38 Search Results for "Berger, Martin"

Document
DOI: 10.4230/LIPIcs.CSL.2026.19
A Unifying Conservation Theorem

Authors: Giulio Fellin

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

Abstract
The relationship between classical and constructive logics has long been illuminated by a series of conservation results, beginning with Kolmogorov’s negative translation and Glivenko’s double negation theorem, and later extended by Kuroda and Segerberg to first-order and minimal logics respectively. These results reveal how certain classical principles can be interpreted or recovered within weaker constructive frameworks, either via translations or through minimal extensions that satisfy specific logical properties. In this paper, we propose a unifying generalisation of these conservation theorems, that consolidates and expands the abstract methods introduced in earlier studies, offering a unified perspective on the interplay between classical provability and constructive reasoning.
Cite as

Giulio Fellin. A Unifying Conservation Theorem. In 34th EACSL Annual Conference on Computer Science Logic (CSL 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 363, pp. 19:1-19:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

Copy BibTex To Clipboard

@InProceedings{fellin:LIPIcs.CSL.2026.19,
  author =	{Fellin, Giulio},
  title =	{{A Unifying Conservation Theorem}},
  booktitle =	{34th EACSL Annual Conference on Computer Science Logic (CSL 2026)},
  pages =	{19:1--19:23},
  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.2026.19},
  URN =		{urn:nbn:de:0030-drops-254431},
  doi =		{10.4230/LIPIcs.CSL.2026.19},
  annote =	{Keywords: double negation, negative translation, conservation, minimal logic, Glivenko’s theorem}
}
Document
DOI: 10.4230/LIPIcs.CSL.2026.23
A Logic for Fresh Labelled Transition Systems

Authors: Mohamed H. Bandukara and Nikos Tzevelekos

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

Abstract
We introduce a Hennessy-Milner logic with recursion for Fresh Labelled Transition Systems (FLTSs). These are nominal labelled transition systems which keep track of the history, i.e. of data values seen so far, and can model fresh data generation. In particular, FLTSs generalise the computations of Fresh-Register Automata, which in turn can be seen as a "regular" class of history-tracking automata operating on infinite input alphabets. The logic we introduce is a modal mu-calculus equipped with infinite disjunctions over arbitrary and fresh data values respectively, while its recursion is parameterised on vectors of data values. It can express a variety of properties, such as the existence of an infinite path of distinct data values, the absence of paths where values are repeated, or the existence of a finite path where some taint property is violated. We study the model-checking problem and its complexity via a reduction to parity games and, using nominal sets techniques, provide an exponential upper bound for it.
Cite as

Mohamed H. Bandukara and Nikos Tzevelekos. A Logic for Fresh Labelled Transition Systems. In 34th EACSL Annual Conference on Computer Science Logic (CSL 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 363, pp. 23:1-23:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

Copy BibTex To Clipboard

@InProceedings{bandukara_et_al:LIPIcs.CSL.2026.23,
  author =	{Bandukara, Mohamed H. and Tzevelekos, Nikos},
  title =	{{A Logic for Fresh Labelled Transition Systems}},
  booktitle =	{34th EACSL Annual Conference on Computer Science Logic (CSL 2026)},
  pages =	{23:1--23:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-411-6},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{363},
  editor =	{Guerrini, Stefano and K\"{o}nig, Barbara},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CSL.2026.23},
  URN =		{urn:nbn:de:0030-drops-254478},
  doi =		{10.4230/LIPIcs.CSL.2026.23},
  annote =	{Keywords: Nominal Transition Systems, Hennessy-Milner Logic, Modal Mu-Calculus, Register Automata, Nominal Sets, Parity Games}
}
Document
DOI: 10.4230/LIPIcs.OPODIS.2025.9
Contention-Aware Cooperation

Authors: Timothé Albouy, Davide Frey, Mathieu Gestin, Michel Raynal, and François Taïani

Published in: LIPIcs, Volume 361, 29th International Conference on Principles of Distributed Systems (OPODIS 2025)

Abstract
As shown by Reliable Broadcast and Consensus, cooperation among a set of independent computing entities (sequential processes) is crucial in fault-tolerant distributed computing. Considering n-process asynchronous message-passing systems where some processes may be Byzantine, this paper introduces a novel cooperation abstraction, Contention-Aware Cooperation (CAC). While Reliable Broadcast is a one-to-n cooperation abstraction and Consensus is an n-to-n cooperation abstraction, CAC is a d-to-n cooperation abstraction where d (1 ≤ d ≤ n) varies with each run and remains unknown to the processes. Correct processes accept the same set of 𝓁 pairs ⟨ v,i ⟩ (v is the value proposed by p_i) from the d proposer processes, where 1 ≤ 𝓁 ≤ d and (as d) 𝓁 remains unknown to the processes (except in specific cases). Those 𝓁 values are accepted one at a time, potentially in different orders at each process. In addition, CAC provides each process with an imperfect oracle that provides insights into the values that they may accept in the future. Interestingly, the CAC abstraction is particularly efficient in favorable circumstances, when the oracle becomes accurate, which processes can detect. To illustrate its practical utility, the paper details two applications leveraging CAC: a fast consensus implementation optimized for low contention (named Cascading Consensus), and a novel naming problem that can be solved under full asynchrony. All algorithms presented require signatures.
Cite as

Timothé Albouy, Davide Frey, Mathieu Gestin, Michel Raynal, and François Taïani. Contention-Aware Cooperation. In 29th International Conference on Principles of Distributed Systems (OPODIS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 361, pp. 9:1-9:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

Copy BibTex To Clipboard

@InProceedings{albouy_et_al:LIPIcs.OPODIS.2025.9,
  author =	{Albouy, Timoth\'{e} and Frey, Davide and Gestin, Mathieu and Raynal, Michel and Ta\"{i}ani, Fran\c{c}ois},
  title =	{{Contention-Aware Cooperation}},
  booktitle =	{29th International Conference on Principles of Distributed Systems (OPODIS 2025)},
  pages =	{9:1--9:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-409-3},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{361},
  editor =	{Arusoaie, Andrei and Onica, Emanuel and Spear, Michael and Tucci-Piergiovanni, Sara},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.OPODIS.2025.9},
  URN =		{urn:nbn:de:0030-drops-251823},
  doi =		{10.4230/LIPIcs.OPODIS.2025.9},
  annote =	{Keywords: Agreement, Asynchronous message-passing system, Byzantine processes, Conflict detection, Consensus, Cooperation abstraction, Distributed computing, Fault tolerance, Optimistically terminating consensus, Short-naming}
}
Document
Invited Paper
DOI: 10.4230/OASIcs.RW.2024/2025.7
Modern Datalog: Concepts, Methods, Applications (Invited Paper)

Authors: Markus Krötzsch

Published in: OASIcs, Volume 138, Joint Proceedings of the 20th and 21st Reasoning Web Summer Schools (RW 2024 & RW 2025)

Abstract
Pure Datalog is arguably the most fundamental rule language, elegant and simple, but also often too limited to be useful in practice. This has motivated the introduction of many new expressive features, ranging from datatypes and related functions, over aggregates and semi-ring generalisations, to existential quantifiers and complex terms. In spite of their variety, all these approaches remain true to the nature of Datalog as a direct, pattern-based way of computing on structured data. We therefore find that a modern notion of Datalog is emerging, distinctly different from other approaches of logic programming and with its own set of related methods and applications. In this course, we introduce Datalog and its most common extensions, and explain when and how these features can be used together (which is often, but not always, safe to do). We further look at modern Datalog systems and some of their primary use cases. Hands-on work with Datalog and its extensions is done with the free Datalog engine https://knowsys.github.io/nemo-doc/. The course is accessible to all audiences and does not assume specific prior knowledge.
Cite as

Markus Krötzsch. Modern Datalog: Concepts, Methods, Applications (Invited Paper). In Joint Proceedings of the 20th and 21st Reasoning Web Summer Schools (RW 2024 & RW 2025). Open Access Series in Informatics (OASIcs), Volume 138, pp. 7:1-7:41, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

Copy BibTex To Clipboard

@InProceedings{krotzsch:OASIcs.RW.2024/2025.7,
  author =	{Kr\"{o}tzsch, Markus},
  title =	{{Modern Datalog: Concepts, Methods, Applications}},
  booktitle =	{Joint Proceedings of the 20th and 21st Reasoning Web Summer Schools (RW 2024 \& RW 2025)},
  pages =	{7:1--7:41},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-405-5},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{138},
  editor =	{Artale, Alessandro and Bienvenu, Meghyn and Garc{\'\i}a, Yazm{\'\i}n Ib\'{a}\~{n}ez and Murlak, Filip},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.RW.2024/2025.7},
  URN =		{urn:nbn:de:0030-drops-250524},
  doi =		{10.4230/OASIcs.RW.2024/2025.7},
  annote =	{Keywords: Datalog, query language, knowlegde representation and reasoning, logic programming, Horn logic, SPARQL, datatypes and aggregation, lecture notes, tutorial}
}
Document
DOI: 10.4230/LIPIcs.ISAAC.2025.15
Parameterized Complexity of Directed Traveling Salesman Problem

Authors: Václav Blažej, Andreas Emil Feldmann, Foivos Fioravantes, Paweł Rzążewski, and Ondřej Suchý

Published in: LIPIcs, Volume 359, 36th International Symposium on Algorithms and Computation (ISAAC 2025)

Abstract
The Directed Traveling Salesman Problem (DTSP) is a variant of the classical Traveling Salesman Problem in which the edges in the graph are directed and a vertex and edge can be visited multiple times. The goal is to find a directed closed walk of minimum length (or total weight) that visits every vertex of the given graph at least once. In a yet more general version, Directed Waypoint Routing Problem (DWRP), some vertices are marked as terminals and we are only required to visit all terminals. Furthermore, each edge has its capacity bounding the number of times this edge can be used by a solution. While both problems (and many other variants of TSP) were extensively investigated, mostly from the approximation point of view, there are surprisingly few results concerning the parameterized complexity. Our starting point is the result of Marx et al. [APPROX/RANDOM 2016] who proved that DTSP is W[1]-hard parameterized by distance to pathwidth 3. In this paper we aim to initiate the systematic complexity study of variants of Directed Traveling Salesman Problem with respect to various, mostly structural, parameters. We show that DWRP is FPT parameterized by the solution size, the feedback edge number and the vertex integrity of the underlying undirected graph. Furthermore, the problem is XP parameterized by treewidth. On the complexity side, we show that the problem is W[1]-hard parameterized by the distance to constant treedepth.
Cite as

Václav Blažej, Andreas Emil Feldmann, Foivos Fioravantes, Paweł Rzążewski, and Ondřej Suchý. Parameterized Complexity of Directed Traveling Salesman Problem. In 36th International Symposium on Algorithms and Computation (ISAAC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 359, pp. 15:1-15:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

Copy BibTex To Clipboard

@InProceedings{blazej_et_al:LIPIcs.ISAAC.2025.15,
  author =	{Bla\v{z}ej, V\'{a}clav and Feldmann, Andreas Emil and Fioravantes, Foivos and Rz\k{a}\.{z}ewski, Pawe{\l} and Such\'{y}, Ond\v{r}ej},
  title =	{{Parameterized Complexity of Directed Traveling Salesman Problem}},
  booktitle =	{36th International Symposium on Algorithms and Computation (ISAAC 2025)},
  pages =	{15:1--15:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-408-6},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{359},
  editor =	{Chen, Ho-Lin and Hon, Wing-Kai and Tsai, Meng-Tsung},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ISAAC.2025.15},
  URN =		{urn:nbn:de:0030-drops-249231},
  doi =		{10.4230/LIPIcs.ISAAC.2025.15},
  annote =	{Keywords: Directed TSP, parameterized complexity, vertex integrity, treedepth}
}
Document
Survey
DOI: 10.4230/TGDK.3.2.1
Resilience in Knowledge Graph Embeddings

Authors: Arnab Sharma, N'Dah Jean Kouagou, and Axel-Cyrille Ngonga Ngomo

Published in: TGDK, Volume 3, Issue 2 (2025). Transactions on Graph Data and Knowledge, Volume 3, Issue 2

Abstract
In recent years, knowledge graphs have gained interest and witnessed widespread applications in various domains, such as information retrieval, question-answering, recommendation systems, amongst others. Large-scale knowledge graphs to this end have demonstrated their utility in effectively representing structured knowledge. To further facilitate the application of machine learning techniques, knowledge graph embedding models have been developed. Such models can transform entities and relationships within knowledge graphs into vectors. However, these embedding models often face challenges related to noise, missing information, distribution shift, adversarial attacks, etc. This can lead to sub-optimal embeddings and incorrect inferences, thereby negatively impacting downstream applications. While the existing literature has focused so far on adversarial attacks on KGE models, the challenges related to the other critical aspects remain unexplored. In this paper, we, first of all, give a unified definition of resilience, encompassing several factors such as generalisation, in-distribution generalization, distribution adaption, and robustness. After formalizing these concepts for machine learning in general, we define them in the context of knowledge graphs. To find the gap in the existing works on resilience in the context of knowledge graphs, we perform a systematic survey, taking into account all these aspects mentioned previously. Our survey results show that most of the existing works focus on a specific aspect of resilience, namely robustness. After categorizing such works based on their respective aspects of resilience, we discuss the challenges and future research directions.
Cite as

Arnab Sharma, N'Dah Jean Kouagou, and Axel-Cyrille Ngonga Ngomo. Resilience in Knowledge Graph Embeddings. In Transactions on Graph Data and Knowledge (TGDK), Volume 3, Issue 2, pp. 1:1-1:38, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

Copy BibTex To Clipboard

@Article{sharma_et_al:TGDK.3.2.1,
  author =	{Sharma, Arnab and Kouagou, N'Dah Jean and Ngomo, Axel-Cyrille Ngonga},
  title =	{{Resilience in Knowledge Graph Embeddings}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{1:1--1:38},
  ISSN =	{2942-7517},
  year =	{2025},
  volume =	{3},
  number =	{2},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.3.2.1},
  URN =		{urn:nbn:de:0030-drops-248117},
  doi =		{10.4230/TGDK.3.2.1},
  annote =	{Keywords: Knowledge graphs, Resilience, Robustness}
}
Document
DOI: 10.4230/OASIcs.SpaceCHI.2025.33
Digital Health for Space: Towards Prevention, Training, Empowerment, and Autonomy

Authors: Mario A. Cypko, Ulrich Straube, Russell J. Andrews, and Oliver Amft

Published in: OASIcs, Volume 130, Advancing Human-Computer Interaction for Space Exploration (SpaceCHI 2025)

Abstract
Future long-duration and deep-space missions will rely on digital health technologies to ensure the health and safety of the crew, as well as to enable the required mission autonomy. This position paper redefines the current paradigms of digital health by emphasizing prevention, self-management, and individual empowerment for health as central challenges for both space and terrestrial medicine. We focus on future mission scenarios and highlight the potential of co-evolving digital health and related technologies, particularly sensing, artificial intelligence (AI), and human-computer interaction (HCI), across the continuum of space medicine: from astronaut selection and training to prevention, diagnostics, therapy, rehabilitation, and long-term care. Future digital health technologies can respond to pressing needs arising from limited medical infrastructure, rising care costs, and increasing demands on healthcare systems in space and on Earth. To structure research and development needs, we introduce a framework with four autonomy levels based on mission distance and communication latency (Earth orbit, Lunar Gateway and Moon vicinity, Mars, and deep space) that illustrate how mission context constrains medical support and dictates system requirements. Using the Lunar Orbital Platform-Gateway as a near-future reference, we discuss how growing communication delays demand greater onboard autonomy and new telemedical strategies. Within the proposed framework, we integrate solutions built around AI-supported decision making, multimodal monitoring, and adaptive HCI, which should be co-designed through human-centered methods to form a cohesive health management ecosystem. The framework opens up synergies for proactive and trustworthy health support under isolation and limited ground contact. The paper consolidates current technological readiness and strategic challenges, offering guidance for space health research and policy, with clear translational benefits for terrestrial care delivery.
Cite as

Mario A. Cypko, Ulrich Straube, Russell J. Andrews, and Oliver Amft. Digital Health for Space: Towards Prevention, Training, Empowerment, and Autonomy. In Advancing Human-Computer Interaction for Space Exploration (SpaceCHI 2025). Open Access Series in Informatics (OASIcs), Volume 130, pp. 33:1-33:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

Copy BibTex To Clipboard

@InProceedings{cypko_et_al:OASIcs.SpaceCHI.2025.33,
  author =	{Cypko, Mario A. and Straube, Ulrich and Andrews, Russell J. and Amft, Oliver},
  title =	{{Digital Health for Space: Towards Prevention, Training, Empowerment, and Autonomy}},
  booktitle =	{Advancing Human-Computer Interaction for Space Exploration (SpaceCHI 2025)},
  pages =	{33:1--33:12},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-384-3},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{130},
  editor =	{Bensch, Leonie and Nilsson, Tommy and Nisser, Martin and Pataranutaporn, Pat and Schmidt, Albrecht and Sumini, Valentina},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.SpaceCHI.2025.33},
  URN =		{urn:nbn:de:0030-drops-240236},
  doi =		{10.4230/OASIcs.SpaceCHI.2025.33},
  annote =	{Keywords: Digital Health in Space, AI-based Decision Support, Wearable Health Monitoring, Human-Computer Interaction (HCI), Autonomous Medical Systems}
}
Document
DOI: 10.4230/LIPIcs.MFCS.2025.63
Shortest Paths in Multimode Graphs

Authors: Yael Kirkpatrick and Virginia Vassilevska Williams

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

Abstract
In this work we study shortest path problems in multimode graphs, a generalization of the min-distance measure introduced by Abboud, Vassilevska W. and Wang in [SODA'16]. A multimode shortest path is the shortest path using one of multiple "modes" of transportation that cannot be combined. This represents real-world scenarios where different modes are not combinable, such as flights operated by different airline alliances. The problem arises naturally in machine learning in the context of learning with multiple embedding. More precisely, a k-multimode graph is a collection of k graphs on the same vertex set and the k-mode distance between two vertices is defined as the minimum among the distances computed in each individual graph. We focus on approximating fundamental graph parameters on these graphs, specifically diameter and radius. In undirected multimode graphs we first show an elegant linear time 3-approximation algorithm for 2-mode diameter. We then extend this idea into a general subroutine that can be used as a part of any α-approximation, and use it to construct a 2 and 2.5 approximation algorithm for 2-mode diameter. For undirected radius, we introduce a general scheme that can compute a 3-approximation of the k-mode radius for any k and runs in near linear time in the case of k = O(1). In the directed case we establish an equivalence between approximating 2-mode diameter on DAGs and approximating the min-diameter, while for general graphs we develop novel techniques and provide a linear time algorithm to determine whether the diameter is finite. We also develop many conditional fine-grained lower bounds for various multimode diameter and radius approximation problems. We are able to show that many of our algorithms are tight under popular fine-grained complexity hypotheses, including our linear time 3-approximation for 3-mode undirected diameter and radius. As part of this effort we propose the first extension to the Hitting Set Hypothesis [SODA'16], which we call the 𝓁-Hitting Set Hypothesis. We use this hypothesis to prove the first parameterized lower bound tradeoff for radius approximation algorithms.
Cite as

Yael Kirkpatrick and Virginia Vassilevska Williams. Shortest Paths in Multimode Graphs. In 50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 345, pp. 63:1-63:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

Copy BibTex To Clipboard

@InProceedings{kirkpatrick_et_al:LIPIcs.MFCS.2025.63,
  author =	{Kirkpatrick, Yael and Vassilevska Williams, Virginia},
  title =	{{Shortest Paths in Multimode Graphs}},
  booktitle =	{50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025)},
  pages =	{63:1--63:16},
  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.2025.63},
  URN =		{urn:nbn:de:0030-drops-241703},
  doi =		{10.4230/LIPIcs.MFCS.2025.63},
  annote =	{Keywords: Graph Algorithms, Shortest Paths, Diameter, Radius, Fine-Grained Complexity}
}
Document
DOI: 10.4230/LIPIcs.CONCUR.2025.23
First-Order Store and Visibility in Name-Passing Calculi

Authors: Daniel Hirschkoff, Iwan Quémerais, and Davide Sangiorgi

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

Abstract
The π-calculus is the paradigmatical name-passing calculus. While being purely name-passing, it allows the representation of higher-order functions and store. We study how π-calculus processes can be controlled so that computations can only involve storage of first-order values. The discipline is enforced by a type system that is based on the notion of visibility, coming from game semantics. We discuss the impact of visibility on the behavioural theory. We propose characterisations of may-testing and barbed equivalence, based on (variants of) trace equivalence and labelled bisimilarity, in the case where computation is sequential, and in the case where computation is well-bracketed.
Cite as

Daniel Hirschkoff, Iwan Quémerais, and Davide Sangiorgi. First-Order Store and Visibility in Name-Passing Calculi. In 36th International Conference on Concurrency Theory (CONCUR 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 348, pp. 23:1-23:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

Copy BibTex To Clipboard

@InProceedings{hirschkoff_et_al:LIPIcs.CONCUR.2025.23,
  author =	{Hirschkoff, Daniel and Qu\'{e}merais, Iwan and Sangiorgi, Davide},
  title =	{{First-Order Store and Visibility in Name-Passing Calculi}},
  booktitle =	{36th International Conference on Concurrency Theory (CONCUR 2025)},
  pages =	{23:1--23:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-389-8},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{348},
  editor =	{Bouyer, Patricia and van de Pol, Jaco},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CONCUR.2025.23},
  URN =		{urn:nbn:de:0030-drops-239737},
  doi =		{10.4230/LIPIcs.CONCUR.2025.23},
  annote =	{Keywords: process calculi, behavioural equivalence, type system}
}
Document
DOI: 10.4230/LIPIcs.WABI.2025.22
Design of Worst-Case-Optimal Spaced Seeds

Authors: Jens Zentgraf and Sven Rahmann

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

Abstract
Read mapping (and alignment) is a fundamental problem in biological sequence analysis. For speed and computational efficiency, many popular read mappers tolerate only a few differences between the read and the corresponding part of the reference genome, which leads to reference bias: Reads with too many differences are not guaranteed to be mapped correctly or at all, because to even consider a genomic position, a sufficiently long exact match (seed) must exist. While pangenomes and their graph-based representations provide one way to avoid reference bias by enlarging the reference, we explore an orthogonal approach and consider stronger substitution-tolerant primitives, namely spaced seeds or gapped k-mers. Given two integers k ≤ w, one considers k selected positions, described by a mask, from each length-w window in a sequence. In the existing literature, masks with certain probabilistic guarantees have been designed for small values of k. Here, for the first time, we take a combinatorial approach from a worst-case perspective. For any mask, using integer linear programs, we find least favorable distributions of sequence changes in two different senses: (1) minimizing the number of unchanged windows; (2) minimizing the number of positions covered by unchanged windows. Then, among all masks or all symmetric masks of a given shape (k,w), we find the set of best masks that maximize these minima. As a result, we obtain robust masks, even for large numbers of changes. We illustrate the properties of these masks by constructing a challenging set of reads that contain many approximately equidistributed substitutions (but no indels) that many existing tools cannot map, even though they are in principle easily mappable (apart from the large number of changes) because they originate from selected non-repetitive regions of the human reference genome. We observe that the majority of these reads can be mapped with a simple alignment-free approach using chosen spaced masks, where seeding approaches based on contiguous k-mers fail.
Cite as

Jens Zentgraf and Sven Rahmann. Design of Worst-Case-Optimal Spaced Seeds. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 22:1-22:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

Copy BibTex To Clipboard

@InProceedings{zentgraf_et_al:LIPIcs.WABI.2025.22,
  author =	{Zentgraf, Jens and Rahmann, Sven},
  title =	{{Design of Worst-Case-Optimal Spaced Seeds}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{22:1--22:17},
  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.2025.22},
  URN =		{urn:nbn:de:0030-drops-239488},
  doi =		{10.4230/LIPIcs.WABI.2025.22},
  annote =	{Keywords: Spaced seed, Gapped k-mer, Integer linear program (ILP), Worst-case design, Reference bias}
}
Document
DOI: 10.4230/LIPIcs.WABI.2025.20
A k-mer-Based Estimator of the Substitution Rate Between Repetitive Sequences

Authors: Haonan Wu, Antonio Blanca, and Paul Medvedev

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

Abstract
K-mer-based analysis of genomic data is ubiquitous, but the presence of repetitive k-mers continues to pose problems for the accuracy of many methods. For example, the Mash tool (Ondov et al. 2016) can accurately estimate the substitution rate between two low-repetitive sequences from their k-mer sketches; however, it is inaccurate on repetitive sequences such as the centromere of a human chromosome. Follow-up work by Blanca et al. (2021) has attempted to model how mutations affect k-mer sets based on strong assumptions that the sequence is non-repetitive and that mutations do not create spurious k-mer matches. However, the theoretical foundations for extending an estimator like Mash to work in the presence of repeat sequences have been lacking. In this work, we relax the non-repetitive assumption and propose a novel estimator for the mutation rate. We derive theoretical bounds on our estimator’s bias. Our experiments show that it remains accurate for repetitive genomic sequences, such as the alpha satellite higher order repeats in centromeres. We demonstrate our estimator’s robustness across diverse datasets and various ranges of the substitution rate and k-mer size. Finally, we show how sketching can be used to avoid dealing with large k-mer sets while retaining accuracy. Our software is available at https://github.com/medvedevgroup/Repeat-Aware_Substitution_Rate_Estimator.
Cite as

Haonan Wu, Antonio Blanca, and Paul Medvedev. A k-mer-Based Estimator of the Substitution Rate Between Repetitive Sequences. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 20:1-20:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

Copy BibTex To Clipboard

@InProceedings{wu_et_al:LIPIcs.WABI.2025.20,
  author =	{Wu, Haonan and Blanca, Antonio and Medvedev, Paul},
  title =	{{A k-mer-Based Estimator of the Substitution Rate Between Repetitive Sequences}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{20:1--20:20},
  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.2025.20},
  URN =		{urn:nbn:de:0030-drops-239465},
  doi =		{10.4230/LIPIcs.WABI.2025.20},
  annote =	{Keywords: k-mers, sketching, mutation rates}
}
Document
DOI: 10.4230/LIPIcs.WABI.2025.7
Sequence Similarity Estimation by Random Subsequence Sketching

Authors: Ke Chen, Vinamratha Pattar, and Mingfu Shao

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

Abstract
Sequence similarity estimation is essential for many bioinformatics tasks, including functional annotation, phylogenetic analysis, and overlap graph construction. Alignment-free methods aim to solve large-scale sequence similarity estimation by mapping sequences to more easily comparable features that can approximate edit distances efficiently. Substrings or k-mers, as the dominant choice of features, face an unavoidable compromise between sensitivity and specificity when selecting the proper k-value. Recently, subsequence-based features have shown improved performance, but they are computationally demanding, and determining the ideal subsequence length remains an intricate art. In this work, we introduce SubseqSketch, a novel alignment-free scheme that maps a sequence to an integer vector, where the entries correspond to dynamic, rather than fixed, lengths of random subsequences. The cosine similarity between these vectors exhibits a strong correlation with the edit similarity between the original sequences. Through experiments on benchmark datasets, we demonstrate that SubseqSketch is both efficient and effective across various alignment-free tasks, including nearest neighbor search and phylogenetic clustering. A C++ implementation of SubseqSketch is openly available at https://github.com/Shao-Group/SubseqSketch.
Cite as

Ke Chen, Vinamratha Pattar, and Mingfu Shao. Sequence Similarity Estimation by Random Subsequence Sketching. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 7:1-7:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

Copy BibTex To Clipboard

@InProceedings{chen_et_al:LIPIcs.WABI.2025.7,
  author =	{Chen, Ke and Pattar, Vinamratha and Shao, Mingfu},
  title =	{{Sequence Similarity Estimation by Random Subsequence Sketching}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{7:1--7:17},
  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.2025.7},
  URN =		{urn:nbn:de:0030-drops-239332},
  doi =		{10.4230/LIPIcs.WABI.2025.7},
  annote =	{Keywords: Alignment-free sequence comparison, Phylogenetic clustering, Nearest neighbor search, Edit distance embedding}
}
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)

Copy BibTex To Clipboard

@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/LIPIcs.SAT.2025.4
Bit-Precise Reasoning with Parametric Bit-Vectors

Authors: Zvika Berger, Yoni Zohar, Aina Niemetz, Mathias Preiner, Andrew Reynolds, Clark Barrett, and Cesare Tinelli

Published in: LIPIcs, Volume 341, 28th International Conference on Theory and Applications of Satisfiability Testing (SAT 2025)

Abstract
The SMT-LIB theory of bit-vectors is restricted to bit-vectors of fixed width. However, several important applications can benefit from reasoning about bit-vectors of symbolic widths, i.e., parametric bit-vectors. Recent work has introduced an approach for solving formulas over parametric bit-vectors, via an eager translation to quantified integer arithmetic with uninterpreted functions. The approach was shown to be successful for several applications, including the bit-width independent verification of compiler optimizations, invertibility conditions, and rewrite rules. We extend and improve that approach in several aspects. Theoretically, we improve expressiveness by defining a new theory of parametric bit-vectors that supports more operators and allows reasoning about the bit-widths themselves. Algorithmically, we introduce a lazy algorithm that avoids the use of uninterpreted functions and quantified axioms for them. Empirically, we show a significant improvement by implementing and evaluating our approach, and comparing it experimentally to the previous one.
Cite as

Zvika Berger, Yoni Zohar, Aina Niemetz, Mathias Preiner, Andrew Reynolds, Clark Barrett, and Cesare Tinelli. Bit-Precise Reasoning with Parametric Bit-Vectors. In 28th International Conference on Theory and Applications of Satisfiability Testing (SAT 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 341, pp. 4:1-4:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

Copy BibTex To Clipboard

@InProceedings{berger_et_al:LIPIcs.SAT.2025.4,
  author =	{Berger, Zvika and Zohar, Yoni and Niemetz, Aina and Preiner, Mathias and Reynolds, Andrew and Barrett, Clark and Tinelli, Cesare},
  title =	{{Bit-Precise Reasoning with Parametric Bit-Vectors}},
  booktitle =	{28th International Conference on Theory and Applications of Satisfiability Testing (SAT 2025)},
  pages =	{4:1--4:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-381-2},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{341},
  editor =	{Berg, Jeremias and Nordstr\"{o}m, Jakob},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SAT.2025.4},
  URN =		{urn:nbn:de:0030-drops-237385},
  doi =		{10.4230/LIPIcs.SAT.2025.4},
  annote =	{Keywords: Satisfiability Modulo Theories, Bit-precise Reasoning, Parametric Bit-vectors}
}
Document
DOI: 10.4230/LIPIcs.SEA.2025.20
SimdMinimizers: Computing Random Minimizers, fast

Authors: Ragnar Groot Koerkamp and Igor Martayan

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

Abstract
Motivation. Because of the rapidly-growing amount of sequencing data, computing sketches of large textual datasets has become an essential preprocessing task. These sketches are typically much smaller than the input sequences, but preserve sufficient information for downstream analysis. Minimizers are an especially popular sketching technique and used in a wide variety of applications. They sample at least one out of every w consecutive k-mers. As DNA sequencers are getting more accurate, some applications can afford to use a larger w and hence sparser and smaller sketches. And as sketches get smaller, their analysis becomes faster, so the time spent sketching the full-sized input becomes more of a bottleneck. Methods. Our library simd-minimizers implements a random minimizer algorithm using SIMD instructions. It supports both AVX2 and NEON architectures. Its main novelty is two-fold. First, it splits the input into 8 chunks that are streamed over in parallel through all steps of the algorithm. This is enabled by using the completely deterministic two-stacks sliding window minimum algorithm, which seems not to have been used before for finding minimizers. Results. Our library is up to 6.8× faster than a scalar implementation of the rescan method when w = 5 is small, and 3.4× faster for larger w = 19. Computing canonical minimizers is less than 50% slower than computing forward minimizers, and over 15× faster than the existing implementation in the minimizer-iter crate. Our library finds all (canonical) minimizers of a 3.2 Gbp human genome in 5.2 (resp. 6.7) seconds.
Cite as

Ragnar Groot Koerkamp and Igor Martayan. SimdMinimizers: Computing Random Minimizers, fast. In 23rd International Symposium on Experimental Algorithms (SEA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 338, pp. 20:1-20:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

Copy BibTex To Clipboard

@InProceedings{grootkoerkamp_et_al:LIPIcs.SEA.2025.20,
  author =	{Groot Koerkamp, Ragnar and Martayan, Igor},
  title =	{{SimdMinimizers: Computing Random Minimizers, fast}},
  booktitle =	{23rd International Symposium on Experimental Algorithms (SEA 2025)},
  pages =	{20:1--20:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-375-1},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{338},
  editor =	{Mutzel, Petra and Prezza, Nicola},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2025.20},
  URN =		{urn:nbn:de:0030-drops-232581},
  doi =		{10.4230/LIPIcs.SEA.2025.20},
  annote =	{Keywords: Minimizers, Randomized algorithms, Sketching, Hashing}
}
  • Refine by Type
  • 38 Document/PDF
  • 29 Document/HTML

  • Refine by Publication Year
  • 3 2026
  • 27 2025
  • 1 2024
  • 1 2023
  • 1 2022
  • Show More...

  • Refine by Author
  • 2 Berger, Martin
  • 2 Cerda, Rémy
  • 2 Vassilevska Williams, Virginia
  • 1 Ajdarów, Michal
  • 1 Albouy, Timothé
  • Show More...

  • Refine by Series/Journal
  • 30 LIPIcs
  • 4 OASIcs
  • 3 LITES
  • 1 TGDK

  • Refine by Classification
  • 5 Applied computing → Bioinformatics
  • 3 Theory of computation → Graph algorithms analysis
  • 3 Theory of computation → Lambda calculus
  • 3 Theory of computation → Logic and verification
  • 3 Theory of computation → Proof theory
  • Show More...

  • Refine by Keyword
  • 3 Taylor expansion
  • 2 Böhm trees
  • 2 Types
  • 2 program approximation
  • 1 802.1Qcr
  • Show More...

Any Issues?
X

Feedback on the Current Page

CAPTCHA

Thanks for your feedback!

Feedback submitted to Dagstuhl Publishing

Could not send message

Please try again later or send an E-mail
© 2023-2026 Schloss Dagstuhl – LZI GmbH Schloss Dagstuhl – LZI GmbH About DROPS Imprint Privacy Contact