18 Search Results for "David, Laurent"

Document
DOI: 10.4230/LIPIcs.GD.2024.26
Storylines with a Protagonist

Authors: Tim Hegemann and Alexander Wolff

Published in: LIPIcs, Volume 320, 32nd International Symposium on Graph Drawing and Network Visualization (GD 2024)

Abstract
Storyline visualizations show interactions between a given set of characters over time. Each character is represented by an x-monotone curve. A meeting is represented by a vertical bar that is crossed by the curves of exactly those characters that participate in the meeting. Therefore, character curves may have to cross each other. In the context of publication networks, we consider storylines where the characters are authors and the meetings are joint publications. We are especially interested in visualizing a group of colleagues centered around an author, the protagonist, who participates in all selected publications. For such instances, we propose a drawing style where the protagonist’s curve is drawn at a prominent position and never crossed by any other author’s curve. We consider two variants of storylines with a protagonist. In the one-sided variant, the protagonist is required to be drawn at the top position. In this restricted setting, we can efficiently compute a drawing with the minimum number of pairwise crossings, whereas we show that it is NP-hard to minimize the number of block crossings (i.e., pairs of blocks of parallel curves that intersect each other). In the two-sided variant, the task is to split the set of co-authors of the protagonist into two groups, and to place the curves of one group above and the curves of the other group below the protagonist’s curve such that the total number of (block) crossings is minimized. As our main result, we present an algorithm for bundling a sequence of pairwise crossings into a sequence of few block crossings (in the absence of meetings). It exploits a connection to a rectangle dissection problem. In the presence of meetings, it yields results that are very close to a lower bound. Based on this bundling algorithm and our exact algorithm for the one-sided variant, we present a new heuristic for computing two-sided storylines with few block crossings. We perform an extensive experimental study using publication data of 81 protagonists from GD 2023 and their most frequent collaborators over the last ten years. Our study shows that, for two-sided storylines with a protagonist, our new heuristic uses fewer block crossings (and fewer pairwise crossings) than two heuristics for block crossing minimization in general storylines.
Cite as

Tim Hegemann and Alexander Wolff. Storylines with a Protagonist. In 32nd International Symposium on Graph Drawing and Network Visualization (GD 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 320, pp. 26:1-26:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{hegemann_et_al:LIPIcs.GD.2024.26,
  author =	{Hegemann, Tim and Wolff, Alexander},
  title =	{{Storylines with a Protagonist}},
  booktitle =	{32nd International Symposium on Graph Drawing and Network Visualization (GD 2024)},
  pages =	{26:1--26:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-343-0},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{320},
  editor =	{Felsner, Stefan and Klein, Karsten},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.GD.2024.26},
  URN =		{urn:nbn:de:0030-drops-213109},
  doi =		{10.4230/LIPIcs.GD.2024.26},
  annote =	{Keywords: Storyline visualization, storyline with a protagonist, crossing minimization, block crossings}
}
Document
DOI: 10.4230/LIPIcs.ECOOP.2024.14
The Performance Effects of Virtual-Machine Instruction Pointer Updates

Authors: M. Anton Ertl and Bernd Paysan

Published in: LIPIcs, Volume 313, 38th European Conference on Object-Oriented Programming (ECOOP 2024)

Abstract
How much performance do VM instruction-pointer (IP) updates cost and how much benefit do we get from optimizing them away? Two decades ago it had little effect on the hardware of the day, but on recent hardware the dependence chain of IP updates can become the critical path on processors with out-of-order execution. In particular, this happens if the VM instructions are light-weight and the application programs are loop-dominated. The present work presents several ways of reducing or eliminating the dependence chains from IP updates, either by breaking the dependence chains with the loop optimization or by reducing the number of IP updates (the c and ci optimizations) or their latency (the b optimization). Some benchmarks see speedups from these optimizations by factors > 2 on most recent cores, while other benchmarks and older cores see more modest results, often in the speedup ranges 1.1-1.3.
Cite as

M. Anton Ertl and Bernd Paysan. The Performance Effects of Virtual-Machine Instruction Pointer Updates. In 38th European Conference on Object-Oriented Programming (ECOOP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 313, pp. 14:1-14:26, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{ertl_et_al:LIPIcs.ECOOP.2024.14,
  author =	{Ertl, M. Anton and Paysan, Bernd},
  title =	{{The Performance Effects of Virtual-Machine Instruction Pointer Updates}},
  booktitle =	{38th European Conference on Object-Oriented Programming (ECOOP 2024)},
  pages =	{14:1--14:26},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-341-6},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{313},
  editor =	{Aldrich, Jonathan and Salvaneschi, Guido},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECOOP.2024.14},
  URN =		{urn:nbn:de:0030-drops-208634},
  doi =		{10.4230/LIPIcs.ECOOP.2024.14},
  annote =	{Keywords: virtual machine, interpreter, out-of-order execution}
}
Document
DOI: 10.4230/LIPIcs.ITP.2024.30
A Coq Formalization of Taylor Models and Power Series for Solving Ordinary Differential Equations

Authors: Sewon Park and Holger Thies

Published in: LIPIcs, Volume 309, 15th International Conference on Interactive Theorem Proving (ITP 2024)

Abstract
In exact real computation real numbers are manipulated exactly without round-off errors, making it well-suited for high precision verified computation. In recent work we propose an axiomatic formalization of exact real computation in the Coq theorem prover. The formalization admits an extended extraction mechanism that lets us extract computational content from constructive parts of proofs to efficient programs built on top of AERN, a Haskell library for exact real computation. Many processes in science and engineering are modeled by ordinary differential equations (ODEs), and often safety-critical applications depend on computing their solutions correctly. The primary goal of the current work is to extend our framework to spaces of functions and to support computation of solutions to ODEs and other essential operators. In numerical mathematics, the most common way to represent continuous functions is to use polynomial approximations. This can be modeled by so-called Taylor models, that encode a function as a polynomial and a rigorous error-bound over some domain. We define types of classical functions that do not hold any computational content and formalize Taylor models to computationally approximate those classical functions. Classical functions are defined in a way to admit classical principles in their constructions and verification. We define various basic operations on Taylor models and verify their correctness based on the classical functions that they approximate. We then shift our interest to analytic functions as a generalization of Taylor models where polynomials are replaced by infinite power series. We use the formalization to develop a theory of non-linear polynomial ODEs. From the proofs we can extract certified exact real computation programs that compute solutions of ODEs on some time interval up to any precision.
Cite as

Sewon Park and Holger Thies. A Coq Formalization of Taylor Models and Power Series for Solving Ordinary Differential Equations. In 15th International Conference on Interactive Theorem Proving (ITP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 309, pp. 30:1-30:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{park_et_al:LIPIcs.ITP.2024.30,
  author =	{Park, Sewon and Thies, Holger},
  title =	{{A Coq Formalization of Taylor Models and Power Series for Solving Ordinary Differential Equations}},
  booktitle =	{15th International Conference on Interactive Theorem Proving (ITP 2024)},
  pages =	{30:1--30:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-337-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{309},
  editor =	{Bertot, Yves and Kutsia, Temur and Norrish, Michael},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITP.2024.30},
  URN =		{urn:nbn:de:0030-drops-207581},
  doi =		{10.4230/LIPIcs.ITP.2024.30},
  annote =	{Keywords: Exact real computation, Taylor models, Analytic functions, Computable analysis, Program extraction}
}
Document
DOI: 10.4230/LIPIcs.ITP.2024.14
End-To-End Formal Verification of a Fast and Accurate Floating-Point Approximation

Authors: Florian Faissole, Paul Geneau de Lamarlière, and Guillaume Melquiond

Published in: LIPIcs, Volume 309, 15th International Conference on Interactive Theorem Proving (ITP 2024)

Abstract
Designing an efficient yet accurate floating-point approximation of a mathematical function is an intricate and error-prone process. This warrants the use of formal methods, especially formal proof, to achieve some degree of confidence in the implementation. Unfortunately, the lack of automation or its poor interplay with the more manual parts of the proof makes it way too costly in practice. This article revisits the issue by proposing a methodology and some dedicated automation, and applies them to the use case of a faithful binary64 approximation of exponential. The peculiarity of this use case is that the target of the formal verification is not a simple modeling of an external code; it is an actual floating-point function defined in the logic of the Coq proof assistant, which is thus usable inside proofs once its correctness has been fully verified. This function presents all the attributes of a state-of-the-art implementation: bit-level manipulations, large tables of constants, obscure floating-point transformations, exceptional values, etc. This function has been integrated into the proof strategies of the CoqInterval library, bringing a 20× speedup with respect to the previous implementation.
Cite as

Florian Faissole, Paul Geneau de Lamarlière, and Guillaume Melquiond. End-To-End Formal Verification of a Fast and Accurate Floating-Point Approximation. In 15th International Conference on Interactive Theorem Proving (ITP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 309, pp. 14:1-14:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{faissole_et_al:LIPIcs.ITP.2024.14,
  author =	{Faissole, Florian and Geneau de Lamarli\`{e}re, Paul and Melquiond, Guillaume},
  title =	{{End-To-End Formal Verification of a Fast and Accurate Floating-Point Approximation}},
  booktitle =	{15th International Conference on Interactive Theorem Proving (ITP 2024)},
  pages =	{14:1--14:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-337-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{309},
  editor =	{Bertot, Yves and Kutsia, Temur and Norrish, Michael},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITP.2024.14},
  URN =		{urn:nbn:de:0030-drops-207420},
  doi =		{10.4230/LIPIcs.ITP.2024.14},
  annote =	{Keywords: Program verification, floating-point arithmetic, formal proof, automated reasoning, mathematical library}
}
Document
DOI: 10.4230/LIPIcs.WABI.2024.5
Memoization on Shared Subtrees Accelerates Computations on Genealogical Forests

Authors: Lukas Hübner and Alexandros Stamatakis

Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)

Abstract
The field of population genetics attempts to advance our understanding of evolutionary processes. It has applications, for example, in medical research, wildlife conservation, and - in conjunction with recent advances in ancient DNA sequencing technology - studying human migration patterns over the past few thousand years. The basic toolbox of population genetics includes genealogical trees, which describe the shared evolutionary history among individuals of the same species. They are calculated on the basis of genetic variations. However, in recombining organisms, a single tree is insufficient to describe the evolutionary history of the whole genome. Instead, a collection of correlated trees can be used, where each describes the evolutionary history of a consecutive region of the genome. The current corresponding state of-the-art data structure, tree sequences, compresses these genealogical trees via edit operations when moving from one tree to the next along the genome instead of storing the full, often redundant, description for each tree. We propose a new data structure, genealogical forests, which compresses the set of genealogical trees into a DAG. In this DAG identical subtrees that are shared across the input trees are encoded only once, thereby allowing for straight-forward memoization of intermediate results. Additionally, we provide a C++ implementation of our proposed data structure, called gfkit, which is 2.1 to 11.2 (median 4.0) times faster than the state-of-the-art tool on empirical and simulated datasets at computing important population genetics statistics such as the Allele Frequency Spectrum, Patterson’s f, the Fixation Index, Tajima’s D, pairwise Lowest Common Ancestors, and others. On Lowest Common Ancestor queries with more than two samples as input, gfkit scales asymptotically better than the state-of-the-art, and is thus up to 990 times faster. In conclusion, our proposed data structure compresses genealogical trees by storing shared subtrees only once, thereby enabling straight-forward memoization of intermediate results, yielding a substantial runtime reduction and a potentially more intuitive data representation over the state-of-the-art. Our improvements will boost the development of novel analyses and models in the field of population genetics and increases scalability to ever-growing genomic datasets.
Cite as

Lukas Hübner and Alexandros Stamatakis. Memoization on Shared Subtrees Accelerates Computations on Genealogical Forests. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 5:1-5:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{hubner_et_al:LIPIcs.WABI.2024.5,
  author =	{H\"{u}bner, Lukas and Stamatakis, Alexandros},
  title =	{{Memoization on Shared Subtrees Accelerates Computations on Genealogical Forests}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{5:1--5:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-340-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{312},
  editor =	{Pissis, Solon P. and Sung, Wing-Kin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2024.5},
  URN =		{urn:nbn:de:0030-drops-206499},
  doi =		{10.4230/LIPIcs.WABI.2024.5},
  annote =	{Keywords: bioinformatics, population genetics, algorithms}
}
Document
DOI: 10.4230/LIPIcs.WABI.2024.19
RNA Inverse Folding Can Be Solved in Linear Time for Structures Without Isolated Stacks or Base Pairs

Authors: Théo Boury, Laurent Bulteau, and Yann Ponty

Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)

Abstract
Inverse folding is a classic instance of negative RNA design which consists in finding a sequence that uniquely folds into a target secondary structure with respect to energy minimization. A breakthrough result of Bonnet et al. shows that, even in simple base pairs-based (BP) models, the decision version of a mildly constrained version of inverse folding is NP-hard. In this work, we show that inverse folding can be solved in linear time for a large collection of targets, including every structure that contains no isolated BP and no isolated stack (or, equivalently, when all helices consist of 3^{+} base pairs). For structures featuring shorter helices, our linear algorithm is no longer guaranteed to produce a solution, but still does so for a large proportion of instances. Our approach introduces a notion of modulo m-separability, generalizing a property pioneered by Hales et al. Separability is a sufficient condition for the existence of a solution to the inverse folding problem. We show that, for any input secondary structure of length n, a modulo m-separated sequence can be produced in time 𝒪(n 2^m) anytime such a sequence exists. Meanwhile, we show that any structure consisting of 3^{+} base pairs is either trivially non-designable, or always admits a modulo-2 separated solution (m = 2). Solution sequences can thus be produced in linear time, and even be uniformly generated within the set of modulo-2 separable sequences.
Cite as

Théo Boury, Laurent Bulteau, and Yann Ponty. RNA Inverse Folding Can Be Solved in Linear Time for Structures Without Isolated Stacks or Base Pairs. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 19:1-19:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{boury_et_al:LIPIcs.WABI.2024.19,
  author =	{Boury, Th\'{e}o and Bulteau, Laurent and Ponty, Yann},
  title =	{{RNA Inverse Folding Can Be Solved in Linear Time for Structures Without Isolated Stacks or Base Pairs}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{19:1--19:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-340-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{312},
  editor =	{Pissis, Solon P. and Sung, Wing-Kin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2024.19},
  URN =		{urn:nbn:de:0030-drops-206632},
  doi =		{10.4230/LIPIcs.WABI.2024.19},
  annote =	{Keywords: RNA structure, String Design, Parameterized Complexity, Uniform Sampling}
}
Document
DOI: 10.4230/LIPIcs.MFCS.2024.12
Generalizing Roberts' Characterization of Unit Interval Graphs

Authors: Virginia Ardévol Martínez, Romeo Rizzi, Abdallah Saffidine, Florian Sikora, and Stéphane Vialette

Published in: LIPIcs, Volume 306, 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)

Abstract
For any natural number d, a graph G is a (disjoint) d-interval graph if it is the intersection graph of (disjoint) d-intervals, the union of d (disjoint) intervals on the real line. Two important subclasses of d-interval graphs are unit and balanced d-interval graphs (where every interval has unit length or all the intervals associated to a same vertex have the same length, respectively). A celebrated result by Roberts gives a simple characterization of unit interval graphs being exactly claw-free interval graphs. Here, we study the generalization of this characterization for d-interval graphs. In particular, we prove that for any d ⩾ 2, if G is a K_{1,2d+1}-free interval graph, then G is a unit d-interval graph. However, somehow surprisingly, under the same assumptions, G is not always a disjoint unit d-interval graph. This implies that the class of disjoint unit d-interval graphs is strictly included in the class of unit d-interval graphs. Finally, we study the relationships between the classes obtained under disjoint and non-disjoint d-intervals in the balanced case and show that the classes of disjoint balanced 2-intervals and balanced 2-intervals coincide, but this is no longer true for d > 2.
Cite as

Virginia Ardévol Martínez, Romeo Rizzi, Abdallah Saffidine, Florian Sikora, and Stéphane Vialette. Generalizing Roberts' Characterization of Unit Interval Graphs. In 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 306, pp. 12:1-12:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{ardevolmartinez_et_al:LIPIcs.MFCS.2024.12,
  author =	{Ard\'{e}vol Mart{\'\i}nez, Virginia and Rizzi, Romeo and Saffidine, Abdallah and Sikora, Florian and Vialette, St\'{e}phane},
  title =	{{Generalizing Roberts' Characterization of Unit Interval Graphs}},
  booktitle =	{49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)},
  pages =	{12:1--12:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-335-5},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{306},
  editor =	{Kr\'{a}lovi\v{c}, Rastislav and Ku\v{c}era, Anton{\'\i}n},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2024.12},
  URN =		{urn:nbn:de:0030-drops-205687},
  doi =		{10.4230/LIPIcs.MFCS.2024.12},
  annote =	{Keywords: Interval graphs, Multiple Interval Graphs, Unit Interval Graphs, Characterization}
}
Document
DOI: 10.4230/LIPIcs.SAT.2024.9
Lazy Reimplication in Chronological Backtracking

Authors: Robin Coutelier, Mathias Fleury, and Laura Kovács

Published in: LIPIcs, Volume 305, 27th International Conference on Theory and Applications of Satisfiability Testing (SAT 2024)

Abstract
Chronological backtracking is an interesting SAT solving technique within CDCL reasoning, as it backtracks less aggressively upon conflicts. However, chronological backtracking is more difficult to maintain due to its weaker SAT solving invariants. This paper introduces a lazy reimplication procedure for missed lower implications in chronological backtracking. Our method saves propagations by reimplying literals on demand, rather than eagerly. Due to its modularity, our work can be replicated in other solvers, as shown by our results in the solvers CaDiCaL and Glucose.
Cite as

Robin Coutelier, Mathias Fleury, and Laura Kovács. Lazy Reimplication in Chronological Backtracking. In 27th International Conference on Theory and Applications of Satisfiability Testing (SAT 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 305, pp. 9:1-9:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{coutelier_et_al:LIPIcs.SAT.2024.9,
  author =	{Coutelier, Robin and Fleury, Mathias and Kov\'{a}cs, Laura},
  title =	{{Lazy Reimplication in Chronological Backtracking}},
  booktitle =	{27th International Conference on Theory and Applications of Satisfiability Testing (SAT 2024)},
  pages =	{9:1--9:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-334-8},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{305},
  editor =	{Chakraborty, Supratik and Jiang, Jie-Hong Roland},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SAT.2024.9},
  URN =		{urn:nbn:de:0030-drops-205313},
  doi =		{10.4230/LIPIcs.SAT.2024.9},
  annote =	{Keywords: Chronological Backtracking, CDCL, Invariants, Watcher Lists}
}
Document
DOI: 10.4230/LIPIcs.SAT.2024.15
Antichain with SAT and Tries

Authors: Lukáš Holík and Pavol Vargovčík

Published in: LIPIcs, Volume 305, 27th International Conference on Theory and Applications of Satisfiability Testing (SAT 2024)

Abstract
We introduce a SAT-enabled version of an antichain algorithm for checking language emptiness of alternating finite automata (AFA) with complex transition relations encoded as compact logical formulae. The SAT solver is used to compute predecessors of AFA configurations, and at the same time, to evaluate the subsumption of newly found configurations in the antichain of the previously found ones. The algorithm could be naively implemented by an incremental SAT solver where the growing antichain is represented by adding new clauses. To make it efficient, we 1) force the SAT solver to prioritize largest/subsumption-strongest predecessors (so that weaker configurations are not even generated), and 2) store the antichain clauses in a special variant of a trie that allows fast subsumption testing. The experimental results suggest that the resulting emptiness checker is very efficient compared to the state of the art and that our techniques improve the performance of the SAT solver.
Cite as

Lukáš Holík and Pavol Vargovčík. Antichain with SAT and Tries. In 27th International Conference on Theory and Applications of Satisfiability Testing (SAT 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 305, pp. 15:1-15:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{holik_et_al:LIPIcs.SAT.2024.15,
  author =	{Hol{\'\i}k, Luk\'{a}\v{s} and Vargov\v{c}{\'\i}k, Pavol},
  title =	{{Antichain with SAT and Tries}},
  booktitle =	{27th International Conference on Theory and Applications of Satisfiability Testing (SAT 2024)},
  pages =	{15:1--15:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-334-8},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{305},
  editor =	{Chakraborty, Supratik and Jiang, Jie-Hong Roland},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SAT.2024.15},
  URN =		{urn:nbn:de:0030-drops-205372},
  doi =		{10.4230/LIPIcs.SAT.2024.15},
  annote =	{Keywords: SAT, Trie, Antichain, Alternating automata, Subset query}
}
Document
DOI: 10.4230/LIPIcs.SEA.2024.8
Practical Computation of Graph VC-Dimension

Authors: David Coudert, Mónika Csikós, Guillaume Ducoffe, and Laurent Viennot

Published in: LIPIcs, Volume 301, 22nd International Symposium on Experimental Algorithms (SEA 2024)

Abstract
For any set system ℋ = (V,ℛ), ℛ ⊆ 2^V, a subset S ⊆ V is called shattered if every S' ⊆ S results from the intersection of S with some set in ℛ. The VC-dimension of ℋ is the size of a largest shattered set in V. In this paper, we focus on the problem of computing the VC-dimension of graphs. In particular, given a graph G = (V,E), the VC-dimension of G is defined as the VC-dimension of (V, N), where N contains each subset of V that can be obtained as the closed neighborhood of some vertex v ∈ V in G. Our main contribution is an algorithm for computing the VC-dimension of any graph, whose effectiveness is shown through experiments on various types of practical graphs, including graphs with millions of vertices. A key aspect of its efficiency resides in the fact that practical graphs have small VC-dimension, up to 8 in our experiments. As a side-product, we present several new bounds relating the graph VC-dimension to other classical graph theoretical notions. We also establish the W[1]-hardness of the graph VC-dimension problem by extending a previous result for arbitrary set systems.
Cite as

David Coudert, Mónika Csikós, Guillaume Ducoffe, and Laurent Viennot. Practical Computation of Graph VC-Dimension. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 8:1-8:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{coudert_et_al:LIPIcs.SEA.2024.8,
  author =	{Coudert, David and Csik\'{o}s, M\'{o}nika and Ducoffe, Guillaume and Viennot, Laurent},
  title =	{{Practical Computation of Graph VC-Dimension}},
  booktitle =	{22nd International Symposium on Experimental Algorithms (SEA 2024)},
  pages =	{8:1--8:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-325-6},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{301},
  editor =	{Liberti, Leo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2024.8},
  URN =		{urn:nbn:de:0030-drops-203731},
  doi =		{10.4230/LIPIcs.SEA.2024.8},
  annote =	{Keywords: VC-dimension, graph, algorithm}
}
Document
DOI: 10.4230/LIPIcs.FSCD.2024.5
The Flower Calculus

Authors: Pablo Donato

Published in: LIPIcs, Volume 299, 9th International Conference on Formal Structures for Computation and Deduction (FSCD 2024)

Abstract
We introduce the flower calculus, a deep inference proof system for intuitionistic first-order logic inspired by Peirce’s existential graphs. It works as a rewriting system over inductive objects called "flowers", that enjoy both a graphical interpretation as topological diagrams, and a textual presentation as nested sequents akin to coherent formulas. Importantly, the calculus dispenses completely with the traditional notion of symbolic connective, operating solely on nested flowers containing atomic predicates. We prove both the soundness of the full calculus and the completeness of an analytic fragment with respect to Kripke semantics. This provides to our knowledge the first analyticity result for a proof system based on existential graphs, adapting semantic cut-elimination techniques to a deep inference setting. Furthermore, the kernel of rules targetted by completeness is fully invertible, a desirable property for both automated and interactive proof search.
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Pablo Donato. The Flower Calculus. In 9th International Conference on Formal Structures for Computation and Deduction (FSCD 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 299, pp. 5:1-5:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{donato:LIPIcs.FSCD.2024.5,
  author =	{Donato, Pablo},
  title =	{{The Flower Calculus}},
  booktitle =	{9th International Conference on Formal Structures for Computation and Deduction (FSCD 2024)},
  pages =	{5:1--5:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-323-2},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{299},
  editor =	{Rehof, Jakob},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FSCD.2024.5},
  URN =		{urn:nbn:de:0030-drops-203343},
  doi =		{10.4230/LIPIcs.FSCD.2024.5},
  annote =	{Keywords: deep inference, graphical calculi, existential graphs, intuitionistic logic, Kripke semantics, cut-elimination}
}
Document
DOI: 10.4230/LIPIcs.FSCD.2024.24
IMELL Cut Elimination with Linear Overhead

Authors: Beniamino Accattoli and Claudio Sacerdoti Coen

Published in: LIPIcs, Volume 299, 9th International Conference on Formal Structures for Computation and Deduction (FSCD 2024)

Abstract
Recently, Accattoli introduced the Exponential Substitution Calculus (ESC) given by untyped proof terms for Intuitionistic Multiplicative Exponential Linear Logic (IMELL), endowed with rewriting rules at-a-distance for cut elimination. He also introduced a new cut elimination strategy, dubbed the good strategy, and showed that its number of steps is a time cost model with polynomial overhead for ESC/IMELL, and the first such one. Here, we refine Accattoli’s result by introducing an abstract machine for ESC and proving that it implements the good strategy and computes cut-free terms/proofs within a linear overhead.
Cite as

Beniamino Accattoli and Claudio Sacerdoti Coen. IMELL Cut Elimination with Linear Overhead. In 9th International Conference on Formal Structures for Computation and Deduction (FSCD 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 299, pp. 24:1-24:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{accattoli_et_al:LIPIcs.FSCD.2024.24,
  author =	{Accattoli, Beniamino and Sacerdoti Coen, Claudio},
  title =	{{IMELL Cut Elimination with Linear Overhead}},
  booktitle =	{9th International Conference on Formal Structures for Computation and Deduction (FSCD 2024)},
  pages =	{24:1--24:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-323-2},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{299},
  editor =	{Rehof, Jakob},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FSCD.2024.24},
  URN =		{urn:nbn:de:0030-drops-203539},
  doi =		{10.4230/LIPIcs.FSCD.2024.24},
  annote =	{Keywords: Lambda calculus, linear logic, abstract machines}
}
Document
DOI: 10.4230/LIPIcs.SAND.2023.4
Computing Temporal Reachability Under Waiting-Time Constraints in Linear Time

Authors: Filippo Brunelli and Laurent Viennot

Published in: LIPIcs, Volume 257, 2nd Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2023)

Abstract
This paper proposes a simple algorithm for computing single-source reachability in a temporal graph under waiting-time constraints, that is when waiting at each node is bounded by some time constraints. Given a space-time representation of a temporal graph, and a source node, the algorithm computes in linear-time which nodes and temporal edges are reachable through a constrained temporal walk from the source.
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Filippo Brunelli and Laurent Viennot. Computing Temporal Reachability Under Waiting-Time Constraints in Linear Time. In 2nd Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 257, pp. 4:1-4:11, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{brunelli_et_al:LIPIcs.SAND.2023.4,
  author =	{Brunelli, Filippo and Viennot, Laurent},
  title =	{{Computing Temporal Reachability Under Waiting-Time Constraints in Linear Time}},
  booktitle =	{2nd Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2023)},
  pages =	{4:1--4:11},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-275-4},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{257},
  editor =	{Doty, David and Spirakis, Paul},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SAND.2023.4},
  URN =		{urn:nbn:de:0030-drops-179402},
  doi =		{10.4230/LIPIcs.SAND.2023.4},
  annote =	{Keywords: temporal reachability, temporal graph, temporal path, temporal walk, waiting-time constraints, restless temporal walk, linear time}
}
Document
DOI: 10.4230/LIPIcs.SAND.2023.7
When Should You Wait Before Updating? - Toward a Robustness Refinement

Authors: Swan Dubois, Laurent Feuilloley, Franck Petit, and Mikaël Rabie

Published in: LIPIcs, Volume 257, 2nd Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2023)

Abstract
Consider a dynamic network and a given distributed problem. At any point in time, there might exist several solutions that are equally good with respect to the problem specification, but that are different from an algorithmic perspective, because some could be easier to update than others when the network changes. In other words, one would prefer to have a solution that is more robust to topological changes in the network; and in this direction the best scenario would be that the solution remains correct despite the dynamic of the network. In [Arnaud Casteigts et al., 2020], the authors introduced a very strong robustness criterion: they required that for any removal of edges that maintain the network connected, the solution remains valid. They focus on the maximal independent set problem, and their approach consists in characterizing the graphs in which there exists a robust solution (the existential problem), or even stronger, where any solution is robust (the universal problem). As the robustness criteria is very demanding, few graphs have a robust solution, and even fewer are such that all of their solutions are robust. In this paper, we ask the following question: Can we have robustness for a larger class of networks, if we bound the number k of edge removals allowed? To answer this question, we consider three classic problems: maximal independent set, minimal dominating set and maximal matching. For the universal problem, the answers for the three cases are surprisingly different. For minimal dominating set, the class does not depend on the number of edges removed. For maximal matching, removing only one edge defines a robust class related to perfect matchings, but for all other bounds k, the class is the same as for an arbitrary number of edge removals. Finally, for maximal independent set, there is a strict hierarchy of classes: the class for the bound k is strictly larger than the class for bound k+1. For the robustness notion of [Arnaud Casteigts et al., 2020], no characterization of the class for the existential problem is known, only a polynomial-time recognition algorithm. We show that the situation is even worse for bounded k: even for k = 1, it is NP-hard to decide whether a graph has a robust maximal independent set.
Cite as

Swan Dubois, Laurent Feuilloley, Franck Petit, and Mikaël Rabie. When Should You Wait Before Updating? - Toward a Robustness Refinement. In 2nd Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 257, pp. 7:1-7:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{dubois_et_al:LIPIcs.SAND.2023.7,
  author =	{Dubois, Swan and Feuilloley, Laurent and Petit, Franck and Rabie, Mika\"{e}l},
  title =	{{When Should You Wait Before Updating? - Toward a Robustness Refinement}},
  booktitle =	{2nd Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2023)},
  pages =	{7:1--7:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-275-4},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{257},
  editor =	{Doty, David and Spirakis, Paul},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SAND.2023.7},
  URN =		{urn:nbn:de:0030-drops-179435},
  doi =		{10.4230/LIPIcs.SAND.2023.7},
  annote =	{Keywords: Robustness, dynamic network, temporal graphs, edge removal, connectivity, footprint, packing/covering problems, maximal independent set, maximal matching, minimum dominating set, perfect matching, NP-hardness}
}
Document
DOI: 10.4230/OASIcs.AUTOMATA.2021.5
Dynamical Algebraic Combinatorics, Asynchronous Cellular Automata, and Toggling Independent Sets

Authors: Laurent David, Colin Defant, Michael Joseph, Matthew Macauley, and Alex McDonough

Published in: OASIcs, Volume 90, 27th IFIP WG 1.5 International Workshop on Cellular Automata and Discrete Complex Systems (AUTOMATA 2021)

Abstract
Though iterated maps and dynamical systems are not new to combinatorics, they have enjoyed a renewed prominence over the past decade through the elevation of the subfield that has become known as dynamical algebraic combinatorics. Some of the problems that have gained popularity can also be cast and analyzed as finite asynchronous cellular automata (CA). However, these two fields are fairly separate, and while there are some individuals who work in both, that is the exception rather than the norm. In this article, we will describe our ongoing work on toggling independent sets on graphs. This will be preceded by an overview of how this project arose from new combinatorial problems involving homomesy, toggling, and resonance. Though the techniques that we explore are directly applicable to ECA rule 1, many of them can be generalized to other cellular automata. Moreover, some of the ideas that we borrow from cellular automata can be adapted to problems in dynamical algebraic combinatorics. It is our hope that this article will inspire new problems in both fields and connections between them.
Cite as

Laurent David, Colin Defant, Michael Joseph, Matthew Macauley, and Alex McDonough. Dynamical Algebraic Combinatorics, Asynchronous Cellular Automata, and Toggling Independent Sets. In 27th IFIP WG 1.5 International Workshop on Cellular Automata and Discrete Complex Systems (AUTOMATA 2021). Open Access Series in Informatics (OASIcs), Volume 90, pp. 5:1-5:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

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@InProceedings{david_et_al:OASIcs.AUTOMATA.2021.5,
  author =	{David, Laurent and Defant, Colin and Joseph, Michael and Macauley, Matthew and McDonough, Alex},
  title =	{{Dynamical Algebraic Combinatorics, Asynchronous Cellular Automata, and Toggling Independent Sets}},
  booktitle =	{27th IFIP WG 1.5 International Workshop on Cellular Automata and Discrete Complex Systems (AUTOMATA 2021)},
  pages =	{5:1--5:16},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-189-4},
  ISSN =	{2190-6807},
  year =	{2021},
  volume =	{90},
  editor =	{Castillo-Ramirez, Alonso and Guillon, Pierre and Perrot, K\'{e}vin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.AUTOMATA.2021.5},
  URN =		{urn:nbn:de:0030-drops-140145},
  doi =		{10.4230/OASIcs.AUTOMATA.2021.5},
  annote =	{Keywords: Asynchronous cellular automata, Covering space, Coxeter element, Dynamical algebraic combinatorics, Group action, Homomesy, Independent set, Resonance, Toggling, Toric equivalence}
}
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