14 Search Results for "Meier, Michael"

Document
DOI: 10.4230/LIPIcs.SoCG.2026.58
On Sparse Representations of 3‑Manifolds

Authors: Kristóf Huszár and Clément Maria

Published in: LIPIcs, Volume 367, 42nd International Symposium on Computational Geometry (SoCG 2026)

Abstract
3-manifolds are commonly represented as triangulations, consisting of abstract tetrahedra whose triangular faces are identified in pairs. The combinatorial sparsity of a triangulation, as measured by the treewidth of its dual graph, plays a fundamental role in the design of parameterized algorithms. In this work, we investigate algorithmic procedures that transform or modify a given triangulation while controlling specific sparsity parameters. First, we revisit a standard, linear-time algorithm that converts a given triangulation into a Heegaard diagram of the underlying 3-manifold, showing that the construction preserves treewidth. We apply this construction to exhibit a fixed-parameter tractable framework for computing Kuperberg’s quantum invariants of 3-manifolds. Second, we present a quasi-linear-time algorithm that retriangulates a given triangulation into one with maximum edge valence of at most nine, while only moderately increasing the treewidth of the dual graph. Combining these two algorithms yields a quasi-linear-time algorithm that produces, from a given triangulation, a Heegaard diagram in which every attaching curve intersects at most nine others.
Cite as

Kristóf Huszár and Clément Maria. On Sparse Representations of 3‑Manifolds. In 42nd International Symposium on Computational Geometry (SoCG 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 367, pp. 58:1-58:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{huszar_et_al:LIPIcs.SoCG.2026.58,
  author =	{Husz\'{a}r, Krist\'{o}f and Maria, Cl\'{e}ment},
  title =	{{On Sparse Representations of 3‑Manifolds}},
  booktitle =	{42nd International Symposium on Computational Geometry (SoCG 2026)},
  pages =	{58:1--58:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-418-5},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{367},
  editor =	{Ahn, Hee-Kap and Hoffmann, Michael and Nayyeri, Amir},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SoCG.2026.58},
  URN =		{urn:nbn:de:0030-drops-258659},
  doi =		{10.4230/LIPIcs.SoCG.2026.58},
  annote =	{Keywords: computational 3-manifold topology, fixed-parameter tractability, Heegaard splittings and diagrams, triangulations, edge valence, treewidth, quantum invariants, tensor networks}
}
Document
DOI: 10.4230/LIPIcs.IPEC.2025.23
Enumeration Kernels for Vertex Cover and Feedback Vertex Set

Authors: Marin Bougeret, Guilherme C. M. Gomes, Vinicius F. dos Santos, and Ignasi Sau

Published in: LIPIcs, Volume 358, 20th International Symposium on Parameterized and Exact Computation (IPEC 2025)

Abstract
Enumerative kernelization is a recent and promising area sitting at the intersection of parameterized complexity and enumeration algorithms. Its study began with the paper of Creignou et al. [Theory Comput. Syst., 2017], and development in the area has started to accelerate with the work of Golovach et al. [J. Comput. Syst. Sci., 2022]. The latter introduced polynomial-delay enumeration kernels and applied them in the study of structural parameterizations of the Matching Cut problem and some variants. Few other results, mostly on Longest Path and some generalizations of Matching Cut, have also been developed. However, little success has been seen in enumeration versions of Vertex Cover and Feedback Vertex Set, some of the most studied problems in kernelization. In this paper, we address this shortcoming. Our first result is a polynomial-delay enumeration kernel with 2k vertices for Enum Vertex Cover, where we wish to list all solutions with at most k vertices. This is obtained by developing a non-trivial lifting algorithm for the classical crown decomposition reduction rule, and directly improves upon the kernel with 𝒪(k²) vertices derived from the work of Creignou et al. Our other result is a polynomial-delay enumeration kernel with 𝒪(k³) vertices and edges for Enum Feedback Vertex Set; the proof is inspired by some ideas of Thomassé [TALG, 2010], but with a weaker bound on the kernel size due to difficulties in applying the q-expansion technique.
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Marin Bougeret, Guilherme C. M. Gomes, Vinicius F. dos Santos, and Ignasi Sau. Enumeration Kernels for Vertex Cover and Feedback Vertex Set. In 20th International Symposium on Parameterized and Exact Computation (IPEC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 358, pp. 23:1-23:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{bougeret_et_al:LIPIcs.IPEC.2025.23,
  author =	{Bougeret, Marin and C. M. Gomes, Guilherme and dos Santos, Vinicius F. and Sau, Ignasi},
  title =	{{Enumeration Kernels for Vertex Cover and Feedback Vertex Set}},
  booktitle =	{20th International Symposium on Parameterized and Exact Computation (IPEC 2025)},
  pages =	{23:1--23:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-407-9},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{358},
  editor =	{Agrawal, Akanksha and van Leeuwen, Erik Jan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.IPEC.2025.23},
  URN =		{urn:nbn:de:0030-drops-251552},
  doi =		{10.4230/LIPIcs.IPEC.2025.23},
  annote =	{Keywords: Kernelization, Enumeration, Vertex cover, Crown decomposition, Feedback vertex set}
}
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
Research
DOI: 10.4230/OASIcs.Grossi.19
Designing Output Sensitive Algorithms for Subgraph Enumeration

Authors: Alessio Conte, Kazuhiro Kurita, Andrea Marino, Giulia Punzi, Takeaki Uno, and Kunihiro Wasa

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

Abstract
The enumeration of all subgraphs respecting some structural property is a fundamental task in theoretical computer science, with practical applications in many branches of data mining and network analysis. It is often of interest to only consider solutions (subgraphs) that are maximal under inclusion, and to achieve output-sensitive complexity, i.e., bounding the running time with respect to the number of subgraphs produced. In this paper, we provide a survey of techniques for designing output-sensitive algorithms for subgraph enumeration, including partition-based approaches such as flashlight search, solution-graph traversal methods such as reverse search, and cost amortization strategies such as push-out amortization. We also briefly discuss classes of efficiency, hardness of enumeration, and variants such as approximate enumeration. The paper is meant as an accessible handbook for learning the basics of the field and as a practical reference for selecting state-of-the-art subgraph enumeration strategies fitting to one’s needs.
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Alessio Conte, Kazuhiro Kurita, Andrea Marino, Giulia Punzi, Takeaki Uno, and Kunihiro Wasa. Designing Output Sensitive Algorithms for Subgraph Enumeration. 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. 19:1-19:40, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{conte_et_al:OASIcs.Grossi.19,
  author =	{Conte, Alessio and Kurita, Kazuhiro and Marino, Andrea and Punzi, Giulia and Uno, Takeaki and Wasa, Kunihiro},
  title =	{{Designing Output Sensitive Algorithms for Subgraph Enumeration}},
  booktitle =	{From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday},
  pages =	{19:1--19:40},
  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.19},
  URN =		{urn:nbn:de:0030-drops-238180},
  doi =		{10.4230/OASIcs.Grossi.19},
  annote =	{Keywords: Graph algorithms, Graph enumeration, Output sensitive enumeration}
}
Document
DOI: 10.4230/LIPIcs.CP.2025.17
Scalable Counting of Minimal Trap Spaces and Fixed Points in Boolean Networks

Authors: Mohimenul Kabir, Van-Giang Trinh, Samuel Pastva, and Kuldeep S Meel

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

Abstract
Boolean Networks (BNs) serve as a fundamental modeling framework for capturing complex dynamical systems across various domains, including systems biology, computational logic, and artificial intelligence. A crucial property of BNs is the presence of trap spaces - subspaces of the state space that, once entered, cannot be exited. Minimal trap spaces, in particular, play a significant role in analyzing the long-term behavior of BNs, making their efficient enumeration and counting essential. The fixed points in BNs are a special case of minimal trap spaces. In this work, we formulate several meaningful counting problems related to minimal trap spaces and fixed points in BNs. These problems provide valuable insights both within BN theory (e.g., in probabilistic reasoning and dynamical analysis) and in broader application areas, including systems biology, abstract argumentation, and logic programming. To address these computational challenges, we propose novel methods based on approximate answer set counting, leveraging techniques from answer set programming. Our approach efficiently approximates the number of minimal trap spaces and the number of fixed points without requiring exhaustive enumeration, making it particularly well-suited for large-scale BNs. Our experimental evaluation on an extensive and diverse set of benchmark instances shows that our methods significantly improve the feasibility of counting minimal trap spaces and fixed points, paving the way for new applications in BN analysis and beyond.
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Mohimenul Kabir, Van-Giang Trinh, Samuel Pastva, and Kuldeep S Meel. Scalable Counting of Minimal Trap Spaces and Fixed Points in Boolean Networks. In 31st International Conference on Principles and Practice of Constraint Programming (CP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 340, pp. 17:1-17:26, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{kabir_et_al:LIPIcs.CP.2025.17,
  author =	{Kabir, Mohimenul and Trinh, Van-Giang and Pastva, Samuel and Meel, Kuldeep S},
  title =	{{Scalable Counting of Minimal Trap Spaces and Fixed Points in Boolean Networks}},
  booktitle =	{31st International Conference on Principles and Practice of Constraint Programming (CP 2025)},
  pages =	{17:1--17:26},
  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.2025.17},
  URN =		{urn:nbn:de:0030-drops-238780},
  doi =		{10.4230/LIPIcs.CP.2025.17},
  annote =	{Keywords: Computational systems biology, Boolean network, Fixed point, Trap space, Answer set counting, Projected counting, Abstract argumentation, Logic programming}
}
Document
DOI: 10.4230/LIPIcs.CSL.2025.10
The Complexity of Second-Order HyperLTL

Authors: Hadar Frenkel and Martin Zimmermann

Published in: LIPIcs, Volume 326, 33rd EACSL Annual Conference on Computer Science Logic (CSL 2025)

Abstract
We determine the complexity of second-order HyperLTL satisfiability, finite-state satisfiability, and model-checking: All three are equivalent to truth in third-order arithmetic. We also consider two fragments of second-order HyperLTL that have been introduced with the aim to facilitate effective model-checking by restricting the sets one can quantify over. The first one restricts second-order quantification to smallest/largest sets that satisfy a guard while the second one restricts second-order quantification further to least fixed points of (first-order) HyperLTL definable functions. All three problems for the first fragment are still equivalent to truth in third-order arithmetic while satisfiability for the second fragment is Σ₁¹-complete, i.e., only as hard as for (first-order) HyperLTL and therefore much less complex. Finally, finite-state satisfiability and model-checking are in Σ₂² and are Σ₁¹-hard, and thus also less complex than for full second-order HyperLTL.
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Hadar Frenkel and Martin Zimmermann. The Complexity of Second-Order HyperLTL. In 33rd EACSL Annual Conference on Computer Science Logic (CSL 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 326, pp. 10:1-10:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{frenkel_et_al:LIPIcs.CSL.2025.10,
  author =	{Frenkel, Hadar and Zimmermann, Martin},
  title =	{{The Complexity of Second-Order HyperLTL}},
  booktitle =	{33rd EACSL Annual Conference on Computer Science Logic (CSL 2025)},
  pages =	{10:1--10:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-362-1},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{326},
  editor =	{Endrullis, J\"{o}rg and Schmitz, Sylvain},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CSL.2025.10},
  URN =		{urn:nbn:de:0030-drops-227679},
  doi =		{10.4230/LIPIcs.CSL.2025.10},
  annote =	{Keywords: HyperLTL, Satisfiability, Model-checking}
}
Document
Survey
DOI: 10.4230/TGDK.2.1.3
Semantic Web: Past, Present, and Future

Authors: Ansgar Scherp, Gerd Groener, Petr Škoda, Katja Hose, and Maria-Esther Vidal

Published in: TGDK, Volume 2, Issue 1 (2024): Special Issue on Trends in Graph Data and Knowledge - Part 2. Transactions on Graph Data and Knowledge, Volume 2, Issue 1

Abstract
Ever since the vision was formulated, the Semantic Web has inspired many generations of innovations. Semantic technologies have been used to share vast amounts of information on the Web, enhance them with semantics to give them meaning, and enable inference and reasoning on them. Throughout the years, semantic technologies, and in particular knowledge graphs, have been used in search engines, data integration, enterprise settings, and machine learning. In this paper, we recap the classical concepts and foundations of the Semantic Web as well as modern and recent concepts and applications, building upon these foundations. The classical topics we cover include knowledge representation, creating and validating knowledge on the Web, reasoning and linking, and distributed querying. We enhance this classical view of the so-called "Semantic Web Layer Cake" with an update of recent concepts that include provenance, security and trust, as well as a discussion of practical impacts from industry-led contributions. We conclude with an outlook on the future directions of the Semantic Web. This is a living document. If you like to contribute, please contact the first author and visit: https://github.com/ascherp/semantic-web-primer
Cite as

Ansgar Scherp, Gerd Groener, Petr Škoda, Katja Hose, and Maria-Esther Vidal. Semantic Web: Past, Present, and Future. In Special Issue on Trends in Graph Data and Knowledge - Part 2. Transactions on Graph Data and Knowledge (TGDK), Volume 2, Issue 1, pp. 3:1-3:37, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@Article{scherp_et_al:TGDK.2.1.3,
  author =	{Scherp, Ansgar and Groener, Gerd and \v{S}koda, Petr and Hose, Katja and Vidal, Maria-Esther},
  title =	{{Semantic Web: Past, Present, and Future}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{3:1--3:37},
  ISSN =	{2942-7517},
  year =	{2024},
  volume =	{2},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.2.1.3},
  URN =		{urn:nbn:de:0030-drops-198607},
  doi =		{10.4230/TGDK.2.1.3},
  annote =	{Keywords: Linked Open Data, Semantic Web Graphs, Knowledge Graphs}
}
Document
Survey
DOI: 10.4230/TGDK.1.1.4
Knowledge Graph Embeddings: Open Challenges and Opportunities

Authors: Russa Biswas, Lucie-Aimée Kaffee, Michael Cochez, Stefania Dumbrava, Theis E. Jendal, Matteo Lissandrini, Vanessa Lopez, Eneldo Loza Mencía, Heiko Paulheim, Harald Sack, Edlira Kalemi Vakaj, and Gerard de Melo

Published in: TGDK, Volume 1, Issue 1 (2023): Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge, Volume 1, Issue 1

Abstract
While Knowledge Graphs (KGs) have long been used as valuable sources of structured knowledge, in recent years, KG embeddings have become a popular way of deriving numeric vector representations from them, for instance, to support knowledge graph completion and similarity search. This study surveys advances as well as open challenges and opportunities in this area. For instance, the most prominent embedding models focus primarily on structural information. However, there has been notable progress in incorporating further aspects, such as semantics, multi-modal, temporal, and multilingual features. Most embedding techniques are assessed using human-curated benchmark datasets for the task of link prediction, neglecting other important real-world KG applications. Many approaches assume a static knowledge graph and are unable to account for dynamic changes. Additionally, KG embeddings may encode data biases and lack interpretability. Overall, this study provides an overview of promising research avenues to learn improved KG embeddings that can address a more diverse range of use cases.
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Russa Biswas, Lucie-Aimée Kaffee, Michael Cochez, Stefania Dumbrava, Theis E. Jendal, Matteo Lissandrini, Vanessa Lopez, Eneldo Loza Mencía, Heiko Paulheim, Harald Sack, Edlira Kalemi Vakaj, and Gerard de Melo. Knowledge Graph Embeddings: Open Challenges and Opportunities. In Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge (TGDK), Volume 1, Issue 1, pp. 4:1-4:32, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@Article{biswas_et_al:TGDK.1.1.4,
  author =	{Biswas, Russa and Kaffee, Lucie-Aim\'{e}e and Cochez, Michael and Dumbrava, Stefania and Jendal, Theis E. and Lissandrini, Matteo and Lopez, Vanessa and Menc{\'\i}a, Eneldo Loza and Paulheim, Heiko and Sack, Harald and Vakaj, Edlira Kalemi and de Melo, Gerard},
  title =	{{Knowledge Graph Embeddings: Open Challenges and Opportunities}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{4:1--4:32},
  year =	{2023},
  volume =	{1},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.1.1.4},
  URN =		{urn:nbn:de:0030-drops-194783},
  doi =		{10.4230/TGDK.1.1.4},
  annote =	{Keywords: Knowledge Graphs, KG embeddings, Link prediction, KG applications}
}
Document
Position
DOI: 10.4230/TGDK.1.1.5
Knowledge Graphs for the Life Sciences: Recent Developments, Challenges and Opportunities

Authors: Jiaoyan Chen, Hang Dong, Janna Hastings, Ernesto Jiménez-Ruiz, Vanessa López, Pierre Monnin, Catia Pesquita, Petr Škoda, and Valentina Tamma

Published in: TGDK, Volume 1, Issue 1 (2023): Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge, Volume 1, Issue 1

Abstract
The term life sciences refers to the disciplines that study living organisms and life processes, and include chemistry, biology, medicine, and a range of other related disciplines. Research efforts in life sciences are heavily data-driven, as they produce and consume vast amounts of scientific data, much of which is intrinsically relational and graph-structured. The volume of data and the complexity of scientific concepts and relations referred to therein promote the application of advanced knowledge-driven technologies for managing and interpreting data, with the ultimate aim to advance scientific discovery. In this survey and position paper, we discuss recent developments and advances in the use of graph-based technologies in life sciences and set out a vision for how these technologies will impact these fields into the future. We focus on three broad topics: the construction and management of Knowledge Graphs (KGs), the use of KGs and associated technologies in the discovery of new knowledge, and the use of KGs in artificial intelligence applications to support explanations (explainable AI). We select a few exemplary use cases for each topic, discuss the challenges and open research questions within these topics, and conclude with a perspective and outlook that summarizes the overarching challenges and their potential solutions as a guide for future research.
Cite as

Jiaoyan Chen, Hang Dong, Janna Hastings, Ernesto Jiménez-Ruiz, Vanessa López, Pierre Monnin, Catia Pesquita, Petr Škoda, and Valentina Tamma. Knowledge Graphs for the Life Sciences: Recent Developments, Challenges and Opportunities. In Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge (TGDK), Volume 1, Issue 1, pp. 5:1-5:33, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@Article{chen_et_al:TGDK.1.1.5,
  author =	{Chen, Jiaoyan and Dong, Hang and Hastings, Janna and Jim\'{e}nez-Ruiz, Ernesto and L\'{o}pez, Vanessa and Monnin, Pierre and Pesquita, Catia and \v{S}koda, Petr and Tamma, Valentina},
  title =	{{Knowledge Graphs for the Life Sciences: Recent Developments, Challenges and Opportunities}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{5:1--5:33},
  year =	{2023},
  volume =	{1},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.1.1.5},
  URN =		{urn:nbn:de:0030-drops-194791},
  doi =		{10.4230/TGDK.1.1.5},
  annote =	{Keywords: Knowledge graphs, Life science, Knowledge discovery, Explainable AI}
}
Document
Position
DOI: 10.4230/TGDK.1.1.2
Large Language Models and Knowledge Graphs: Opportunities and Challenges

Authors: Jeff Z. Pan, Simon Razniewski, Jan-Christoph Kalo, Sneha Singhania, Jiaoyan Chen, Stefan Dietze, Hajira Jabeen, Janna Omeliyanenko, Wen Zhang, Matteo Lissandrini, Russa Biswas, Gerard de Melo, Angela Bonifati, Edlira Vakaj, Mauro Dragoni, and Damien Graux

Published in: TGDK, Volume 1, Issue 1 (2023): Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge, Volume 1, Issue 1

Abstract
Large Language Models (LLMs) have taken Knowledge Representation - and the world - by storm. This inflection point marks a shift from explicit knowledge representation to a renewed focus on the hybrid representation of both explicit knowledge and parametric knowledge. In this position paper, we will discuss some of the common debate points within the community on LLMs (parametric knowledge) and Knowledge Graphs (explicit knowledge) and speculate on opportunities and visions that the renewed focus brings, as well as related research topics and challenges.
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Jeff Z. Pan, Simon Razniewski, Jan-Christoph Kalo, Sneha Singhania, Jiaoyan Chen, Stefan Dietze, Hajira Jabeen, Janna Omeliyanenko, Wen Zhang, Matteo Lissandrini, Russa Biswas, Gerard de Melo, Angela Bonifati, Edlira Vakaj, Mauro Dragoni, and Damien Graux. Large Language Models and Knowledge Graphs: Opportunities and Challenges. In Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge (TGDK), Volume 1, Issue 1, pp. 2:1-2:38, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@Article{pan_et_al:TGDK.1.1.2,
  author =	{Pan, Jeff Z. and Razniewski, Simon and Kalo, Jan-Christoph and Singhania, Sneha and Chen, Jiaoyan and Dietze, Stefan and Jabeen, Hajira and Omeliyanenko, Janna and Zhang, Wen and Lissandrini, Matteo and Biswas, Russa and de Melo, Gerard and Bonifati, Angela and Vakaj, Edlira and Dragoni, Mauro and Graux, Damien},
  title =	{{Large Language Models and Knowledge Graphs: Opportunities and Challenges}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{2:1--2:38},
  year =	{2023},
  volume =	{1},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.1.1.2},
  URN =		{urn:nbn:de:0030-drops-194766},
  doi =		{10.4230/TGDK.1.1.2},
  annote =	{Keywords: Large Language Models, Pre-trained Language Models, Knowledge Graphs, Ontology, Retrieval Augmented Language Models}
}
Document
DOI: 10.4230/LIPIcs.ESA.2019.46
Obviously Strategyproof Mechanisms for Machine Scheduling

Authors: Diodato Ferraioli, Adrian Meier, Paolo Penna, and Carmine Ventre

Published in: LIPIcs, Volume 144, 27th Annual European Symposium on Algorithms (ESA 2019)

Abstract
Catering to the incentives of people with limited rationality is a challenging research direction that requires novel paradigms to design mechanisms and approximation algorithms. Obviously strategyproof (OSP) mechanisms have recently emerged as the concept of interest to this research agenda. However, the majority of the literature in the area has either highlighted the shortcomings of OSP or focused on the "right" definition rather than on the construction of these mechanisms. We here give the first set of tight results on the approximation guarantee of OSP mechanisms for scheduling related machines. By extending the well-known cycle monotonicity technique, we are able to concentrate on the algorithmic component of OSP mechanisms and provide some novel paradigms for their design.
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Diodato Ferraioli, Adrian Meier, Paolo Penna, and Carmine Ventre. Obviously Strategyproof Mechanisms for Machine Scheduling. In 27th Annual European Symposium on Algorithms (ESA 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 144, pp. 46:1-46:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)

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@InProceedings{ferraioli_et_al:LIPIcs.ESA.2019.46,
  author =	{Ferraioli, Diodato and Meier, Adrian and Penna, Paolo and Ventre, Carmine},
  title =	{{Obviously Strategyproof Mechanisms for Machine Scheduling}},
  booktitle =	{27th Annual European Symposium on Algorithms (ESA 2019)},
  pages =	{46:1--46:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-124-5},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{144},
  editor =	{Bender, Michael A. and Svensson, Ola 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.2019.46},
  URN =		{urn:nbn:de:0030-drops-111677},
  doi =		{10.4230/LIPIcs.ESA.2019.46},
  annote =	{Keywords: Bounded Rationality, Extensive-form Mechanisms, Approximate Mechanism Design}
}
Document
DOI: 10.4230/DagSemProc.10061.5
Proof Complexity of Propositional Default Logic

Authors: Olaf Beyersdorff, Arne Meier, Sebastian Müller, Michael Thomas, and Heribert Vollmer

Published in: Dagstuhl Seminar Proceedings, Volume 10061, Circuits, Logic, and Games (2010)

Abstract
Default logic is one of the most popular and successful formalisms for non-monotonic reasoning. In 2002, Bonatti and Olivetti introduced several sequent calculi for credulous and skeptical reasoning in propositional default logic. In this paper we examine these calculi from a proof-complexity perspective. In particular, we show that the calculus for credulous reasoning obeys almost the same bounds on the proof size as Gentzen's system LK. Hence proving lower bounds for credulous reasoning will be as hard as proving lower bounds for LK. On the other hand, we show an exponential lower bound to the proof size in Bonatti and Olivetti's enhanced calculus for skeptical default reasoning.
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Olaf Beyersdorff, Arne Meier, Sebastian Müller, Michael Thomas, and Heribert Vollmer. Proof Complexity of Propositional Default Logic. In Circuits, Logic, and Games. Dagstuhl Seminar Proceedings, Volume 10061, pp. 1-14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2010)

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@InProceedings{beyersdorff_et_al:DagSemProc.10061.5,
  author =	{Beyersdorff, Olaf and Meier, Arne and M\"{u}ller, Sebastian and Thomas, Michael and Vollmer, Heribert},
  title =	{{Proof Complexity of Propositional Default Logic}},
  booktitle =	{Circuits, Logic, and Games},
  pages =	{1--14},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2010},
  volume =	{10061},
  editor =	{Benjamin Rossman and Thomas Schwentick and Denis Th\'{e}rien and Heribert Vollmer},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.10061.5},
  URN =		{urn:nbn:de:0030-drops-25261},
  doi =		{10.4230/DagSemProc.10061.5},
  annote =	{Keywords: Proof complexity, default logic, sequent calculus}
}
Document
DOI: 10.4230/DagSemProc.10061.6
The Complexity of Reasoning for Fragments of Autoepistemic Logic

Authors: Nadia Creignou, Arne Meier, Michael Thomas, and Heribert Vollmer

Published in: Dagstuhl Seminar Proceedings, Volume 10061, Circuits, Logic, and Games (2010)

Abstract
Autoepistemic logic extends propositional logic by the modal operator L. A formula that is preceded by an L is said to be "believed". The logic was introduced by Moore 1985 for modeling an ideally rational agent's behavior and reasoning about his own beliefs. In this paper we analyze all Boolean fragments of autoepistemic logic with respect to the computational complexity of the three most common decision problems expansion existence, brave reasoning and cautious reasoning. As a second contribution we classify the computational complexity of counting the number of stable expansions of a given knowledge base. To the best of our knowledge this is the first paper analyzing the counting problem for autoepistemic logic.
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Nadia Creignou, Arne Meier, Michael Thomas, and Heribert Vollmer. The Complexity of Reasoning for Fragments of Autoepistemic Logic. In Circuits, Logic, and Games. Dagstuhl Seminar Proceedings, Volume 10061, pp. 1-10, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2010)

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@InProceedings{creignou_et_al:DagSemProc.10061.6,
  author =	{Creignou, Nadia and Meier, Arne and Thomas, Michael and Vollmer, Heribert},
  title =	{{The Complexity of Reasoning for Fragments of Autoepistemic Logic}},
  booktitle =	{Circuits, Logic, and Games},
  pages =	{1--10},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2010},
  volume =	{10061},
  editor =	{Benjamin Rossman and Thomas Schwentick and Denis Th\'{e}rien and Heribert Vollmer},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.10061.6},
  URN =		{urn:nbn:de:0030-drops-25234},
  doi =		{10.4230/DagSemProc.10061.6},
  annote =	{Keywords: Autoepistemic logic, computational complexity, nonmonotonic reasoning, Post's lattice}
}
Document
DOI: 10.4230/DagSemProc.08102.2
2. 08102 Working Group – Early Warning Systems

Authors: Joachim Biskup, Bernhard Hämmerli, Michael Meier, Sebastian Schmerl, Jens Tölle, and Michael Vogel

Published in: Dagstuhl Seminar Proceedings, Volume 8102, Perspectives Workshop: Network Attack Detection and Defense (2008)

Abstract
Early Warning Systems aim at detecting unclassified but potentially harmful sys-tem behavior based on preliminary indications and are complementary to Intrusion Detection Systems. Both kinds of systems try to detect, identify and react before pos-sible damage occurs and contribute to an integrated and aggregated situation report (big picture). A particular emphasis of Early Warning Systems is to establish hypotheses and predictions as well as to generate advises in still not completely understood situations. Thus the term early has two meanings, a) to start early in time aiming to minimize damage, and b) to process uncertain and incomplete information.
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Joachim Biskup, Bernhard Hämmerli, Michael Meier, Sebastian Schmerl, Jens Tölle, and Michael Vogel. 2. 08102 Working Group – Early Warning Systems. In Perspectives Workshop: Network Attack Detection and Defense. Dagstuhl Seminar Proceedings, Volume 8102, pp. 1-2, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2008)

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@InProceedings{biskup_et_al:DagSemProc.08102.2,
  author =	{Biskup, Joachim and H\"{a}mmerli, Bernhard and Meier, Michael and Schmerl, Sebastian and T\"{o}lle, Jens and Vogel, Michael},
  title =	{{2. 08102 Working Group – Early Warning Systems}},
  booktitle =	{Perspectives Workshop: Network Attack Detection and Defense},
  pages =	{1--2},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2008},
  volume =	{8102},
  editor =	{Georg Carle and Falko Dressler and Richard A. Kemmerer and Hartmut K\"{o}nig and Christopher Kruegel},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.08102.2},
  URN =		{urn:nbn:de:0030-drops-14936},
  doi =		{10.4230/DagSemProc.08102.2},
  annote =	{Keywords: Intrusion detection and prevention, attack response and countermeasures, reactive security, automated security, survivability and self-protection, ma network monitoring, flow analysis, denial of service detection and response, event correlation}
}
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