25 Search Results for "Simpson, Michael"

Document
DOI: 10.4230/LIPIcs.STACS.2026.5
On the Complexity of Language Membership for Probabilistic Words

Authors: Antoine Amarilli, Mikaël Monet, Paul Raphaël, and Sylvain Salvati

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

Abstract
We study the membership problem to context-free languages L (CFLs) on probabilistic words, that specify for each position a probability distribution on the letters (assuming independence across positions). Our task is to compute, given a probabilistic word, what is the probability that a word drawn according to the distribution belongs to L. This problem generalizes the problem of counting how many words of length n belong to L, or of counting how many completions of a partial word belong to L. We show that this problem is in polynomial time for unambiguous context-free languages (uCFLs), but can be #P-hard already for unions of two linear uCFLs. More generally, we show that the problem is in polynomial time for so-called poly-slicewise-unambiguous languages, where given a length n we can tractably compute an uCFL for the words of length n in the language. This class includes some inherently ambiguous languages, and implies the tractability of bounded CFLs and of languages recognized by unambiguous polynomial-time counter automata; but we show that the problem can be #P-hard for nondeterministic counter automata, even for Parikh automata with a single counter. We then introduce classes of circuits from knowledge compilation which we use for tractable counting, and show that this covers the tractability of poly-slicewise-unambiguous languages and of some CFLs that are not poly-slicewise-unambiguous. Extending these circuits with negation further allows us to show tractability for the language of primitive words, and for the language of concatenations of two palindromes. We finally show the conditional undecidability of the meta-problem that asks, given a CFG, whether the probabilistic membership problem for that CFG is tractable or #P-hard.
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Antoine Amarilli, Mikaël Monet, Paul Raphaël, and Sylvain Salvati. On the Complexity of Language Membership for Probabilistic Words. In 43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 364, pp. 5:1-5:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{amarilli_et_al:LIPIcs.STACS.2026.5,
  author =	{Amarilli, Antoine and Monet, Mika\"{e}l and Rapha\"{e}l, Paul and Salvati, Sylvain},
  title =	{{On the Complexity of Language Membership for Probabilistic Words}},
  booktitle =	{43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026)},
  pages =	{5:1--5:21},
  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.2026.5},
  URN =		{urn:nbn:de:0030-drops-254943},
  doi =		{10.4230/LIPIcs.STACS.2026.5},
  annote =	{Keywords: Automaton, probabilistic words, context-free grammar, membership problem}
}
Document
DOI: 10.4230/LIPIcs.CSL.2026.18
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.
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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
DOI: 10.4230/LIPIcs.CSL.2026.15
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.
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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
DOI: 10.4230/LIPIcs.CSL.2026.47
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.
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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
DOI: 10.4230/LIPIcs.ITCS.2026.52
Diffie-Hellman Key Exchange from Commutativity to Group Laws

Authors: Dung Hoang Duong, Youming Qiao, and Chuanqi Zhang

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

Abstract
In Diffie-Hellman key exchange, the commutativity of power operations is instrumental in the agreement of keys. Viewing commutativity as a law in abelian groups, we propose Diffie-Hellman key exchange in the group action framework (Brassard-Yung, Crypto'90; Ji-Qiao-Song-Yun, TCC'19), for actions of non-abelian groups with laws. The security of this protocol is shown, following Fischlin, Günther, Schmidt, and Warinschi (IEEE S&P'16), based on a pseudorandom group action assumption. A concrete instantiation is proposed based on the monomial code equivalence problem.
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Dung Hoang Duong, Youming Qiao, and Chuanqi Zhang. Diffie-Hellman Key Exchange from Commutativity to Group Laws. In 17th Innovations in Theoretical Computer Science Conference (ITCS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 362, pp. 52:1-52:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{duong_et_al:LIPIcs.ITCS.2026.52,
  author =	{Duong, Dung Hoang and Qiao, Youming and Zhang, Chuanqi},
  title =	{{Diffie-Hellman Key Exchange from Commutativity to Group Laws}},
  booktitle =	{17th Innovations in Theoretical Computer Science Conference (ITCS 2026)},
  pages =	{52:1--52:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-410-9},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{362},
  editor =	{Saraf, Shubhangi},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITCS.2026.52},
  URN =		{urn:nbn:de:0030-drops-253396},
  doi =		{10.4230/LIPIcs.ITCS.2026.52},
  annote =	{Keywords: Diffie-Hellman, Key Exchange, Group Laws, Group Actions, Code Equivalence}
}
Document
DOI: 10.4230/LIPIcs.MFCS.2025.36
Counting Distinct Square Substrings in Sublinear Time

Authors: Panagiotis Charalampopoulos, Manal Mohamed, Jakub Radoszewski, Wojciech Rytter, Tomasz Waleń, and Wiktor Zuba

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

Abstract
We show that the number of distinct squares in a packed string of length n over an alphabet of size σ can be computed in 𝒪(n/log_{σ}n) time in the word-RAM model of computation. This paper is the first to introduce a sublinear time algorithm for the packed version of squares counting. The packed representation of a string of length n over an alphabet of size σ is given as a sequence of 𝒪(n/ log_{σ} n) machine words in the word-RAM model (a machine word consists of ω ≥ log₂ n bits). Previously it was known how to count distinct squares in 𝒪(n) time [Gusfield and Stoye, JCSS 2004], even for a string over an integer alphabet, see [Crochemore et al., TCS 2014; Bannai et al., CPM 2017; Charalampopoulos et al., SPIRE 2020]. We use techniques of squares extraction from runs described by Crochemore et al. [TCS 2014]. However, the packed model requires novel approaches. In particular, we need an 𝒪(n/log_{σ}n) sized representation of all long-period runs (runs with periods that are Ω(log_{σ}n)) which guarantees sublinear time counting of potentially linearly-many implied squares. The long-period runs with a string period that is periodic itself (called layer runs) are an obstacle, since their number can be Ω(n). Fortunately, the number of all other long-period runs is 𝒪(n/log_{σ}n) and we can construct an implicit representation of all long-period runs in 𝒪(n/log_{σ}n) time by adopting the insights of Amir et al. [ESA 2019], combined with sublinear time tools provided by the PILLAR model of computations in case of packed strings. We count squares in layer runs in sublinear time by exploiting combinatorial properties of types of pyramidally-shaped groups of layer runs. As a by-product, we discover several new structural properties of runs. Another difficulty is to compute, in sublinear time, locations of Lyndon roots of runs in packed strings, which is needed for grouping of runs that can generate equal squares. To overcome this difficulty, we introduce sparse-Lyndon roots which are based on the notion of string synchronizers proposed by Kempa and Kociumaka [STOC 2019].
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Panagiotis Charalampopoulos, Manal Mohamed, Jakub Radoszewski, Wojciech Rytter, Tomasz Waleń, and Wiktor Zuba. Counting Distinct Square Substrings in Sublinear Time. In 50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 345, pp. 36:1-36:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{charalampopoulos_et_al:LIPIcs.MFCS.2025.36,
  author =	{Charalampopoulos, Panagiotis and Mohamed, Manal and Radoszewski, Jakub and Rytter, Wojciech and Wale\'{n}, Tomasz and Zuba, Wiktor},
  title =	{{Counting Distinct Square Substrings in Sublinear Time}},
  booktitle =	{50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025)},
  pages =	{36:1--36:19},
  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.2025.36},
  URN =		{urn:nbn:de:0030-drops-241439},
  doi =		{10.4230/LIPIcs.MFCS.2025.36},
  annote =	{Keywords: square in a string, packed model, run (maximal repetition), Lyndon word}
}
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.CONCUR.2025.17
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.
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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
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
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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/OASIcs.Manzini.3
BWT for String Collections

Authors: Davide Cenzato, Zsuzsanna Lipták, Nadia Pisanti, Giovanna Rosone, and Marinella Sciortino

Published in: OASIcs, Volume 131, The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday (2025)

Abstract
We survey the different methods used for extending the BWT to collections of strings, following largely [Cenzato and Lipták, CPM 2022, Bioinformatics 2024]. We analyze the specific aspects and combinatorial properties of the resulting BWT variants and give a categorization of publicly available tools for computing the BWT of string collections. We show how the specific method used impacts on the resulting transform, including the number of runs, and on the dynamicity of the transform with respect to adding or removing strings from the collection. We then focus on the number of runs of these BWT variants and present the optimal BWT introduced in [Cenzato et al., DCC 2023], which implements an algorithm originally proposed by [Bentley et al., ESA 2020] to minimize the number of BWT-runs. We also discuss several recent heuristics and study their impact on the compression of biological sequences. We conclude with an overview of the applications and the impact of the BWT of string collections in bioinformatics.
Cite as

Davide Cenzato, Zsuzsanna Lipták, Nadia Pisanti, Giovanna Rosone, and Marinella Sciortino. BWT for String Collections. In The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday. Open Access Series in Informatics (OASIcs), Volume 131, pp. 3:1-3:29, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{cenzato_et_al:OASIcs.Manzini.3,
  author =	{Cenzato, Davide and Lipt\'{a}k, Zsuzsanna and Pisanti, Nadia and Rosone, Giovanna and Sciortino, Marinella},
  title =	{{BWT for String Collections}},
  booktitle =	{The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday},
  pages =	{3:1--3:29},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-390-4},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{131},
  editor =	{Ferragina, Paolo and Gagie, Travis and Navarro, Gonzalo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.Manzini.3},
  URN =		{urn:nbn:de:0030-drops-239113},
  doi =		{10.4230/OASIcs.Manzini.3},
  annote =	{Keywords: Burrows-Wheeler transform, Extended Burrows-Wheeler transform, compressed text indexes, text compression, string collections, bioinformatics}
}
Document
DOI: 10.4230/OASIcs.Manzini.1
BWT and Combinatorics on Words

Authors: Gabriele Fici, Sabrina Mantaci, Antonio Restivo, Giuseppe Romana, Giovanna Rosone, and Marinella Sciortino

Published in: OASIcs, Volume 131, The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday (2025)

Abstract
The Burrows-Wheeler Transform (BWT) is a reversible transformation on words (strings) introduced in 1994 in the context of data compression, which is a permutation of the characters in the word. Its clustering effect, i.e., the remarkable property of grouping identical characters (BWT runs) when they share common contexts, has made it a powerful tool for boosting compression performances and enabling efficient pattern searching in highly repetitive string collections. In this chapter, we analyze the Burrows-Wheeler transform under the combinatorial point of view, and we survey known properties and connections with different aspects of combinatorics on words. In particular, we focus on the properties of words in relation to the number of their BWT runs. The value r, which counts the number of BWT runs, impacts both compression performance and indexing efficiency, and is considered a measure to evaluate the above-mentioned clustering effect and, consequently, the repetitiveness of a word. We give an overview of the results relating r to other combinatorial repetitiveness measures related to the factor complexity. The chapter also explores extremal cases of the clustering effect. Finally, some results on the sensitivity of the measure r are considered, where the effects of combinatorial operations are studied, such as reversal, edits, and the application of morphisms.
Cite as

Gabriele Fici, Sabrina Mantaci, Antonio Restivo, Giuseppe Romana, Giovanna Rosone, and Marinella Sciortino. BWT and Combinatorics on Words. In The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday. Open Access Series in Informatics (OASIcs), Volume 131, pp. 1:1-1:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{fici_et_al:OASIcs.Manzini.1,
  author =	{Fici, Gabriele and Mantaci, Sabrina and Restivo, Antonio and Romana, Giuseppe and Rosone, Giovanna and Sciortino, Marinella},
  title =	{{BWT and Combinatorics on Words}},
  booktitle =	{The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday},
  pages =	{1:1--1:23},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-390-4},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{131},
  editor =	{Ferragina, Paolo and Gagie, Travis and Navarro, Gonzalo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.Manzini.1},
  URN =		{urn:nbn:de:0030-drops-239090},
  doi =		{10.4230/OASIcs.Manzini.1},
  annote =	{Keywords: Burrows-Wheeler Transform, Combinatorics on Words, Clustering Effect, BWT Runs}
}
Document
DOI: 10.4230/OASIcs.Manzini.7
Algorithms for Computing Very Large BWTs: a Short Survey

Authors: Diego Díaz-Domínguez, Lavinia Egidi, Veronica Guerrini, Felipe A. Louza, and Giovanna Rosone

Published in: OASIcs, Volume 131, The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday (2025)

Abstract
The Burrows-Wheeler Transform (BWT) is a fundamental string transformation that, although initially introduced for data compression, has been extensively utilized across various domains, including text indexing and pattern matching within large datasets. Although the BWT construction is linear, the constants make the task impractical for large datasets, and as highlighted by Ferragina et al. [Paolo Ferragina et al., 2012], "to use it, one must first build it!". Thus, the construction of the BWT remains a significant challenge. For these reasons, during the past three decades there has been a succession of new algorithms for its construction using techniques that work in external memory or that use text compression. In this survey, we revise some of the most important advancements and tools presented in the past years for computing large BWTs exploiting external memory or text compression approaches without using additional information about the data.
Cite as

Diego Díaz-Domínguez, Lavinia Egidi, Veronica Guerrini, Felipe A. Louza, and Giovanna Rosone. Algorithms for Computing Very Large BWTs: a Short Survey. In The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday. Open Access Series in Informatics (OASIcs), Volume 131, pp. 7:1-7:28, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{diazdominguez_et_al:OASIcs.Manzini.7,
  author =	{D{\'\i}az-Dom{\'\i}nguez, Diego and Egidi, Lavinia and Guerrini, Veronica and Louza, Felipe A. and Rosone, Giovanna},
  title =	{{Algorithms for Computing Very Large BWTs: a Short Survey}},
  booktitle =	{The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday},
  pages =	{7:1--7:28},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-390-4},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{131},
  editor =	{Ferragina, Paolo and Gagie, Travis and Navarro, Gonzalo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.Manzini.7},
  URN =		{urn:nbn:de:0030-drops-239151},
  doi =		{10.4230/OASIcs.Manzini.7},
  annote =	{Keywords: Burrows-Wheeler transform, Extended Burrows-Wheeler transform, external memory, text compression, longest common prefix}
}
Document
DOI: 10.4230/LIPIcs.SEA.2025.2
IBB: Fast Burrows-Wheeler Transform Construction for Length-Diverse DNA Data

Authors: Enno Adler, Stefan Böttcher, Rita Hartel, and Cederic Alexander Steininger

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

Abstract
The Burrows-Wheeler transform (BWT) is integral to the FM-index, which is used extensively in text compression, indexing, pattern search, and bioinformatic problems as de novo assembly and read alignment. Thus, efficient construction of the BWT in terms of time and memory usage is key to these applications. We present a novel external-memory algorithm called Improved-Bucket Burrows-Wheeler transform (IBB) for constructing the BWT of DNA datasets with highly diverse sequence lengths. IBB uses a right-aligned approach to efficiently handle sequences of varying lengths, a tree-based data structure to manage relative insert positions and ranks, and fine buckets to reduce the necessary amount of input and output to external memory. Our experiments demonstrate that IBB is 10% to 40% faster than the best existing state-of-the-art BWT construction algorithms on most datasets while maintaining competitive memory consumption.
Cite as

Enno Adler, Stefan Böttcher, Rita Hartel, and Cederic Alexander Steininger. IBB: Fast Burrows-Wheeler Transform Construction for Length-Diverse DNA Data. In 23rd International Symposium on Experimental Algorithms (SEA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 338, pp. 2:1-2:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{adler_et_al:LIPIcs.SEA.2025.2,
  author =	{Adler, Enno and B\"{o}ttcher, Stefan and Hartel, Rita and Steininger, Cederic Alexander},
  title =	{{IBB: Fast Burrows-Wheeler Transform Construction for Length-Diverse DNA Data}},
  booktitle =	{23rd International Symposium on Experimental Algorithms (SEA 2025)},
  pages =	{2:1--2:18},
  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.2025.2},
  URN =		{urn:nbn:de:0030-drops-232402},
  doi =		{10.4230/LIPIcs.SEA.2025.2},
  annote =	{Keywords: burrows-wheeler transform, self-indexes, external-memory}
}
Document
Invited Talk
DOI: 10.4230/LIPIcs.FSCD.2025.1
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}
}
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