and Peyrot, Lo\"{i}c and Sacerdoti Coen, Claudio},
  title =	{{The Cost of Skeletal Call-By-Need, Smoothly}},
  booktitle =	{10th International Conference on Formal Structures for Computation and Deduction (FSCD 2025)},
  pages =	{5:1--5:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-374-4},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{337},
  editor =	{Fern\'{a}ndez, Maribel},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FSCD.2025.5},
  URN =		{urn:nbn:de:0030-drops-236206},
  doi =		{10.4230/LIPIcs.FSCD.2025.5},
  annote =	{Keywords: \lambda-calculus, abstract machines, call-by-need, cost models}
}
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