35 Search Results for "Anderson, Daniel"

Document
DOI: 10.4230/LIPIcs.ESA.2025.76
A 3.3904-Competitive Online Algorithm for List Update with Uniform Costs

Authors: Mateusz Basiak, Marcin Bienkowski, Martin Böhm, Marek Chrobak, Łukasz Jeż, Jiří Sgall, and Agnieszka Tatarczuk

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

Abstract
We consider the List Update problem where the cost of each swap is assumed to be 1. This is in contrast to the "standard" model, in which an algorithm is allowed to swap the requested item with previous items for free. We construct an online algorithm Full-Or-Partial-Move (FPM), whose competitive ratio is at most 3.3904, improving over the previous best known bound of 4.
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Mateusz Basiak, Marcin Bienkowski, Martin Böhm, Marek Chrobak, Łukasz Jeż, Jiří Sgall, and Agnieszka Tatarczuk. A 3.3904-Competitive Online Algorithm for List Update with Uniform Costs. In 33rd Annual European Symposium on Algorithms (ESA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 351, pp. 76:1-76:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{basiak_et_al:LIPIcs.ESA.2025.76,
  author =	{Basiak, Mateusz and Bienkowski, Marcin and B\"{o}hm, Martin and Chrobak, Marek and Je\.{z}, {\L}ukasz and Sgall, Ji\v{r}{\'\i} and Tatarczuk, Agnieszka},
  title =	{{A 3.3904-Competitive Online Algorithm for List Update with Uniform Costs}},
  booktitle =	{33rd Annual European Symposium on Algorithms (ESA 2025)},
  pages =	{76:1--76:15},
  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.2025.76},
  URN =		{urn:nbn:de:0030-drops-245442},
  doi =		{10.4230/LIPIcs.ESA.2025.76},
  annote =	{Keywords: List update, work functions, amortized analysis, online algorithms, competitive analysis}
}
Document
DOI: 10.4230/OASIcs.SpaceCHI.2025.20
Navigating Exoplanetary Systems in Augmented Reality: Preliminary Insights on ExoAR

Authors: Bryson Lawton, Frank Maurer, and Daniel Zielasko

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

Abstract
With thousands of exoplanets now confirmed by space missions such as NASA’s Kepler and TESS, scientific interest and public curiosity about these distant worlds continue to grow. However, current visualization tools for exploring exoplanetary systems often lack sufficient scientific accuracy or interactive features, limiting their educational effectiveness and analytical utility. To help address this gap, we developed ExoAR, an augmented reality tool designed to offer immersive, scientifically sound visualizations of all known exoplanetary systems using data directly sourced from NASA’s Exoplanet Archive. By leveraging augmented reality’s strengths, ExoAR enables users to immerse themselves in interactive, dynamic 3D models of these planetary systems with data-driven representations of planets and their host stars. The application also allows users to adjust various visualization scales independently, a capability designed to aid comprehension of comparative astronomical properties such as orbital mechanics, planetary sizes, and stellar classifications. To begin assessing ExoAR’s potential as an educational and analytical tool and inform future iterations, a pilot user study was conducted. Its findings indicate that participants found ExoAR improved user engagement and spatial understanding compared to NASA’s Eyes on Exoplanets application, a non-immersive exoplanetary system visualization tool. This work-in-progress paper presents these early insights, acknowledges current system limitations, and outlines future directions for more rigorously evaluating and further improving ExoAR’s capabilities for both educational and scientific communities.
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Bryson Lawton, Frank Maurer, and Daniel Zielasko. Navigating Exoplanetary Systems in Augmented Reality: Preliminary Insights on ExoAR. In Advancing Human-Computer Interaction for Space Exploration (SpaceCHI 2025). Open Access Series in Informatics (OASIcs), Volume 130, pp. 20:1-20:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{lawton_et_al:OASIcs.SpaceCHI.2025.20,
  author =	{Lawton, Bryson and Maurer, Frank and Zielasko, Daniel},
  title =	{{Navigating Exoplanetary Systems in Augmented Reality: Preliminary Insights on ExoAR}},
  booktitle =	{Advancing Human-Computer Interaction for Space Exploration (SpaceCHI 2025)},
  pages =	{20:1--20:13},
  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.2025.20},
  URN =		{urn:nbn:de:0030-drops-240106},
  doi =		{10.4230/OASIcs.SpaceCHI.2025.20},
  annote =	{Keywords: Immersive Analytics, Data Visualization, Astronomy, Astrophysics, Exoplanet, Augmented Reality, AR}
}
Document
DOI: 10.4230/OASIcs.SpaceCHI.2025.30
A Research Framework to Develop a Real-Time Synchrony Index to Monitor Team Cohesion and Performance in Long-Duration Space Exploration

Authors: Federico Nemmi, Emma Chabani, Laure Boyer, Charlie Madier, and Daniel Lewkowicz

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

Abstract
As humanity prepares for long-distance space exploration, optimizing group performance, the ability of a group to achieve its goals efficiently, is critical. Astronaut crews will endure isolation, confinement, and operational stress, making group synchrony - the alignment of behaviors, emotions, and physiological states - a key factor in mission success. Synchrony influences team cohesion, performance, and resilience, necessitating effective crew management strategies. This paper proposes a framework for a real-time, unobtrusive index of group synchrony to support astronauts and mission control. Research indicates that team cohesion fluctuates in isolated environments, with reduced communication and interpersonal conflicts emerging over time. A system tracking synchrony could mitigate these issues, providing proactive support and improving remote management. Additionally, it could serve as a cognitive and physiological feedback tool for astronauts and a decision-making aid for mission control, enhancing well-being and efficiency. Our approach integrates behavioral and physiological synchrony measures to assess team cohesion and performance. We propose a multi-modal synchrony index combining movement coordination, communication patterns, and physiological signals such as heart rate, electrodermal activity, and EEG. This index will be validated across different tasks to ensure applicability across diverse mission scenarios. By developing a robust synchrony index, we address a fundamental challenge in space missions: sustaining team effectiveness under extreme conditions. Beyond space exploration, our findings could benefit high-risk, high-isolation teams in submarine crews, polar expeditions, and remote research groups. Our collaboration with the Centre National d'Etudes Spatiales, the Institut de Médecine et de Physiologie Spatiales, and the Toulouse University Hospital marks the first step, with experimental data collection starting this year. Ultimately, this research fosters more adaptive, responsive, and resilient teams for future space missions.
Cite as

Federico Nemmi, Emma Chabani, Laure Boyer, Charlie Madier, and Daniel Lewkowicz. A Research Framework to Develop a Real-Time Synchrony Index to Monitor Team Cohesion and Performance in Long-Duration Space Exploration. In Advancing Human-Computer Interaction for Space Exploration (SpaceCHI 2025). Open Access Series in Informatics (OASIcs), Volume 130, pp. 30:1-30:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{nemmi_et_al:OASIcs.SpaceCHI.2025.30,
  author =	{Nemmi, Federico and Chabani, Emma and Boyer, Laure and Madier, Charlie and Lewkowicz, Daniel},
  title =	{{A Research Framework to Develop a Real-Time Synchrony Index to Monitor Team Cohesion and Performance in Long-Duration Space Exploration}},
  booktitle =	{Advancing Human-Computer Interaction for Space Exploration (SpaceCHI 2025)},
  pages =	{30:1--30:16},
  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.2025.30},
  URN =		{urn:nbn:de:0030-drops-240200},
  doi =		{10.4230/OASIcs.SpaceCHI.2025.30},
  annote =	{Keywords: Performance, Synchronie, Crew monitoring, Cohesion}
}
Document
DOI: 10.4230/OASIcs.SpaceCHI.2025.22
Mixed-Initiative Dynamic Autonomy Through Variable Levels of Immersion and Control (MIDA-VIC): A New Paradigm for Collaborative Robotic Teleoperation in Space Exploration

Authors: Hans-Christian Jetter, Leon Raule, Jens Gerken, and Sören Pirk

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

Abstract
In this position paper, we propose the new control paradigm and conceptual framework MIDA-VIC for collaborative robotic teleoperation in space exploration and beyond. Such teleoperation is a complex and demanding team effort with distributed responsibilities that require both efficient human-robot and human-human collaboration. To address these challenges, we propose a new paradigm of mixed-initiative dynamic autonomy for robotic teleoperation. It exploits recent advances in human-computer interaction (HCI), human-robot interaction (HRI), augmented and virtual reality (AR/VR), and artificial intelligence (AI) research. By integrating methods from multiple fields, our paradigm allows human operators to choose their preferred level of immersion, from traditional 2D graphical user interfaces (GUIs) to fully immersive AR/VR environments. It also supports a dynamic adjustment of the level of control, ranging from direct motor commands (e.g., using a joystick) to high-level task delegation using AI (e.g., instructing the robot via natural language to select a path or explore autonomously). In addition, we propose a mixed-initiative paradigm in which a robot can also take the initiative, request human assistance, and propose the specific level of immersion and control to the human operator that it currently considers useful for effective and efficient collaboration.
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Hans-Christian Jetter, Leon Raule, Jens Gerken, and Sören Pirk. Mixed-Initiative Dynamic Autonomy Through Variable Levels of Immersion and Control (MIDA-VIC): A New Paradigm for Collaborative Robotic Teleoperation in Space Exploration. In Advancing Human-Computer Interaction for Space Exploration (SpaceCHI 2025). Open Access Series in Informatics (OASIcs), Volume 130, pp. 22:1-22:10, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{jetter_et_al:OASIcs.SpaceCHI.2025.22,
  author =	{Jetter, Hans-Christian and Raule, Leon and Gerken, Jens and Pirk, S\"{o}ren},
  title =	{{Mixed-Initiative Dynamic Autonomy Through Variable Levels of Immersion and Control (MIDA-VIC): A New Paradigm for Collaborative Robotic Teleoperation in Space Exploration}},
  booktitle =	{Advancing Human-Computer Interaction for Space Exploration (SpaceCHI 2025)},
  pages =	{22:1--22:10},
  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.2025.22},
  URN =		{urn:nbn:de:0030-drops-240122},
  doi =		{10.4230/OASIcs.SpaceCHI.2025.22},
  annote =	{Keywords: Collaboration, Teleoperation, Robot, Space Exploration}
}
Document
RANDOM
DOI: 10.4230/LIPIcs.APPROX/RANDOM.2025.48
Sharp Thresholds for the Overlap Gap Property: Ising p-Spin Glass and Random k-SAT

Authors: Eren C. Kızıldağ

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

Abstract
The Ising p-spin glass and random k-SAT are two canonical examples of disordered systems that play a central role in understanding the link between geometric features of optimization landscapes and computational tractability. Both models exhibit hard regimes where all known polynomial-time algorithms fail and possess the multi Overlap Gap Property (m-OGP), an intricate geometrical property that rigorously rules out a broad class of algorithms exhibiting input stability. We establish that, in both models, the symmetric m-OGP undergoes a sharp phase transition, and we pinpoint its exact threshold. For the Ising p-spin glass, our results hold for all sufficiently large p; for the random k-SAT, they apply to all k growing mildly with the number of Boolean variables. Notably, our findings yield qualitative insights into the power of OGP-based arguments. A particular consequence for the Ising p-spin glass is that the strength of the m-OGP in establishing algorithmic hardness grows without bound as m increases. These are the first sharp threshold results for the m-OGP. Our analysis hinges on a judicious application of the second moment method, enhanced by concentration. While a direct second moment calculation fails, we overcome this via a refined approach that leverages an argument of Frieze [Frieze, 1990] and exploiting concentration properties of carefully constructed random variables.
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Eren C. Kızıldağ. Sharp Thresholds for the Overlap Gap Property: Ising p-Spin Glass and Random k-SAT. In Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 353, pp. 48:1-48:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{kizildag:LIPIcs.APPROX/RANDOM.2025.48,
  author =	{K{\i}z{\i}lda\u{g}, Eren C.},
  title =	{{Sharp Thresholds for the Overlap Gap Property: Ising p-Spin Glass and Random k-SAT}},
  booktitle =	{Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025)},
  pages =	{48:1--48:16},
  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.2025.48},
  URN =		{urn:nbn:de:0030-drops-244147},
  doi =		{10.4230/LIPIcs.APPROX/RANDOM.2025.48},
  annote =	{Keywords: spin glasses, p-spin model, random constraint satisfaction problems, overlap gap property, phase transitions, computational complexity}
}
Document
DOI: 10.4230/LIPIcs.TQC.2025.9
Efficient Quantum Pseudorandomness from Hamiltonian Phase States

Authors: John Bostanci, Jonas Haferkamp, Dominik Hangleiter, and Alexander Poremba

Published in: LIPIcs, Volume 350, 20th Conference on the Theory of Quantum Computation, Communication and Cryptography (TQC 2025)

Abstract
Quantum pseudorandomness has found applications in many areas of quantum information, ranging from entanglement theory, to models of scrambling phenomena in chaotic quantum systems, and, more recently, in the foundations of quantum cryptography. Kretschmer (TQC '21) showed that both pseudorandom states and pseudorandom unitaries exist even in a world without classical one-way functions. To this day, however, all known constructions require classical cryptographic building blocks which are themselves synonymous with the existence of one-way functions, and which are also challenging to implement on realistic quantum hardware. In this work, we seek to make progress on both of these fronts simultaneously - by decoupling quantum pseudorandomness from classical cryptography altogether. We introduce a quantum hardness assumption called the Hamiltonian Phase State (HPS) problem, which is the task of decoding output states of a random instantaneous quantum polynomial-time (IQP) circuit. Hamiltonian phase states can be generated very efficiently using only Hadamard gates, single-qubit Z rotations and CNOT circuits. We show that the hardness of our problem reduces to a worst-case version of the problem, and we provide evidence that our assumption is plausibly fully quantum; meaning, it cannot be used to construct one-way functions. We also show information-theoretic hardness when only few copies of HPS are available by proving an approximate t-design property of our ensemble. Finally, we show that our HPS assumption and its variants allow us to efficiently construct many pseudorandom quantum primitives, ranging from pseudorandom states, to quantum pseudoentanglement, to pseudorandom unitaries, and even primitives such as public-key encryption with quantum keys.
Cite as

John Bostanci, Jonas Haferkamp, Dominik Hangleiter, and Alexander Poremba. Efficient Quantum Pseudorandomness from Hamiltonian Phase States. In 20th Conference on the Theory of Quantum Computation, Communication and Cryptography (TQC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 350, pp. 9:1-9:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{bostanci_et_al:LIPIcs.TQC.2025.9,
  author =	{Bostanci, John and Haferkamp, Jonas and Hangleiter, Dominik and Poremba, Alexander},
  title =	{{Efficient Quantum Pseudorandomness from Hamiltonian Phase States}},
  booktitle =	{20th Conference on the Theory of Quantum Computation, Communication and Cryptography (TQC 2025)},
  pages =	{9:1--9:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-392-8},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{350},
  editor =	{Fefferman, Bill},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.TQC.2025.9},
  URN =		{urn:nbn:de:0030-drops-240586},
  doi =		{10.4230/LIPIcs.TQC.2025.9},
  annote =	{Keywords: Quantum pseudorandomness, quantum phase states, quantum cryptography}
}
Document
DOI: 10.4230/LIPIcs.WADS.2025.43
On the Complexity of Finding 1-Center Spanning Trees

Authors: Pin-Hsian Lee, Meng-Tsung Tsai, and Hung-Lung Wang

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

Abstract
We consider the problem of finding a spanning tree T of a given undirected graph G such that any other spanning tree can be obtained from T by removing k edges and subsequently adding k edges, where k is minimized over all spanning trees of G. We refer to this minimum k as the treeradius of G. Treeradius is an interesting graph parameter with natural interpretations: (1) It is the smallest radius of a Hamming ball centered at an extreme point of the spanning tree polytope that covers the entire polytope. (2) Any graph with bounded treeradius also has bounded treewidth. Consequently, if a problem admits a fixed-parameter algorithm parameterized by treewidth, it also admits a fixed-parameter algorithm parameterized by treeradius. In this paper, we show that computing the exact treeradius for n-vertex graphs requires 2^Ω(n) time under the Exponential Time Hypothesis (ETH) and does not admit a PTAS, with an inapproximability bound of 1153/1152, unless P = NP. This hardness result is surprising, as treeradius has significantly higher ETH complexity compared to analogous problems on shortest path polytopes and star subgraph polytopes.
Cite as

Pin-Hsian Lee, Meng-Tsung Tsai, and Hung-Lung Wang. On the Complexity of Finding 1-Center Spanning Trees. In 19th International Symposium on Algorithms and Data Structures (WADS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 349, pp. 43:1-43:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{lee_et_al:LIPIcs.WADS.2025.43,
  author =	{Lee, Pin-Hsian and Tsai, Meng-Tsung and Wang, Hung-Lung},
  title =	{{On the Complexity of Finding 1-Center Spanning Trees}},
  booktitle =	{19th International Symposium on Algorithms and Data Structures (WADS 2025)},
  pages =	{43:1--43:19},
  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.2025.43},
  URN =		{urn:nbn:de:0030-drops-242743},
  doi =		{10.4230/LIPIcs.WADS.2025.43},
  annote =	{Keywords: Treeradius, Spanning tree polytope, Shortest s, t-path polytope}
}
Document
DOI: 10.4230/LIPIcs.MFCS.2025.39
Right-Linear Lattices: An Algebraic Theory of ω-Regular Languages, with Fixed Points

Authors: Anupam Das and Abhishek De

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

Abstract
Alternating parity automata (APAs) provide a robust formalism for modelling infinite behaviours and play a central role in formal verification. Despite their widespread use, the algebraic theory underlying APAs has remained largely unexplored. In recent work [Anupam Das and Abhishek De, 2024], a notation for non-deterministic finite automata (NFAs) was introduced, along with a sound and complete axiomatisation of their equational theory via right-linear algebras. In this paper, we extend that line of work to the setting of infinite words. In particular, we present a dualised syntax, yielding a notation for APAs based on right-linear lattice expressions, and provide a natural axiomatisation of their equational theory with respect to the standard language model of ω-regular languages. The design of this axiomatisation is guided by the theory of fixed point logics; in fact, the completeness factors cleanly through the completeness of the linear-time μ-calculus.
Cite as

Anupam Das and Abhishek De. Right-Linear Lattices: An Algebraic Theory of ω-Regular Languages, with Fixed Points. In 50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 345, pp. 39:1-39:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{das_et_al:LIPIcs.MFCS.2025.39,
  author =	{Das, Anupam and De, Abhishek},
  title =	{{Right-Linear Lattices: An Algebraic Theory of \omega-Regular Languages, with Fixed Points}},
  booktitle =	{50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025)},
  pages =	{39:1--39:17},
  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.2025.39},
  URN =		{urn:nbn:de:0030-drops-241461},
  doi =		{10.4230/LIPIcs.MFCS.2025.39},
  annote =	{Keywords: omega-languages, regular languages, fixed points, Kleene algebras, right-linear grammars}
}
Document
DOI: 10.4230/LIPIcs.DNA.31.3
Reachability in Deletion-Only Chemical Reaction Networks

Authors: Bin Fu, Timothy Gomez, Ryan Knobel, Austin Luchsinger, Aiden Massie, Marco Rodriguez, Adrian Salinas, Robert Schweller, and Tim Wylie

Published in: LIPIcs, Volume 347, 31st International Conference on DNA Computing and Molecular Programming (DNA 31) (2025)

Abstract
For general discrete Chemical Reaction Networks (CRNs), the fundamental problem of reachability - the question of whether a target configuration can be produced from a given initial configuration - was recently shown to be Ackermann-complete. However, many open questions remain about which features of the CRN model drive this complexity. We study a restricted class of CRNs with void rules, reactions that only decrease species counts. We further examine this regime in the motivated model of step CRNs, which allow additional species to be introduced in discrete stages. With and without steps, we characterize the complexity of the reachability problem for CRNs with void rules. We show that, without steps, reachability remains polynomial-time solvable for bimolecular systems but becomes NP-complete for larger reactions. Conversely, with just a single step, reachability becomes NP-complete even for bimolecular systems. Our results provide a nearly complete classification of void-rule reachability problems into tractable and intractable cases, with only a single exception.
Cite as

Bin Fu, Timothy Gomez, Ryan Knobel, Austin Luchsinger, Aiden Massie, Marco Rodriguez, Adrian Salinas, Robert Schweller, and Tim Wylie. Reachability in Deletion-Only Chemical Reaction Networks. In 31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 3:1-3:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{fu_et_al:LIPIcs.DNA.31.3,
  author =	{Fu, Bin and Gomez, Timothy and Knobel, Ryan and Luchsinger, Austin and Massie, Aiden and Rodriguez, Marco and Salinas, Adrian and Schweller, Robert and Wylie, Tim},
  title =	{{Reachability in Deletion-Only Chemical Reaction Networks}},
  booktitle =	{31st International Conference on DNA Computing and Molecular Programming (DNA 31)},
  pages =	{3:1--3:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-399-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{347},
  editor =	{Schaeffer, Josie and Zhang, Fei},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.31.3},
  URN =		{urn:nbn:de:0030-drops-238521},
  doi =		{10.4230/LIPIcs.DNA.31.3},
  annote =	{Keywords: CRN, Chemical Reaction Network, Reachability, Void Reactions}
}
Document
DOI: 10.4230/LIPIcs.CONCUR.2025.17
Just Verification of Mutual Exclusion Algorithms

Authors: Rob van Glabbeek, Bas Luttik, and Myrthe S. C. Spronck

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

Abstract
We verify the correctness of a variety of mutual exclusion algorithms through model checking. We look at algorithms where communication is via shared read/write registers, where those registers can be atomic or non-atomic. For the verification of liveness properties, it is necessary to assume a completeness criterion to eliminate spurious counterexamples. We use justness as completeness criterion. Justness depends on a concurrency relation; we consider several such relations, modelling different assumptions on the working of the shared registers. We present executions demonstrating the violation of correctness properties by several algorithms, and in some cases suggest improvements.
Cite as

Rob van Glabbeek, Bas Luttik, and Myrthe S. C. Spronck. Just Verification of Mutual Exclusion Algorithms. In 36th International Conference on Concurrency Theory (CONCUR 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 348, pp. 17:1-17:25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{vanglabbeek_et_al:LIPIcs.CONCUR.2025.17,
  author =	{van Glabbeek, Rob and Luttik, Bas and Spronck, Myrthe S. C.},
  title =	{{Just Verification of Mutual Exclusion Algorithms}},
  booktitle =	{36th International Conference on Concurrency Theory (CONCUR 2025)},
  pages =	{17:1--17:25},
  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.2025.17},
  URN =		{urn:nbn:de:0030-drops-239670},
  doi =		{10.4230/LIPIcs.CONCUR.2025.17},
  annote =	{Keywords: Mutual exclusion, safe registers, regular registers, overlapping reads and writes, atomicity, safety, liveness, starvation freedom, justness, model checking, mCRL2}
}
Document
DOI: 10.4230/LIPIcs.GIScience.2025.18
U-Prithvi: Integrating a Foundation Model and U-Net for Enhanced Flood Inundation Mapping

Authors: Vit Kostejn, Yamil Essus, Jenna Abrahamson, and Ranga Raju Vatsavai

Published in: LIPIcs, Volume 346, 13th International Conference on Geographic Information Science (GIScience 2025)

Abstract
In recent years, large pre-trained models, commonly referred to as foundation models, have become increasingly popular for various tasks leveraging transfer learning. This trend has expanded to remote sensing, where transformer-based foundation models such as Prithvi, msGFM, and SatSwinMAE have been utilized for a range of applications. While these transformer-based models, particularly the Prithvi model, exhibit strong generalization capabilities, they have limitations on capturing fine-grained details compared to convolutional neural network architectures like U-Net in segmentation tasks. In this paper, we propose a novel architecture, U-Prithvi, which combines the strengths of the Prithvi transformer with those of U-Net. We introduce a RandomHalfMaskLayer to ensure balanced learning from both models during training. Our approach is evaluated on the Sen1Floods11 dataset for flood inundation mapping, and experimental results demonstrate better performance of U-Prithvi over both individual models, achieving improved performance on out-of-sample data. While this principle is illustrated using the Prithvi model, it is easily adaptable to other foundation models.
Cite as

Vit Kostejn, Yamil Essus, Jenna Abrahamson, and Ranga Raju Vatsavai. U-Prithvi: Integrating a Foundation Model and U-Net for Enhanced Flood Inundation Mapping. In 13th International Conference on Geographic Information Science (GIScience 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 346, pp. 18:1-18:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{kostejn_et_al:LIPIcs.GIScience.2025.18,
  author =	{Kostejn, Vit and Essus, Yamil and Abrahamson, Jenna and Vatsavai, Ranga Raju},
  title =	{{U-Prithvi: Integrating a Foundation Model and U-Net for Enhanced Flood Inundation Mapping}},
  booktitle =	{13th International Conference on Geographic Information Science (GIScience 2025)},
  pages =	{18:1--18:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-378-2},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{346},
  editor =	{Sila-Nowicka, Katarzyna and Moore, Antoni and O'Sullivan, David and Adams, Benjamin and Gahegan, Mark},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.GIScience.2025.18},
  URN =		{urn:nbn:de:0030-drops-238479},
  doi =		{10.4230/LIPIcs.GIScience.2025.18},
  annote =	{Keywords: GeoAI, flood mapping, foundation model, U-Net, Prithvi}
}
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.WABI.2025.6
Fast Pseudoalignment Queries on Compressed Colored de Bruijn Graphs

Authors: Alessio Campanelli, Giulio Ermanno Pibiri, and Rob Patro

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

Abstract
Motivation. Indexes for the colored de Bruijn graph (c-dBG) play a crucial role in computational biology by facilitating complex tasks such as read mapping and assembly. These indexes map k-mers (substrings of length k) appearing in a large collection of reference strings to the set of identifiers of the strings where they appear. These sets, colloquially referred to as color sets, tend to occupy large quantities of memory, especially for large pangenomes. Our previous work thus focused on leveraging the repetitiveness of the color sets to improve the space effectiveness of the resulting index. As a matter of fact, repetition-aware indexes can be up to one order of magnitude smaller on large pangenomes compared to indexes that do not exploit such repetitiveness. Such improved space effectiveness, on the other hand, imposes an overhead at query time when performing tasks such as pseudoalignment that require the collection and processing of multiple related color sets. Methods. In this paper, we show how to avoid this overhead. We devise novel query algorithms tailored for the specific repetition-aware representations adopted by the Fulgor index, a state-of-the-art c-dBG index, to significantly improve its pseudoalignment efficiency and without consuming additional space. Results. Our results indicate that with increasing redundancy in the pangenomes, the compression factor provided by the Fulgor index increases, while the relative query time actually reduces. For example, while the space of the Fulgor index improves by 2.5× with repetition-aware compression and its query time improves by 1.6× on a collection of 5,000 Salmonella Enterica genomes, these factors become (6.1×,2.8×) and (11.2×,3.2×) for 50,000 and 150,000 genomes respectively. For an even larger collection of 300,000 genomes, we obtained an index that is 22.3× smaller and 2.2× faster.
Cite as

Alessio Campanelli, Giulio Ermanno Pibiri, and Rob Patro. Fast Pseudoalignment Queries on Compressed Colored de Bruijn Graphs. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 6:1-6:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{campanelli_et_al:LIPIcs.WABI.2025.6,
  author =	{Campanelli, Alessio and Pibiri, Giulio Ermanno and Patro, Rob},
  title =	{{Fast Pseudoalignment Queries on Compressed Colored de Bruijn Graphs}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{6:1--6:21},
  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.2025.6},
  URN =		{urn:nbn:de:0030-drops-239327},
  doi =		{10.4230/LIPIcs.WABI.2025.6},
  annote =	{Keywords: Colored de Bruijn graphs, Pseudoalignment, Repetition-aware compression}
}
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)

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@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.SEA.2025.4
U-Index: A Universal Indexing Framework for Matching Long Patterns

Authors: Lorraine A. K. Ayad, Gabriele Fici, Ragnar Groot Koerkamp, Grigorios Loukides, Rob Patro, Giulio Ermanno Pibiri, and Solon P. Pissis

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

Abstract
Motivation. Text indexing is a fundamental and well-studied problem. Classic solutions to this problem either replace the original text with a compressed representation, e.g., the FM-index and its variants, or keep it uncompressed but attach some redundancy - an index - to accelerate matching, e.g., the suffix array. The former solutions thus retain excellent compressed space, but are practically slow to construct and query. The latter approaches, instead, sacrifice space efficiency but are typically faster; for example, the suffix array takes much more space than the text itself for commonly used alphabets, like ASCII or DNA, but it is very fast to construct and query. Methods. In this paper, we show that efficient text indexing can be achieved using just a small extra space on top of the original text, provided that the query patterns are sufficiently long. More specifically, we develop a new indexing paradigm in which a sketch of a query pattern is first matched against a sketch of the text. Once candidate matches are retrieved, they are verified using the original text. This paradigm is thus universal in the sense that it allows us to use any solution to index the sketched text, like a suffix array, FM-index, or r-index. Results. We explore both the theory and the practice of this universal framework. With an extensive experimental analysis, we show that, surprisingly, universal indexes can be constructed much faster than their unsketched counterparts and take a fraction of the space, as a direct consequence of (i) having a lower bound on the length of patterns and (ii) working in sketch space. Furthermore, these data structures have the potential of retaining or even improving query time, because matching against the sketched text is faster and verifying candidates can be theoretically done in constant time per occurrence (or, in practice, by short and cache-friendly scans of the text). Finally, we discuss some important applications of this novel indexing paradigm to computational biology. We hypothesize that such indexes will be particularly effective when the queries are sufficiently long, and so we demonstrate applications in long-read mapping.
Cite as

Lorraine A. K. Ayad, Gabriele Fici, Ragnar Groot Koerkamp, Grigorios Loukides, Rob Patro, Giulio Ermanno Pibiri, and Solon P. Pissis. U-Index: A Universal Indexing Framework for Matching Long Patterns. In 23rd International Symposium on Experimental Algorithms (SEA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 338, pp. 4:1-4:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{ayad_et_al:LIPIcs.SEA.2025.4,
  author =	{Ayad, Lorraine A. K. and Fici, Gabriele and Groot Koerkamp, Ragnar and Loukides, Grigorios and Patro, Rob and Pibiri, Giulio Ermanno and Pissis, Solon P.},
  title =	{{U-Index: A Universal Indexing Framework for Matching Long Patterns}},
  booktitle =	{23rd International Symposium on Experimental Algorithms (SEA 2025)},
  pages =	{4:1--4:18},
  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.2025.4},
  URN =		{urn:nbn:de:0030-drops-232420},
  doi =		{10.4230/LIPIcs.SEA.2025.4},
  annote =	{Keywords: Text Indexing, Sketching, Minimizers, Hashing}
}
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