23 Search Results for "Wilson, James B."

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.ITCS.2026.63
Perfect Simulation of Las Vegas Algorithms via Local Computation

Authors: Xinyu Fu, Yonggang Jiang, and Yitong Yin

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

Abstract
The notion of Las Vegas algorithms was introduced by Babai (1979) and can be defined in two ways: - In Babai’s original definition, a randomized algorithm is called Las Vegas if it has a finitely bounded running time and certifiable random failure. - Another definition widely accepted today is that Las Vegas algorithms refer to zero-error randomized algorithms with random running times. The equivalence between the two definitions is straightforward. Specifically, for randomized algorithms with certifiable failures, repeatedly running the algorithm until no failure is encountered allows for faithful simulation of the correct output when it executes successfully. We show that a similar perfect simulation can also be achieved in distributed local computation. Specifically, in the LOCAL model, with a polylogarithmic overhead in time complexity, any Las Vegas algorithm with finitely bounded running time and locally certifiable failures can be converted to a zero error Las Vegas algorithm. This transformed algorithm faithfully reproduces the correct output of the original algorithm in successful executions. This is achieved by a reduction to a distributed sampling problem under the Lovász Local Lemma (LLL), where the objective is to sample from the joint distribution of random variables avoiding all bad events. We then design the first efficient algorithm to solve this sampling problem in the LOCAL model.
Cite as

Xinyu Fu, Yonggang Jiang, and Yitong Yin. Perfect Simulation of Las Vegas Algorithms via Local Computation. In 17th Innovations in Theoretical Computer Science Conference (ITCS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 362, pp. 63:1-63:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{fu_et_al:LIPIcs.ITCS.2026.63,
  author =	{Fu, Xinyu and Jiang, Yonggang and Yin, Yitong},
  title =	{{Perfect Simulation of Las Vegas Algorithms via Local Computation}},
  booktitle =	{17th Innovations in Theoretical Computer Science Conference (ITCS 2026)},
  pages =	{63:1--63:22},
  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.2026.63},
  URN =		{urn:nbn:de:0030-drops-253503},
  doi =		{10.4230/LIPIcs.ITCS.2026.63},
  annote =	{Keywords: Las Vegas algorithms, perfect simulation, Lov\'{a}sz Local Lemma, sampling}
}
Document
DOI: 10.4230/LIPIcs.ITCS.2026.92
A Combinatorial Characterization of Constant Mixing Time

Authors: Lap Chi Lau and Raymond Liu

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

Abstract
Classical spectral graph theory characterizes graphs with logarithmic mixing time. In this work, we present a combinatorial characterization of graphs with constant mixing time. The combinatorial characterization is based on the small-set bipartite density condition, which is weaker than having near-optimal spectral radius and is stronger than having near-optimal small-set vertex expansion.
Cite as

Lap Chi Lau and Raymond Liu. A Combinatorial Characterization of Constant Mixing Time. In 17th Innovations in Theoretical Computer Science Conference (ITCS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 362, pp. 92:1-92:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{lau_et_al:LIPIcs.ITCS.2026.92,
  author =	{Lau, Lap Chi and Liu, Raymond},
  title =	{{A Combinatorial Characterization of Constant Mixing Time}},
  booktitle =	{17th Innovations in Theoretical Computer Science Conference (ITCS 2026)},
  pages =	{92:1--92:13},
  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.2026.92},
  URN =		{urn:nbn:de:0030-drops-253792},
  doi =		{10.4230/LIPIcs.ITCS.2026.92},
  annote =	{Keywords: Random walks, mixing time, bipartite density, spectral graph theory}
}
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.GD.2025.37
Show Me Your Best Side: Characteristics of User-Preferred Perspectives for 3D Graph Drawings

Authors: Lucas Joos, Gavin J. Mooney, Maximilian T. Fischer, Daniel A. Keim, Falk Schreiber, Helen C. Purchase, and Karsten Klein

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

Abstract
The visual analysis of graphs in 3D has become increasingly popular, accelerated by the rise of immersive technology, such as augmented and virtual reality. Unlike 2D drawings, 3D graph layouts are highly viewpoint-dependent, making perspective selection critical for revealing structural and relational patterns. Despite its importance, there is limited empirical evidence guiding what constitutes an effective or preferred viewpoint from the user’s perspective. In this paper, we present a systematic investigation into user-preferred viewpoints in 3D graph visualisations. We conducted a controlled study with 23 participants in a virtual reality environment, where users selected their most and least preferred viewpoints for 36 different graphs varying in size and layout. From this data, enriched by qualitative feedback, we distil common strategies underlying viewpoint choice. We further analyse the alignment of user preferences with classical 2D aesthetic criteria (e.g., Crossings), 3D-specific measures (e.g., Node-Node Occlusion), and introduce a novel measure capturing the perceivability of a graph’s principal axes (Isometric Viewpoint Deviation). Our data-driven analysis indicates that Stress, Crossings, Gabriel Ratio, Edge-Node Overlap, and Isometric Viewpoint Deviation are key indicators of viewpoint preference. Beyond our findings, we contribute a publicly available dataset consisting of the graphs and computed aesthetic measures, supporting further research and the development of viewpoint evaluation measures for 3D graph drawing.
Cite as

Lucas Joos, Gavin J. Mooney, Maximilian T. Fischer, Daniel A. Keim, Falk Schreiber, Helen C. Purchase, and Karsten Klein. Show Me Your Best Side: Characteristics of User-Preferred Perspectives for 3D Graph Drawings. In 33rd International Symposium on Graph Drawing and Network Visualization (GD 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 357, pp. 37:1-37:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{joos_et_al:LIPIcs.GD.2025.37,
  author =	{Joos, Lucas and Mooney, Gavin J. and Fischer, Maximilian T. and Keim, Daniel A. and Schreiber, Falk and Purchase, Helen C. and Klein, Karsten},
  title =	{{Show Me Your Best Side: Characteristics of User-Preferred Perspectives for 3D Graph Drawings}},
  booktitle =	{33rd International Symposium on Graph Drawing and Network Visualization (GD 2025)},
  pages =	{37:1--37:19},
  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.2025.37},
  URN =		{urn:nbn:de:0030-drops-250236},
  doi =		{10.4230/LIPIcs.GD.2025.37},
  annote =	{Keywords: Graph Aesthetics, Immersive 3D, Node-Link Diagrams, Empirical Evaluation}
}
Document
DOI: 10.4230/LIPIcs.ESA.2025.43
Edge Clique Partition and Cover Beyond Independence

Authors: Fedor V. Fomin, Petr A. Golovach, Danil Sagunov, and Kirill Simonov

Published in: LIPIcs, Volume 351, 33rd Annual European Symposium on Algorithms (ESA 2025)

Abstract
Covering and partitioning the edges of a graph into cliques are classical problems at the intersection of combinatorial optimization and graph theory, having been studied through a range of algorithmic and complexity-theoretic lenses. Despite the well-known fixed-parameter tractability of these problems when parameterized by the total number of cliques, such a parameterization often fails to be meaningful for sparse graphs. In many real-world instances, on the other hand, the minimum number of cliques in an edge cover or partition can be very close to the size of a maximum independent set α(G). Motivated by this observation, we investigate above-α parameterizations of the edge clique cover and partition problems. Concretely, we introduce and study Edge Clique Cover Above Independent Set (ECC/α) and Edge Clique Partition Above Independent Set (ECP/α), where the goal is to cover or partition all edges of a graph using at most α(G) + k cliques, and k is the parameter. Our main results reveal a distinct complexity landscape for the two variants. We show that ECP/α is fixed-parameter tractable, whereas ECC/α is NP-complete for all k ≥ 2, yet can be solved in polynomial time for k ∈ {0,1}. These findings highlight intriguing differences between the two problems when viewed through the lens of parameterization above a natural lower bound. Finally, we demonstrate that ECC/α becomes fixed-parameter tractable when parameterized by k + ω(G), where ω(G) is the size of a maximum clique of the graph G. This result is particularly relevant for sparse graphs, in which ω is typically small. For H-minor free graphs, we design a subexponential algorithm of running time f(H)^√k ⋅ n^𝒪(1).
Cite as

Fedor V. Fomin, Petr A. Golovach, Danil Sagunov, and Kirill Simonov. Edge Clique Partition and Cover Beyond Independence. In 33rd Annual European Symposium on Algorithms (ESA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 351, pp. 43:1-43:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{fomin_et_al:LIPIcs.ESA.2025.43,
  author =	{Fomin, Fedor V. and Golovach, Petr A. and Sagunov, Danil and Simonov, Kirill},
  title =	{{Edge Clique Partition and Cover Beyond Independence}},
  booktitle =	{33rd Annual European Symposium on Algorithms (ESA 2025)},
  pages =	{43:1--43:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-395-9},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{351},
  editor =	{Benoit, Anne and Kaplan, Haim and Wild, Sebastian and Herman, Grzegorz},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2025.43},
  URN =		{urn:nbn:de:0030-drops-245113},
  doi =		{10.4230/LIPIcs.ESA.2025.43},
  annote =	{Keywords: edge clique partition, edge clique cover, independence number, parameterized complexity, above guarantee}
}
Document
RANDOM
DOI: 10.4230/LIPIcs.APPROX/RANDOM.2025.60
Sink-Free Orientations: A Local Sampler with Applications

Authors: Konrad Anand, Graham Freifeld, Heng Guo, Chunyang Wang, and Jiaheng Wang

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

Abstract
For sink-free orientations in graphs of minimum degree at least 3, we show that there is a deterministic approximate counting algorithm that runs in time O((n^33/ε^32)log(n/ε)), a near-linear time sampling algorithm, and a randomised approximate counting algorithm that runs in time O((n/ε)²log(n/ε)), where n denotes the number of vertices of the input graph and 0 < ε < 1 is the desired accuracy. All three algorithms are based on a local implementation of the sink popping method (Cohn, Pemantle, and Propp, 2002) under the partial rejection sampling framework (Guo, Jerrum, and Liu, 2019).
Cite as

Konrad Anand, Graham Freifeld, Heng Guo, Chunyang Wang, and Jiaheng Wang. Sink-Free Orientations: A Local Sampler with Applications. In Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 353, pp. 60:1-60:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{anand_et_al:LIPIcs.APPROX/RANDOM.2025.60,
  author =	{Anand, Konrad and Freifeld, Graham and Guo, Heng and Wang, Chunyang and Wang, Jiaheng},
  title =	{{Sink-Free Orientations: A Local Sampler with Applications}},
  booktitle =	{Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025)},
  pages =	{60:1--60:19},
  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.2025.60},
  URN =		{urn:nbn:de:0030-drops-244267},
  doi =		{10.4230/LIPIcs.APPROX/RANDOM.2025.60},
  annote =	{Keywords: Sink-free orientations, local sampling, deterministic counting}
}
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)

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@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.2025.10
DiVerG: Scalable Distance Index for Validation of Paired-End Alignments in Sequence Graphs

Authors: Ali Ghaffaari, Alexander Schönhuth, and Tobias Marschall

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

Abstract
Determining the distance between two loci within a genomic region is a recurrent operation in various tasks in computational genomics. A notable example of this task arises in paired-end read mapping as a form of validation of distances between multiple alignments. While straightforward for a single genome, graph-based reference structures render the operation considerably more involved. Given the sheer number of such queries in a typical read mapping experiment, an efficient algorithm for answering distance queries is crucial. In this paper, we introduce DiVerG, a compact data structure as well as a fast and scalable algorithm, for constructing distance indexes for general sequence graphs on multi-core CPU and many-core GPU architectures. DiVerG is based on PairG [Jain et al., 2019], but overcomes the limitations of PairG by exploiting the extensive potential for improvements in terms of scalability and space efficiency. As a consequence, DiVerG can process substantially larger datasets, such as whole human genomes, which are unmanageable by PairG. DiVerG offers faster index construction time and consistently faster query time with gains proportional to the size of the underlying compact data structure. We demonstrate that our method performs favorably on multiple real datasets at various scales. DiVerG achieves superior performance over PairG; e.g. resulting to 2.5-4x speed-up in query time, 44-340x smaller index size, and 3-50x faster construction time for the genome graph of the MHC region, as a particularly variable region of the human genome. The implementation is available at: https://github.com/cartoonist/diverg
Cite as

Ali Ghaffaari, Alexander Schönhuth, and Tobias Marschall. DiVerG: Scalable Distance Index for Validation of Paired-End Alignments in Sequence Graphs. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 10:1-10:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{ghaffaari_et_al:LIPIcs.WABI.2025.10,
  author =	{Ghaffaari, Ali and Sch\"{o}nhuth, Alexander and Marschall, Tobias},
  title =	{{DiVerG: Scalable Distance Index for Validation of Paired-End Alignments in Sequence Graphs}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{10:1--10:24},
  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.2025.10},
  URN =		{urn:nbn:de:0030-drops-239369},
  doi =		{10.4230/LIPIcs.WABI.2025.10},
  annote =	{Keywords: Sequence graph, distance index, read mapping, sparse matrix}
}
Document
DOI: 10.4230/LIPIcs.SAT.2025.13
Random Local Access for Sampling k-SAT Solutions

Authors: Dingding Dong and Nitya Mani

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

Abstract
We present a sublinear time algorithm that gives random local access to the uniform distribution over satisfying assignments to an arbitrary k-SAT formula Φ, at exponential clause density. Our algorithm provides memory-less query access to variable assignments, such that the output variable assignments consistently emulate a single global satisfying assignment whose law is close to the uniform distribution over satisfying assignments to Φ. Random local access and related models have been studied for a wide variety of natural Gibbs distributions and random graphical processes. Here, we establish feasibility of random local access models for one of the most canonical such sample spaces, the set of satisfying assignments to a k-SAT formula. Our algorithm proceeds by leveraging the local uniformity of the uniform distribution over satisfying assignments to Φ. We randomly partition the variables into two subsets, so that each clause has sufficiently many variables from each set to preserve local uniformity. We then sample some variables by simulating a systematic scan Glauber dynamics backward in time, greedily constructing the necessary intermediate steps. We sample the other variables by first conducting a search for a polylogarithmic-sized local component, which we iteratively grow to identify a small subformula from which we can efficiently sample using the appropriate marginal distribution. This two-pronged approach enables us to sample individual variable assignments without constructing a full solution.
Cite as

Dingding Dong and Nitya Mani. Random Local Access for Sampling k-SAT Solutions. In 28th International Conference on Theory and Applications of Satisfiability Testing (SAT 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 341, pp. 13:1-13:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{dong_et_al:LIPIcs.SAT.2025.13,
  author =	{Dong, Dingding and Mani, Nitya},
  title =	{{Random Local Access for Sampling k-SAT Solutions}},
  booktitle =	{28th International Conference on Theory and Applications of Satisfiability Testing (SAT 2025)},
  pages =	{13:1--13:24},
  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.2025.13},
  URN =		{urn:nbn:de:0030-drops-237474},
  doi =		{10.4230/LIPIcs.SAT.2025.13},
  annote =	{Keywords: sublinear time algorithms, random generation, k-SAT, local computation}
}
Document
Track A: Algorithms, Complexity and Games
DOI: 10.4230/LIPIcs.ICALP.2025.13
Quantum Speedup for Sampling Random Spanning Trees

Authors: Simon Apers, Minbo Gao, Zhengfeng Ji, and Chenghua Liu

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

Abstract
We present a quantum algorithm for sampling random spanning trees from a weighted graph in Õ(√{mn}) time, where n and m denote the number of vertices and edges, respectively. Our algorithm has sublinear runtime for dense graphs and achieves a quantum speedup over the best-known classical algorithm, which runs in Õ(m) time. The approach carefully combines, on one hand, a classical method based on "large-step" random walks for reduced mixing time and, on the other hand, quantum algorithmic techniques, including quantum graph sparsification and a sampling-without-replacement variant of Hamoudi’s multiple-state preparation. We also establish a matching lower bound, proving the optimality of our algorithm up to polylogarithmic factors. These results highlight the potential of quantum computing in accelerating fundamental graph sampling problems.
Cite as

Simon Apers, Minbo Gao, Zhengfeng Ji, and Chenghua Liu. Quantum Speedup for Sampling Random Spanning Trees. In 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 334, pp. 13:1-13:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{apers_et_al:LIPIcs.ICALP.2025.13,
  author =	{Apers, Simon and Gao, Minbo and Ji, Zhengfeng and Liu, Chenghua},
  title =	{{Quantum Speedup for Sampling Random Spanning Trees}},
  booktitle =	{52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)},
  pages =	{13:1--13:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-372-0},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{334},
  editor =	{Censor-Hillel, Keren and Grandoni, Fabrizio and Ouaknine, Jo\"{e}l and Puppis, Gabriele},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2025.13},
  URN =		{urn:nbn:de:0030-drops-233907},
  doi =		{10.4230/LIPIcs.ICALP.2025.13},
  annote =	{Keywords: Quantum Computing, Quantum Algorithms, Random Spanning Trees}
}
Document
Track A: Algorithms, Complexity and Games
DOI: 10.4230/LIPIcs.ICALP.2025.125
Unbalanced Random Matching Markets with Partial Preferences

Authors: Aditya Potukuchi and Shikha Singh

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

Abstract
Properties of stable matchings in the popular random-matching-market model have been studied for over 50 years. In a random matching market, each agent has complete preferences drawn uniformly and independently at random. Wilson (1972), Knuth (1976) and Pittel (1989) proved that in balanced random matching markets, the proposers are matched to their ln nth choice on average. In this paper, we consider competitive markets with n jobs and n+k candidates, and partial lists where each agent only ranks their top d choices. Despite the long history of the problem, the following fundamental question remains unanswered for these generalized markets: what is the tight threshold on list length d that results in a perfect stable matching with high probability? In this paper, we answer this question exactly - we prove a sharp threshold d₀ = ln n ⋅ ln (n+k)/(k+1) on the existence of perfect stable matchings when k = o(n). That is, we show that if d < (1-ε) d₀, then no stable matching matches all jobs; moreover, if d > (1+ ε) d₀, then all jobs are matched in every stable matching with high probability. This bound improves and generalizes recent results by Kanoria, Min and Qian (2021). Furthermore, we extend the line of work studying the effect of imbalance on the expected rank of the proposers (termed the "stark effect of competition"). We establish the regime in unbalanced markets that forces this stark effect to take shape in markets with partial preferences.
Cite as

Aditya Potukuchi and Shikha Singh. Unbalanced Random Matching Markets with Partial Preferences. In 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 334, pp. 125:1-125:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{potukuchi_et_al:LIPIcs.ICALP.2025.125,
  author =	{Potukuchi, Aditya and Singh, Shikha},
  title =	{{Unbalanced Random Matching Markets with Partial Preferences}},
  booktitle =	{52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)},
  pages =	{125:1--125:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-372-0},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{334},
  editor =	{Censor-Hillel, Keren and Grandoni, Fabrizio and Ouaknine, Jo\"{e}l and Puppis, Gabriele},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2025.125},
  URN =		{urn:nbn:de:0030-drops-235025},
  doi =		{10.4230/LIPIcs.ICALP.2025.125},
  annote =	{Keywords: stable matching, probabilistic method, Gale-Shapley algorithm}
}
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
DOI: 10.4230/LIPIcs.STACS.2025.39
A Quasi-Polynomial Time Algorithm for Multi-Arrival on Tree-Like Multigraphs

Authors: Ebrahim Ghorbani, Jonah Leander Hoff, and Matthias Mnich

Published in: LIPIcs, Volume 327, 42nd International Symposium on Theoretical Aspects of Computer Science (STACS 2025)

Abstract
Propp machines, or rotor-router models, are a classic tool to simulate random systems in forms of Markov chains by deterministic systems. To this end, the nodes of the Markov chain are replaced by switching nodes, which maintain a queue over their outgoing arcs, and a particle sent through the system traverses the top arc of the queue which is then moved to the end of the queue and the particle arrives at the next node. A key question to answer about such systems is whether a single particle can reach a particular target node, given as input an initial configuration of the queues at all switching nodes. This question was introduced by Dohrau et al. (2017) under the name of Arrival. A major open question is whether Arrival can be solved in polynomial time, as it is known to lie in NP ∩ co-NP; yet the fastest known algorithm for general instances takes subexponential time (Gärtner et al., ICALP 2021). We consider a generalized version of Arrival introduced by Auger et al. (RP 2023), which requires routing multiple (potentially exponentially many) particles through a rotor graph. The Multi-Arrival problem is to determine the particle configuration that results from moving all particles from a given initial configuration to sinks. Auger et al. showed that for path-like rotor graphs with a certain uniform rotor order, the problem can be solved in polynomial time. Our main result is a quasi-polynomial-time algorithm for Multi-Arrival on tree-like rotor graphs for arbitrary rotor orders. Tree-like rotor graphs are directed multigraphs which can be obtained from undirected trees by replacing each edge by an arbitrary number of arcs in either or both directions. For trees of bounded contracted height, such as paths, the algorithm runs in polynomial time and thereby generalizes the result by Auger et al.. Moreover, we give a polynomial-time algorithm for Multi-Arrival on tree-like rotor graphs without parallel arcs.
Cite as

Ebrahim Ghorbani, Jonah Leander Hoff, and Matthias Mnich. A Quasi-Polynomial Time Algorithm for Multi-Arrival on Tree-Like Multigraphs. In 42nd International Symposium on Theoretical Aspects of Computer Science (STACS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 327, pp. 39:1-39:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{ghorbani_et_al:LIPIcs.STACS.2025.39,
  author =	{Ghorbani, Ebrahim and Leander Hoff, Jonah and Mnich, Matthias},
  title =	{{A Quasi-Polynomial Time Algorithm for Multi-Arrival on Tree-Like Multigraphs}},
  booktitle =	{42nd International Symposium on Theoretical Aspects of Computer Science (STACS 2025)},
  pages =	{39:1--39:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-365-2},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{327},
  editor =	{Beyersdorff, Olaf and Pilipczuk, Micha{\l} and Pimentel, Elaine 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.2025.39},
  URN =		{urn:nbn:de:0030-drops-228658},
  doi =		{10.4230/LIPIcs.STACS.2025.39},
  annote =	{Keywords: Arrival, Rotor-routing, Tree-like Multigraph, Path-Like Multigraph, Fixed-Parameter Tractability}
}
Document
Vision
DOI: 10.4230/TGDK.1.1.9
Trust, Accountability, and Autonomy in Knowledge Graph-Based AI for Self-Determination

Authors: Luis-Daniel Ibáñez, John Domingue, Sabrina Kirrane, Oshani Seneviratne, Aisling Third, and Maria-Esther Vidal

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 Graphs (KGs) have emerged as fundamental platforms for powering intelligent decision-making and a wide range of Artificial Intelligence (AI) services across major corporations such as Google, Walmart, and AirBnb. KGs complement Machine Learning (ML) algorithms by providing data context and semantics, thereby enabling further inference and question-answering capabilities. The integration of KGs with neuronal learning (e.g., Large Language Models (LLMs)) is currently a topic of active research, commonly named neuro-symbolic AI. Despite the numerous benefits that can be accomplished with KG-based AI, its growing ubiquity within online services may result in the loss of self-determination for citizens as a fundamental societal issue. The more we rely on these technologies, which are often centralised, the less citizens will be able to determine their own destinies. To counter this threat, AI regulation, such as the European Union (EU) AI Act, is being proposed in certain regions. The regulation sets what technologists need to do, leading to questions concerning How the output of AI systems can be trusted? What is needed to ensure that the data fuelling and the inner workings of these artefacts are transparent? How can AI be made accountable for its decision-making? This paper conceptualises the foundational topics and research pillars to support KG-based AI for self-determination. Drawing upon this conceptual framework, challenges and opportunities for citizen self-determination are illustrated and analysed in a real-world scenario. As a result, we propose a research agenda aimed at accomplishing the recommended objectives.
Cite as

Luis-Daniel Ibáñez, John Domingue, Sabrina Kirrane, Oshani Seneviratne, Aisling Third, and Maria-Esther Vidal. Trust, Accountability, and Autonomy in Knowledge Graph-Based AI for Self-Determination. In Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge (TGDK), Volume 1, Issue 1, pp. 9:1-9:32, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@Article{ibanez_et_al:TGDK.1.1.9,
  author =	{Ib\'{a}\~{n}ez, Luis-Daniel and Domingue, John and Kirrane, Sabrina and Seneviratne, Oshani and Third, Aisling and Vidal, Maria-Esther},
  title =	{{Trust, Accountability, and Autonomy in Knowledge Graph-Based AI for Self-Determination}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{9:1--9:32},
  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.1.1.9},
  URN =		{urn:nbn:de:0030-drops-194839},
  doi =		{10.4230/TGDK.1.1.9},
  annote =	{Keywords: Trust, Accountability, Autonomy, AI, Knowledge Graphs}
}
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