26 Search Results for "Mitchell, Scott A."

Document
Research
DOI: 10.4230/TGDK.4.1.1
On the Computational Cost of Knowledge Graph Embeddings

Authors: Victor Charpenay, Mansour Zoubeirou A Mayaki, and Antoine Zimmermann

Published in: TGDK, Volume 4, Issue 1 (2026). Transactions on Graph Data and Knowledge, Volume 4, Issue 1

Abstract
Over a decade, numerous Knowledge Graph Embedding (KGE) models have been designed and evaluated on reference datasets, always with increasing performance. In this paper, we re-evaluate these models with respect to their computational efficiency during training, by estimating the computational cost of the procedure expressed in floating-point operations. We design a cost model based on analytical expressions and apply it on a collection of 20 KGE models, representative of the state-of-the-art. We show that dimensionality or parameter efficiency, used in the literature to compare models with each other, are not suitable to evaluate the true cost of models. Through fixed-budget experiments, a novel approach to evaluate KGE models based on cost estimates, we re-assess the relative performance of model families compared to the state-of-the-art. Bilinear models such as ComplEx underperform with a low computational budget while hyperbolic linear models appear to offer no particular benefit compared to simpler Euclidian models, especially the MuRE model. Neural models, such as ConvE or CompGCN, achieve reasonable performance in the literature but their high computational cost appears unnecessary when compared with other models. The trade-off between efficiency and expressivity of both linear and neural models is to be further explored.
Cite as

Victor Charpenay, Mansour Zoubeirou A Mayaki, and Antoine Zimmermann. On the Computational Cost of Knowledge Graph Embeddings. In Transactions on Graph Data and Knowledge (TGDK), Volume 4, Issue 1, pp. 1:1-1:30, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@Article{charpenay_et_al:TGDK.4.1.1,
  author =	{Charpenay, Victor and Zoubeirou A Mayaki, Mansour and Zimmermann, Antoine},
  title =	{{On the Computational Cost of Knowledge Graph Embeddings}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{1:1--1:30},
  ISSN =	{2942-7517},
  year =	{2026},
  volume =	{4},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.4.1.1},
  URN =		{urn:nbn:de:0030-drops-256863},
  doi =		{10.4230/TGDK.4.1.1},
  annote =	{Keywords: Knowledge Graph Embedding, Parameter Efficiency, Computational Budget, Green AI}
}
Document
DOI: 10.4230/LIPIcs.CSL.2026.26
ε-Distance via Lévy-Prokhorov Lifting

Authors: Josée Desharnais and Ana Sokolova

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

Abstract
The most studied and accepted pseudometric for probabilistic processes is one based on the Kantorovich distance between distributions. It comes with many theoretical and motivating results, in particular it is the fixpoint of a given functional and defines a functor on (complete) pseudometric spaces. It is also the foundation for a categorical lifting of pseudometrics. Other notions of behavioural pseudometrics have also been proposed, one of them (ε-distance) based on ε-bisimulation. ε-Distance has the advantages that it is intuitively easy to understand, it relates systems that are conceptually close (for example, an imperfect implementation is close to its specification), and it comes equipped with a natural notion of ε-coupling. Finally, this distance is easy to compute. We show that ε-distance is also the greatest fixpoint of a functional and provides a functor. The latter is obtained by replacing the Kantorovich distance in the lifting functor with the Lévy-Prokhorov distance. In addition, we show that ε-couplings and ε-bisimulations have an appealing coalgebraic characterization.
Cite as

Josée Desharnais and Ana Sokolova. ε-Distance via Lévy-Prokhorov Lifting. In 34th EACSL Annual Conference on Computer Science Logic (CSL 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 363, pp. 26:1-26:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{desharnais_et_al:LIPIcs.CSL.2026.26,
  author =	{Desharnais, Jos\'{e}e and Sokolova, Ana},
  title =	{{\epsilon-Distance via L\'{e}vy-Prokhorov Lifting}},
  booktitle =	{34th EACSL Annual Conference on Computer Science Logic (CSL 2026)},
  pages =	{26:1--26:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-411-6},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{363},
  editor =	{Guerrini, Stefano and K\"{o}nig, Barbara},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CSL.2026.26},
  URN =		{urn:nbn:de:0030-drops-254506},
  doi =		{10.4230/LIPIcs.CSL.2026.26},
  annote =	{Keywords: L\'{e}vy-Prokhorov metric, behavioural distance, epsilon-bisimulation, reactive probabilistic transition systems, discrete labelled Markov processes, coalgebraic epsilon-(bi)simulation}
}
Document
DOI: 10.4230/LIPIcs.ITCS.2026.52
Diffie-Hellman Key Exchange from Commutativity to Group Laws

Authors: Dung Hoang Duong, Youming Qiao, and Chuanqi Zhang

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

Abstract
In Diffie-Hellman key exchange, the commutativity of power operations is instrumental in the agreement of keys. Viewing commutativity as a law in abelian groups, we propose Diffie-Hellman key exchange in the group action framework (Brassard-Yung, Crypto'90; Ji-Qiao-Song-Yun, TCC'19), for actions of non-abelian groups with laws. The security of this protocol is shown, following Fischlin, Günther, Schmidt, and Warinschi (IEEE S&P'16), based on a pseudorandom group action assumption. A concrete instantiation is proposed based on the monomial code equivalence problem.
Cite as

Dung Hoang Duong, Youming Qiao, and Chuanqi Zhang. Diffie-Hellman Key Exchange from Commutativity to Group Laws. In 17th Innovations in Theoretical Computer Science Conference (ITCS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 362, pp. 52:1-52:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{duong_et_al:LIPIcs.ITCS.2026.52,
  author =	{Duong, Dung Hoang and Qiao, Youming and Zhang, Chuanqi},
  title =	{{Diffie-Hellman Key Exchange from Commutativity to Group Laws}},
  booktitle =	{17th Innovations in Theoretical Computer Science Conference (ITCS 2026)},
  pages =	{52:1--52:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-410-9},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{362},
  editor =	{Saraf, Shubhangi},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITCS.2026.52},
  URN =		{urn:nbn:de:0030-drops-253396},
  doi =		{10.4230/LIPIcs.ITCS.2026.52},
  annote =	{Keywords: Diffie-Hellman, Key Exchange, Group Laws, Group Actions, Code Equivalence}
}
Document
DOI: 10.4230/LIPIcs.ITCS.2026.93
Analyzing the Economic Impact of Decentralization on Users

Authors: Amit Levy, S. Matthew Weinberg, and Chenghan Zhou

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

Abstract
We model the ultimate price paid by users of a decentralized ledger as resulting from a two-stage game where Miners (/Proposers/etc.) first purchase blockspace via a Tullock contest, and then price that space to users. When analyzing our distributed ledger model, we find: - A characterization of all possible pure equilibria (although pure equilibria are not guaranteed to exist). - A natural sufficient condition, implied by Regularity (à la [Myerson, 1981]), for existence of a "market-clearing" pure equilibrium where Miners choose to sell all space allocated by the Distributed Ledger Protocol, and that this equilibrium is unique. - The market share of the largest miner is the relevant "measure of decentralization" to determine whether a market-clearing pure equilibrium exists. - Block rewards do not impact users' prices at equilibrium, when pure equilibria exist. But, higher block rewards can cause pure equilibria to exist. We also discuss aspects of our model and how they relate to blockchains deployed in practice. For example, only "patient" users (who are happy for their transactions to enter the blockchain under any miner) would enjoy the conclusions highlighted by our model, whereas "impatient" users (who are interested only for their transaction to be included in the very next block) still face monopoly pricing.
Cite as

Amit Levy, S. Matthew Weinberg, and Chenghan Zhou. Analyzing the Economic Impact of Decentralization on Users. In 17th Innovations in Theoretical Computer Science Conference (ITCS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 362, pp. 93:1-93:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{levy_et_al:LIPIcs.ITCS.2026.93,
  author =	{Levy, Amit and Weinberg, S. Matthew and Zhou, Chenghan},
  title =	{{Analyzing the Economic Impact of Decentralization on Users}},
  booktitle =	{17th Innovations in Theoretical Computer Science Conference (ITCS 2026)},
  pages =	{93:1--93:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-410-9},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{362},
  editor =	{Saraf, Shubhangi},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITCS.2026.93},
  URN =		{urn:nbn:de:0030-drops-253805},
  doi =		{10.4230/LIPIcs.ITCS.2026.93},
  annote =	{Keywords: Blockchain, Cryptocurrency, Blockspace Markets, Decentralization, Distributed Ledgers, Equilibrium Analysis, Tullock Contests}
}
Document
Survey
DOI: 10.4230/TGDK.3.2.1
Resilience in Knowledge Graph Embeddings

Authors: Arnab Sharma, N'Dah Jean Kouagou, and Axel-Cyrille Ngonga Ngomo

Published in: TGDK, Volume 3, Issue 2 (2025). Transactions on Graph Data and Knowledge, Volume 3, Issue 2

Abstract
In recent years, knowledge graphs have gained interest and witnessed widespread applications in various domains, such as information retrieval, question-answering, recommendation systems, amongst others. Large-scale knowledge graphs to this end have demonstrated their utility in effectively representing structured knowledge. To further facilitate the application of machine learning techniques, knowledge graph embedding models have been developed. Such models can transform entities and relationships within knowledge graphs into vectors. However, these embedding models often face challenges related to noise, missing information, distribution shift, adversarial attacks, etc. This can lead to sub-optimal embeddings and incorrect inferences, thereby negatively impacting downstream applications. While the existing literature has focused so far on adversarial attacks on KGE models, the challenges related to the other critical aspects remain unexplored. In this paper, we, first of all, give a unified definition of resilience, encompassing several factors such as generalisation, in-distribution generalization, distribution adaption, and robustness. After formalizing these concepts for machine learning in general, we define them in the context of knowledge graphs. To find the gap in the existing works on resilience in the context of knowledge graphs, we perform a systematic survey, taking into account all these aspects mentioned previously. Our survey results show that most of the existing works focus on a specific aspect of resilience, namely robustness. After categorizing such works based on their respective aspects of resilience, we discuss the challenges and future research directions.
Cite as

Arnab Sharma, N'Dah Jean Kouagou, and Axel-Cyrille Ngonga Ngomo. Resilience in Knowledge Graph Embeddings. In Transactions on Graph Data and Knowledge (TGDK), Volume 3, Issue 2, pp. 1:1-1:38, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@Article{sharma_et_al:TGDK.3.2.1,
  author =	{Sharma, Arnab and Kouagou, N'Dah Jean and Ngomo, Axel-Cyrille Ngonga},
  title =	{{Resilience in Knowledge Graph Embeddings}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{1:1--1:38},
  ISSN =	{2942-7517},
  year =	{2025},
  volume =	{3},
  number =	{2},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.3.2.1},
  URN =		{urn:nbn:de:0030-drops-248117},
  doi =		{10.4230/TGDK.3.2.1},
  annote =	{Keywords: Knowledge graphs, Resilience, Robustness}
}
Document
DOI: 10.4230/OASIcs.SpaceCHI.2025.7
Unbound Human-Machine Interfaces for Interaction in Weightless Environments

Authors: Jessica R. Cauchard

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

Abstract
User interfaces are subject to the rules of physics (e.g., Newton and Archimedes' laws) relevant to the environment they are in. As such, most interfaces and interaction techniques have been designed for Earth surface. However, when interacting with technology in weightless environments, such as in space, both human and machine will be subject to different physical constraints. For instance, underwater or in Space, people can experience spatial disorientation, which will in turn affect how they use a system. This position paper conceptualizes unbound Human-Machine Interfaces (HMIs) as interfaces where either, or both, human and machine are located beyond Earth surface. In particular, it describes how traditional HCI needs to be rethought for interaction in weightless environments and how theoretical models such as joint cognition can support future developments of unbound interfaces.
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Jessica R. Cauchard. Unbound Human-Machine Interfaces for Interaction in Weightless Environments. In Advancing Human-Computer Interaction for Space Exploration (SpaceCHI 2025). Open Access Series in Informatics (OASIcs), Volume 130, pp. 7:1-7:8, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{cauchard:OASIcs.SpaceCHI.2025.7,
  author =	{Cauchard, Jessica R.},
  title =	{{Unbound Human-Machine Interfaces for Interaction in Weightless Environments}},
  booktitle =	{Advancing Human-Computer Interaction for Space Exploration (SpaceCHI 2025)},
  pages =	{7:1--7:8},
  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.2025.7},
  URN =		{urn:nbn:de:0030-drops-239970},
  doi =		{10.4230/OASIcs.SpaceCHI.2025.7},
  annote =	{Keywords: human-robot interaction, gravity, space, interaction technique}
}
Document
DOI: 10.4230/LIPIcs.WADS.2025.39
Sweeping a Domain with Line-Of-Sight Between Covisible Agents

Authors: Kien C. Huynh, Joseph S. B. Mitchell, and Valentin Polishchuk

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

Abstract
We consider sweeping a polygonal domain using variable-length segments whose endpoints can be considered to be mobile agents moving with bounded speeds; a point in the domain is swept when it belongs to one of the segments. The objective is to sweep the domain as quickly as possible. We show that the problem is NP-hard even in simple polygons and even for a single segment (two agents), and give constant-factor approximation algorithms, both for simple polygons and polygons with holes. Our approximations are obtained by introducing a new type of "window partition" of the polygon, which may find other applications. For domains with holes, our results are based on a non-trivial topological argument proving a surprising fact: a connected subset of the domain, whose points are swept but not directly touched by the agents, may contain at most one hole.
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Kien C. Huynh, Joseph S. B. Mitchell, and Valentin Polishchuk. Sweeping a Domain with Line-Of-Sight Between Covisible Agents. In 19th International Symposium on Algorithms and Data Structures (WADS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 349, pp. 39:1-39:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{huynh_et_al:LIPIcs.WADS.2025.39,
  author =	{Huynh, Kien C. and Mitchell, Joseph S. B. and Polishchuk, Valentin},
  title =	{{Sweeping a Domain with Line-Of-Sight Between Covisible Agents}},
  booktitle =	{19th International Symposium on Algorithms and Data Structures (WADS 2025)},
  pages =	{39:1--39:22},
  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.2025.39},
  URN =		{urn:nbn:de:0030-drops-242706},
  doi =		{10.4230/LIPIcs.WADS.2025.39},
  annote =	{Keywords: Polygon sweeping, collaborating agents, motion coordination, makespan optimization}
}
Document
DOI: 10.4230/LIPIcs.MFCS.2025.46
Guarding Offices with Maximum Dispersion

Authors: Sándor P. Fekete, Kai Kobbe, Dominik Krupke, Joseph S. B. Mitchell, Christian Rieck, and Christian Scheffer

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

Abstract
We investigate the Dispersive Art Gallery Problem with vertex guards and rectangular visibility (r-visibility) for a class of orthogonal polygons that reflect the properties of real-world floor plans: these office-like polygons consist of rectangular rooms and corridors. In the dispersive variant of the Art Gallery Problem, the objective is not to minimize the number of guards but to maximize the minimum geodesic L₁-distance between any two guards, called the dispersion distance. Our main contributions are as follows. We prove that determining whether a vertex guard set can achieve a dispersion distance of 4 in office-like polygons is NP-complete, where vertices of the polygon are restricted to integer coordinates. Additionally, we present a simple worst-case optimal algorithm that guarantees a dispersion distance of 3 in polynomial time. Our complexity result extends to polyominoes, resolving an open question posed by Rieck and Scheffer [Christian Rieck and Christian Scheffer, 2024]. When vertex coordinates are allowed to be rational, we establish analogous results, proving that achieving a dispersion distance of 2+ε is NP-hard for any ε > 0, while the classic Art Gallery Problem remains solvable in polynomial time for this class of polygons. Furthermore, we give a straightforward polynomial-time algorithm that computes worst-case optimal solutions with a dispersion distance 2. On the other hand, for the more restricted class of hole-free independent office-like polygons, we propose a dynamic programming approach that computes optimal solutions. Moreover, we demonstrate that the problem is practically tractable for arbitrary orthogonal polygons. To this end, we compare solvers based on SAT, CP, and MIP formulations. Notably, SAT solvers efficiently compute optimal solutions for randomly generated instances with up to 1600 vertices in under 15s.
Cite as

Sándor P. Fekete, Kai Kobbe, Dominik Krupke, Joseph S. B. Mitchell, Christian Rieck, and Christian Scheffer. Guarding Offices with Maximum Dispersion. In 50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 345, pp. 46:1-46:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{fekete_et_al:LIPIcs.MFCS.2025.46,
  author =	{Fekete, S\'{a}ndor P. and Kobbe, Kai and Krupke, Dominik and Mitchell, Joseph S. B. and Rieck, Christian and Scheffer, Christian},
  title =	{{Guarding Offices with Maximum Dispersion}},
  booktitle =	{50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025)},
  pages =	{46:1--46:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-388-1},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{345},
  editor =	{Gawrychowski, Pawe{\l} and Mazowiecki, Filip and Skrzypczak, Micha{\l}},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2025.46},
  URN =		{urn:nbn:de:0030-drops-241530},
  doi =		{10.4230/LIPIcs.MFCS.2025.46},
  annote =	{Keywords: Dispersive Art Gallery Problem, vertex guards, office-like polygons, orthogonal polygons, polyominoes, NP-completeness, worst-case optimality, dynamic programming, SAT solver}
}
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.WABI.2025.10
DiVerG: Scalable Distance Index for Validation of Paired-End Alignments in Sequence Graphs

Authors: Ali Ghaffaari, Alexander Schönhuth, and Tobias Marschall

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

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

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

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@InProceedings{ghaffaari_et_al:LIPIcs.WABI.2025.10,
  author =	{Ghaffaari, Ali and Sch\"{o}nhuth, Alexander and Marschall, Tobias},
  title =	{{DiVerG: Scalable Distance Index for Validation of Paired-End Alignments in Sequence Graphs}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{10:1--10:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-386-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{344},
  editor =	{Brejov\'{a}, Bro\v{n}a and Patro, Rob},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2025.10},
  URN =		{urn:nbn:de:0030-drops-239369},
  doi =		{10.4230/LIPIcs.WABI.2025.10},
  annote =	{Keywords: Sequence graph, distance index, read mapping, sparse matrix}
}
Document
DOI: 10.4230/LIPIcs.WABI.2025.11
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.8
Enumeration of Ordered Trees with Leaf Restrictions

Authors: Yasuaki Kobayashi, Dominik Köppl, Yasuko Matsui, Hirotaka Ono, Toshiki Saitoh, and Yushi Uno

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

Abstract
An α-ary tree for a constant α ≥ 2 is a rooted tree in which each node has at most α children. A node having no children is called a leaf. For a given rooted tree and a node v, the number of edges from the root to v is called the depth of v. We call a vector w = (w_1,w_2,…, w_d) of nonnegative integers an (α-ary) distribution if there is an α-ary tree T such that the number of leaves at each depth i ∈ [1..d] in T is w_i. Although not every vector of nonnegative integers is a distribution, a distribution can be associated with many α-ary trees. In this paper, we present an algorithm to enumerate all α-ary trees for a given distribution. Our algorithm reports the first tree in O(d + ∑_{i = 1}^d w_i) time, and then each subsequent α-ary tree in O(max_{i = 1}^d w_i) time by representing each tree as the difference from the previous one. The algorithm can be restricted to computing all trees that are full, i.e., trees whose nodes have exactly α or no children.
Cite as

Yasuaki Kobayashi, Dominik Köppl, Yasuko Matsui, Hirotaka Ono, Toshiki Saitoh, and Yushi Uno. Enumeration of Ordered Trees with Leaf Restrictions. 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. 8:1-8:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{kobayashi_et_al:OASIcs.Grossi.8,
  author =	{Kobayashi, Yasuaki and K\"{o}ppl, Dominik and Matsui, Yasuko and Ono, Hirotaka and Saitoh, Toshiki and Uno, Yushi},
  title =	{{Enumeration of Ordered Trees with Leaf Restrictions}},
  booktitle =	{From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday},
  pages =	{8:1--8:19},
  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.8},
  URN =		{urn:nbn:de:0030-drops-238077},
  doi =		{10.4230/OASIcs.Grossi.8},
  annote =	{Keywords: binary trees, ordered trees, rooted trees, enumeration algorithm, constant-time delay}
}
Document
DOI: 10.4230/LIPIcs.CP.2025.35
Unite and Lead: Finding Disjunctive Cliques for Scheduling Problems

Authors: Konstantin Sidorov, Imko Marijnissen, and Emir Demirović

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

Abstract
Constraint programming solvers have seen much success in scheduling problems owing to their efficient reasoning over constraints to solve complex problems in practice. Many algorithms have been proposed for propagating information from a single constraint. However, inferring and exchanging information across multiple constraints can provide deeper insight into the global structure of a problem. In this work, we propose to exchange information amongst constraints by inferring the disjointness of tasks in scheduling problems from many constraints. We do this by (i) augmenting existing propagators, such as the Cumulative and nogoods, to report when pairs of tasks are disjoint, and (ii) leveraging this information by introducing the SelectiveDisjunctive propagator which generates a lower bound on the earliest completion time of cliques of disjoint tasks to determine conflicts. This allows us to aggregate disjointness information spanning multiple constraints to gain a better global overview of the problem, as well as more precise local information. We also identify a problem structure where an LCG solver reasoning over Cumulative constraints separately, without any reformulations, requires an exponential amount of time to prove infeasibility, which we both justify theoretically and show empirically; on the other hand, our approach solves those instances in polynomial time. On particular known RCPSP and RCPSP/max benchmarks, our approach significantly reduces the number of conflicts required to prove optimality when resource contention is high. Additionally, we discover new lower bounds for 16 RCPSP/max instances (closing six of them) and four RCPSP instances (closing one), as well as new upper bounds for two RCPSP/max instances and four RCPSP instances. Furthermore, we empirically analyse our proposed approach to determine which features are beneficial for performance, showing that finding cliques is one of the main bottlenecks and that detecting disjointness during search can lead to improved bounds on certain instances, but it generally negatively impacts learning. This work paves the way for reasoning over the disjointness of tasks inferred from a variety of standard constraints to discover novel information sourced from multiple constraints during search.
Cite as

Konstantin Sidorov, Imko Marijnissen, and Emir Demirović. Unite and Lead: Finding Disjunctive Cliques for Scheduling Problems. In 31st International Conference on Principles and Practice of Constraint Programming (CP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 340, pp. 35:1-35:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{sidorov_et_al:LIPIcs.CP.2025.35,
  author =	{Sidorov, Konstantin and Marijnissen, Imko and Demirovi\'{c}, Emir},
  title =	{{Unite and Lead: Finding Disjunctive Cliques for Scheduling Problems}},
  booktitle =	{31st International Conference on Principles and Practice of Constraint Programming (CP 2025)},
  pages =	{35:1--35:24},
  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.2025.35},
  URN =		{urn:nbn:de:0030-drops-238969},
  doi =		{10.4230/LIPIcs.CP.2025.35},
  annote =	{Keywords: Constraint Programming, Lazy Clause Generation, Propagation, Scheduling, Cumulative, Disjunctive}
}
Document
DOI: 10.4230/LIPIcs.CCC.2025.12
New Lower-Bounds for Quantum Computation with Non-Collapsing Measurements

Authors: David Miloschewsky and Supartha Podder

Published in: LIPIcs, Volume 339, 40th Computational Complexity Conference (CCC 2025)

Abstract
Aaronson, Bouland, Fitzsimons and Lee [Scott Aaronson et al., 2014] introduced the complexity class PDQP (which was original labeled naCQP), an alteration of BQP enhanced with the ability to obtain non-collapsing measurements, samples of quantum states without collapsing them. Although SZK ⊆ PDQP, it still requires Ω(N^(1/4)) queries to solve unstructured search. We formulate an alternative equivalent definition of PDQP, which we use to prove the positive weighted adversary lower-bounding method, establishing multiple tighter bounds and a trade-off between queries and non-collapsing measurements. We utilize the technique in order to analyze the query complexity of the well-studied majority and element distinctness problems. Additionally, we prove a tight Θ(N^(1/3)) bound on search. Furthermore, we use the lower-bound to explore PDQP under query restrictions, finding that when combined with non-adaptive queries, we limit the speed-up in several cases.
Cite as

David Miloschewsky and Supartha Podder. New Lower-Bounds for Quantum Computation with Non-Collapsing Measurements. In 40th Computational Complexity Conference (CCC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 339, pp. 12:1-12:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{miloschewsky_et_al:LIPIcs.CCC.2025.12,
  author =	{Miloschewsky, David and Podder, Supartha},
  title =	{{New Lower-Bounds for Quantum Computation with Non-Collapsing Measurements}},
  booktitle =	{40th Computational Complexity Conference (CCC 2025)},
  pages =	{12:1--12:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-379-9},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{339},
  editor =	{Srinivasan, Srikanth},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CCC.2025.12},
  URN =		{urn:nbn:de:0030-drops-237067},
  doi =		{10.4230/LIPIcs.CCC.2025.12},
  annote =	{Keywords: Non-collapsing measurements, Quantum lower-bounds, Quantum adversary method}
}
Document
DOI: 10.4230/LIPIcs.SEA.2025.20
SimdMinimizers: Computing Random Minimizers, fast

Authors: Ragnar Groot Koerkamp and Igor Martayan

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

Abstract
Motivation. Because of the rapidly-growing amount of sequencing data, computing sketches of large textual datasets has become an essential preprocessing task. These sketches are typically much smaller than the input sequences, but preserve sufficient information for downstream analysis. Minimizers are an especially popular sketching technique and used in a wide variety of applications. They sample at least one out of every w consecutive k-mers. As DNA sequencers are getting more accurate, some applications can afford to use a larger w and hence sparser and smaller sketches. And as sketches get smaller, their analysis becomes faster, so the time spent sketching the full-sized input becomes more of a bottleneck. Methods. Our library simd-minimizers implements a random minimizer algorithm using SIMD instructions. It supports both AVX2 and NEON architectures. Its main novelty is two-fold. First, it splits the input into 8 chunks that are streamed over in parallel through all steps of the algorithm. This is enabled by using the completely deterministic two-stacks sliding window minimum algorithm, which seems not to have been used before for finding minimizers. Results. Our library is up to 6.8× faster than a scalar implementation of the rescan method when w = 5 is small, and 3.4× faster for larger w = 19. Computing canonical minimizers is less than 50% slower than computing forward minimizers, and over 15× faster than the existing implementation in the minimizer-iter crate. Our library finds all (canonical) minimizers of a 3.2 Gbp human genome in 5.2 (resp. 6.7) seconds.
Cite as

Ragnar Groot Koerkamp and Igor Martayan. SimdMinimizers: Computing Random Minimizers, fast. In 23rd International Symposium on Experimental Algorithms (SEA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 338, pp. 20:1-20:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{grootkoerkamp_et_al:LIPIcs.SEA.2025.20,
  author =	{Groot Koerkamp, Ragnar and Martayan, Igor},
  title =	{{SimdMinimizers: Computing Random Minimizers, fast}},
  booktitle =	{23rd International Symposium on Experimental Algorithms (SEA 2025)},
  pages =	{20:1--20:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-375-1},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{338},
  editor =	{Mutzel, Petra and Prezza, Nicola},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2025.20},
  URN =		{urn:nbn:de:0030-drops-232581},
  doi =		{10.4230/LIPIcs.SEA.2025.20},
  annote =	{Keywords: Minimizers, Randomized algorithms, Sketching, Hashing}
}
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