10 Search Results for "Kohler, Matthias"

Document
DOI: 10.4230/LIPIcs.FUN.2026.19
Sinks and Ladders: ARRIVAL and SSG with Two Vertices per Level

Authors: Bernd Gärtner, Sebastian Haslebacher, and Hung P. Hoang

Published in: LIPIcs, Volume 366, 13th International Conference on Fun with Algorithms (FUN 2026)

Abstract
ARRIVAL is the problem of deciding whether a token, following a deterministic process, eventually reaches a designated destination. While the problem is known to lie in NP ∩ CoNP, whether it can be solved in polynomial time remains a major open question. In this article, we study ladders, a class of graphs that constitutes a family of worst-case instances for many existing algorithms, including the currently best known algorithm by Gärtner, Haslebacher, and Hoang (ICALP 2021). We show that ARRIVAL restricted to ladders can be solved in polynomial time, and we further extend this result to stopping binary simple stochastic games (SSG).
Cite as

Bernd Gärtner, Sebastian Haslebacher, and Hung P. Hoang. Sinks and Ladders: ARRIVAL and SSG with Two Vertices per Level. In 13th International Conference on Fun with Algorithms (FUN 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 366, pp. 19:1-19:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{gartner_et_al:LIPIcs.FUN.2026.19,
  author =	{G\"{a}rtner, Bernd and Haslebacher, Sebastian and Hoang, Hung P.},
  title =	{{Sinks and Ladders: ARRIVAL and SSG with Two Vertices per Level}},
  booktitle =	{13th International Conference on Fun with Algorithms (FUN 2026)},
  pages =	{19:1--19:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-417-8},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{366},
  editor =	{Iacono, John},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FUN.2026.19},
  URN =		{urn:nbn:de:0030-drops-257385},
  doi =		{10.4230/LIPIcs.FUN.2026.19},
  annote =	{Keywords: ARRIVAL, Rotor-Routing, Simple Stochastic Games}
}
Document
Research
DOI: 10.4230/TGDK.3.3.4
Mining Inter-Document Argument Structures in Scientific Papers for an Argument Web

Authors: Florian Ruosch, Cristina Sarasua, and Abraham Bernstein

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

Abstract
In Argument Mining, predicting argumentative relations between texts (or spans) remains one of the most challenging aspects, even more so in the cross-document setting. This paper makes three key contributions to advance research in this domain. We first extend an existing dataset, the Sci-Arg corpus, by annotating it with explicit inter-document argumentative relations, thereby allowing arguments to be distributed over several documents forming an Argument Web; these new annotations are published using Semantic Web technologies (RDF, OWL). Second, we explore and evaluate three automated approaches for predicting these inter-document argumentative relations, establishing critical baselines on the new dataset. We find that a simple classifier based on discourse indicators with access to context outperforms neural methods. Third, we conduct a comparative analysis of these approaches for both intra- and inter-document settings, identifying statistically significant differences in results that indicate the necessity of distinguishing between these two scenarios. Our findings highlight significant challenges in this complex domain and open crucial avenues for future research on the Argument Web of Science, particularly for those interested in leveraging Semantic Web technologies and knowledge graphs to understand scholarly discourse. With this, we provide the first stepping stones in the form of a benchmark dataset, three baseline methods, and an initial analysis for a systematic exploration of this field relevant to the Web of Data and Science.
Cite as

Florian Ruosch, Cristina Sarasua, and Abraham Bernstein. Mining Inter-Document Argument Structures in Scientific Papers for an Argument Web. In Transactions on Graph Data and Knowledge (TGDK), Volume 3, Issue 3, pp. 4:1-4:33, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@Article{ruosch_et_al:TGDK.3.3.4,
  author =	{Ruosch, Florian and Sarasua, Cristina and Bernstein, Abraham},
  title =	{{Mining Inter-Document Argument Structures in Scientific Papers for an Argument Web}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{4:1--4:33},
  ISSN =	{2942-7517},
  year =	{2025},
  volume =	{3},
  number =	{3},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.3.3.4},
  URN =		{urn:nbn:de:0030-drops-252159},
  doi =		{10.4230/TGDK.3.3.4},
  annote =	{Keywords: Argument Mining, Large Language Models, Knowledge Graphs, Link Prediction}
}
Document
DOI: 10.4230/LIPIcs.ISAAC.2025.48
Quadratic Kernel for Cliques or Trees Vertex Deletion

Authors: Soh Kumabe

Published in: LIPIcs, Volume 359, 36th International Symposium on Algorithms and Computation (ISAAC 2025)

Abstract
We consider Cliques or Trees Vertex Deletion, which is a hybrid of two fundamental parameterized problems: Cluster Vertex Deletion and Feedback Vertex Set. In this problem, we are given an undirected graph G and an integer k, and asked to find a vertex subset X of size at most k such that each connected component of G-X is either a clique or a tree. Jacob et al. (ISAAC, 2024) provided a kernel of O(k⁵) vertices for this problem, which was recently improved to O(k⁴) by Tsur (IPL, 2025). Our main result is a kernel of O(k²) vertices. This result closes the gap between the kernelization result for Feedback Vertex Set, which corresponds to the case where each connected component of G-X must be a tree. Although both cluster vertex deletion number and feedback vertex set number are well-studied structural parameters, little attention has been given to parameters that generalize both of them. In fact, the lowest common well-known generalization of them is clique-width, which is a highly general parameter. To fill the gap here, we initiate the study of the cliques or trees vertex deletion number as a structural parameter. We prove that Longest Cycle, which is a fundamental problem that does not admit o(n^k)-time algorithm unless ETH fails when k is the clique-width, becomes fixed-parameter tractable when parameterized by the cliques or trees vertex deletion number.
Cite as

Soh Kumabe. Quadratic Kernel for Cliques or Trees Vertex Deletion. In 36th International Symposium on Algorithms and Computation (ISAAC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 359, pp. 48:1-48:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{kumabe:LIPIcs.ISAAC.2025.48,
  author =	{Kumabe, Soh},
  title =	{{Quadratic Kernel for Cliques or Trees Vertex Deletion}},
  booktitle =	{36th International Symposium on Algorithms and Computation (ISAAC 2025)},
  pages =	{48:1--48:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-408-6},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{359},
  editor =	{Chen, Ho-Lin and Hon, Wing-Kai and Tsai, Meng-Tsung},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ISAAC.2025.48},
  URN =		{urn:nbn:de:0030-drops-249568},
  doi =		{10.4230/LIPIcs.ISAAC.2025.48},
  annote =	{Keywords: Fixed-Parameter Tractability, Kernelization, Deletion to Scattered Graph Classes, Cluster Vertex Deletion, Feedback Vertex Set}
}
Document
Track A: Algorithms, Complexity and Games
DOI: 10.4230/LIPIcs.ICALP.2025.32
Light Edge Fault Tolerant Graph Spanners

Authors: Greg Bodwin, Michael Dinitz, Ama Koranteng, and Lily Wang

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

Abstract
There has recently been significant interest in fault tolerant spanners, which are spanners that still maintain their stretch guarantees after some nodes or edges fail. This work has culminated in an almost complete understanding of the three-way tradeoff between stretch, sparsity, and number of faults tolerated. However, despite some progress in metric settings, there have been no results to date on the tradeoff in general graphs between stretch, lightness, and number of faults tolerated. We initiate the study of light edge fault tolerant (EFT) graph spanners, obtaining the first such results. First, we observe that lightness can be unbounded if we use the traditional definition (normalizing by the MST). We then argue that a natural definition of fault-tolerant lightness is to instead normalize by a min-weight fault tolerant connectivity preserver; essentially, a fault-tolerant version of the MST. However, even with this, we show that it is still not generally possible to construct f-EFT spanners whose weight compares reasonably to the weight of a min-weight f-EFT connectivity preserver. In light of this lower bound, it is natural to then consider bicriteria notions of lightness, where we compare the weight of an f-EFT spanner to a min-weight (f' > f)-EFT connectivity preserver. The most interesting question is to determine the minimum value of f' that allows for reasonable lightness upper bounds. Our main result is a precise answer to this question: f' = 2f. In particular, we show that the lightness can be untenably large (roughly n/k for a k-spanner) if one normalizes by the min-weight (2f-1)-EFT connectivity preserver. But if one normalizes by the min-weight 2f-EFT connectivity preserver, then we show that the lightness is bounded by just O(f^{1/2}) times the non-fault tolerant lightness (roughly n^{1/k} for a (1+ε)(2k-1)-spanner).
Cite as

Greg Bodwin, Michael Dinitz, Ama Koranteng, and Lily Wang. Light Edge Fault Tolerant Graph Spanners. In 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 334, pp. 32:1-32:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{bodwin_et_al:LIPIcs.ICALP.2025.32,
  author =	{Bodwin, Greg and Dinitz, Michael and Koranteng, Ama and Wang, Lily},
  title =	{{Light Edge Fault Tolerant Graph Spanners}},
  booktitle =	{52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)},
  pages =	{32:1--32:20},
  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.2025.32},
  URN =		{urn:nbn:de:0030-drops-234093},
  doi =		{10.4230/LIPIcs.ICALP.2025.32},
  annote =	{Keywords: Fault Tolerant Spanners, Light Spanners}
}
Document
Track A: Algorithms, Complexity and Games
DOI: 10.4230/LIPIcs.ICALP.2025.95
ARRIVAL: Recursive Framework & 𝓁₁-Contraction

Authors: Sebastian Haslebacher

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

Abstract
ARRIVAL is the problem of deciding which out of two possible destinations will be reached first by a token that moves deterministically along the edges of a directed graph, according to so-called switching rules. It is known to lie in NP ∩ CoNP, but not known to lie in 𝖯. The state-of-the-art algorithm due to Gärtner et al. (ICALP `21) runs in time 2^{𝒪(√n log n)} on an n-vertex graph. We prove that ARRIVAL can be solved in time 2^{𝒪(k log² n)} on n-vertex graphs of treewidth k. Our algorithm is derived by adapting a simple recursive algorithm for a generalization of ARRIVAL called G-ARRIVAL. This simple recursive algorithm acts as a framework from which we can also rederive the subexponential upper bound of Gärtner et al. Our second result is a reduction from G-ARRIVAL to the problem of finding an approximate fixed point of an 𝓁₁-contracting function f : [0, 1]ⁿ → [0, 1]ⁿ. Finding such fixed points is a well-studied problem in the case of the 𝓁₂-metric and the 𝓁_∞-metric, but little is known about the 𝓁₁-case. Both of our results highlight parallels between ARRIVAL and the Simple Stochastic Games (SSG) problem. Concretely, Chatterjee et al. (SODA `23) gave an algorithm for SSG parameterized by treewidth that achieves a similar bound as we do for ARRIVAL, and SSG is known to reduce to 𝓁_∞-contraction.
Cite as

Sebastian Haslebacher. ARRIVAL: Recursive Framework & 𝓁₁-Contraction. In 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 334, pp. 95:1-95:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{haslebacher:LIPIcs.ICALP.2025.95,
  author =	{Haslebacher, Sebastian},
  title =	{{ARRIVAL: Recursive Framework \& 𝓁₁-Contraction}},
  booktitle =	{52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)},
  pages =	{95:1--95:17},
  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.2025.95},
  URN =		{urn:nbn:de:0030-drops-234723},
  doi =		{10.4230/LIPIcs.ICALP.2025.95},
  annote =	{Keywords: ARRIVAL, G-ARRIVAL, Deterministic Random Walk, Rotor-Routing, 𝓁₁-Contraction, Banach Fixed Point}
}
Document
DOI: 10.4230/LIPIcs.STACS.2025.39
A Quasi-Polynomial Time Algorithm for Multi-Arrival on Tree-Like Multigraphs

Authors: Ebrahim Ghorbani, Jonah Leander Hoff, and Matthias Mnich

Published in: LIPIcs, Volume 327, 42nd International Symposium on Theoretical Aspects of Computer Science (STACS 2025)

Abstract
Propp machines, or rotor-router models, are a classic tool to simulate random systems in forms of Markov chains by deterministic systems. To this end, the nodes of the Markov chain are replaced by switching nodes, which maintain a queue over their outgoing arcs, and a particle sent through the system traverses the top arc of the queue which is then moved to the end of the queue and the particle arrives at the next node. A key question to answer about such systems is whether a single particle can reach a particular target node, given as input an initial configuration of the queues at all switching nodes. This question was introduced by Dohrau et al. (2017) under the name of Arrival. A major open question is whether Arrival can be solved in polynomial time, as it is known to lie in NP ∩ co-NP; yet the fastest known algorithm for general instances takes subexponential time (Gärtner et al., ICALP 2021). We consider a generalized version of Arrival introduced by Auger et al. (RP 2023), which requires routing multiple (potentially exponentially many) particles through a rotor graph. The Multi-Arrival problem is to determine the particle configuration that results from moving all particles from a given initial configuration to sinks. Auger et al. showed that for path-like rotor graphs with a certain uniform rotor order, the problem can be solved in polynomial time. Our main result is a quasi-polynomial-time algorithm for Multi-Arrival on tree-like rotor graphs for arbitrary rotor orders. Tree-like rotor graphs are directed multigraphs which can be obtained from undirected trees by replacing each edge by an arbitrary number of arcs in either or both directions. For trees of bounded contracted height, such as paths, the algorithm runs in polynomial time and thereby generalizes the result by Auger et al.. Moreover, we give a polynomial-time algorithm for Multi-Arrival on tree-like rotor graphs without parallel arcs.
Cite as

Ebrahim Ghorbani, Jonah Leander Hoff, and Matthias Mnich. A Quasi-Polynomial Time Algorithm for Multi-Arrival on Tree-Like Multigraphs. In 42nd International Symposium on Theoretical Aspects of Computer Science (STACS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 327, pp. 39:1-39:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{ghorbani_et_al:LIPIcs.STACS.2025.39,
  author =	{Ghorbani, Ebrahim and Leander Hoff, Jonah and Mnich, Matthias},
  title =	{{A Quasi-Polynomial Time Algorithm for Multi-Arrival on Tree-Like Multigraphs}},
  booktitle =	{42nd International Symposium on Theoretical Aspects of Computer Science (STACS 2025)},
  pages =	{39:1--39:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-365-2},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{327},
  editor =	{Beyersdorff, Olaf and Pilipczuk, Micha{\l} and Pimentel, Elaine and Thắng, Nguy\~{ê}n Kim},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.STACS.2025.39},
  URN =		{urn:nbn:de:0030-drops-228658},
  doi =		{10.4230/LIPIcs.STACS.2025.39},
  annote =	{Keywords: Arrival, Rotor-routing, Tree-like Multigraph, Path-Like Multigraph, Fixed-Parameter Tractability}
}
Document
DOI: 10.4230/LIPIcs.ITCS.2025.11
Rank Lower Bounds on Non-Local Quantum Computation

Authors: Vahid R. Asadi, Eric Culf, and Alex May

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

Abstract
A non-local quantum computation (NLQC) replaces an interaction between two quantum systems with a single simultaneous round of communication and shared entanglement. We study two classes of NLQC, f-routing and f-BB84, which are of relevance to classical information theoretic cryptography and quantum position-verification. We give the first non-trivial lower bounds on entanglement in both settings, but are restricted to lower bounding protocols with perfect correctness. Within this setting, we give a lower bound on the Schmidt rank of any entangled state that completes these tasks for a given function f(x,y) in terms of the rank of a matrix g(x,y) whose entries are zero when f(x,y) = 0, and strictly positive otherwise. This also leads to a lower bound on the Schmidt rank in terms of the non-deterministic quantum communication complexity of f(x,y). Because of a relationship between f-routing and the conditional disclosure of secrets (CDS) primitive studied in information theoretic cryptography, we obtain a new technique for lower bounding the randomness complexity of CDS.
Cite as

Vahid R. Asadi, Eric Culf, and Alex May. Rank Lower Bounds on Non-Local Quantum Computation. In 16th Innovations in Theoretical Computer Science Conference (ITCS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 325, pp. 11:1-11:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{asadi_et_al:LIPIcs.ITCS.2025.11,
  author =	{Asadi, Vahid R. and Culf, Eric and May, Alex},
  title =	{{Rank Lower Bounds on Non-Local Quantum Computation}},
  booktitle =	{16th Innovations in Theoretical Computer Science Conference (ITCS 2025)},
  pages =	{11:1--11:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-361-4},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{325},
  editor =	{Meka, Raghu},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITCS.2025.11},
  URN =		{urn:nbn:de:0030-drops-226399},
  doi =		{10.4230/LIPIcs.ITCS.2025.11},
  annote =	{Keywords: Non-local quantum computation, quantum position-verification, conditional disclosure of secrets}
}
Document
Resource Paper
DOI: 10.4230/TGDK.2.2.7
Whelk: An OWL EL+RL Reasoner Enabling New Use Cases

Authors: James P. Balhoff and Christopher J. Mungall

Published in: TGDK, Volume 2, Issue 2 (2024): Special Issue on Resources for Graph Data and Knowledge. Transactions on Graph Data and Knowledge, Volume 2, Issue 2

Abstract
Many tasks in the biosciences rely on reasoning with large OWL terminologies (Tboxes), often combined with even larger databases. In particular, a common task is retrieval queries that utilize relational expressions; for example, “find all genes expressed in the brain or any part of the brain”. Automated reasoning on these ontologies typically relies on scalable reasoners targeting the EL subset of OWL, such as ELK. While the introduction of ELK has been transformative in the incorporation of reasoning into bio-ontology quality control and production pipelines, we have encountered limitations when applying it to use cases involving high throughput query answering or reasoning about datasets describing instances (Aboxes). Whelk is a fast OWL reasoner for combined EL+RL reasoning. As such, it is particularly useful for many biological ontology tasks, particularly those characterized by large Tboxes using the EL subset of OWL, combined with Aboxes targeting the RL subset of OWL. Whelk is implemented in Scala and utilizes immutable functional data structures, which provides advantages when performing incremental or dynamic reasoning tasks. Whelk supports querying complex class expressions at a substantially greater rate than ELK, and can answer queries or perform incremental reasoning tasks in parallel, enabling novel applications of OWL reasoning.
Cite as

James P. Balhoff and Christopher J. Mungall. Whelk: An OWL EL+RL Reasoner Enabling New Use Cases. In Special Issue on Resources for Graph Data and Knowledge. Transactions on Graph Data and Knowledge (TGDK), Volume 2, Issue 2, pp. 7:1-7:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@Article{balhoff_et_al:TGDK.2.2.7,
  author =	{Balhoff, James P. and Mungall, Christopher J.},
  title =	{{Whelk: An OWL EL+RL Reasoner Enabling New Use Cases}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{7:1--7:17},
  ISSN =	{2942-7517},
  year =	{2024},
  volume =	{2},
  number =	{2},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.2.2.7},
  URN =		{urn:nbn:de:0030-drops-225918},
  doi =		{10.4230/TGDK.2.2.7},
  annote =	{Keywords: Web Ontology Language, OWL, Semantic Web, ontology, reasoner}
}
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
DOI: 10.4230/LIPIcs.ICALP.2017.33
Reordering Buffer Management with a Logarithmic Guarantee in General Metric Spaces

Authors: Matthias Kohler and Harald Räcke

Published in: LIPIcs, Volume 80, 44th International Colloquium on Automata, Languages, and Programming (ICALP 2017)

Abstract
In the reordering buffer management problem a sequence of requests arrive online in a finite metric space, and have to be processed by a single server. This server is equipped with a request buffer of size k and can decide at each point in time, which request from its buffer to serve next. Servicing of a request is simply done by moving the server to the location of the request. The goal is to process all requests while minimizing the total distance that the server is traveling inside the metric space. In this paper we present a deterministic algorithm for the reordering buffer management problem that achieves a competitive ratio of O(log Delta + min {log n,log k}) in a finite metric space of n points and aspect ratio Delta. This is the first algorithm that works for general metric spaces and has just a logarithmic dependency on the relevant parameters. The guarantee is memory-robust, i.e., the competitive ratio decreases only slightly when the buffer-size of the optimum is increased to h=(1+\epsilon)k. For memory robust guarantees our bounds are close to optimal.
Cite as

Matthias Kohler and Harald Räcke. Reordering Buffer Management with a Logarithmic Guarantee in General Metric Spaces. In 44th International Colloquium on Automata, Languages, and Programming (ICALP 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 80, pp. 33:1-33:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)

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@InProceedings{kohler_et_al:LIPIcs.ICALP.2017.33,
  author =	{Kohler, Matthias and R\"{a}cke, Harald},
  title =	{{Reordering Buffer Management with a Logarithmic Guarantee in General Metric Spaces}},
  booktitle =	{44th International Colloquium on Automata, Languages, and Programming (ICALP 2017)},
  pages =	{33:1--33:12},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-041-5},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{80},
  editor =	{Chatzigiannakis, Ioannis and Indyk, Piotr and Kuhn, Fabian and Muscholl, Anca},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2017.33},
  URN =		{urn:nbn:de:0030-drops-73882},
  doi =		{10.4230/LIPIcs.ICALP.2017.33},
  annote =	{Keywords: Online algorithms, reordering buffer, metric spaces, scheduling}
}
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