19 Search Results for "Silva, Gil"

Document
DOI: 10.4230/LIPIcs.CPM.2026.14
Hardness Results on Characteristics for Elastic-Degenerate Strings

Authors: Dominik Köppl and Jannik Olbrich

Published in: LIPIcs, Volume 369, 37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026)

Abstract
Generalizations of plain strings have been proposed as a compact way to represent a collection of nearly identical sequences or to express uncertainty at specific text positions by enumerating all possibilities. While a plain string stores a character at each of its positions, generalizations consider a set of characters (indeterminate strings), a set of strings of equal length (generalized degenerate strings, or shortly GD strings), or a set of strings of arbitrary lengths (elastic-degenerate strings, or shortly ED strings). These generalizations are of importance to compactly represent such type of data, and find applications in bioinformatics for representing and maintaining a set of genetic sequences of the same taxonomy or a multiple sequence alignment. To be of use, attention has been drawn to answering various query types such as pattern matching or measuring similarity of ED strings by generalizing techniques known to plain strings. However, for some types of queries, it has been shown that a generalization of a polynomial-time solvable query on classic strings becomes NP-hard on ED strings, e.g. [Russo et al., 2022]. In that light, we wonder about other types of queries that are of particular interest to bioinformatics: unique substrings, absent words, anti-powers, longest previous factors, and Lempel-Ziv-like compression schemes. While we obtain a polynomial time algorithm for a variation of longest previous factors, we show that all other problems are NP-hard to compute, some of them even under the restriction that the input can be modeled as an indeterminate or GD string.
Cite as

Dominik Köppl and Jannik Olbrich. Hardness Results on Characteristics for Elastic-Degenerate Strings. In 37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 369, pp. 14:1-14:25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{koppl_et_al:LIPIcs.CPM.2026.14,
  author =	{K\"{o}ppl, Dominik and Olbrich, Jannik},
  title =	{{Hardness Results on Characteristics for Elastic-Degenerate Strings}},
  booktitle =	{37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026)},
  pages =	{14:1--14:25},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-420-8},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{369},
  editor =	{Bille, Philip 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.CPM.2026.14},
  URN =		{urn:nbn:de:0030-drops-259409},
  doi =		{10.4230/LIPIcs.CPM.2026.14},
  annote =	{Keywords: Elastic-degenerate strings, NP-hardness, longest common factor, minimal unique substring, minimal absent word, anti-power, longest previous factor}
}
Document
DOI: 10.4230/LIPIcs.SoCG.2026.93
Simplicial Approximation to CW Complexes with Spherical Delaunay Triangulations

Authors: Raphaël Tinarrage

Published in: LIPIcs, Volume 367, 42nd International Symposium on Computational Geometry (SoCG 2026)

Abstract
Simplicial approximation provides a framework for constructing simplicial complexes that are homotopy equivalent to a given manifold, provided a CW structure is explicitly known. However, its conventional implementation quickly becomes intractable on a computer: barycentric subdivision produces poorly shaped simplices, and the star condition introduces many vertices. To address these limitations, this article develops a subdivision scheme based on spherical Delaunay triangulations, which attains better refinement properties than barycentric subdivisions. Moreover, the star condition is reframed as two independent problems, one geometric and the other combinatorial, respectively tackled in the language of locally equiconnected spaces and the list homomorphism problem, allowing an exponential reduction in the number of vertices. Via a prototype implementation, we obtain simplicial complexes homotopy equivalent to Grassmannians and Stiefel manifolds up to dimension 5.
Cite as

Raphaël Tinarrage. Simplicial Approximation to CW Complexes with Spherical Delaunay Triangulations. In 42nd International Symposium on Computational Geometry (SoCG 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 367, pp. 93:1-93:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{tinarrage:LIPIcs.SoCG.2026.93,
  author =	{Tinarrage, Rapha\"{e}l},
  title =	{{Simplicial Approximation to CW Complexes with Spherical Delaunay Triangulations}},
  booktitle =	{42nd International Symposium on Computational Geometry (SoCG 2026)},
  pages =	{93:1--93:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-418-5},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{367},
  editor =	{Ahn, Hee-Kap and Hoffmann, Michael and Nayyeri, Amir},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SoCG.2026.93},
  URN =		{urn:nbn:de:0030-drops-258991},
  doi =		{10.4230/LIPIcs.SoCG.2026.93},
  annote =	{Keywords: Triangulation of manifolds, Simplicial approximation, CW complexes, Delaunay complexes, List homomorphism problem, Topological Data Analysis}
}
Document
DOI: 10.4230/LIPIcs.ITCS.2026.35
Symmetric Quantum Computation

Authors: Davi Castro-Silva, Tom Gur, and Sergii Strelchuk

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

Abstract
We introduce a systematic study of symmetric quantum circuits, a new restricted model of quantum computation that preserves the symmetries of the problems it solves. This model is well-adapted for studying the role of symmetry in quantum speedups, extending a central notion of symmetric computation studied in the classical setting. Our results establish that symmetric quantum circuits are fundamentally more powerful than their classical counterparts. First, we give efficient symmetric circuits for key quantum techniques such as amplitude amplification, phase estimation and linear combination of unitaries. In addition, we show how the task of symmetric state preparation can be performed efficiently in several natural cases. Finally, we demonstrate an exponential separation in the symmetric setting for the problem XOR-SAT, which requires exponential-size symmetric classical circuits but can be solved by polynomial-size symmetric quantum circuits.
Cite as

Davi Castro-Silva, Tom Gur, and Sergii Strelchuk. Symmetric Quantum Computation. In 17th Innovations in Theoretical Computer Science Conference (ITCS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 362, pp. 35:1-35:10, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{castrosilva_et_al:LIPIcs.ITCS.2026.35,
  author =	{Castro-Silva, Davi and Gur, Tom and Strelchuk, Sergii},
  title =	{{Symmetric Quantum Computation}},
  booktitle =	{17th Innovations in Theoretical Computer Science Conference (ITCS 2026)},
  pages =	{35:1--35:10},
  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.2026.35},
  URN =		{urn:nbn:de:0030-drops-253223},
  doi =		{10.4230/LIPIcs.ITCS.2026.35},
  annote =	{Keywords: Quantum computing, complexity theory, symmetries}
}
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
RANDOM
DOI: 10.4230/LIPIcs.APPROX/RANDOM.2025.44
Density Frankl–Rödl on the Sphere

Authors: Venkatesan Guruswami and Shilun Li

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

Abstract
We establish a density variant of the Frankl–Rödl theorem on the sphere 𝕊^{n-1}, which concerns avoiding pairs of vectors with a specific distance, or equivalently, a prescribed inner product. In particular, we establish lower bounds on the probability that a randomly chosen pair of such vectors lies entirely within a measurable subset A ⊆ 𝕊^{n-1} of sufficiently large measure. Additionally, we prove a density version of spherical avoidance problems, which generalize from pairwise avoidance to broader configurations with prescribed pairwise inner products. Our framework encompasses a class of configurations we call inductive configurations, which include simplices with any prescribed inner product -1 < r < 1. As a consequence of our density statement, we show that all inductive configurations are sphere Ramsey.
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Venkatesan Guruswami and Shilun Li. Density Frankl–Rödl on the Sphere. In Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 353, pp. 44:1-44:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{guruswami_et_al:LIPIcs.APPROX/RANDOM.2025.44,
  author =	{Guruswami, Venkatesan and Li, Shilun},
  title =	{{Density Frankl–R\"{o}dl on the Sphere}},
  booktitle =	{Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025)},
  pages =	{44:1--44:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-397-3},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{353},
  editor =	{Ene, Alina and Chattopadhyay, Eshan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.APPROX/RANDOM.2025.44},
  URN =		{urn:nbn:de:0030-drops-244108},
  doi =		{10.4230/LIPIcs.APPROX/RANDOM.2025.44},
  annote =	{Keywords: Frankl–R\"{o}dl, Sphere Ramsey, Sphere Avoidance, Reverse Hypercontractivity, Forbidden Angles}
}
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.
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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
Research
DOI: 10.4230/TGDK.3.1.4
CoaKG: A Contextualized Knowledge Graph Approach for Exploratory Search and Decision Making

Authors: Veronica dos Santos, Daniel Schwabe, Altigran Soares da Silva, and Sérgio Lifschitz

Published in: TGDK, Volume 3, Issue 1 (2025). Transactions on Graph Data and Knowledge, Volume 3, Issue 1

Abstract
In decision-making scenarios, an information need arises due to a knowledge gap when a decision-maker needs more knowledge to make a decision. Users may take the initiative to acquire knowledge to fill this gap through exploratory search approaches using Knowledge Graphs (KGs) as information sources, but their queries can be incomplete, inaccurate, and ambiguous. Although KGs have great potential for exploratory search, they are incomplete by nature. Besides, for both Crowd-sourced KGs and KGs constructed by integrating several different information sources of varying quality to be effectively consumed, there is a need for a Trust Layer. Our research aims to enrich and allow querying KGs to support context-aware exploration in decision-making scenarios. We propose a layered architecture for Context Augmented Knowledge Graphs-based Decision Support Systems with a Knowledge Layer that operates under a Dual Open World Assumption (DOWA). Under DOWA, the evaluation of the truthfulness of the information obtained from KGs depends on the context of its claims and the tasks carried out or intended (purpose). The Knowledge Layer comprises a Context Augmented KG (CoaKG) and a CoaKG Query Engine. The CoaKG contains contextual mappings to identify explicit context and rules to infer implicit context. The CoaKG Query Engine is designed as a query-answering approach that retrieves all contextualized answers from the CoaKG. A Proof of Concept (PoC) based on Wikidata was developed to evaluate the effectiveness of the Knowledge Layer.
Cite as

Veronica dos Santos, Daniel Schwabe, Altigran Soares da Silva, and Sérgio Lifschitz. CoaKG: A Contextualized Knowledge Graph Approach for Exploratory Search and Decision Making. In Transactions on Graph Data and Knowledge (TGDK), Volume 3, Issue 1, pp. 4:1-4:27, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@Article{dossantos_et_al:TGDK.3.1.4,
  author =	{dos Santos, Veronica and Schwabe, Daniel and da Silva, Altigran Soares and Lifschitz, S\'{e}rgio},
  title =	{{CoaKG: A Contextualized Knowledge Graph Approach for Exploratory Search and Decision Making}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{4:1--4:27},
  ISSN =	{2942-7517},
  year =	{2025},
  volume =	{3},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.3.1.4},
  URN =		{urn:nbn:de:0030-drops-236685},
  doi =		{10.4230/TGDK.3.1.4},
  annote =	{Keywords: Knowledge Graphs, Context Search, Decision Support}
}
Document
Experience Paper
DOI: 10.4230/LIPIcs.ECOOP.2025.37
RacerF: Lightweight Static Data Race Detection for C Code (Experience Paper)

Authors: Tomáš Dacík and Tomáš Vojnar

Published in: LIPIcs, Volume 333, 39th European Conference on Object-Oriented Programming (ECOOP 2025)

Abstract
We present RacerF, a novel static analyser for thread-modular data race detection. The approach behind RacerF exploits static analysis of sequential program behaviour whose results are generalised for multi-threaded programs using a combination of lightweight under- and over-approximating methods. The tool is implemented as a plugin of the Frama-C platform and can leverage several analysis backends, most notably the Frama-C’s abstract interpreter EVA. Although our methods are mostly heuristic without providing formal guarantees, our experimental evaluation shows that even for intricate programs, RacerF can provide very precise results competitive with more heavyweight approaches while being faster than them.
Cite as

Tomáš Dacík and Tomáš Vojnar. RacerF: Lightweight Static Data Race Detection for C Code (Experience Paper). In 39th European Conference on Object-Oriented Programming (ECOOP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 333, pp. 37:1-37:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{dacik_et_al:LIPIcs.ECOOP.2025.37,
  author =	{Dac{\'\i}k, Tom\'{a}\v{s} and Vojnar, Tom\'{a}\v{s}},
  title =	{{RacerF: Lightweight Static Data Race Detection for C Code}},
  booktitle =	{39th European Conference on Object-Oriented Programming (ECOOP 2025)},
  pages =	{37:1--37:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-373-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{333},
  editor =	{Aldrich, Jonathan and Silva, Alexandra},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECOOP.2025.37},
  URN =		{urn:nbn:de:0030-drops-233298},
  doi =		{10.4230/LIPIcs.ECOOP.2025.37},
  annote =	{Keywords: concurrency, data race detection, static analysis}
}
Document
DOI: 10.4230/LIPIcs.ECOOP.2025.4
Ensuring Convergence and Invariants Without Coordination

Authors: Dina Borrego, Nuno Preguiça, Elisa Gonzalez Boix, and Carla Ferreira

Published in: LIPIcs, Volume 333, 39th European Conference on Object-Oriented Programming (ECOOP 2025)

Abstract
The CAP theorem demonstrates a trade-off between consistency and availability (and, by extension, latency) in systems where network partitions are unavoidable, such as in cloud computing and local-first software. While adopting weak consistency can preserve availability, it may result in inconsistencies that compromise application correctness. Replicated data types provide a principled, coordination-free approach to guarantee convergence but do not consider application invariants. Existing methods for maintaining invariants in replicated systems either rely on coordination - undermining the benefits of weak consistency - or suffer from limited applicability. This paper introduces the No-Op framework, a generic approach for enforcing consistency without coordination while guaranteeing both convergence and invariant preservation. The core idea of the No-Op approach is to resolve conflicts among concurrent operations by prioritising one operation over the other according to programmer-defined conflict resolution policies. This prioritisation transforms the less-preferred operation into a no-side-effect operation, ensuring conflict-free execution. We formalise the model underlying the No-Op framework and introduce a replication protocol built upon it, accompanied by a formal proof of correctness for both the framework and the protocol. Furthermore, we demonstrate the framework’s applicability by showcasing the design of widely used replicated data types and the preservation of a wide range of application invariants.
Cite as

Dina Borrego, Nuno Preguiça, Elisa Gonzalez Boix, and Carla Ferreira. Ensuring Convergence and Invariants Without Coordination. In 39th European Conference on Object-Oriented Programming (ECOOP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 333, pp. 4:1-4:29, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{borrego_et_al:LIPIcs.ECOOP.2025.4,
  author =	{Borrego, Dina and Pregui\c{c}a, Nuno and Gonzalez Boix, Elisa and Ferreira, Carla},
  title =	{{Ensuring Convergence and Invariants Without Coordination}},
  booktitle =	{39th European Conference on Object-Oriented Programming (ECOOP 2025)},
  pages =	{4:1--4:29},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-373-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{333},
  editor =	{Aldrich, Jonathan and Silva, Alexandra},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECOOP.2025.4},
  URN =		{urn:nbn:de:0030-drops-232978},
  doi =		{10.4230/LIPIcs.ECOOP.2025.4},
  annote =	{Keywords: distributed systems, conflict resolution, RDTs, invariant preservation}
}
Document
Pearl/Brave New Idea
DOI: 10.4230/LIPIcs.ECOOP.2025.41
Shouting at Memory: Where Did My Write Go? (Pearl/Brave New Idea)

Authors: Vasileios Klimis

Published in: LIPIcs, Volume 333, 39th European Conference on Object-Oriented Programming (ECOOP 2025)

Abstract
Non-Volatile Memory (NVM) promises persistent data, but verifying that promise on real hardware is challenging due to opaque caching and internal buffers like Intel’s WPQ, which obscure the true state of writes. Traditional validation methods often fall short. This paper introduces a novel perspective: leveraging the subtle timing variations of memory accesses as a direct probe into write persistence. We present a software technique, inspired by echolocation, that uses high-resolution timers to measure memory load latencies. These timings act as distinct signatures ("echoes") revealing whether a write’s data resides in volatile caches or has reached the NVM persistence domain. This offers a non-invasive method to track write progression towards durability. To reliably interpret these potentially noisy timing signatures and systematically explore complex persistence behaviours, we integrate this echolocation probe into an active model learning framework. This synergy enables the automated inference of a system’s actual persistency semantics directly from black-box hardware observations. The approach is hardware-agnostic, adaptive, and scalable. Preliminary experiments on Intel x86 - a platform where persistence validation is notably challenged by the opaque Write Pending Queue (WPQ) - demonstrate the feasibility of our technique. We observed distinct latency clusters differentiating volatile cache accesses from those reaching the persistence domain. This combined approach offers a promising path towards robust and automated validation of NVM persistency across diverse architectures.
Cite as

Vasileios Klimis. Shouting at Memory: Where Did My Write Go? (Pearl/Brave New Idea). In 39th European Conference on Object-Oriented Programming (ECOOP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 333, pp. 41:1-41:26, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{klimis:LIPIcs.ECOOP.2025.41,
  author =	{Klimis, Vasileios},
  title =	{{Shouting at Memory: Where Did My Write Go?}},
  booktitle =	{39th European Conference on Object-Oriented Programming (ECOOP 2025)},
  pages =	{41:1--41:26},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-373-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{333},
  editor =	{Aldrich, Jonathan and Silva, Alexandra},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECOOP.2025.41},
  URN =		{urn:nbn:de:0030-drops-233339},
  doi =		{10.4230/LIPIcs.ECOOP.2025.41},
  annote =	{Keywords: Persistency Memory Semantics, Fuzz Testing, Model Learning}
}
Document
DOI: 10.4230/LIPIcs.SoCG.2025.68
Persistent (Co)Homology in Matrix Multiplication Time

Authors: Dmitriy Morozov and Primoz Skraba

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

Abstract
Most algorithms for computing persistent homology do so by tracking cycles that represent homology classes. There are many choices of such cycles, and specific choices have found different uses in applications. Although it is known that persistence diagrams can be computed in matrix multiplication time for the more general case of zigzag persistent homology [Milosavljević et al., 2011], it is not clear how to extract cycle representatives, especially if specific representatives are desired. In this paper, we provide the same matrix multiplication bound for computing representatives for the two choices common in applications in the case of ordinary persistent (co)homology. We first provide a fast version of the reduction algorithm, which is simpler than the algorithm in [Milosavljević et al., 2011], but returns a different set of representatives than the standard algorithm [Edelsbrunner et al., 2002]. We then give a fast version of a variant called the row algorithm [De Silva et al., 2011], which returns the same representatives as the standard algorithm.
Cite as

Dmitriy Morozov and Primoz Skraba. Persistent (Co)Homology in Matrix Multiplication Time. In 41st International Symposium on Computational Geometry (SoCG 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 332, pp. 68:1-68:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{morozov_et_al:LIPIcs.SoCG.2025.68,
  author =	{Morozov, Dmitriy and Skraba, Primoz},
  title =	{{Persistent (Co)Homology in Matrix Multiplication Time}},
  booktitle =	{41st International Symposium on Computational Geometry (SoCG 2025)},
  pages =	{68:1--68:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-370-6},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{332},
  editor =	{Aichholzer, Oswin and Wang, Haitao},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SoCG.2025.68},
  URN =		{urn:nbn:de:0030-drops-232204},
  doi =		{10.4230/LIPIcs.SoCG.2025.68},
  annote =	{Keywords: persistent homology, matrix multiplication, cycle representatives}
}
Document
DOI: 10.4230/LIPIcs.CPM.2025.17
On the Compressiveness of the Burrows-Wheeler Transform

Authors: Hideo Bannai, Tomohiro I, and Yuto Nakashima

Published in: LIPIcs, Volume 331, 36th Annual Symposium on Combinatorial Pattern Matching (CPM 2025)

Abstract
The Burrows-Wheeler transform (BWT) is a reversible transform that converts a string w into another string BWT(w). The size of the run-length encoded BWT (RLBWT) can be interpreted as a measure of repetitiveness in the class of representations called dictionary compression which are essentially representations based on copy and paste operations. In this paper, we shed new light on the compressiveness of BWT and the bijective BWT (BBWT). We first extend previous results on the relations of their run-length compressed sizes r and r_B. We also show that the so-called "clustering effect" of BWT and BBWT can be captured by measures other than empirical entropy or run-length encoding. In particular, we show that BWT and BBWT do not increase the repetitiveness of the string with respect to various measures based on dictionary compression by more than a polylogarithmic factor. Furthermore, we show that there exists an infinite family of strings that are maximally incompressible by any dictionary compression measure, but become very compressible after applying BBWT. An interesting implication of this result is that it is possible to transcend dictionary compression in some cases by simply applying BBWT before applying dictionary compression.
Cite as

Hideo Bannai, Tomohiro I, and Yuto Nakashima. On the Compressiveness of the Burrows-Wheeler Transform. In 36th Annual Symposium on Combinatorial Pattern Matching (CPM 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 331, pp. 17:1-17:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{bannai_et_al:LIPIcs.CPM.2025.17,
  author =	{Bannai, Hideo and I, Tomohiro and Nakashima, Yuto},
  title =	{{On the Compressiveness of the Burrows-Wheeler Transform}},
  booktitle =	{36th Annual Symposium on Combinatorial Pattern Matching (CPM 2025)},
  pages =	{17:1--17:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-369-0},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{331},
  editor =	{Bonizzoni, Paola and M\"{a}kinen, Veli},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2025.17},
  URN =		{urn:nbn:de:0030-drops-231116},
  doi =		{10.4230/LIPIcs.CPM.2025.17},
  annote =	{Keywords: Data Compression, Bijective Burrows-Wheeler Transform, Fibonacci words}
}
Document
Resource Paper
DOI: 10.4230/TGDK.2.2.4
FAIR Jupyter: A Knowledge Graph Approach to Semantic Sharing and Granular Exploration of a Computational Notebook Reproducibility Dataset

Authors: Sheeba Samuel and Daniel Mietchen

Published in: TGDK, Volume 2, Issue 2 (2024): Special Issue on Resources for Graph Data and Knowledge. Transactions on Graph Data and Knowledge, Volume 2, Issue 2

Abstract
The way in which data are shared can affect their utility and reusability. Here, we demonstrate how data that we had previously shared in bulk can be mobilized further through a knowledge graph that allows for much more granular exploration and interrogation. The original dataset is about the computational reproducibility of GitHub-hosted Jupyter notebooks associated with biomedical publications. It contains rich metadata about the publications, associated GitHub repositories and Jupyter notebooks, and the notebooks' reproducibility. We took this dataset, converted it into semantic triples and loaded these into a triple store to create a knowledge graph - FAIR Jupyter - that we made accessible via a web service. This enables granular data exploration and analysis through queries that can be tailored to specific use cases. Such queries may provide details about any of the variables from the original dataset, highlight relationships between them or combine some of the graph’s content with materials from corresponding external resources. We provide a collection of example queries addressing a range of use cases in research and education. We also outline how sets of such queries can be used to profile specific content types, either individually or by class. We conclude by discussing how such a semantically enhanced sharing of complex datasets can both enhance their FAIRness - i.e., their findability, accessibility, interoperability, and reusability - and help identify and communicate best practices, particularly with regards to data quality, standardization, automation and reproducibility.
Cite as

Sheeba Samuel and Daniel Mietchen. FAIR Jupyter: A Knowledge Graph Approach to Semantic Sharing and Granular Exploration of a Computational Notebook Reproducibility Dataset. In Special Issue on Resources for Graph Data and Knowledge. Transactions on Graph Data and Knowledge (TGDK), Volume 2, Issue 2, pp. 4:1-4:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@Article{samuel_et_al:TGDK.2.2.4,
  author =	{Samuel, Sheeba and Mietchen, Daniel},
  title =	{{FAIR Jupyter: A Knowledge Graph Approach to Semantic Sharing and Granular Exploration of a Computational Notebook Reproducibility Dataset}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{4:1--4:24},
  ISSN =	{2942-7517},
  year =	{2024},
  volume =	{2},
  number =	{2},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.2.2.4},
  URN =		{urn:nbn:de:0030-drops-225886},
  doi =		{10.4230/TGDK.2.2.4},
  annote =	{Keywords: Knowledge Graph, Computational reproducibility, Jupyter notebooks, FAIR data, PubMed Central, GitHub, Python, SPARQL}
}
Document
Survey
DOI: 10.4230/TGDK.2.1.1
Towards Representing Processes and Reasoning with Process Descriptions on the Web

Authors: Andreas Harth, Tobias Käfer, Anisa Rula, Jean-Paul Calbimonte, Eduard Kamburjan, and Martin Giese

Published in: TGDK, Volume 2, Issue 1 (2024): Special Issue on Trends in Graph Data and Knowledge - Part 2. Transactions on Graph Data and Knowledge, Volume 2, Issue 1

Abstract
We work towards a vocabulary to represent processes and temporal logic specifications as graph-structured data. Different fields use incompatible terminologies for describing essentially the same process-related concepts. In addition, processes can be represented from different perspectives and levels of abstraction: both state-centric and event-centric perspectives offer distinct insights into the underlying processes. In this work, we strive to unify the representation of processes and related concepts by leveraging the power of knowledge graphs. We survey approaches to representing processes and reasoning with process descriptions from different fields and provide a selection of scenarios to help inform the scope of a unified representation of processes. We focus on processes that can be executed and observed via web interfaces. We propose to provide a representation designed to combine state-centric and event-centric perspectives while incorporating temporal querying and reasoning capabilities on temporal logic specifications. A standardised vocabulary and representation for processes and temporal specifications would contribute towards bridging the gap between the terminologies from different fields and fostering the broader application of methods involving temporal logics, such as formal verification and program synthesis.
Cite as

Andreas Harth, Tobias Käfer, Anisa Rula, Jean-Paul Calbimonte, Eduard Kamburjan, and Martin Giese. Towards Representing Processes and Reasoning with Process Descriptions on the Web. In Special Issue on Trends in Graph Data and Knowledge - Part 2. Transactions on Graph Data and Knowledge (TGDK), Volume 2, Issue 1, pp. 1:1-1:32, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@Article{harth_et_al:TGDK.2.1.1,
  author =	{Harth, Andreas and K\"{a}fer, Tobias and Rula, Anisa and Calbimonte, Jean-Paul and Kamburjan, Eduard and Giese, Martin},
  title =	{{Towards Representing Processes and Reasoning with Process Descriptions on the Web}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{1:1--1:32},
  ISSN =	{2942-7517},
  year =	{2024},
  volume =	{2},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.2.1.1},
  URN =		{urn:nbn:de:0030-drops-198583},
  doi =		{10.4230/TGDK.2.1.1},
  annote =	{Keywords: Process modelling, Process ontology, Temporal logic, Web services}
}
Document
Vision
DOI: 10.4230/TGDK.1.1.3
Knowledge Engineering Using Large Language Models

Authors: Bradley P. Allen, Lise Stork, and Paul Groth

Published in: TGDK, Volume 1, Issue 1 (2023): Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge, Volume 1, Issue 1

Abstract
Knowledge engineering is a discipline that focuses on the creation and maintenance of processes that generate and apply knowledge. Traditionally, knowledge engineering approaches have focused on knowledge expressed in formal languages. The emergence of large language models and their capabilities to effectively work with natural language, in its broadest sense, raises questions about the foundations and practice of knowledge engineering. Here, we outline the potential role of LLMs in knowledge engineering, identifying two central directions: 1) creating hybrid neuro-symbolic knowledge systems; and 2) enabling knowledge engineering in natural language. Additionally, we formulate key open research questions to tackle these directions.
Cite as

Bradley P. Allen, Lise Stork, and Paul Groth. Knowledge Engineering Using Large Language Models. In Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge (TGDK), Volume 1, Issue 1, pp. 3:1-3:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@Article{allen_et_al:TGDK.1.1.3,
  author =	{Allen, Bradley P. and Stork, Lise and Groth, Paul},
  title =	{{Knowledge Engineering Using Large Language Models}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{3:1--3:19},
  ISSN =	{2942-7517},
  year =	{2023},
  volume =	{1},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.1.1.3},
  URN =		{urn:nbn:de:0030-drops-194777},
  doi =		{10.4230/TGDK.1.1.3},
  annote =	{Keywords: knowledge engineering, large language models}
}
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