22 Search Results for "Williams, Brian C."

Document
DOI: 10.4230/OASIcs.DX.2025.3
Combining Dynamic Slicing and Spectrum-Based Fault Localization - A First Experimental Evaluation

Authors: Jonas Schleich and Franz Wotawa

Published in: OASIcs, Volume 136, 36th International Conference on Principles of Diagnosis and Resilient Systems (DX 2025)

Abstract
Identifying and localizing bugs in programs has always been considered a complex but essential topic. Whereas the former has led to substantial progress in areas like formal verification and testing with a high degree of automation, the latter has not been satisfactorily automated. Approaches like program slicing, model-based diagnosis, and, more recently, spectrum-based fault localization can be used to find possible causes of a misbehaving program automatically, but often come with high computational complexity or a larger list of diagnoses, which require additional manual effort. In this paper, we present the first experimental results of an approach that combines program slicing with spectrum-based fault localization aiming at improving the outcome of automated debugging methods. In contrast to previous work, where we illustrated potential improvements only by considering a particular use case, we present an evaluation based on 22 different example programs in this paper. The approach improves the wasted effort on average by around 5 to 15% on average.
Cite as

Jonas Schleich and Franz Wotawa. Combining Dynamic Slicing and Spectrum-Based Fault Localization - A First Experimental Evaluation. In 36th International Conference on Principles of Diagnosis and Resilient Systems (DX 2025). Open Access Series in Informatics (OASIcs), Volume 136, pp. 3:1-3:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{schleich_et_al:OASIcs.DX.2025.3,
  author =	{Schleich, Jonas and Wotawa, Franz},
  title =	{{Combining Dynamic Slicing and Spectrum-Based Fault Localization - A First Experimental Evaluation}},
  booktitle =	{36th International Conference on Principles of Diagnosis and Resilient Systems (DX 2025)},
  pages =	{3:1--3:18},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-394-2},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{136},
  editor =	{Quinones-Grueiro, Marcos and Biswas, Gautam and Pill, Ingo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.DX.2025.3},
  URN =		{urn:nbn:de:0030-drops-247927},
  doi =		{10.4230/OASIcs.DX.2025.3},
  annote =	{Keywords: Software fault localization, program slicing, spectrum-based fault localization, automated debugging}
}
Document
DOI: 10.4230/OASIcs.DX.2025.1
Beyond Static Diagnosis: A Temporal ASP Framework for HVAC Fault Detection

Authors: Roxane Koitz-Hristov, Liliana Marie Prikler, and Franz Wotawa

Published in: OASIcs, Volume 136, 36th International Conference on Principles of Diagnosis and Resilient Systems (DX 2025)

Abstract
Improving sustainability in the building sector requires more efficient operation of energy-intensive systems such as Heating, Ventilation, and Air Conditioning (HVAC). We present a novel diagnostic framework for HVAC systems that integrates Answer Set Programming (ASP) with Functional Event Calculus (FEC). Our approach exploits the declarative nature of ASP for modeling and incorporates FEC to capture temporal system dynamics. We demonstrate the feasibility of our approach through a case study on a real-world heating system, where we model key components and system constraints. Our evaluation on nominal and faulty traces shows that exploiting ASP in combination with FEC can identify plausible diagnoses. Moreover, we explore the difference between static and rolling-window strategies and provide insights into runtime versus soundness on those variants. Our work provides a step toward the practical application of ASP-based temporal reasoning in building diagnostics.
Cite as

Roxane Koitz-Hristov, Liliana Marie Prikler, and Franz Wotawa. Beyond Static Diagnosis: A Temporal ASP Framework for HVAC Fault Detection. In 36th International Conference on Principles of Diagnosis and Resilient Systems (DX 2025). Open Access Series in Informatics (OASIcs), Volume 136, pp. 1:1-1:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{koitzhristov_et_al:OASIcs.DX.2025.1,
  author =	{Koitz-Hristov, Roxane and Prikler, Liliana Marie and Wotawa, Franz},
  title =	{{Beyond Static Diagnosis: A Temporal ASP Framework for HVAC Fault Detection}},
  booktitle =	{36th International Conference on Principles of Diagnosis and Resilient Systems (DX 2025)},
  pages =	{1:1--1:20},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-394-2},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{136},
  editor =	{Quinones-Grueiro, Marcos and Biswas, Gautam and Pill, Ingo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.DX.2025.1},
  URN =		{urn:nbn:de:0030-drops-247901},
  doi =		{10.4230/OASIcs.DX.2025.1},
  annote =	{Keywords: Model-based diagnosis, Answer set programming, HVAC, Modeling for diagnosis, Experimental evaluation}
}
Document
PhD Panel
DOI: 10.4230/OASIcs.DX.2025.16
Unsupervised Multimodal Learning for Fault Diagnosis and Prognosis - Application to Radiotherapy Systems (PhD Panel)

Authors: Kélian Poujade, Louise Travé-Massuyès, Jérémy Pirard, and Laure Vieillevigne

Published in: OASIcs, Volume 136, 36th International Conference on Principles of Diagnosis and Resilient Systems (DX 2025)

Abstract
Modern complex systems, such as radiotherapy machines, require robust strategies for fault detection, diagnosis, and prognosis to ensure operational continuity and patient safety. While data-driven methods have gained traction, few studies address diagnostic and prognostic tasks using multimodal operational data under unsupervised or semi-supervised learning settings. This gap is particularly critical given the scarcity of labeled failure data in real-world environments. This work aims to design a unified approach for fault detection, diagnosis, and prognosis using multimodal data in the absence of complete labeling. To this end, autoencoders (AEs) are employed due to their suitability for unsupervised and self-supervised learning, flexibility in handling heterogeneous data, and ability to construct latent representations optimized for various downstream tasks. A specific implementation based on a Long Short-Term Memory β-Variational Autoencoder (LSTM-β-VAE) was developed to detect anomalies in machine logs. This framework is applied to TomoTherapy® systems - a highly complex and under-explored use case within the radiotherapy domain. Initial results demonstrate strong anomaly detection performance on both a public benchmark dataset (HDFS) and a proprietary dataset derived from real-world TomoTherapy® machine faults. Beyond methodology, the paper includes a concise literature review of multimodal learning and data-driven diagnosis and prognosis with a focus on AEs. Based on this review, key research directions are identified for the continuation of the thesis, especially the integration of explainable AI as a means to enhance diagnosis capabilities in the absence of labeled faults.
Cite as

Kélian Poujade, Louise Travé-Massuyès, Jérémy Pirard, and Laure Vieillevigne. Unsupervised Multimodal Learning for Fault Diagnosis and Prognosis - Application to Radiotherapy Systems (PhD Panel). In 36th International Conference on Principles of Diagnosis and Resilient Systems (DX 2025). Open Access Series in Informatics (OASIcs), Volume 136, pp. 16:1-16:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{poujade_et_al:OASIcs.DX.2025.16,
  author =	{Poujade, K\'{e}lian and Trav\'{e}-Massuy\`{e}s, Louise and Pirard, J\'{e}r\'{e}my and Vieillevigne, Laure},
  title =	{{Unsupervised Multimodal Learning for Fault Diagnosis and Prognosis - Application to Radiotherapy Systems}},
  booktitle =	{36th International Conference on Principles of Diagnosis and Resilient Systems (DX 2025)},
  pages =	{16:1--16:17},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-394-2},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{136},
  editor =	{Quinones-Grueiro, Marcos and Biswas, Gautam and Pill, Ingo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.DX.2025.16},
  URN =		{urn:nbn:de:0030-drops-248058},
  doi =		{10.4230/OASIcs.DX.2025.16},
  annote =	{Keywords: Artificial Intelligence, Diagnosis, Prognosis, Radiotherapy machines}
}
Document
Short Paper
DOI: 10.4230/LIPIcs.TIME.2025.14
QualiNet: Acquiring Bird’s Eye View Qualitative Spatial Representation from 2D Images in Automated Vehicle Perception (Short Paper)

Authors: Nassim Belmecheri

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

Abstract
We present QualiNet, an end-to-end deep learning framework that acquires Bird’s Eye View (BEV) qualitative spatial relations directly from 2D images, eliminating the need for depth sensors. The system combines 2D object detection, masking, and classification to infer Rectangle Algebra (RA) and Qualitative Distance Calculus (QDC) relations. Evaluated on NuScenes and PandaSet datasets, QualiNet achieves 91% accuracy for RA, 80% for QDC, and 99% top-2 accuracy, demonstrating robust performance for automated vehicle perception.
Cite as

Nassim Belmecheri. QualiNet: Acquiring Bird’s Eye View Qualitative Spatial Representation from 2D Images in Automated Vehicle Perception (Short Paper). In 32nd International Symposium on Temporal Representation and Reasoning (TIME 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 355, pp. 14:1-14:6, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{belmecheri:LIPIcs.TIME.2025.14,
  author =	{Belmecheri, Nassim},
  title =	{{QualiNet: Acquiring Bird’s Eye View Qualitative Spatial Representation from 2D Images in Automated Vehicle Perception}},
  booktitle =	{32nd International Symposium on Temporal Representation and Reasoning (TIME 2025)},
  pages =	{14:1--14:6},
  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.2025.14},
  URN =		{urn:nbn:de:0030-drops-244608},
  doi =		{10.4230/LIPIcs.TIME.2025.14},
  annote =	{Keywords: Qualitative Spatial Representation, Deep Learning, Computer vision, Qualitative Scene Understanding, Spatio-temporal representation and reasoning models (including moving objects tracking)}
}
Document
Short Paper
DOI: 10.4230/LIPIcs.TIME.2025.20
Temporal Considerations in DJ Mix Information Retrieval and Generation (Short Paper)

Authors: Alexander Williams, Gregor Meehan, Stefan Lattner, Johan Pauwels, and Mathieu Barthet

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

Abstract
Music is the art of arranging sounds in time so as to produce a continuous, unified, and evocative composition. Electronic dance music (EDM) is a collection of musical sub-genres produced using computers and electronic instruments and often presented through the medium of DJing, where tracks are curated and mixed sequentially into a continuous stream of music to offer unique listening and dancing experiences over time periods ranging from several minutes to several hours. A DJ’s actions and decisions occur at several levels of temporal granularity, from real-time audio manipulation (e.g. of tempo) for smooth inter-track transitions to long-term planning of track selection and sequencing for mix content and flow. While human DJs can instinctively operate across these different temporal resolutions, replicating this capability in an end-to-end automated DJing system presents significant challenges. In this paper, we analyse existing works in DJ mix information retrieval and generation from this temporal perspective. We first explain the close link between DJing and the temporal notion of musical rhythm, then describe a framework for categorising DJing actions by temporal granularity. Using this framework, we summarise and contrast potential approaches for automating and augmenting sequential DJ decision making, and discuss the unique characteristics of DJ mix track selection as a sequential recommendation task. In doing so, we hope to facilitate the implementation of more robust and complete automated DJing systems in future research.
Cite as

Alexander Williams, Gregor Meehan, Stefan Lattner, Johan Pauwels, and Mathieu Barthet. Temporal Considerations in DJ Mix Information Retrieval and Generation (Short Paper). In 32nd International Symposium on Temporal Representation and Reasoning (TIME 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 355, pp. 20:1-20:8, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{williams_et_al:LIPIcs.TIME.2025.20,
  author =	{Williams, Alexander and Meehan, Gregor and Lattner, Stefan and Pauwels, Johan and Barthet, Mathieu},
  title =	{{Temporal Considerations in DJ Mix Information Retrieval and Generation}},
  booktitle =	{32nd International Symposium on Temporal Representation and Reasoning (TIME 2025)},
  pages =	{20:1--20:8},
  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.2025.20},
  URN =		{urn:nbn:de:0030-drops-244662},
  doi =		{10.4230/LIPIcs.TIME.2025.20},
  annote =	{Keywords: Music Information Retrieval, Computational Creativity, Recommender Systems, Electronic Dance Music, DJ}
}
Document
DOI: 10.4230/OASIcs.SpaceCHI.2025.10
A Postcard from Mars: Exploring Interplanetary Communications in Virtual Reality

Authors: Adalberto L. Simeone

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

Abstract
In this paper we present an Immersive Speculative Enactment focused on the theme of interplanetary communications. These are a novel approach extending conventional Speculative Enactments to Virtual Reality. We created a narrative-based scenario in which participants played the role of human colonists on either Mars or the Moon, to explore a possible future in which interplanetary communication becomes a necessity. To enact this scenario, we created a VR interactive experience to elicit feedback on the idea of communicating across planets. Through an exploratory qualitative analysis of this immersive enactment, we found that while the future envisioned was seen as too distant to prompt realistic behaviour from all participants, the enactment helped us and the participants to reflect on the experience. We discuss these findings, drawing potential implications for the improvement of the feeling of "really being there" even in implausible situations and further contribute reflections on the role of ISEs in space-related scenarios.
Cite as

Adalberto L. Simeone. A Postcard from Mars: Exploring Interplanetary Communications in Virtual Reality. In Advancing Human-Computer Interaction for Space Exploration (SpaceCHI 2025). Open Access Series in Informatics (OASIcs), Volume 130, pp. 10:1-10:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{simeone:OASIcs.SpaceCHI.2025.10,
  author =	{Simeone, Adalberto L.},
  title =	{{A Postcard from Mars: Exploring Interplanetary Communications in Virtual Reality}},
  booktitle =	{Advancing Human-Computer Interaction for Space Exploration (SpaceCHI 2025)},
  pages =	{10:1--10:16},
  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.2025.10},
  URN =		{urn:nbn:de:0030-drops-240002},
  doi =		{10.4230/OASIcs.SpaceCHI.2025.10},
  annote =	{Keywords: Immersive Speculative Enactments, Interplanetary Communications, Virtual Reality}
}
Document
DOI: 10.4230/OASIcs.SpaceCHI.2025.27
Assessing the Use of Mixed Reality as a Valid Tool for Human-Robot Interaction Studies in the Context of Space Exploration

Authors: Enrico Guerra, Sebastian Thomas Büttner, Alper Beşer, and Michael Prilla

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

Abstract
Mixed Reality (MR) is a technology with strong potential for advancing research in Human-Robot Interaction (HRI) for space exploration. Apart from the efficiency and high flexibility MR can offer, we argue that its benefits for HRI research in space contexts lies particularly in its ability to aid human-in-the-loop development, offer realistic hybrid simulations, and foster broader participation in HRI research in the space exploration context. However, we believe that this is only plausible if MR-based simulations can yield comparable results to fully physical approaches in human-centred studies. In this position paper, we highlight several arguments in favour of MR as a tool for space HRI research, while emphasising the importance of the open question regarding its scientific validity. We believe MR could become a central tool for preparing for future human-robotic space exploration missions and significantly diversify research in this domain.
Cite as

Enrico Guerra, Sebastian Thomas Büttner, Alper Beşer, and Michael Prilla. Assessing the Use of Mixed Reality as a Valid Tool for Human-Robot Interaction Studies in the Context of Space Exploration. In Advancing Human-Computer Interaction for Space Exploration (SpaceCHI 2025). Open Access Series in Informatics (OASIcs), Volume 130, pp. 27:1-27:11, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{guerra_et_al:OASIcs.SpaceCHI.2025.27,
  author =	{Guerra, Enrico and B\"{u}ttner, Sebastian Thomas and Be\c{s}er, Alper and Prilla, Michael},
  title =	{{Assessing the Use of Mixed Reality as a Valid Tool for Human-Robot Interaction Studies in the Context of Space Exploration}},
  booktitle =	{Advancing Human-Computer Interaction for Space Exploration (SpaceCHI 2025)},
  pages =	{27:1--27:11},
  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.2025.27},
  URN =		{urn:nbn:de:0030-drops-240175},
  doi =		{10.4230/OASIcs.SpaceCHI.2025.27},
  annote =	{Keywords: Mixed Reality, Augmented Reality, Human-Robot Interaction, Space Exploration, Validity}
}
Document
DOI: 10.4230/LIPIcs.WADS.2025.49
On the I/O Complexity of the Cocke-Younger-Kasami Algorithm and of a Family of Related Dynamic Programming Algorithms

Authors: Lorenzo De Stefani and Vedant Gupta

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

Abstract
Asymptotically tight lower bounds are derived for the Input/Output (I/O) complexity of a class of dynamic programming algorithms, including matrix chain multiplication, optimal polygon triangulation, and the construction of optimal binary search trees. Assuming no recomputation of intermediate values, we establish an Ω(n³/(√M B)) I/O lower bound, where n denotes the size of the input and M denotes the size of the available fast memory (cache). When recomputation is allowed, we show that the same bound holds for M < cn, where c is a positive constant. In the case where M ≥ 2n, we show an Ω(n/B) I/O lower bound. We also discuss algorithms for which the number of executed I/O operations matches asymptotically each of the presented lower bounds, which are thus asymptotically tight. Additionally, we refine our general method to obtain a lower bound for the I/O complexity of the Cocke-Younger-Kasami algorithm, where the size of the grammar impacts the I/O complexity. An upper bound with asymptotically matching performance in many cases is also provided.
Cite as

Lorenzo De Stefani and Vedant Gupta. On the I/O Complexity of the Cocke-Younger-Kasami Algorithm and of a Family of Related Dynamic Programming Algorithms. In 19th International Symposium on Algorithms and Data Structures (WADS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 349, pp. 49:1-49:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{destefani_et_al:LIPIcs.WADS.2025.49,
  author =	{De Stefani, Lorenzo and Gupta, Vedant},
  title =	{{On the I/O Complexity of the Cocke-Younger-Kasami Algorithm and of a Family of Related Dynamic Programming Algorithms}},
  booktitle =	{19th International Symposium on Algorithms and Data Structures (WADS 2025)},
  pages =	{49:1--49:24},
  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.2025.49},
  URN =		{urn:nbn:de:0030-drops-242800},
  doi =		{10.4230/LIPIcs.WADS.2025.49},
  annote =	{Keywords: I/O complexity, Dynamic Programming Algorithms, Lower Bounds, Recomputation, Cocke-Younger-Kasami}
}
Document
DOI: 10.4230/LIPIcs.DNA.31.4
Differentiable Programming of Indexed Chemical Reaction Networks and Reaction-Diffusion Systems

Authors: Inhoo Lee, Salvador Buse, and Erik Winfree

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

Abstract
Many molecular systems are best understood in terms of prototypical species and reactions. The central dogma and related biochemistry are rife with examples: gene i is transcribed into RNA i, which is translated into protein i; kinase n phosphorylates substrate m; protein p dimerizes with protein q. Engineered nucleic acid systems also often have this form: oligonucleotide i hybridizes to complementary oligonucleotide j; signal strand n displaces the output of seesaw gate m; hairpin p triggers the opening of target q. When there are many variants of a small number of prototypes, it can be conceptually cleaner and computationally more efficient to represent the full system in terms of indexed species (e.g. for dimerization, M_p, D_pq) and indexed reactions (M_p + M_q → D_pq). Here, we formalize the Indexed Chemical Reaction Network (ICRN) model and describe a Python software package designed to simulate such systems in the well-mixed and reaction-diffusion settings, using a differentiable programming framework originally developed for large-scale neural network models, taking advantage of GPU acceleration when available. Notably, this framework makes it straightforward to train the models’ initial conditions and rate constants to optimize a target behavior, such as matching experimental data, performing a computation, or exhibiting spatial pattern formation. The natural map of indexed chemical reaction networks onto neural network formalisms provides a tangible yet general perspective for translating concepts and techniques from the theory and practice of neural computation into the design of biomolecular systems.
Cite as

Inhoo Lee, Salvador Buse, and Erik Winfree. Differentiable Programming of Indexed Chemical Reaction Networks and Reaction-Diffusion Systems. In 31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 4:1-4:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{lee_et_al:LIPIcs.DNA.31.4,
  author =	{Lee, Inhoo and Buse, Salvador and Winfree, Erik},
  title =	{{Differentiable Programming of Indexed Chemical Reaction Networks and Reaction-Diffusion Systems}},
  booktitle =	{31st International Conference on DNA Computing and Molecular Programming (DNA 31)},
  pages =	{4:1--4:23},
  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.31.4},
  URN =		{urn:nbn:de:0030-drops-238534},
  doi =		{10.4230/LIPIcs.DNA.31.4},
  annote =	{Keywords: Differentiable Programming, Chemical Reaction Networks, Reaction-Diffusion Systems}
}
Document
DOI: 10.4230/LIPIcs.CONCUR.2025.6
Omega-Regular Verification and Control for Distributional Specifications in MDPs

Authors: S. Akshay, Ouldouz Neysari, and Ðorđe Žikelić

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

Abstract
A classical approach to studying Markov decision processes (MDPs) is to view them as state transformers. However, MDPs can also be viewed as distribution transformers, where an MDP under a strategy generates a sequence of probability distributions over MDP states. This view arises in several applications, even as the probabilistic model checking problem becomes much harder compared to the classical state transformer counterpart. It is known that even distributional reachability and safety problems become computationally intractable (Skolem- and positivity-hard). To address this challenge, recent works focused on sound but possibly incomplete methods for verification and control of MDPs under the distributional view. However, existing automated methods are applicable only to distributional reachability, safety and reach-avoidance specifications. In this work, we present the first automated method for verification and control of MDPs with respect to distributional omega-regular specifications. To achieve this, we propose a novel notion of distributional certificates, which are sound and complete proof rules for proving that an MDP under a distributionally memoryless strategy satisfies some distributional omega-regular specification. We then use our distributional certificates to design the first fully automated algorithms for verification and control of MDPs with respect to distributional omega-regular specifications. Our algorithms follow a template-based synthesis approach and provide soundness and relative completeness guarantees, while running in PSPACE. Our prototype implementation demonstrates practical applicability of our algorithms to challenging examples collected from the literature.
Cite as

S. Akshay, Ouldouz Neysari, and Ðorđe Žikelić. Omega-Regular Verification and Control for Distributional Specifications in MDPs. In 36th International Conference on Concurrency Theory (CONCUR 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 348, pp. 6:1-6:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{akshay_et_al:LIPIcs.CONCUR.2025.6,
  author =	{Akshay, S. and Neysari, Ouldouz and \v{Z}ikeli\'{c}, Ðor{\d}e},
  title =	{{Omega-Regular Verification and Control for Distributional Specifications in MDPs}},
  booktitle =	{36th International Conference on Concurrency Theory (CONCUR 2025)},
  pages =	{6:1--6:19},
  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.2025.6},
  URN =		{urn:nbn:de:0030-drops-239562},
  doi =		{10.4230/LIPIcs.CONCUR.2025.6},
  annote =	{Keywords: MDPs, Distributional objectives, \omega-regularity, Certificates}
}
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
Research
DOI: 10.4230/OASIcs.Grossi.20
Subsequence-Based Indices for Genome Sequence Analysis

Authors: Giovanni Buzzega, Alessio Conte, Veronica Guerrini, Giulia Punzi, Giovanna Rosone, and Lorenzo Tattini

Published in: OASIcs, Volume 132, From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday (2025)

Abstract
Compact indices are a fundamental tool in string analysis, even more so in bioinformatics, where genomic sequences can reach billions in length. This paper presents some recent results in which Roberto Grossi has been involved, showing how some of these indices do more than just efficiently represent data, but rather are able to bring out salient information within it, which can be exploited for their downstream analysis. Specifically, we first review a recently-introduced method [Guerrini et al., 2023] that employs the Burrows-Wheeler Transform to build reasonably accurate phylogenetic trees in an assembly-free scenario. We then describe a recent practical tool [Buzzega et al., 2025] for indexing Maximal Common Subsequences between strings, which can enable analysis of genomic sequence similarity. Experimentally, we show that the results produced by the one index are consistent with the expectations about the results of the other index.
Cite as

Giovanni Buzzega, Alessio Conte, Veronica Guerrini, Giulia Punzi, Giovanna Rosone, and Lorenzo Tattini. Subsequence-Based Indices for Genome Sequence Analysis. In From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday. Open Access Series in Informatics (OASIcs), Volume 132, pp. 20:1-20:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{buzzega_et_al:OASIcs.Grossi.20,
  author =	{Buzzega, Giovanni and Conte, Alessio and Guerrini, Veronica and Punzi, Giulia and Rosone, Giovanna and Tattini, Lorenzo},
  title =	{{Subsequence-Based Indices for Genome Sequence Analysis}},
  booktitle =	{From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday},
  pages =	{20:1--20:21},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-391-1},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{132},
  editor =	{Conte, Alessio and Marino, Andrea and Rosone, Giovanna and Vitter, Jeffrey Scott},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.Grossi.20},
  URN =		{urn:nbn:de:0030-drops-238199},
  doi =		{10.4230/OASIcs.Grossi.20},
  annote =	{Keywords: String Indices, Burrows-Wheeler Transform, Maximal Common Subsequences, Sequence Analysis, Phylogeny}
}
Document
Track A: Algorithms, Complexity and Games
DOI: 10.4230/LIPIcs.ICALP.2025.117
Incremental Approximate Single-Source Shortest Paths with Predictions

Authors: Samuel McCauley, Benjamin Moseley, Aidin Niaparast, Helia Niaparast, and Shikha Singh

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

Abstract
The algorithms-with-predictions framework has been used extensively to develop online algorithms with improved beyond-worst-case competitive ratios. Recently, there is growing interest in leveraging predictions for designing data structures with improved beyond-worst-case running times. In this paper, we study the fundamental data structure problem of maintaining approximate shortest paths in incremental graphs in the algorithms-with-predictions model. Given a sequence σ of edges that are inserted one at a time, the goal is to maintain approximate shortest paths from the source to each vertex in the graph at each time step. Before any edges arrive, the data structure is given a prediction of the online edge sequence σ̂ which is used to "warm start" its state. As our main result, we design a learned algorithm that maintains (1+ε)-approximate single-source shortest paths, which runs in Õ(m η log W/ε) time, where W is the weight of the heaviest edge and η is the prediction error. We show these techniques immediately extend to the all-pairs shortest-path setting as well. Our algorithms are consistent (performing nearly as fast as the offline algorithm) when predictions are nearly perfect, have a smooth degradation in performance with respect to the prediction error and, in the worst case, match the best offline algorithm up to logarithmic factors. That is, the algorithms are "ideal" in the algorithms-with-predictions model. As a building block, we study the offline incremental approximate single-source shortest-path (SSSP) problem. In the offline incremental SSSP problem, the edge sequence σ is known a priori and the goal is to construct a data structure that can efficiently return the length of the shortest paths in the intermediate graph G_t consisting of the first t edges, for all t. Note that the offline incremental problem is defined in the worst-case setting (without predictions) and is of independent interest.
Cite as

Samuel McCauley, Benjamin Moseley, Aidin Niaparast, Helia Niaparast, and Shikha Singh. Incremental Approximate Single-Source Shortest Paths with Predictions. In 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 334, pp. 117:1-117:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{mccauley_et_al:LIPIcs.ICALP.2025.117,
  author =	{McCauley, Samuel and Moseley, Benjamin and Niaparast, Aidin and Niaparast, Helia and Singh, Shikha},
  title =	{{Incremental Approximate Single-Source Shortest Paths with Predictions}},
  booktitle =	{52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)},
  pages =	{117:1--117:20},
  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.2025.117},
  URN =		{urn:nbn:de:0030-drops-234946},
  doi =		{10.4230/LIPIcs.ICALP.2025.117},
  annote =	{Keywords: Algorithms with Predictions, Shortest Paths, Approximation Algorithms, Dynamic Graph Algorithms}
}
Document
DOI: 10.4230/LIPIcs.ITCS.2025.96
Formulations and Constructions of Remote State Preparation with Verifiability, with Applications

Authors: Jiayu Zhang

Published in: LIPIcs, Volume 325, 16th Innovations in Theoretical Computer Science Conference (ITCS 2025)

Abstract
Remote state preparation with verifiability (RSPV) is an important quantum cryptographic primitive [Alexandru Gheorghiu and Thomas Vidick, 2019; Jiayu Zhang, 2022]. In this primitive, a client would like to prepare a quantum state (sampled or chosen from a state family) on the server side, such that ideally the client knows its full description, while the server holds and only holds the state itself. In this work we make several contributions on its formulations, constructions and applications. In more detail: - We first work on the definitions and abstract properties of the RSPV problem. We select and compare different variants of definitions [Bennett et al., 2001; Alexandru Gheorghiu and Thomas Vidick, 2019; Jiayu Zhang, 2022; Alexandru Gheorghiu et al., 2022], and study their basic properties (like composability and amplification). - We also study a closely related question of how to certify the server’s operations (instead of solely the states). We introduce a new notion named remote operator application with verifiability (ROAV). We compare this notion with related existing definitions [Summers and Werner, 1987; Dominic Mayers and Andrew Chi-Chih Yao, 2004; Zhengfeng Ji et al., 2021; Tony Metger and Thomas Vidick, 2021; Anand Natarajan and Tina Zhang, 2023], study its abstract properties and leave its concrete constructions for further works. - Building on the abstract properties and existing results [Zvika Brakerski et al., 2023], we construct a series of new RSPV protocols. Our constructions not only simplify existing results [Alexandru Gheorghiu and Thomas Vidick, 2019] but also cover new state families, for example, states in the form of 1/√2 (|0⟩ + |x_0⟩ + |1⟩ |x_1⟩). All these constructions rely only on the existence of weak NTCF [Zvika Brakerski et al., 2020; Navid Alamati et al., 2022], without additional requirements like the adaptive hardcore bit property [Zvika Brakerski et al., 2018; Navid Alamati et al., 2022]. - As a further application, we show that the classical verification of quantum computations (CVQC) problem [Dorit Aharonov et al., 2010; Urmila Mahadev, 2018] could be constructed from assumptions on group actions [Navid Alamati et al., 2020]. This is achieved by combining our results on RSPV with group-action-based instantiation of weak NTCF [Navid Alamati et al., 2022], and then with the quantum-gadget-assisted quantum verification protocol [Ferracin et al., 2018].
Cite as

Jiayu Zhang. Formulations and Constructions of Remote State Preparation with Verifiability, with Applications. In 16th Innovations in Theoretical Computer Science Conference (ITCS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 325, pp. 96:1-96:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{zhang:LIPIcs.ITCS.2025.96,
  author =	{Zhang, Jiayu},
  title =	{{Formulations and Constructions of Remote State Preparation with Verifiability, with Applications}},
  booktitle =	{16th Innovations in Theoretical Computer Science Conference (ITCS 2025)},
  pages =	{96:1--96:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-361-4},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{325},
  editor =	{Meka, Raghu},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITCS.2025.96},
  URN =		{urn:nbn:de:0030-drops-227245},
  doi =		{10.4230/LIPIcs.ITCS.2025.96},
  annote =	{Keywords: Quantum Cryptography, Remote State Preparation, Self-testing, Verification of Quantum Computations}
}
Document
DOI: 10.4230/LIPIcs.OPODIS.2024.24
Hash & Adjust: Competitive Demand-Aware Consistent Hashing

Authors: Arash Pourdamghani, Chen Avin, Robert Sama, Maryam Shiran, and Stefan Schmid

Published in: LIPIcs, Volume 324, 28th International Conference on Principles of Distributed Systems (OPODIS 2024)

Abstract
Distributed systems often serve dynamic workloads and resource demands evolve over time. Such a temporal behavior stands in contrast to the static and demand-oblivious nature of most data structures used by these systems. In this paper, we are particularly interested in consistent hashing, a fundamental building block in many large distributed systems. Our work is motivated by the hypothesis that a more adaptive approach to consistent hashing can leverage structure in the demand, and hence improve storage utilization and reduce access time. We initiate the study of demand-aware consistent hashing. Our main contribution is H&A, a constant-competitive online algorithm (i.e., it comes with provable performance guarantees over time). H&A is demand-aware and optimizes its internal structure to enable faster access times, while offering a high utilization of storage. We further evaluate H&A empirically.
Cite as

Arash Pourdamghani, Chen Avin, Robert Sama, Maryam Shiran, and Stefan Schmid. Hash & Adjust: Competitive Demand-Aware Consistent Hashing. In 28th International Conference on Principles of Distributed Systems (OPODIS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 324, pp. 24:1-24:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{pourdamghani_et_al:LIPIcs.OPODIS.2024.24,
  author =	{Pourdamghani, Arash and Avin, Chen and Sama, Robert and Shiran, Maryam and Schmid, Stefan},
  title =	{{Hash \& Adjust: Competitive Demand-Aware Consistent Hashing}},
  booktitle =	{28th International Conference on Principles of Distributed Systems (OPODIS 2024)},
  pages =	{24:1--24:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-360-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{324},
  editor =	{Bonomi, Silvia and Galletta, Letterio and Rivi\`{e}re, Etienne and Schiavoni, Valerio},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.OPODIS.2024.24},
  URN =		{urn:nbn:de:0030-drops-225607},
  doi =		{10.4230/LIPIcs.OPODIS.2024.24},
  annote =	{Keywords: Consistent hashing, demand-awareness, online algorithms}
}
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