27 Search Results for "Jones, Christopher B."

Document
DOI: 10.4230/LIPIcs.TIME.2025.13
Temporal Ensemble Logic for Integrative Representation of the Entirety of Clinical Trials

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

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

Abstract
Clinical trials are typically specified with protocols that define eligibility criteria, treatment regimens, follow-up schedules, and outcome assessments. Temporality is a hallmark of all clinical trials, reflected within and across trial components, with complex dependencies unfolding across multiple time points. Despite their importance, clinical trial protocols are described in free-text format, limiting their semantic precision and the ability to support automated reasoning, leverage data across studies and sites, or simulate trial execution under varying assumptions using Real-World Data. This paper introduces a formalized representation of clinical trials using Temporal Ensemble Logic (TEL). TEL incorporates metricized modal operators, such as "always until t" (□_t) and "possibly until t" (◇_t), where t is a time-length parameter, to offer a logical framework for capturing phenotypes in biomedicine. TEL is more expressive in syntax than classical linear temporal logic (LTL) while maintaining the simplicity of semantic structures. The attributes of TEL are exploited in this paper to formally represent not only individual clinical trial components, but also the timing and sequential dependencies of these components as a whole. Modeling strategies and demonstration case studies are provided to show that TEL can represent the entirety of clinical trials, whereby providing a formal logical framework that can be used to represent the intricate temporal dependencies in trial structure specification. Since clinical trials are a cornerstone of evidence-based medicine, serving as the scientific basis for evaluating the safety, efficacy, and comparative effectiveness of therapeutic interventions, results reported here can serve as a stepping stone that leads to scalable, consistent, and reproducible representation and simulation of clinical trials across all disease domains.
Cite as

Xiaojin Li, Yan Huang, Rashmie Abeysinghe, Zenan Sun, Hongyu Chen, Pengze Li, Xing He, Shiqiang Tao, Cui Tao, Jiang Bian, Licong Cui, and Guo-Qiang Zhang. Temporal Ensemble Logic for Integrative Representation of the Entirety of Clinical Trials. In 32nd International Symposium on Temporal Representation and Reasoning (TIME 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 355, pp. 13:1-13:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{li_et_al:LIPIcs.TIME.2025.13,
  author =	{Li, Xiaojin and Huang, Yan and Abeysinghe, Rashmie and Sun, Zenan and Chen, Hongyu and Li, Pengze and He, Xing and Tao, Shiqiang and Tao, Cui and Bian, Jiang and Cui, Licong and Zhang, Guo-Qiang},
  title =	{{Temporal Ensemble Logic for Integrative Representation of the Entirety of Clinical Trials}},
  booktitle =	{32nd International Symposium on Temporal Representation and Reasoning (TIME 2025)},
  pages =	{13:1--13:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-401-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{355},
  editor =	{Vidal, Thierry and Wa{\l}\k{e}ga, Przemys{\l}aw Andrzej},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.TIME.2025.13},
  URN =		{urn:nbn:de:0030-drops-244595},
  doi =		{10.4230/LIPIcs.TIME.2025.13},
  annote =	{Keywords: Temporal ensemble logic, Clinical trials, Logic-based modeling}
}
Document
DOI: 10.4230/LIPIcs.ESA.2025.106
On Estimating the Quantum 𝓁_α Distance

Authors: Yupan Liu and Qisheng Wang

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

Abstract
We study the computational complexity of estimating the quantum 𝓁_α distance T_α(ρ₀,ρ₁), defined via the Schatten α-norm ‖A‖_α := tr(|A|^α)^{1/α}, given poly(n)-size state-preparation circuits of n-qubit quantum states ρ₀ and ρ₁. This quantity serves as a lower bound on the trace distance for α > 1. For any constant α > 1, we develop an efficient rank-independent quantum estimator for T_α(ρ₀,ρ₁) with time complexity poly(n), achieving an exponential speedup over the prior best results of exp(n) due to Wang, Guan, Liu, Zhang, and Ying (IEEE Trans. Inf. Theory 2024). Our improvement leverages efficiently computable uniform polynomial approximations of signed positive power functions within quantum singular value transformation, thereby eliminating the dependence on the rank of the states. Our quantum algorithm reveals a dichotomy in the computational complexity of the Quantum State Distinguishability Problem with Schatten α-norm (QSD_α), which involves deciding whether T_α(ρ₀,ρ₁) is at least 2/5 or at most 1/5. This dichotomy arises between the cases of constant α > 1 and α = 1: - For any 1+Ω(1) ≤ α ≤ O(1), QSD_α is BQP-complete. - For any 1 ≤ α ≤ 1+1/n, QSD_α is QSZK-complete, implying that no efficient quantum estimator for T_α(ρ₀,ρ₁) exists unless BQP = QSZK. The hardness results follow from reductions based on new rank-dependent inequalities for the quantum 𝓁_α distance with 1 ≤ α ≤ ∞, which are of independent interest.
Cite as

Yupan Liu and Qisheng Wang. On Estimating the Quantum 𝓁_α Distance. In 33rd Annual European Symposium on Algorithms (ESA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 351, pp. 106:1-106:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{liu_et_al:LIPIcs.ESA.2025.106,
  author =	{Liu, Yupan and Wang, Qisheng},
  title =	{{On Estimating the Quantum 𝓁\underline\alpha Distance}},
  booktitle =	{33rd Annual European Symposium on Algorithms (ESA 2025)},
  pages =	{106:1--106:19},
  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.2025.106},
  URN =		{urn:nbn:de:0030-drops-245758},
  doi =		{10.4230/LIPIcs.ESA.2025.106},
  annote =	{Keywords: quantum algorithms, quantum state testing, trace distance, Schatten norm}
}
Document
DOI: 10.4230/LIPIcs.ESA.2025.37
Hardness of Computation of Quantum Invariants on 3-Manifolds with Restricted Topology

Authors: Henrique Ennes and Clément Maria

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

Abstract
Quantum invariants in low-dimensional topology offer a wide variety of valuable invariants about knots and 3-manifolds, presented by explicit formulas that are readily computable. Their computational complexity has been actively studied and is tightly connected to topological quantum computing. In this article, we prove that for any 3-manifold quantum invariant in the Reshetikhin-Turaev model, there is a deterministic polynomial time algorithm that, given as input an arbitrary closed 3-manifold M, outputs a closed 3-manifold M' with the same quantum invariant, such that M' is hyperbolic, contains no low genus embedded incompressible surface, and is presented by a strongly irreducible Heegaard diagram. Our construction relies on properties of Heegaard splittings and the Hempel distance. At the level of computational complexity, this proves that the hardness of computing a given quantum invariant of 3-manifolds is preserved even when severely restricting the topology and the combinatorics of the input. This positively answers a question raised by Samperton [Samperton, 2023].
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Henrique Ennes and Clément Maria. Hardness of Computation of Quantum Invariants on 3-Manifolds with Restricted Topology. In 33rd Annual European Symposium on Algorithms (ESA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 351, pp. 37:1-37:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{ennes_et_al:LIPIcs.ESA.2025.37,
  author =	{Ennes, Henrique and Maria, Cl\'{e}ment},
  title =	{{Hardness of Computation of Quantum Invariants on 3-Manifolds with Restricted Topology}},
  booktitle =	{33rd Annual European Symposium on Algorithms (ESA 2025)},
  pages =	{37:1--37:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-395-9},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{351},
  editor =	{Benoit, Anne and Kaplan, Haim and Wild, Sebastian and Herman, Grzegorz},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2025.37},
  URN =		{urn:nbn:de:0030-drops-245057},
  doi =		{10.4230/LIPIcs.ESA.2025.37},
  annote =	{Keywords: 3-manifold, Heegaard splitting, Hempel distance, Quantum invariant, polynomial time reduction}
}
Document
DOI: 10.4230/OASIcs.SpaceCHI.2025.15
Integrating Human-In-The-Loop AI to Tackle Space Communication Delay Challenges

Authors: Nikos Mavrakis, Effie Lai-Chong Law, and Hubert P. H. Shum

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

Abstract
Deep space missions face significant communication delays that disrupt both operational workflows and psychological support for crew members. Unlike low Earth orbit operations, delays ranging from several minutes to nearly an hour make real-time communication with mission control infeasible, forcing crews to act with greater independence under uncertain conditions. This position paper examines how human-in-the-loop AI, digital twins, and edge AI can be integrated to mitigate these delays while maintaining astronaut autonomy and engagement. We argue that human-in-the-loop AI enables decision-making processes that are responsive to local context while remaining adaptable to changing mission demands. Digital twins offer real-time simulation and predictive modelling capabilities, allowing astronauts to explore options and troubleshoot without waiting for ground input. Edge AI brings computation closer to data sources, enabling low-latency inference onboard spacecraft for time-critical decisions. These ideas are explored through two use cases: using deepfakes to support emotionally resonant communication with loved ones, and applying visual-language models for onboard fault diagnosis and adaptive task replanning. We conclude with reflections on system design challenges under constrained and high-stakes conditions.
Cite as

Nikos Mavrakis, Effie Lai-Chong Law, and Hubert P. H. Shum. Integrating Human-In-The-Loop AI to Tackle Space Communication Delay Challenges. In Advancing Human-Computer Interaction for Space Exploration (SpaceCHI 2025). Open Access Series in Informatics (OASIcs), Volume 130, pp. 15:1-15:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{mavrakis_et_al:OASIcs.SpaceCHI.2025.15,
  author =	{Mavrakis, Nikos and Law, Effie Lai-Chong and Shum, Hubert P. H.},
  title =	{{Integrating Human-In-The-Loop AI to Tackle Space Communication Delay Challenges}},
  booktitle =	{Advancing Human-Computer Interaction for Space Exploration (SpaceCHI 2025)},
  pages =	{15:1--15:16},
  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.2025.15},
  URN =		{urn:nbn:de:0030-drops-240051},
  doi =		{10.4230/OASIcs.SpaceCHI.2025.15},
  annote =	{Keywords: Human-in-the-loop AI, communication delays, human spaceflight}
}
Document
DOI: 10.4230/OASIcs.SpaceCHI.2025.26
Movement in Low Gravity (MoLo) – LUNA: Biomechanical Modelling to Mitigate Lunar Surface Operation Risks

Authors: David Andrew Green

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

Abstract
The Artemis programme seeks to develop and test concepts, hardware and approaches to support long term habitation of the Lunar surface, and future missions to Mars. In preparation for the Artemis missions determination of tasks to be performed, the functional requirements of such tasks and as mission duration extends whether physiological deconditioning becomes functionally significant, compromising the crew member’s ability to perform critical tasks on the surface, and/or upon return to earth [MoLo-LUNA – leveraging the Molo programme (and several other activities) - could become a key supporting activity for LUNA incl. validation of the Puppeteer offloading system itself via creation of a complementary MoLo-LUNA-LAB. Furthermore, the MoLo-LUNA programme could become a key facilitator of simulator suit instrumentation/definition, broader astronaut training activities and mission architecture development – including Artemis mission simulations. By employing a Puppeteer system external to the LUNA chamber hall it will optimise utilisation and cost-effectiveness of LUNA, and as such represents a critical service to future LUNA stakeholders. Furthermore, MoLo-LUNA would generate a unique data set that can be leveraged to predict de-conditioning on the Lunar surface - and thereby optimise functionality, and minimise mission risk – including informing the need for, and prescription of exercise countermeasures on the Lunar Surface and in transit. Thus, MoLo-LUNA offers a unique opportunity to place LUNA, and ESA as a key ongoing provider of evidence to define, optimise and support crew Artemis surface missions.
Cite as

David Andrew Green. Movement in Low Gravity (MoLo) – LUNA: Biomechanical Modelling to Mitigate Lunar Surface Operation Risks. In Advancing Human-Computer Interaction for Space Exploration (SpaceCHI 2025). Open Access Series in Informatics (OASIcs), Volume 130, pp. 26:1-26:11, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{green:OASIcs.SpaceCHI.2025.26,
  author =	{Green, David Andrew},
  title =	{{Movement in Low Gravity (MoLo) – LUNA: Biomechanical Modelling to Mitigate Lunar Surface Operation Risks}},
  booktitle =	{Advancing Human-Computer Interaction for Space Exploration (SpaceCHI 2025)},
  pages =	{26:1--26:11},
  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.2025.26},
  URN =		{urn:nbn:de:0030-drops-240166},
  doi =		{10.4230/OASIcs.SpaceCHI.2025.26},
  annote =	{Keywords: Locomotion, hypogravity, modelling, Lunar}
}
Document
DOI: 10.4230/LIPIcs.WADS.2025.32
Fantastic Flips and Where to Find Them: A General Framework for Parameterized Local Search on Partitioning Problems

Authors: Niels Grüttemeier, Nils Morawietz, and Frank Sommer

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

Abstract
Parameterized local search combines classic local search heuristics with the paradigm of parameterized algorithmics. While most local search algorithms aim to improve given solutions by performing one single operation on a given solution, the parameterized approach aims to improve a solution by performing k simultaneous operations. Herein, k is a parameter called search radius for which the value can be chosen by a user. One major goal in the field of parameterized local search is to outline the trade-off between the size of k and the running time of the local search step. In this work, we introduce an abstract framework that generalizes natural parameterized local search approaches for a large class of partitioning problems: Given n items that are partitioned into b bins and a target function that evaluates the quality of the current partition, one asks whether it is possible to improve the solution by removing up to k items from their current bins and reassigning them to other bins. Among others, our framework applies for the local search versions of problems like Cluster Editing, Vector Bin Packing, and Nash Social Welfare. Motivated by a real-world application of the problem Vector Bin Packing, we introduce a parameter called number of types τ ≤ n and show that all problems fitting in our framework can be solved in τ^k ⋅ 2^𝒪(k) ⋅ |I|^𝒪(1) time, where |I| denotes the total input size. In case of Cluster Editing, the parameter τ generalizes the well-known parameter neighborhood diversity of the input graph. We complement these algorithms by showing that for all considered problems, an algorithm significantly improving over our algorithm with running time τ^k ⋅ 2^𝒪(k) ⋅ |I|^𝒪(1) would contradict the Exponential Time Hypothesis. Additionally, we show that even on very restricted instances, all considered problems are W[1]-hard when parameterized by the search radius k alone. In case of the local search version of Vector Bin Packing, we provide an even stronger W[1]-hardness result.
Cite as

Niels Grüttemeier, Nils Morawietz, and Frank Sommer. Fantastic Flips and Where to Find Them: A General Framework for Parameterized Local Search on Partitioning Problems. In 19th International Symposium on Algorithms and Data Structures (WADS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 349, pp. 32:1-32:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{gruttemeier_et_al:LIPIcs.WADS.2025.32,
  author =	{Gr\"{u}ttemeier, Niels and Morawietz, Nils and Sommer, Frank},
  title =	{{Fantastic Flips and Where to Find Them: A General Framework for Parameterized Local Search on Partitioning Problems}},
  booktitle =	{19th International Symposium on Algorithms and Data Structures (WADS 2025)},
  pages =	{32:1--32:20},
  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.2025.32},
  URN =		{urn:nbn:de:0030-drops-242631},
  doi =		{10.4230/LIPIcs.WADS.2025.32},
  annote =	{Keywords: Flip-Neighborhood, Cluster Editing, Vector Bin Packing, Vertex Cover, NP-hard problem, Max c-Cut}
}
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.GIScience.2025.12
Large Multi-Modal Model Cartographic Map Comprehension for Textual Locality Georeferencing

Authors: Kalana Wijegunarathna, Kristin Stock, and Christopher B. Jones

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

Abstract
Millions of biological sample records collected in the last few centuries archived in natural history collections are un-georeferenced. Georeferencing complex locality descriptions associated with these collection samples is a highly labour-intensive task collection agencies struggle with. None of the existing automated methods exploit maps that are an essential tool for georeferencing complex relations. We present preliminary experiments and results of a novel method that exploits multi-modal capabilities of recent Large Multi-Modal Models (LMM). This method enables the model to visually contextualize spatial relations it reads in the locality description. We use a grid-based approach to adapt these auto-regressive models for this task in a zero-shot setting. Our experiments conducted on a small manually annotated dataset show impressive results for our approach (∼1 km Average distance error) compared to uni-modal georeferencing with Large Language Models and existing georeferencing tools. The paper also discusses the findings of the experiments in light of an LMM’s ability to comprehend fine-grained maps. Motivated by these results, a practical framework is proposed to integrate this method into a georeferencing workflow.
Cite as

Kalana Wijegunarathna, Kristin Stock, and Christopher B. Jones. Large Multi-Modal Model Cartographic Map Comprehension for Textual Locality Georeferencing. In 13th International Conference on Geographic Information Science (GIScience 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 346, pp. 12:1-12:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{wijegunarathna_et_al:LIPIcs.GIScience.2025.12,
  author =	{Wijegunarathna, Kalana and Stock, Kristin and Jones, Christopher B.},
  title =	{{Large Multi-Modal Model Cartographic Map Comprehension for Textual Locality Georeferencing}},
  booktitle =	{13th International Conference on Geographic Information Science (GIScience 2025)},
  pages =	{12:1--12:19},
  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.2025.12},
  URN =		{urn:nbn:de:0030-drops-238412},
  doi =		{10.4230/LIPIcs.GIScience.2025.12},
  annote =	{Keywords: Large Multi-Modal Models, Large Language Models, LLM, Georeferencing, Natural History collections}
}
Document
DOI: 10.4230/LIPIcs.GIScience.2025.3
Enriching Location Representation with Detailed Semantic Information

Authors: Junyuan Liu, Xinglei Wang, and Tao Cheng

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

Abstract
Spatial representations that capture both structural and semantic characteristics of urban environments are essential for urban modeling. Traditional spatial embeddings often prioritize spatial proximity while underutilizing fine-grained contextual information from places. To address this limitation, we introduce CaLLiPer+, an extension of the CaLLiPer model that systematically integrates Point-of-Interest (POI) names alongside categorical labels within a multimodal contrastive learning framework. We evaluate its effectiveness on two downstream tasks - land use classification and socioeconomic status distribution mapping - demonstrating consistent performance gains of 4% to 11% over baseline methods. Additionally, we show that incorporating POI names enhances location retrieval, enabling models to capture complex urban concepts with greater precision. Ablation studies further reveal the complementary role of POI names and the advantages of leveraging pretrained text encoders for spatial representations. Overall, our findings highlight the potential of integrating fine-grained semantic attributes and multimodal learning techniques to advance the development of urban foundation models.
Cite as

Junyuan Liu, Xinglei Wang, and Tao Cheng. Enriching Location Representation with Detailed Semantic Information. In 13th International Conference on Geographic Information Science (GIScience 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 346, pp. 3:1-3:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{liu_et_al:LIPIcs.GIScience.2025.3,
  author =	{Liu, Junyuan and Wang, Xinglei and Cheng, Tao},
  title =	{{Enriching Location Representation with Detailed Semantic Information}},
  booktitle =	{13th International Conference on Geographic Information Science (GIScience 2025)},
  pages =	{3:1--3:15},
  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.2025.3},
  URN =		{urn:nbn:de:0030-drops-238322},
  doi =		{10.4230/LIPIcs.GIScience.2025.3},
  annote =	{Keywords: Location Embedding, Contrastive Learning, Pretrained Model}
}
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
Short Paper
DOI: 10.4230/LIPIcs.CP.2025.43
Scheduling Telescope Observations for the European Southern Observatory (Short Paper)

Authors: Michael Prümm, Peter Nightingale, and Felix Ulrich-Oltean

Published in: LIPIcs, Volume 340, 31st International Conference on Principles and Practice of Constraint Programming (CP 2025)

Abstract
The European Southern Observatory (ESO) provides state-of-the-art large telescope facilities at three sites in Chile, supported by 16 European member states. Astronomers submit proposals for sets of observations which are reviewed and ranked based on scientific merit, then a schedule is constructed respecting the ranking and aiming to make the fullest use of the various telescopes and numerous instruments. Currently a schedule covers six months, but in the near future ESO will switch to annual schedules. Here we examine the most challenging scheduling problem encountered by ESO: scheduling the operations of the Very Large Telescope Interferometer (VLTI) on Paranal, Chile. Tasks to be scheduled include observations performed by ESO staff, "visitor mode" periods where astronomers visit the site to use the telescopes, various maintenance tasks, and reconfiguration tasks taking multiple days. Typically a VLTI six-month schedule would contain approximately 450 activities. We explore global constraint models and a SAT encoding of the problem.
Cite as

Michael Prümm, Peter Nightingale, and Felix Ulrich-Oltean. Scheduling Telescope Observations for the European Southern Observatory (Short Paper). In 31st International Conference on Principles and Practice of Constraint Programming (CP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 340, pp. 43:1-43:10, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{prumm_et_al:LIPIcs.CP.2025.43,
  author =	{Pr\"{u}mm, Michael and Nightingale, Peter and Ulrich-Oltean, Felix},
  title =	{{Scheduling Telescope Observations for the European Southern Observatory}},
  booktitle =	{31st International Conference on Principles and Practice of Constraint Programming (CP 2025)},
  pages =	{43:1--43:10},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-380-5},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{340},
  editor =	{de la Banda, Maria Garcia},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CP.2025.43},
  URN =		{urn:nbn:de:0030-drops-239041},
  doi =		{10.4230/LIPIcs.CP.2025.43},
  annote =	{Keywords: Modelling, Constraint Programming, Scheduling, SAT, Global Constraints}
}
Document
DOI: 10.4230/LIPIcs.ECRTS.2025.14
Task-To-Processor Assignment for Real-Time Mixed-Critical Networked Systems Using Inductive Logic Programming

Authors: Marcus Gualtieri, Christian Juette, and Dakshina Dasari

Published in: LIPIcs, Volume 335, 37th Euromicro Conference on Real-Time Systems (ECRTS 2025)

Abstract
Task-to-processor assignment is an essential aspect of configuring real-time, distributed systems, since an improper assignment can adversely affect latency. Model-based, heuristic, and data-driven approaches have been proposed to solve the task-to-processor assignment problem. However, model-based and heuristic approaches require revision if the system changes, and data-driven approaches require training on a lot of data and setting nonintuitive hyper-parameters. We explore a hybrid approach which takes both a system description and data: we use inductive logic programming in an active learning algorithm to search for assignments which satisfy a real-time requirement. By using both domain knowledge and data, the system finds solutions quickly, and changes are not required when using the tool on different systems. Furthermore, the output is a human-readable description of a set of predicted satisfactory assignments. Readable solution sets are useful for analyzing the system, since we can easily compare solution sets across different setups. We evaluate our approach on real systems with mixed-critical network flows. We show that task-to-processor assignment can significantly influence latency by comparing optimal fixed assignments to the default Linux scheduler. We show that our approach finds assignments that are within 10% of optimal with up to 10× fewer system tests, compared to random search. Our algorithm also performs favorably to load balancing and neural network baselines.
Cite as

Marcus Gualtieri, Christian Juette, and Dakshina Dasari. Task-To-Processor Assignment for Real-Time Mixed-Critical Networked Systems Using Inductive Logic Programming. In 37th Euromicro Conference on Real-Time Systems (ECRTS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 335, pp. 14:1-14:26, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{gualtieri_et_al:LIPIcs.ECRTS.2025.14,
  author =	{Gualtieri, Marcus and Juette, Christian and Dasari, Dakshina},
  title =	{{Task-To-Processor Assignment for Real-Time Mixed-Critical Networked Systems Using Inductive Logic Programming}},
  booktitle =	{37th Euromicro Conference on Real-Time Systems (ECRTS 2025)},
  pages =	{14:1--14:26},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-377-5},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{335},
  editor =	{Mancuso, Renato},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECRTS.2025.14},
  URN =		{urn:nbn:de:0030-drops-235925},
  doi =		{10.4230/LIPIcs.ECRTS.2025.14},
  annote =	{Keywords: Real-Time Distributed Systems, Auto-Configuration, Task-to-Processor Mapping, Inductive Logic Programming, Active Learning}
}
Document
DOI: 10.4230/LIPIcs.ECRTS.2025.17
Theoretical Foundations of Utility Accrual for Real-Time Systems

Authors: Jian-Jia Chen, Junjie Shi, Mario Günzel, Georg von der Brüggen, Kuan-Hsun Chen, and Peter Bella

Published in: LIPIcs, Volume 335, 37th Euromicro Conference on Real-Time Systems (ECRTS 2025)

Abstract
Providing guaranteed quantification of properties of soft real-time systems is important in practice to ensure that a system performs correctly most of the time. We study utility accrual for real-time systems, in which the utility of a real-time job is defined as a time utility function with respect to its response time. Essentially, we answer the fundamental questions: Does the utility accrual of a periodic real-time task in the long run converge to a single value? If yes, to which value? We first show that concrete problem instances exist where evaluating the utility accrual by simulating the scheduling algorithm or conducting scheduling experiments in a long run is erroneous. Afterwards, we show how to construct a Markov chain to model the interactions between the scheduling policy, the probabilistic workload of a periodic real-time task, the service provided by the system to serve the task, and the effect on the utility accrual. For such a Markov chain, we also provide the theoretical fundamentals to determine whether the utility accrual converges in the long run and the derivation of the utility accrual if it converges.
Cite as

Jian-Jia Chen, Junjie Shi, Mario Günzel, Georg von der Brüggen, Kuan-Hsun Chen, and Peter Bella. Theoretical Foundations of Utility Accrual for Real-Time Systems. In 37th Euromicro Conference on Real-Time Systems (ECRTS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 335, pp. 17:1-17:26, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{chen_et_al:LIPIcs.ECRTS.2025.17,
  author =	{Chen, Jian-Jia and Shi, Junjie and G\"{u}nzel, Mario and von der Br\"{u}ggen, Georg and Chen, Kuan-Hsun and Bella, Peter},
  title =	{{Theoretical Foundations of Utility Accrual for Real-Time Systems}},
  booktitle =	{37th Euromicro Conference on Real-Time Systems (ECRTS 2025)},
  pages =	{17:1--17:26},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-377-5},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{335},
  editor =	{Mancuso, Renato},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECRTS.2025.17},
  URN =		{urn:nbn:de:0030-drops-235950},
  doi =		{10.4230/LIPIcs.ECRTS.2025.17},
  annote =	{Keywords: Soft Real-Time Systems, Utility Accrual, Markov Chains, Dismiss Points}
}
Document
Track A: Algorithms, Complexity and Games
DOI: 10.4230/LIPIcs.ICALP.2025.29
Guessing Efficiently for Constrained Subspace Approximation

Authors: Aditya Bhaskara, Sepideh Mahabadi, Madhusudhan Reddy Pittu, Ali Vakilian, and David P. Woodruff

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

Abstract
In this paper we study constrained subspace approximation problem. Given a set of n points {a₁,…,a_n} in ℝ^d, the goal of the subspace approximation problem is to find a k dimensional subspace that best approximates the input points. More precisely, for a given p ≥ 1, we aim to minimize the pth power of the 𝓁_p norm of the error vector (‖a₁-Pa₁‖,…,‖a_n-Pa_n‖), where P denotes the projection matrix onto the subspace and the norms are Euclidean. In constrained subspace approximation (CSA), we additionally have constraints on the projection matrix P. In its most general form, we require P to belong to a given subset 𝒮 that is described explicitly or implicitly. We introduce a general framework for constrained subspace approximation. Our approach, that we term coreset-guess-solve, yields either (1+ε)-multiplicative or ε-additive approximations for a variety of constraints. We show that it provides new algorithms for partition-constrained subspace approximation with applications to fair subspace approximation, k-means clustering, and projected non-negative matrix factorization, among others. Specifically, while we reconstruct the best known bounds for k-means clustering in Euclidean spaces, we improve the known results for the remainder of the problems.
Cite as

Aditya Bhaskara, Sepideh Mahabadi, Madhusudhan Reddy Pittu, Ali Vakilian, and David P. Woodruff. Guessing Efficiently for Constrained Subspace Approximation. In 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 334, pp. 29:1-29:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{bhaskara_et_al:LIPIcs.ICALP.2025.29,
  author =	{Bhaskara, Aditya and Mahabadi, Sepideh and Pittu, Madhusudhan Reddy and Vakilian, Ali and Woodruff, David P.},
  title =	{{Guessing Efficiently for Constrained Subspace Approximation}},
  booktitle =	{52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)},
  pages =	{29:1--29:20},
  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.2025.29},
  URN =		{urn:nbn:de:0030-drops-234068},
  doi =		{10.4230/LIPIcs.ICALP.2025.29},
  annote =	{Keywords: parameterized complexity, low rank approximation, fairness, non-negative matrix factorization, clustering}
}
Document
Track A: Algorithms, Complexity and Games
DOI: 10.4230/LIPIcs.ICALP.2025.102
Fourier Analysis of Iterative Algorithms

Authors: Chris Jones and Lucas Pesenti

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

Abstract
We study a general class of nonlinear iterative algorithms which includes power iteration, belief propagation and approximate message passing, and many forms of gradient descent. When the input is a random matrix with i.i.d. entries, we use Boolean Fourier analysis to analyze these algorithms as low-degree polynomials in the entries of the input matrix. Each symmetrized Fourier character represents all monomials with a certain shape as specified by a small graph, which we call a Fourier diagram. We prove fundamental asymptotic properties of the Fourier diagrams: over the randomness of the input, all diagrams with cycles are negligible; the tree-shaped diagrams form a basis of asymptotically independent Gaussian vectors; and, when restricted to the trees, iterative algorithms exactly follow an idealized Gaussian dynamic. We use this to prove a state evolution formula, giving a "complete" asymptotic description of the algorithm’s trajectory. The restriction to tree-shaped monomials mirrors the assumption of the cavity method, a 40-year-old non-rigorous technique in statistical physics which has served as one of the most important techniques in the field. We demonstrate how to implement cavity method derivations by 1) restricting the iteration to its tree approximation, and 2) observing that heuristic cavity method-type arguments hold rigorously on the simplified iteration. Our proofs use combinatorial arguments similar to the trace method from random matrix theory. Finally, we push the diagram analysis to a number of iterations that scales with the dimension n of the input matrix, proving that the tree approximation still holds for a simple variant of power iteration all the way up to n^{Ω(1)} iterations.
Cite as

Chris Jones and Lucas Pesenti. Fourier Analysis of Iterative Algorithms. In 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 334, pp. 102:1-102:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{jones_et_al:LIPIcs.ICALP.2025.102,
  author =	{Jones, Chris and Pesenti, Lucas},
  title =	{{Fourier Analysis of Iterative Algorithms}},
  booktitle =	{52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)},
  pages =	{102:1--102:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-372-0},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{334},
  editor =	{Censor-Hillel, Keren and Grandoni, Fabrizio and Ouaknine, Jo\"{e}l and Puppis, Gabriele},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2025.102},
  URN =		{urn:nbn:de:0030-drops-234791},
  doi =		{10.4230/LIPIcs.ICALP.2025.102},
  annote =	{Keywords: Iterative Algorithms, Message-passing Algorithms, Random Matrix Theory}
}
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