72 Search Results for "Martin, Marcel"

Document
DOI: 10.4230/LIPIcs.SEA.2026.20
QuadRank: Engineering a High Throughput Rank

Authors: Ragnar Groot Koerkamp

Published in: LIPIcs, Volume 371, 24th International Symposium on Experimental Algorithms (SEA 2026)

Abstract
Motivation. Given a text, a query rank(q, c) counts the number of occurrences of character c among the first q characters of the text. Space-efficient methods to answer these rank queries form an important building block in many succinct data structures. For example, the FM-index [Ferragina and Manzini, 2000] is a widely used data structure that uses rank queries to locate all occurrences of a pattern in a text. In bioinformatics applications, the goal is usually to process large inputs as fast as possible. Thus, data structures should have high throughput when used with many threads. Contributions. We first survey existing results on rank data structures. For the σ = 2 binary alphabet, we then develop BiRank, which has 3.28% space overhead. BiRank merges the central ideas of two recent papers: (1) we interleave (inline) offsets in each cache line of the underlying bit vector [Laws et al., 2024], reducing cache misses, and (2) these offsets are to the middle of each block so that only half of each needs popcounting [Gottlieb and Reinert, 2025]. In QuadRank (14.4% overhead), we extend these techniques to the σ = 4 (DNA) alphabet. Both data structures typically require only a single cache miss per query, making them highly suitable for high-throughput and memory-bound settings. To enable efficient batch-processing, we support prefetching the cache lines required to answer upcoming queries. Results. BiRank and QuadRank are around 1.5× and 2× faster than similar-overhead methods that do not use interleaving. Prefetching gives an additional 2× speedup, at which point the dual-channel DDR4 RAM bandwidth becomes a hard limit on the total throughput. With prefetching, both methods outperform all other methods apart from SPIDER [Laws et al., 2024] by 2×. When using QuadRank with prefetching in a toy count-only FM-index, QuadFm, this results in a smaller size and up to 4× speedup over Genedex, a state-of-the-art batching FM-index implementation. Conclusion. Optimizing data structures for high throughput, by minimizing cache misses and branch-misses and adding support for prefetching, can result in significant speedups when benchmarks are adjusted accordingly.
Cite as

Ragnar Groot Koerkamp. QuadRank: Engineering a High Throughput Rank. In 24th International Symposium on Experimental Algorithms (SEA 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 371, pp. 20:1-20:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{grootkoerkamp:LIPIcs.SEA.2026.20,
  author =	{Groot Koerkamp, Ragnar},
  title =	{{QuadRank: Engineering a High Throughput Rank}},
  booktitle =	{24th International Symposium on Experimental Algorithms (SEA 2026)},
  pages =	{20:1--20:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-422-2},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{371},
  editor =	{Aum\"{u}ller, Martin and Finocchi, Irene},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2026.20},
  URN =		{urn:nbn:de:0030-drops-260248},
  doi =		{10.4230/LIPIcs.SEA.2026.20},
  annote =	{Keywords: Rank, Succinct Data Structures, Cache Performance, Prefetching}
}
Document
DOI: 10.4230/LITES.11.1.1
A Survey of Real-Time Support, Analysis, and Advancements in ROS 2

Authors: Daniel Casini, Jian-Jia Chen, Jing Li, Federico Reghenzani, and Harun Teper

Published in: LITES, Volume 11, Issue 1 (2026). Leibniz Transactions on Embedded Systems, Volume 11, Issue 1

Abstract
The Robot Operating System 2 (ROS 2) has emerged as a relevant middleware framework for robotic applications, offering modularity, distributed execution, and communication. In the last six years, ROS 2 has drawn increasing attention from the real-time systems community and industry. This survey presents a comprehensive overview of research efforts that analyze, enhance, and extend ROS 2 to support real-time execution. We first provide a detailed description of the internal scheduling mechanisms of ROS 2 and its layered architecture, including the interaction with DDS-based communication and other communication middleware. We then review key contributions from the literature, covering timing analysis for both single- and multi-threaded executors, metrics such as response time, reaction time, and data age, and different communication modes. The survey also discusses community-driven enhancements to the ROS 2 runtime, including new executor algorithm designs, real-time GPU management, and microcontroller support via micro-ROS. Furthermore, we summarize techniques for bounding DDS communication delays, message filters, and profiling tools that have been developed to support analysis and experimentation. To help systematize this growing body of work, we introduce taxonomies that classify the surveyed contributions based on different criteria. This survey aims to guide both researchers and practitioners in understanding and improving the real-time capabilities of ROS 2.
Cite as

Daniel Casini, Jian-Jia Chen, Jing Li, Federico Reghenzani, and Harun Teper. A Survey of Real-Time Support, Analysis, and Advancements in ROS 2. In LITES, Volume 11, Issue 1 (2026). Leibniz Transactions on Embedded Systems, Volume 11, Issue 1, pp. 1:1-1:37, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@Article{casini_et_al:LITES.11.1.1,
  author =	{Casini, Daniel and Chen, Jian-Jia and Li, Jing and Reghenzani, Federico and Teper, Harun},
  title =	{{A Survey of Real-Time Support, Analysis, and Advancements in ROS 2}},
  journal =	{Leibniz Transactions on Embedded Systems},
  pages =	{1:1--1:37},
  ISSN =	{2199-2002},
  year =	{2026},
  volume =	{11},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LITES.11.1.1},
  URN =		{urn:nbn:de:0030-drops-257914},
  doi =		{10.4230/LITES.11.1.1},
  annote =	{Keywords: ROS 2, middleware, real-time, timing predictability, publish-subscribe}
}
Document
DOI: 10.4230/LIPIcs.STACS.2026.60
The Asymptotic Size of Finite Irreducible Semigroups of Rational Matrices

Authors: Stefan Kiefer and Andrew Ryzhikov

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

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

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

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@InProceedings{kiefer_et_al:LIPIcs.STACS.2026.60,
  author =	{Kiefer, Stefan and Ryzhikov, Andrew},
  title =	{{The Asymptotic Size of Finite Irreducible Semigroups of Rational Matrices}},
  booktitle =	{43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026)},
  pages =	{60:1--60:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-412-3},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{364},
  editor =	{Mahajan, Meena and Manea, Florin and McIver, Annabelle and Thắng, Nguy\~{ê}n Kim},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.STACS.2026.60},
  URN =		{urn:nbn:de:0030-drops-255496},
  doi =		{10.4230/LIPIcs.STACS.2026.60},
  annote =	{Keywords: finite matrix semigroups, irreducible matrix semigroups, matrix mortality, aperiodic semigroups, unambiguous automata, transition monoids}
}
Document
DOI: 10.4230/LIPIcs.CSL.2026.43
Kamp Theorem for Pomset Languages of Higher Dimensional Automata

Authors: Emily Clement, Enzo Erlich, and Jérémy Ledent

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

Abstract
Temporal logics are a powerful tool to specify properties of computational systems. For concurrent programs, Higher Dimensional Automata (HDA) are a very expressive model of non-interleaving concurrency. HDA recognize languages of partially ordered multisets, or pomsets. Recent work has shown that Monadic Second Order (MSO) logic is as expressive as HDA for pomset languages. In the case of words, Kamp’s theorem states that First Order (FO) logic is as expressive as Linear Temporal Logic (LTL). In this paper, we extend this result to pomsets. To do so, we first investigate the class of pomset languages that are definable in FO. As expected, this is a strict subclass of MSO-definable languages. Then, we define a Linear Temporal Logic for pomsets (LTL_Poms), and show that it is equivalent to FO.
Cite as

Emily Clement, Enzo Erlich, and Jérémy Ledent. Kamp Theorem for Pomset Languages of Higher Dimensional Automata. In 34th EACSL Annual Conference on Computer Science Logic (CSL 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 363, pp. 43:1-43:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{clement_et_al:LIPIcs.CSL.2026.43,
  author =	{Clement, Emily and Erlich, Enzo and Ledent, J\'{e}r\'{e}my},
  title =	{{Kamp Theorem for Pomset Languages of Higher Dimensional Automata}},
  booktitle =	{34th EACSL Annual Conference on Computer Science Logic (CSL 2026)},
  pages =	{43:1--43:22},
  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.2026.43},
  URN =		{urn:nbn:de:0030-drops-254685},
  doi =		{10.4230/LIPIcs.CSL.2026.43},
  annote =	{Keywords: Higher dimensional automata, temporal logic, Kamp’s theorem}
}
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.
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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)

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@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/DagMan.11.1.19
Conversational Agents: A Framework for Evaluation (CAFE) (Dagstuhl Perspectives Workshop 24352)

Authors: Christine Bauer, Li Chen, Nicola Ferro, Norbert Fuhr, Avishek Anand, Timo Breuer, Guglielmo Faggioli, Ophir Frieder, Hideo Joho, Jussi Karlgren, Johannes Kiesel, Bart P. Knijnenburg, Aldo Lipani, Lien Michiels, Andrea Papenmeier, Maria Soledad Pera, Mark Sanderson, Scott Sanner, Benno Stein, Johanne R. Trippas, Karin Verspoor, and Martijn C. Willemsen

Published in: Dagstuhl Manifestos, Volume 11, Issue 1 (2025)

Abstract
During the workshop, we deeply discussed what CONversational Information ACcess (CONIAC) is and its unique features, proposing a world model abstracting it, and defined the Conversational Agents Framework for Evaluation (CAFE) for the evaluation of CONIAC systems, consisting of six major components: 1) goals of the system’s stakeholders, 2) user tasks to be studied in the evaluation, 3) aspects of the users carrying out the tasks, 4) evaluation criteria to be considered, 5) evaluation methodology to be applied, and 6) measures for the quantitative criteria chosen.
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Christine Bauer, Li Chen, Nicola Ferro, Norbert Fuhr, Avishek Anand, Timo Breuer, Guglielmo Faggioli, Ophir Frieder, Hideo Joho, Jussi Karlgren, Johannes Kiesel, Bart P. Knijnenburg, Aldo Lipani, Lien Michiels, Andrea Papenmeier, Maria Soledad Pera, Mark Sanderson, Scott Sanner, Benno Stein, Johanne R. Trippas, Karin Verspoor, and Martijn C. Willemsen. Conversational Agents: A Framework for Evaluation (CAFE) (Dagstuhl Perspectives Workshop 24352). In Dagstuhl Manifestos, Volume 11, Issue 1, pp. 19-67, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@Article{bauer_et_al:DagMan.11.1.19,
  author =	{Bauer, Christine and Chen, Li and Ferro, Nicola and Fuhr, Norbert and Anand, Avishek and Breuer, Timo and Faggioli, Guglielmo and Frieder, Ophir and Joho, Hideo and Karlgren, Jussi and Kiesel, Johannes and Knijnenburg, Bart P. and Lipani, Aldo and Michiels, Lien and Papenmeier, Andrea and Pera, Maria Soledad and Sanderson, Mark and Sanner, Scott and Stein, Benno and Trippas, Johanne R. and Verspoor, Karin and Willemsen, Martijn C.},
  title =	{{Conversational Agents: A Framework for Evaluation (CAFE) (Dagstuhl Perspectives Workshop 24352)}},
  pages =	{19--67},
  journal =	{Dagstuhl Manifestos},
  ISSN =	{2193-2433},
  year =	{2025},
  volume =	{11},
  number =	{1},
  editor =	{Bauer, Christine and Chen, Li and Ferro, Nicola and Fuhr, Norbert and Anand, Avishek and Breuer, Timo and Faggioli, Guglielmo and Frieder, Ophir and Joho, Hideo and Karlgren, Jussi and Kiesel, Johannes and Knijnenburg, Bart P. and Lipani, Aldo and Michiels, Lien and Papenmeier, Andrea and Pera, Maria Soledad and Sanderson, Mark and Sanner, Scott and Stein, Benno and Trippas, Johanne R. and Verspoor, Karin and Willemsen, Martijn C.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagMan.11.1.19},
  URN =		{urn:nbn:de:0030-drops-252722},
  doi =		{10.4230/DagMan.11.1.19},
  annote =	{Keywords: Conversational Agents, Evaluation, Information Access}
}
Document
DOI: 10.4230/LIPIcs.IPEC.2025.16
Designing Compact ILPs via Fast Witness Verification

Authors: Michał Włodarczyk

Published in: LIPIcs, Volume 358, 20th International Symposium on Parameterized and Exact Computation (IPEC 2025)

Abstract
The standard formalization of preprocessing in parameterized complexity is given by kernelization. In this work, we depart from this paradigm and study a different type of preprocessing for problems without polynomial kernels, still aiming at producing instances that are easily solvable in practice. Specifically, we ask for which parameterized problems an instance (I,k) can be reduced in polynomial time to an integer linear program (ILP) with poly(k) constraints. We show that this property coincides with the parameterized complexity class WK[1], previously studied in the context of Turing kernelization lower bounds. In turn, the class WK[1] enjoys an elegant characterization in terms of witness verification protocols: a yes-instance should admit a witness of size poly(k) that can be verified in time poly(k). By combining known data structures with new ideas, we design such protocols for several problems, such as r-Way Cut, Vertex Multiway Cut, Steiner Tree, and Minimum Common String Partition, thus showing that they can be modeled by compact ILPs. We also present explicit ILP and MILP formulations for Weighted Vertex Cover on graphs with small (unweighted) vertex cover number. We believe that these results will provide a background for a systematic study of ILP-oriented preprocessing procedures for parameterized problems.
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Michał Włodarczyk. Designing Compact ILPs via Fast Witness Verification. In 20th International Symposium on Parameterized and Exact Computation (IPEC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 358, pp. 16:1-16:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{wlodarczyk:LIPIcs.IPEC.2025.16,
  author =	{W{\l}odarczyk, Micha{\l}},
  title =	{{Designing Compact ILPs via Fast Witness Verification}},
  booktitle =	{20th International Symposium on Parameterized and Exact Computation (IPEC 2025)},
  pages =	{16:1--16:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-407-9},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{358},
  editor =	{Agrawal, Akanksha and van Leeuwen, Erik Jan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.IPEC.2025.16},
  URN =		{urn:nbn:de:0030-drops-251481},
  doi =		{10.4230/LIPIcs.IPEC.2025.16},
  annote =	{Keywords: integer programming, kernelization, nondeterminism, multiway cut}
}
Document
DOI: 10.4230/LIPIcs.GD.2025.30
Universal Quality Metrics for Graph Drawings: Which Graphs Excite Us Most?

Authors: Gavin J. Mooney, Tim Hegemann, Alexander Wolff, Michael Wybrow, and Helen C. Purchase

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

Abstract
Graphs are drawn for various purposes, and drawings are meant to display various features of a graph (such as planarity, Hamiltonicity). Still, there is a long history in measuring the quality of a graph drawing. Most of the metrics that have been implemented and used in large studies assume that graphs are drawn straight-line. Most of the studies use randomly generated graphs or one of very few existing benchmark sets that consist of graphs with a specific technical background (e.g., telecommunication networks). In this paper, we extend ten commonly used metrics to node-link diagrams where edges can be curves or polygonal chains. We implement these measures and use them to evaluate a new collection of graph drawings that we have extracted from 27 proceedings of the Graph Drawing conference using an automated pipeline. We compare the "metrics landscape" of our new benchmark set, the GD-collection-v1, which seems to mostly contain manually drawn graphs, to the metric landscape of a benchmark set with randomly generated graphs and computer-generated straight-line drawings that has been used in a recent study [Mooney et al.; PacificVis 2024]. Comparing the GD-collection-v1 with the Mooney at al. dataset reveals a distinct metrics landscape: GD drawings come from much smaller graphs (median vertex number 11 vs. 48) and therefore attain higher medians on most readability metrics. For example, Neighbourhood Preservation (0.5 vs. 0.239) is markedly higher in the GD-collection-v1. We also find that a large proportion of extracted drawings contain curved and/or polygonal edges (57%), motivating the extended metric definitions.
Cite as

Gavin J. Mooney, Tim Hegemann, Alexander Wolff, Michael Wybrow, and Helen C. Purchase. Universal Quality Metrics for Graph Drawings: Which Graphs Excite Us Most?. In 33rd International Symposium on Graph Drawing and Network Visualization (GD 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 357, pp. 30:1-30:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{mooney_et_al:LIPIcs.GD.2025.30,
  author =	{Mooney, Gavin J. and Hegemann, Tim and Wolff, Alexander and Wybrow, Michael and Purchase, Helen C.},
  title =	{{Universal Quality Metrics for Graph Drawings: Which Graphs Excite Us Most?}},
  booktitle =	{33rd International Symposium on Graph Drawing and Network Visualization (GD 2025)},
  pages =	{30:1--30:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-403-1},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{357},
  editor =	{Dujmovi\'{c}, Vida and Montecchiani, Fabrizio},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.GD.2025.30},
  URN =		{urn:nbn:de:0030-drops-250162},
  doi =		{10.4230/LIPIcs.GD.2025.30},
  annote =	{Keywords: Graph drawing metrics, metric landscape, straight-line drawings, polyline drawings, curved drawings, automated extraction of graph drawings}
}
Document
DOI: 10.4230/LIPIcs.TIME.2025.13
Temporal Ensemble Logic for Integrative Representation of the Entirety of Clinical Trials

Authors: Xiaojin Li, Yan Huang, Rashmie Abeysinghe, Zenan Sun, Hongyu Chen, Pengze Li, Xing He, Shiqiang Tao, Cui Tao, Jiang Bian, Licong Cui, and Guo-Qiang Zhang

Published in: LIPIcs, Volume 355, 32nd International Symposium on Temporal Representation and Reasoning (TIME 2025)

Abstract
Clinical trials are typically specified with protocols that define eligibility criteria, treatment regimens, follow-up schedules, and outcome assessments. Temporality is a hallmark of all clinical trials, reflected within and across trial components, with complex dependencies unfolding across multiple time points. Despite their importance, clinical trial protocols are described in free-text format, limiting their semantic precision and the ability to support automated reasoning, leverage data across studies and sites, or simulate trial execution under varying assumptions using Real-World Data. This paper introduces a formalized representation of clinical trials using Temporal Ensemble Logic (TEL). TEL incorporates metricized modal operators, such as "always until t" (□_t) and "possibly until t" (◇_t), where t is a time-length parameter, to offer a logical framework for capturing phenotypes in biomedicine. TEL is more expressive in syntax than classical linear temporal logic (LTL) while maintaining the simplicity of semantic structures. The attributes of TEL are exploited in this paper to formally represent not only individual clinical trial components, but also the timing and sequential dependencies of these components as a whole. Modeling strategies and demonstration case studies are provided to show that TEL can represent the entirety of clinical trials, whereby providing a formal logical framework that can be used to represent the intricate temporal dependencies in trial structure specification. Since clinical trials are a cornerstone of evidence-based medicine, serving as the scientific basis for evaluating the safety, efficacy, and comparative effectiveness of therapeutic interventions, results reported here can serve as a stepping stone that leads to scalable, consistent, and reproducible representation and simulation of clinical trials across all disease domains.
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Xiaojin Li, Yan Huang, Rashmie Abeysinghe, Zenan Sun, Hongyu Chen, Pengze Li, Xing He, Shiqiang Tao, Cui Tao, Jiang Bian, Licong Cui, and Guo-Qiang Zhang. Temporal Ensemble Logic for Integrative Representation of the Entirety of Clinical Trials. In 32nd International Symposium on Temporal Representation and Reasoning (TIME 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 355, pp. 13:1-13:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{li_et_al:LIPIcs.TIME.2025.13,
  author =	{Li, Xiaojin and Huang, Yan and Abeysinghe, Rashmie and Sun, Zenan and Chen, Hongyu and Li, Pengze and He, Xing and Tao, Shiqiang and Tao, Cui and Bian, Jiang and Cui, Licong and Zhang, Guo-Qiang},
  title =	{{Temporal Ensemble Logic for Integrative Representation of the Entirety of Clinical Trials}},
  booktitle =	{32nd International Symposium on Temporal Representation and Reasoning (TIME 2025)},
  pages =	{13:1--13:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-401-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{355},
  editor =	{Vidal, Thierry and Wa{\l}\k{e}ga, Przemys{\l}aw Andrzej},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.TIME.2025.13},
  URN =		{urn:nbn:de:0030-drops-244595},
  doi =		{10.4230/LIPIcs.TIME.2025.13},
  annote =	{Keywords: Temporal ensemble logic, Clinical trials, Logic-based modeling}
}
Document
DOI: 10.4230/LIPIcs.TIME.2025.5
Higher-Order Timed Automata and Tail Recursion

Authors: Florian Bruse

Published in: LIPIcs, Volume 355, 32nd International Symposium on Temporal Representation and Reasoning (TIME 2025)

Abstract
Timed Automata (TA) are a popular formalism to model systems in dense linear time. However, due to their finite state-space, they can only model systems with a finitary logical behavior. There are extensions to e.g., timed pushdown systems and timed recursive state machines. Higher-Order Recursion Schemes (HORS) are another popular model for infinite-state, non-regular systems, naturally stratified by their type-theoretic order. We recently introduced Real-Time Recursion schemes as an approximation of HORS to real-time systems. This paper updates Real-Time Recursion Schemes into Higher-Order Timed Automata, a formalism that defines a tree-shaped timed automaton, which is more suitable to model actual systems. We show that the model-checking problem against the timed version of the modal mu-calculus exhibits the expected complexity bounds, i.e., an increase by one exponential towards the untimed version. We also show that, in the presence of tail recursion, half an exponential can be recovered, mirroring similar gains in the untimed setting. We also give a matching lower bound for the special case of order-1 HORTA. We conjecture that this can be generalized for all orders.
Cite as

Florian Bruse. Higher-Order Timed Automata and Tail Recursion. In 32nd International Symposium on Temporal Representation and Reasoning (TIME 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 355, pp. 5:1-5:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{bruse:LIPIcs.TIME.2025.5,
  author =	{Bruse, Florian},
  title =	{{Higher-Order Timed Automata and Tail Recursion}},
  booktitle =	{32nd International Symposium on Temporal Representation and Reasoning (TIME 2025)},
  pages =	{5:1--5:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-401-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{355},
  editor =	{Vidal, Thierry and Wa{\l}\k{e}ga, Przemys{\l}aw Andrzej},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.TIME.2025.5},
  URN =		{urn:nbn:de:0030-drops-244519},
  doi =		{10.4230/LIPIcs.TIME.2025.5},
  annote =	{Keywords: Timed Automata, Higher-Order Recursion Schemes, Tree Automata, Tail Recursion}
}
Document
DOI: 10.4230/OASIcs.Programming.2025.8
Fuzzing as Editor Feedback

Authors: Marcel Garus, Jens Lincke, and Robert Hirschfeld

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

Abstract
Live programming requires concrete examples, but coming up with examples takes effort. However, there are ways to execute code without specifying examples, such as fuzzing. Fuzzing is a technique that synthesizes program inputs to find bugs in security-critical software. While fuzzing focuses on finding crashes, it also produces valid inputs as a byproduct. Our approach is to make use of this to show examples, including edge cases, directly in the editor. To provide examples for individual pieces of code, we implement fuzzing at the granularity of functions. We integrate it into the compiler pipeline and language tooling of Martinaise, a custom programming language with a limited feature set. Initially, our examples are random and then mutate based on coverage feedback to reach interesting code locations and become smaller. We evaluate our tool in small case studies, showing generated examples for numbers, strings, and composite objects. Our fuzzed examples still feel synthetic, but since they are grounded in the dynamic behavior of code, they can cover the entire execution and show edge cases.
Cite as

Marcel Garus, Jens Lincke, and Robert Hirschfeld. Fuzzing as Editor Feedback. In Companion Proceedings of the 9th International Conference on the Art, Science, and Engineering of Programming (Programming 2025). Open Access Series in Informatics (OASIcs), Volume 134, pp. 8:1-8:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{garus_et_al:OASIcs.Programming.2025.8,
  author =	{Garus, Marcel and Lincke, Jens and Hirschfeld, Robert},
  title =	{{Fuzzing as Editor Feedback}},
  booktitle =	{Companion Proceedings of the 9th International Conference on the Art, Science, and Engineering of Programming (Programming 2025)},
  pages =	{8:1--8:15},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-382-9},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{134},
  editor =	{Edwards, Jonathan and Perera, Roly and Petricek, Tomas},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.Programming.2025.8},
  URN =		{urn:nbn:de:0030-drops-242926},
  doi =		{10.4230/OASIcs.Programming.2025.8},
  annote =	{Keywords: Fuzzing, Example-based Programming, Babylonian Programming, Dynamic Analysis, Code Coverage, Randomized Testing, Function-Level Fuzzing}
}
Document
DOI: 10.4230/OASIcs.Programming.2025.13
Dimensions of Examples: Toward a Framework for Qualifying Examples in Programming

Authors: Toni Mattis, Lukas Böhme, Stefan Ramson, Tom Beckmann, Martin C. Rinard, and Robert Hirschfeld

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

Abstract
Programming requires understanding, using, and changing abstract source code and other representations of programs. Concrete examples demonstrate a particular instance of their abstract behavior. Hence, they play an important role in program comprehension, specification, and testing of requirements. Authoring examples entails a range of - often implicit - decisions about the content and presentation of the example. In this work, we attempt to structure this decision space by describing a set of dimensions that characterize examples in programming. As the manual effort of creating examples is increasingly automated, e.g., through the use of generative AI, we expect this catalog of dimensions to help users and tool developers parametrize, guide, and evaluate the generation of examples in terms of the vocabulary we present here.
Cite as

Toni Mattis, Lukas Böhme, Stefan Ramson, Tom Beckmann, Martin C. Rinard, and Robert Hirschfeld. Dimensions of Examples: Toward a Framework for Qualifying Examples in Programming. In Companion Proceedings of the 9th International Conference on the Art, Science, and Engineering of Programming (Programming 2025). Open Access Series in Informatics (OASIcs), Volume 134, pp. 13:1-13:11, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{mattis_et_al:OASIcs.Programming.2025.13,
  author =	{Mattis, Toni and B\"{o}hme, Lukas and Ramson, Stefan and Beckmann, Tom and Rinard, Martin C. and Hirschfeld, Robert},
  title =	{{Dimensions of Examples: Toward a Framework for Qualifying Examples in Programming}},
  booktitle =	{Companion Proceedings of the 9th International Conference on the Art, Science, and Engineering of Programming (Programming 2025)},
  pages =	{13:1--13:11},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-382-9},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{134},
  editor =	{Edwards, Jonathan and Perera, Roly and Petricek, Tomas},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.Programming.2025.13},
  URN =		{urn:nbn:de:0030-drops-242973},
  doi =		{10.4230/OASIcs.Programming.2025.13},
  annote =	{Keywords: Examples, Live Programming, Evaluation}
}
Document
DOI: 10.4230/OASIcs.Programming.2025.15
Encouraging Experimentation Through Programming by Proximity

Authors: Tom Beckmann, Leonard Geier, Stefan Ramson, Marcel Taeumel, and Robert Hirschfeld

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

Abstract
Exploratory programming involves evaluating a variety of approaches to identify those that advance the problem understanding. For this purpose, we investigated a notation for code designed to encourage experimentation with elements of a program. In our proof-of-concept, we evaluate the idea of program elements connecting by mere proximity through small case studies. We identify multiple constraints to enable connection through proximity and its limitations.
Cite as

Tom Beckmann, Leonard Geier, Stefan Ramson, Marcel Taeumel, and Robert Hirschfeld. Encouraging Experimentation Through Programming by Proximity. In Companion Proceedings of the 9th International Conference on the Art, Science, and Engineering of Programming (Programming 2025). Open Access Series in Informatics (OASIcs), Volume 134, pp. 15:1-15:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{beckmann_et_al:OASIcs.Programming.2025.15,
  author =	{Beckmann, Tom and Geier, Leonard and Ramson, Stefan and Taeumel, Marcel and Hirschfeld, Robert},
  title =	{{Encouraging Experimentation Through Programming by Proximity}},
  booktitle =	{Companion Proceedings of the 9th International Conference on the Art, Science, and Engineering of Programming (Programming 2025)},
  pages =	{15:1--15:15},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-382-9},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{134},
  editor =	{Edwards, Jonathan and Perera, Roly and Petricek, Tomas},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.Programming.2025.15},
  URN =		{urn:nbn:de:0030-drops-242991},
  doi =		{10.4230/OASIcs.Programming.2025.15},
  annote =	{Keywords: Visual Programming, Proximity, Experimentation Support}
}
Document
DOI: 10.4230/OASIcs.ICPEC.2025.11
Rethinking IoT Education: Is the Concept Truly Grasped?

Authors: Tomáš Kormaník and Jaroslav Porubän

Published in: OASIcs, Volume 133, 6th International Computer Programming Education Conference (ICPEC 2025)

Abstract
This paper focuses on the topic of the Internet of Things (abbr. IoT) in the context of higher education and academic understanding of it. When briefly looking at the IoT course curriculum at our department, we suspected that the curriculum contents are not adhering to the definition of IoT. The goal of our work was to pinpoint the correct definition of IoT, which can be used to bring contents of the IoT courses as close to the truth as possible. Secondarily, we reviewed available articles and reviews of formerly and currently taught IoT or related courses and evaluated whether their approach and contents were correct when considering the definition of IoT. We summarise the issues present in existing works and identify which specific parts are problematic, according to our assessment. Improving IoT courses is crucial since it shapes a student’s understanding of the IoT paradigm and allows them to use it or even develop it in the future. Provisioning our students with a needed set of skills will make them more suitable for research, development, and industry-related futures.
Cite as

Tomáš Kormaník and Jaroslav Porubän. Rethinking IoT Education: Is the Concept Truly Grasped?. In 6th International Computer Programming Education Conference (ICPEC 2025). Open Access Series in Informatics (OASIcs), Volume 133, pp. 11:1-11:8, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{kormanik_et_al:OASIcs.ICPEC.2025.11,
  author =	{Korman{\'\i}k, Tom\'{a}\v{s} and Porub\"{a}n, Jaroslav},
  title =	{{Rethinking IoT Education: Is the Concept Truly Grasped?}},
  booktitle =	{6th International Computer Programming Education Conference (ICPEC 2025)},
  pages =	{11:1--11:8},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-393-5},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{133},
  editor =	{Queir\'{o}s, Ricardo and Pinto, M\'{a}rio and Portela, Filipe and Sim\~{o}es, Alberto},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.ICPEC.2025.11},
  URN =		{urn:nbn:de:0030-drops-240411},
  doi =		{10.4230/OASIcs.ICPEC.2025.11},
  annote =	{Keywords: Internet of Things, Informatics Education, Higher Education, Computer Science Education}
}
Document
DOI: 10.4230/LIPIcs.WADS.2025.45
Fast Kd-Trees for the Kullback-Leibler Divergence and Other Decomposable Bregman Divergences

Authors: Tuyen Pham and Hubert Wagner

Published in: LIPIcs, Volume 349, 19th International Symposium on Algorithms and Data Structures (WADS 2025)

Abstract
The contributions of the paper span theoretical and implementational results. First, we prove that Kd-trees can be extended to ℝ^d with the distance measured by an arbitrary Bregman divergence. Perhaps surprisingly, this shows that the triangle inequality is not necessary for correct pruning in Kd-trees. Second, we offer an efficient algorithm and C++ implementation for nearest neighbour search for decomposable Bregman divergences. The implementation supports the Kullback-Leibler divergence (relative entropy) which is a popular distance between probability vectors and is commonly used in statistics and machine learning. This is a step toward broadening the usage of computational geometry algorithms. Our benchmarks show that our implementation efficiently handles both exact and approximate nearest neighbour queries. Compared to a linear search, we achieve two orders of magnitude speedup for practical scenarios in dimension up to 100. Our solution is simpler and more efficient than competing methods.
Cite as

Tuyen Pham and Hubert Wagner. Fast Kd-Trees for the Kullback-Leibler Divergence and Other Decomposable Bregman Divergences. In 19th International Symposium on Algorithms and Data Structures (WADS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 349, pp. 45:1-45:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{pham_et_al:LIPIcs.WADS.2025.45,
  author =	{Pham, Tuyen and Wagner, Hubert},
  title =	{{Fast Kd-Trees for the Kullback-Leibler Divergence and Other Decomposable Bregman Divergences}},
  booktitle =	{19th International Symposium on Algorithms and Data Structures (WADS 2025)},
  pages =	{45:1--45:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-398-0},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{349},
  editor =	{Morin, Pat and Oh, Eunjin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WADS.2025.45},
  URN =		{urn:nbn:de:0030-drops-242766},
  doi =		{10.4230/LIPIcs.WADS.2025.45},
  annote =	{Keywords: Kd-tree, k-d tree, nearest neighbour search, Bregman divergence, decomposable Bregman divergence, KL divergence, relative entropy, cross entropy, Shannon’s entropy}
}
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