24 Search Results for "Bell, Paul C."

Document
DOI: 10.4230/LIPIcs.STACS.2026.23
Simple Circuit Extensions for XOR in PTIME

Authors: Marco Carmosino, Ngu Dang, and Tim Jackman

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

Abstract
The Minimum Circuit Size Problem for Partial Functions (MCSP^*) is hard assuming the Exponential Time Hypothesis (ETH) (Ilango, 2020). This breakthrough result leveraged a characterization of the optimal {∧, ∨, ¬} circuits for n-bit OR (OR_n) and a reduction from the partial f-Simple Extension Problem where f = OR_n. It remains open to extend that reduction to show ETH-hardness of total MCSP. However, Ilango observed that the total f-Simple Extension Problem is easy whenever f is computed by read-once formulas (like OR_n). Therefore, extending Ilango’s proof to total MCSP would require replacing OR_n with a more complex but similarly well-understood Boolean function. This work shows that the f-Simple Extension problem remains easy when f is the next natural candidate: XOR_n. We first develop a fixed-parameter tractable algorithm for the f-Simple Extension Problem that is efficient whenever the optimal circuits for f are (1) linear in size, (2) polynomially "few" and efficiently enumerable in the truth-table size (up to isomorphism and permutation of inputs), and (3) all have constant bounded fan-out. XOR_n satisfies all three of these conditions. When ¬ gates count towards circuit size, optimal XOR_n circuits are binary trees of n-1 subcircuits computing (¬)XOR₂ (Kombarov, 2011). We extend this characterization when ¬ gates do not contribute the circuit size. Thus, the XOR-Simple Extension Problem is in polynomial time under both measures of circuit complexity. We conclude by discussing conjectures about the complexity of the f-Simple Extension problem for each explicit function f with known and unrestricted circuit lower bounds over the DeMorgan basis. Examining the conditions under which our Simple Extension Solver is efficient, we argue that multiplexer functions (MUX) are the most promising candidate for ETH-hardness of a Simple Extension Problem, towards proving ETH-hardness of total MCSP.
Cite as

Marco Carmosino, Ngu Dang, and Tim Jackman. Simple Circuit Extensions for XOR in PTIME. In 43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 364, pp. 23:1-23:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{carmosino_et_al:LIPIcs.STACS.2026.23,
  author =	{Carmosino, Marco and Dang, Ngu and Jackman, Tim},
  title =	{{Simple Circuit Extensions for XOR in PTIME}},
  booktitle =	{43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026)},
  pages =	{23:1--23:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-412-3},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{364},
  editor =	{Mahajan, Meena and Manea, Florin and McIver, Annabelle and Thắng, Nguy\~{ê}n Kim},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.STACS.2026.23},
  URN =		{urn:nbn:de:0030-drops-255127},
  doi =		{10.4230/LIPIcs.STACS.2026.23},
  annote =	{Keywords: Minimum Circuit Size Problem, Circuit Lower Bounds, Exponential Time Hypothesis}
}
Document
DOI: 10.4230/LIPIcs.STACS.2026.60
The Asymptotic Size of Finite Irreducible Semigroups of Rational Matrices

Authors: Stefan Kiefer and Andrew Ryzhikov

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

Abstract
We study finite semigroups of n × n matrices with rational entries. Such semigroups provide a rich generalization of transition monoids of unambiguous (and, in particular, deterministic) finite automata. In this paper we determine the maximum size of finite semigroups of rational n × n matrices, with the goal of shedding more light on the structure of such matrix semigroups. While in general such semigroups can be arbitrarily large in terms of n, a classical result of Schützenberger from 1962 implies an upper bound of 2^{𝒪(n² log n)} for irreducible semigroups, i.e., the only subspaces of ℚⁿ that are invariant for all matrices in the semigroup are ℚⁿ and the subspace consisting only of the zero vector. Irreducible matrix semigroups can be viewed as the building blocks of general matrix semigroups, and as such play an important role in mathematics and computer science. From the point of view of automata theory, they generalize strongly connected automata. Using a very different technique from that of Schützenberger, we improve the upper bound on the cardinality to 3^{n²}. This is the main result of the paper. The bound is in some sense tight, as we show that there exists, for every n, a finite irreducible semigroup with 3^{⌊ n²/4 ⌋} rational matrices. Our main result also leads to an improvement of a bound, due to Almeida and Steinberg, on the mortality threshold. The mortality threshold is a number 𝓁 such that if the zero matrix is in the semigroup, then the zero matrix can be written as a product of at most 𝓁 matrices from any subset that generates the semigroup.
Cite as

Stefan Kiefer and Andrew Ryzhikov. The Asymptotic Size of Finite Irreducible Semigroups of Rational Matrices. In 43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 364, pp. 60:1-60:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{kiefer_et_al:LIPIcs.STACS.2026.60,
  author =	{Kiefer, Stefan and Ryzhikov, Andrew},
  title =	{{The Asymptotic Size of Finite Irreducible Semigroups of Rational Matrices}},
  booktitle =	{43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026)},
  pages =	{60:1--60:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-412-3},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{364},
  editor =	{Mahajan, Meena and Manea, Florin and McIver, Annabelle and Thắng, Nguy\~{ê}n Kim},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.STACS.2026.60},
  URN =		{urn:nbn:de:0030-drops-255496},
  doi =		{10.4230/LIPIcs.STACS.2026.60},
  annote =	{Keywords: finite matrix semigroups, irreducible matrix semigroups, matrix mortality, aperiodic semigroups, unambiguous automata, transition monoids}
}
Document
DOI: 10.4230/LIPIcs.CSL.2026.45
Reasoning About Quality in Hyperproperties

Authors: Samuel Graepler, Benjamin Monmege, and Jean-Marc Talbot

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

Abstract
Hyperproperties allow one to specify properties of systems that inherently involve not single executions of the system, but several of them at once: observational determinism and non-inference are two examples of such properties used to study the security of systems. Logics like HyperLTL have been studied in the past to model check hyperproperties of systems. However, most of the time, requiring strict security properties is actually ineffective as systems do not meet such requirements. To overcome this issue, we introduce qualitative reasoning in HyperLTL, inspired by a similar work on LTL by Almagor, Boker and Kupferman [Almagor et al., 2016] where a formula has a value in the interval [0, 1], obtained by considering either a propositional quality (how much the specification is satisfied), or a temporal quality (when the specification is satisfied). We show decidability of the approximated model checking problem, as well as the model checking of large fragments.
Cite as

Samuel Graepler, Benjamin Monmege, and Jean-Marc Talbot. Reasoning About Quality in Hyperproperties. In 34th EACSL Annual Conference on Computer Science Logic (CSL 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 363, pp. 45:1-45:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{graepler_et_al:LIPIcs.CSL.2026.45,
  author =	{Graepler, Samuel and Monmege, Benjamin and Talbot, Jean-Marc},
  title =	{{Reasoning About Quality in Hyperproperties}},
  booktitle =	{34th EACSL Annual Conference on Computer Science Logic (CSL 2026)},
  pages =	{45:1--45:18},
  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.2026.45},
  URN =		{urn:nbn:de:0030-drops-254704},
  doi =		{10.4230/LIPIcs.CSL.2026.45},
  annote =	{Keywords: Hyperlogics, Automata-based model checking, Quantitative verification}
}
Document
Research
DOI: 10.4230/TGDK.3.3.4
Mining Inter-Document Argument Structures in Scientific Papers for an Argument Web

Authors: Florian Ruosch, Cristina Sarasua, and Abraham Bernstein

Published in: TGDK, Volume 3, Issue 3 (2025). Transactions on Graph Data and Knowledge, Volume 3, Issue 3

Abstract
In Argument Mining, predicting argumentative relations between texts (or spans) remains one of the most challenging aspects, even more so in the cross-document setting. This paper makes three key contributions to advance research in this domain. We first extend an existing dataset, the Sci-Arg corpus, by annotating it with explicit inter-document argumentative relations, thereby allowing arguments to be distributed over several documents forming an Argument Web; these new annotations are published using Semantic Web technologies (RDF, OWL). Second, we explore and evaluate three automated approaches for predicting these inter-document argumentative relations, establishing critical baselines on the new dataset. We find that a simple classifier based on discourse indicators with access to context outperforms neural methods. Third, we conduct a comparative analysis of these approaches for both intra- and inter-document settings, identifying statistically significant differences in results that indicate the necessity of distinguishing between these two scenarios. Our findings highlight significant challenges in this complex domain and open crucial avenues for future research on the Argument Web of Science, particularly for those interested in leveraging Semantic Web technologies and knowledge graphs to understand scholarly discourse. With this, we provide the first stepping stones in the form of a benchmark dataset, three baseline methods, and an initial analysis for a systematic exploration of this field relevant to the Web of Data and Science.
Cite as

Florian Ruosch, Cristina Sarasua, and Abraham Bernstein. Mining Inter-Document Argument Structures in Scientific Papers for an Argument Web. In Transactions on Graph Data and Knowledge (TGDK), Volume 3, Issue 3, pp. 4:1-4:33, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@Article{ruosch_et_al:TGDK.3.3.4,
  author =	{Ruosch, Florian and Sarasua, Cristina and Bernstein, Abraham},
  title =	{{Mining Inter-Document Argument Structures in Scientific Papers for an Argument Web}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{4:1--4:33},
  ISSN =	{2942-7517},
  year =	{2025},
  volume =	{3},
  number =	{3},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.3.3.4},
  URN =		{urn:nbn:de:0030-drops-252159},
  doi =		{10.4230/TGDK.3.3.4},
  annote =	{Keywords: Argument Mining, Large Language Models, Knowledge Graphs, Link Prediction}
}
Document
DOI: 10.4230/LIPIcs.GD.2025.24
String Graph Obstacles of High Girth and of Bounded Degree

Authors: Maria Chudnovsky, David Eppstein, and David Fischer

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

Abstract
A string graph is the intersection graph of curves in the plane. Kratochvíl previously showed the existence of infinitely many obstacles: graphs that are not string graphs but for which any edge contraction or vertex deletion produces a string graph. Kratochvíl’s obstacles contain arbitrarily large cliques, so they have girth three and unbounded degree. We extend this line of working by studying obstacles among graphs of restricted girth and/or degree. We construct an infinite family of obstacles of girth four; in addition, our construction is K_{2,3}-subgraph-free and near-planar (planar plus one edge). Furthermore, we prove that there is a subcubic obstacle of girth three, and that there are no subcubic obstacles of high girth. We characterize the subcubic string graphs as having a matching whose contraction yields a planar graph, and based on this characterization we find a linear-time algorithm for recognizing subcubic string graphs of bounded treewidth.
Cite as

Maria Chudnovsky, David Eppstein, and David Fischer. String Graph Obstacles of High Girth and of Bounded Degree. In 33rd International Symposium on Graph Drawing and Network Visualization (GD 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 357, pp. 24:1-24:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{chudnovsky_et_al:LIPIcs.GD.2025.24,
  author =	{Chudnovsky, Maria and Eppstein, David and Fischer, David},
  title =	{{String Graph Obstacles of High Girth and of Bounded Degree}},
  booktitle =	{33rd International Symposium on Graph Drawing and Network Visualization (GD 2025)},
  pages =	{24:1--24:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-403-1},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{357},
  editor =	{Dujmovi\'{c}, Vida and Montecchiani, Fabrizio},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.GD.2025.24},
  URN =		{urn:nbn:de:0030-drops-250108},
  doi =		{10.4230/LIPIcs.GD.2025.24},
  annote =	{Keywords: string graphs, induced minors, forbidden minors, sparsity, triangle-free graphs, near-planar graphs}
}
Document
DOI: 10.4230/OASIcs.Programming.2025.23
The Pyttern Program Query Language

Authors: Julien Liénard, Kim Mens, and Siegfried Nijssen

Published in: OASIcs, Volume 134, Companion Proceedings of the 9th International Conference on the Art, Science, and Engineering of Programming (Programming 2025)

Abstract
Despite the availability of numerous tools and languages for detecting structural patterns in programs, their complexity often presents a steep learning curve. This highlights the need for a program query language that is easier to learn, use, and read while remaining sufficiently expressive for defining and detecting relevant structural coding patterns in program code. To address this challenge, we present Pyttern, a query language that extends Python syntax with regular-expression-inspired wildcards, enabling intuitive pattern-based querying of Python code. Its implementation relies upon a custom pushdown automaton describing how to match patterns over program parse trees, thus providing a robust foundation for structural code analysis. We evaluate Pyttern’s usability and effectiveness through a study involving 35 master’s students, who were asked to write seven different patterns to identify known programming misconceptions. The results demonstrate that Pyttern is both easy to learn and practical to use, at least for analysing small-scale programs.
Cite as

Julien Liénard, Kim Mens, and Siegfried Nijssen. The Pyttern Program Query Language. In Companion Proceedings of the 9th International Conference on the Art, Science, and Engineering of Programming (Programming 2025). Open Access Series in Informatics (OASIcs), Volume 134, pp. 23:1-23:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{lienard_et_al:OASIcs.Programming.2025.23,
  author =	{Li\'{e}nard, Julien and Mens, Kim and Nijssen, Siegfried},
  title =	{{The Pyttern Program Query Language}},
  booktitle =	{Companion Proceedings of the 9th International Conference on the Art, Science, and Engineering of Programming (Programming 2025)},
  pages =	{23:1--23:15},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-382-9},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{134},
  editor =	{Edwards, Jonathan and Perera, Roly and Petricek, Tomas},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.Programming.2025.23},
  URN =		{urn:nbn:de:0030-drops-243075},
  doi =		{10.4230/OASIcs.Programming.2025.23},
  annote =	{Keywords: Pyttern, Program Query Languages, Python, Pattern Matching, Parse Tree, Pushdown Automaton, Static Code Analysis, Wildcards, Tree Pattern Matching}
}
Document
DOI: 10.4230/LIPIcs.MFCS.2025.62
The Complexity of Reachability Problems in Strongly Connected Finite Automata

Authors: Stefan Kiefer and Andrew Ryzhikov

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

Abstract
Several reachability problems in finite automata, such as completeness of NFAs and synchronisation of total DFAs, correspond to fundamental properties of sets of nonnegative matrices. In particular, the two mentioned properties correspond to matrix mortality and ergodicity, which ask whether there exists a product of the input matrices that is equal to, respectively, the zero matrix and a matrix with a column of strictly positive entries only. The case where the input automaton is strongly connected (that is, the corresponding set of nonnegative matrices is irreducible) frequently appears in applications and often admits better properties than the general case. In this paper, we address the existence of such properties from the computational complexity point of view, and develop a versatile technique to show that several NL-complete problems remain NL-complete in the strongly connected case. In particular, we show that deciding if a binary total DFA is synchronising is NL-complete even if it is promised to be strongly connected, and that deciding completeness of a binary unambiguous NFA with very limited nondeterminism is NL-complete under the same promise.
Cite as

Stefan Kiefer and Andrew Ryzhikov. The Complexity of Reachability Problems in Strongly Connected Finite Automata. In 50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 345, pp. 62:1-62:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{kiefer_et_al:LIPIcs.MFCS.2025.62,
  author =	{Kiefer, Stefan and Ryzhikov, Andrew},
  title =	{{The Complexity of Reachability Problems in Strongly Connected Finite Automata}},
  booktitle =	{50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025)},
  pages =	{62:1--62:19},
  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.2025.62},
  URN =		{urn:nbn:de:0030-drops-241690},
  doi =		{10.4230/LIPIcs.MFCS.2025.62},
  annote =	{Keywords: unambiguous automata, nonnegative matrices, irreducible matrix sets, strongly connected automata, matrix monoids, mortality, completeness, synchronisation, ergodicity}
}
Document
DOI: 10.4230/LIPIcs.MFCS.2025.61
Quantum Relaxations of CSP and Structure Isomorphism

Authors: Amin Karamlou

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

Abstract
We investigate quantum relaxations of two key decision problems in computer science: the constraint satisfaction problem (CSP) and the structure isomorphism problem. CSP asks whether a homomorphism exists between two relational structures, while structure isomorphism seeks an isomorphism between them. In recent years, it has become increasingly apparent that many special cases of CSP can be reformulated in terms of the existence of perfect classical strategies in non-local games, a key topic of study in quantum information theory. These games have allowed us to study quantum advantage in relation to many important decision problems, such as the k-colouring problem, and the problem of solving binary constraint systems. Abramsky et al. (2017) have shown that all of these games can be seen as special instances of a non-local CSP game. Moreover, they show that perfect quantum strategies in this CSP game can be viewed as Kleisli morphisms of a graded monad on the category of relational structures, which they dub the quantum monad. In this way, the quantum monad provides a categorical characterisation of quantum advantage for the non-local CSP game. In this work we solidify and expand the results of Abramsky et al., answering several of their open questions. Firstly, we compare the definition of quantum graph homomorphisms arising from this work with an earlier definition of the concept due to Mančinska and Roberson and show that there are graphs which exhibit quantum advantage under one definition but not the other. Our second contribution is to extend the results of Abramsky et al. which only hold in the tensor product framework of quantum mechanics to the commuting operator framework. Next, we study a non-local structure isomorphism game, which generalises the well-studied graph isomorphism game. We show how the construction of the quantum monad can be refined to provide categorical semantics for quantum strategies in this game. This results in a category where morphisms coincide with quantum homomorphisms and isomorphisms coincide with quantum isomorphisms.
Cite as

Amin Karamlou. Quantum Relaxations of CSP and Structure Isomorphism. In 50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 345, pp. 61:1-61:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{karamlou:LIPIcs.MFCS.2025.61,
  author =	{Karamlou, Amin},
  title =	{{Quantum Relaxations of CSP and Structure Isomorphism}},
  booktitle =	{50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025)},
  pages =	{61:1--61:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-388-1},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{345},
  editor =	{Gawrychowski, Pawe{\l} and Mazowiecki, Filip and Skrzypczak, Micha{\l}},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2025.61},
  URN =		{urn:nbn:de:0030-drops-241686},
  doi =		{10.4230/LIPIcs.MFCS.2025.61},
  annote =	{Keywords: CSP, graph isomorphism, quantum information, non-local game, quantum graph homomorphism, monad}
}
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.2025.11
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.2
A Survey of the Bijective Burrows-Wheeler Transform

Authors: Hideo Bannai, Dominik Köppl, and Zsuzsanna Lipták

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

Abstract
The Bijective BWT (BBWT), conceived by Scott in 2007, later summarized in a preprint by Gil and Scott in 2009 (arXiv 2012), is a variant of the Burrows-Wheeler Transform which is bijective: every string is the BBWT of some string. Indeed, the BBWT of a string is the extended BWT [Mantaci et al., 2007] of the factors of its Lyndon factorization. The BBWT has been receiving increasing interest in recent years. In this paper, we survey existing research on the BBWT, starting with its history and motivation. We then present algorithmic topics including construction algorithms with various complexities and an index on top of the BBWT for pattern matching. We subsequently address some properties of the BBWT as a compressor, discussing robustness to operations such as reversal, edits, rotation, as well as compression power. We close with listing other bijective variants of the BWT and open problems concerning the BBWT.
Cite as

Hideo Bannai, Dominik Köppl, and Zsuzsanna Lipták. A Survey of the Bijective Burrows-Wheeler Transform. In The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday. Open Access Series in Informatics (OASIcs), Volume 131, pp. 2:1-2:26, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{bannai_et_al:OASIcs.Manzini.2,
  author =	{Bannai, Hideo and K\"{o}ppl, Dominik and Lipt\'{a}k, Zsuzsanna},
  title =	{{A Survey of the Bijective Burrows-Wheeler Transform}},
  booktitle =	{The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday},
  pages =	{2:1--2:26},
  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.2},
  URN =		{urn:nbn:de:0030-drops-239100},
  doi =		{10.4230/OASIcs.Manzini.2},
  annote =	{Keywords: Burrows-Wheeler Transform, compression, text indexing, repetitiveness measure, Lyndon words, index construction algorithms, bijective string transformation}
}
Document
DOI: 10.4230/LIPIcs.CCC.2025.4
Hardness of Clique Approximation for Monotone Circuits

Authors: Jarosław Błasiok and Linus Meierhöfer

Published in: LIPIcs, Volume 339, 40th Computational Complexity Conference (CCC 2025)

Abstract
We consider a problem of approximating the size of the largest clique in a graph, using a monotone circuit. Concretely, we focus on distinguishing a random Erdős–Rényi graph 𝒢_{n,p}, with p = n^{-2/(α-1)} chosen st. with high probability it does not even contain an α-clique, from a random clique on β vertices (where α ≤ β). Using the approximation method of Razborov, Alon and Boppana showed in their influential work in 1987 that as long as √{α} β < n^{1-δ}/log n, this problem requires a monotone circuit of size n^Ω(δ√α), implying a lower bound of 2^Ω̃(n^{1/3}) for the exact version of the problem Clique_k when k≈ n^{2/3}. Recently, Cavalar, Kumar, and Rossman improved their result by showing a tight lower bound n^Ω(k), in a limited range k ≤ n^{1/3}, implying a comparable 2^Ω̃(n^{1/3}) lower bound after choosing the largest admissible k. We combine the ideas of Cavalar, Kumar and Rossman with recent breakthrough results on sunflower conjecture by Alweiss, Lovett, Wu, and Zhang to show that as long as α β < n^{1-δ}/log n, any monotone circuit rejecting 𝒢_{n,p} graph while accepting a β-clique needs to have size at least n^Ω(δ²α); this implies a stronger 2^Ω̃(√n) lower bound for the unrestricted version of the problem. We complement this result with a construction of an explicit monotone circuit of size O(n^{δ² α/2}) which rejects 𝒢_{n,p}, and accepts any graph containing β-clique whenever β > n^{1-δ}. In particular, those two theorems give a precise characterization of the smallest β-clique that can be distinguished from 𝒢_{n, 1/2}: when β > n / 2^{C √{log n}}, there is a polynomial-size circuit that solves it, while for β < n / 2^ω(√{log n}) every circuit needs size n^ω(1).
Cite as

Jarosław Błasiok and Linus Meierhöfer. Hardness of Clique Approximation for Monotone Circuits. In 40th Computational Complexity Conference (CCC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 339, pp. 4:1-4:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{blasiok_et_al:LIPIcs.CCC.2025.4,
  author =	{B{\l}asiok, Jaros{\l}aw and Meierh\"{o}fer, Linus},
  title =	{{Hardness of Clique Approximation for Monotone Circuits}},
  booktitle =	{40th Computational Complexity Conference (CCC 2025)},
  pages =	{4:1--4:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-379-9},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{339},
  editor =	{Srinivasan, Srikanth},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CCC.2025.4},
  URN =		{urn:nbn:de:0030-drops-236987},
  doi =		{10.4230/LIPIcs.CCC.2025.4},
  annote =	{Keywords: circuit lower bounds, monotone circuits, sunflower conjecture}
}
Document
DOI: 10.4230/LIPIcs.CCC.2025.14
On the Automatability of Tree-Like k-DNF Resolution

Authors: Gaia Carenini and Susanna F. de Rezende

Published in: LIPIcs, Volume 339, 40th Computational Complexity Conference (CCC 2025)

Abstract
A proof system 𝒫 is said to be automatable in time f(N) if there exists an algorithm that given as input an unsatisfiable formula F outputs a refutation of F in the proof system 𝒫 in time f(N), where N is the size of the smallest 𝒫-refutation of F plus the size of F. Atserias and Bonet (ECCC 2002), observed that tree-like k-DNF resolution is automatable in time N^{c⋅klog N} for a universal constant c. We show that, under the randomized exponential-time hypothesis (rETH), this is tight up to a O(log k)-factor in the exponent, i.e., we prove that tree-like k-DNF resolution, for k at most logarithmic in the number of variables of F, is not automatable in time N^o((k/log k)⋅log N) unless rETH is false. Our proof builds on the non-automatability results for resolution by Atserias and Müller (FOCS 2019), for algebraic proof systems by de Rezende, Göös, Nordström, Pitassi, Robere and Sokolov (STOC 2021), and for tree-like resolution by de Rezende (LAGOS 2021).
Cite as

Gaia Carenini and Susanna F. de Rezende. On the Automatability of Tree-Like k-DNF Resolution. In 40th Computational Complexity Conference (CCC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 339, pp. 14:1-14:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{carenini_et_al:LIPIcs.CCC.2025.14,
  author =	{Carenini, Gaia and de Rezende, Susanna F.},
  title =	{{On the Automatability of Tree-Like k-DNF Resolution}},
  booktitle =	{40th Computational Complexity Conference (CCC 2025)},
  pages =	{14:1--14:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-379-9},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{339},
  editor =	{Srinivasan, Srikanth},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CCC.2025.14},
  URN =		{urn:nbn:de:0030-drops-237081},
  doi =		{10.4230/LIPIcs.CCC.2025.14},
  annote =	{Keywords: Proof Complexity, Tree-like k-DNF Resolution, Automatability}
}
Document
Track B: Automata, Logic, Semantics, and Theory of Programming
DOI: 10.4230/LIPIcs.ICALP.2025.139
Minimality and Computability of Languages of G-Shifts

Authors: Djamel Eddine Amir and Benjamin Hellouin de Menibus

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

Abstract
Motivated by the notion of strong computable type for sets in computable analysis, we define the notion of strong computable type for G-shifts, where G is a finitely generated group with decidable word problem. A G-shift has strong computable type if one can compute its language from the complement of its language. We obtain a characterization of G-shifts with strong computable type in terms of a notion of minimality with respect to properties with a bounded computational complexity. We provide a self-contained direct proof, and also explain how this characterization can be obtained from an existing similar characterization for sets by Amir and Hoyrup, and discuss its connexions with results by Jeandel on closure spaces. We apply this characterization to several classes of shifts that are minimal with respect to specific properties. This provides a unifying approach that not only generalizes many existing results but also has the potential to yield new findings effortlessly. In contrast to the case of sets, we prove that strong computable type for G-shifts is preserved under products. We conclude by discussing some generalizations and future directions.
Cite as

Djamel Eddine Amir and Benjamin Hellouin de Menibus. Minimality and Computability of Languages of G-Shifts. In 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 334, pp. 139:1-139:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{amir_et_al:LIPIcs.ICALP.2025.139,
  author =	{Amir, Djamel Eddine and Hellouin de Menibus, Benjamin},
  title =	{{Minimality and Computability of Languages of G-Shifts}},
  booktitle =	{52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)},
  pages =	{139:1--139:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-372-0},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{334},
  editor =	{Censor-Hillel, Keren and Grandoni, Fabrizio and Ouaknine, Jo\"{e}l and Puppis, Gabriele},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2025.139},
  URN =		{urn:nbn:de:0030-drops-235161},
  doi =		{10.4230/LIPIcs.ICALP.2025.139},
  annote =	{Keywords: shifts, subshifts, minimal shifts, computable language, computability, strong computable type, descriptive complexity}
}
Document
Track A: Algorithms, Complexity and Games
DOI: 10.4230/LIPIcs.ICALP.2025.60
Random Reed-Solomon Codes Achieve the Half-Singleton Bound for Insertions and Deletions over Linear-Sized Alphabets

Authors: Roni Con, Zeyu Guo, Ray Li, and Zihan Zhang

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

Abstract
In this paper, we prove that with high probability, random Reed-Solomon codes approach the half-Singleton bound - the optimal rate versus error tradeoff for linear insdel codes - with linear-sized alphabets. More precisely, we prove that, for any ε > 0 and positive integers n and k, with high probability, random Reed-Solomon codes of length n and dimension k can correct (1-ε)n-2k+1 adversarial insdel errors over alphabets of size n+2^{poly(1/ε)}k. This significantly improves upon the alphabet size demonstrated in the work of Con, Shpilka, and Tamo (IEEE TIT, 2023), who showed the existence of Reed-Solomon codes with exponential alphabet size Õ(binom(n,2k-1)²) precisely achieving the half-Singleton bound. Our methods are inspired by recent works on list-decoding Reed-Solomon codes. Brakensiek-Gopi-Makam (STOC 2023) showed that random Reed-Solomon codes are list-decodable up to capacity with exponential-sized alphabets, and Guo-Zhang (FOCS 2023) and Alrabiah-Guruswami-Li (STOC 2024) improved the alphabet-size to linear. We achieve a similar alphabet-size reduction by similarly establishing strong bounds on the probability that certain random rectangular matrices are full rank. To accomplish this in our insdel context, our proof combines the random matrix techniques from list-decoding with structural properties of Longest Common Subsequences.
Cite as

Roni Con, Zeyu Guo, Ray Li, and Zihan Zhang. Random Reed-Solomon Codes Achieve the Half-Singleton Bound for Insertions and Deletions over Linear-Sized Alphabets. In 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 334, pp. 60:1-60:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{con_et_al:LIPIcs.ICALP.2025.60,
  author =	{Con, Roni and Guo, Zeyu and Li, Ray and Zhang, Zihan},
  title =	{{Random Reed-Solomon Codes Achieve the Half-Singleton Bound for Insertions and Deletions over Linear-Sized Alphabets}},
  booktitle =	{52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)},
  pages =	{60:1--60:21},
  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.2025.60},
  URN =		{urn:nbn:de:0030-drops-234372},
  doi =		{10.4230/LIPIcs.ICALP.2025.60},
  annote =	{Keywords: coding theory, error-correcting codes, Reed-Solomon codes, insdel, insertion-deletion errors, half-Singleton bound}
}
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