11 Search Results for "Cooper, Jacob W."

Document
DOI: 10.4230/LIPIcs.ITCS.2026.61
Random Unitaries in Constant (Quantum) Time

Authors: Ben Foxman, Natalie Parham, Francisca Vasconcelos, and Henry Yuen

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

Abstract
Random unitaries are a central object of study in quantum information, with applications to quantum computation, quantum many-body physics, and quantum cryptography. Recent work has constructed unitary designs and pseudorandom unitaries (PRUs) using Θ(log log n)-depth unitary circuits with two-qubit gates. In this work, we show that unitary designs and PRUs can be efficiently constructed in several well-studied models of constant-time quantum computation (i.e., the time complexity on the quantum computer is independent of the system size). These models are constant-depth circuits augmented with certain nonlocal operations, such as (a) many-qubit TOFFOLI gates, (b) many-qubit FANOUT gates, or (c) mid-circuit measurements with classical feedforward control. Recent advances in quantum computing hardware suggest experimental feasibility of these models in the near future. Our results demonstrate that unitary designs and PRUs can be constructed in much weaker circuit models than previously thought. Furthermore, our construction of PRUs in constant-depth with many-qubit TOFFOLI gates shows that, under cryptographic assumptions, there is no polynomial-time learning algorithm for the circuit class QAC⁰. Finally, our results suggest a new approach towards proving that PARITY is not computable in QAC⁰, a long-standing question in quantum complexity theory.
Cite as

Ben Foxman, Natalie Parham, Francisca Vasconcelos, and Henry Yuen. Random Unitaries in Constant (Quantum) Time. In 17th Innovations in Theoretical Computer Science Conference (ITCS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 362, pp. 61:1-61:25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{foxman_et_al:LIPIcs.ITCS.2026.61,
  author =	{Foxman, Ben and Parham, Natalie and Vasconcelos, Francisca and Yuen, Henry},
  title =	{{Random Unitaries in Constant (Quantum) Time}},
  booktitle =	{17th Innovations in Theoretical Computer Science Conference (ITCS 2026)},
  pages =	{61:1--61:25},
  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.2026.61},
  URN =		{urn:nbn:de:0030-drops-253481},
  doi =		{10.4230/LIPIcs.ITCS.2026.61},
  annote =	{Keywords: Quantum Information, Pseudorandomness, Circuit Complexity}
}
Document
Invited Talk
DOI: 10.4230/LIPIcs.IPEC.2025.1
A Brief History of Parameterized Algorithms for Block-Structured Integer Programs (Invited Talk)

Authors: Martin Koutecký

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

Abstract
Integer Programming (IP) is a fundamental but computationally hard problem. Still, certain efficiently solvable subclasses have been identified over time, most notably totally unimodular IPs in the 1950s, and fixed-dimension IPs in the 1980s. Starting around the year 2000, a stream of research has identified block-structured IPs as yet another tractable subclass. In this paper, we give a brief and incomplete review of this history, with a focus on several of the author’s contributions.
Cite as

Martin Koutecký. A Brief History of Parameterized Algorithms for Block-Structured Integer Programs (Invited Talk). In 20th International Symposium on Parameterized and Exact Computation (IPEC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 358, pp. 1:1-1:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{koutecky:LIPIcs.IPEC.2025.1,
  author =	{Kouteck\'{y}, Martin},
  title =	{{A Brief History of Parameterized Algorithms for Block-Structured Integer Programs}},
  booktitle =	{20th International Symposium on Parameterized and Exact Computation (IPEC 2025)},
  pages =	{1:1--1:20},
  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.2025.1},
  URN =		{urn:nbn:de:0030-drops-251338},
  doi =		{10.4230/LIPIcs.IPEC.2025.1},
  annote =	{Keywords: Integer Programming, Parameterized Algorithm, Graver Basis, Treedepth, n-fold, tree-fold, 2-stage stochastic, multistage stochastic, Mixed-Integer Programming}
}
Document
DOI: 10.4230/LIPIcs.FSTTCS.2025.21
Overlay Network Construction: Improved Overall and Node-Wise Message Complexity

Authors: Yi-Jun Chang, Yanyu Chen, and Gopinath Mishra

Published in: LIPIcs, Volume 360, 45th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2025)

Abstract
We consider the problem of constructing distributed overlay networks, where nodes in a reconfigurable system can create or sever connections with nodes whose identifiers they know. Initially, each node knows only its own and its neighbors' identifiers, forming a local channel, while the evolving structure is termed the global channel. The goal is to reconfigure any connected graph into a desired topology, such as a bounded-degree expander graph or a well-formed tree (WFT) with a constant maximum degree and logarithmic diameter, minimizing the total number of rounds and message complexity. This problem mirrors real-world peer-to-peer network construction, where creating robust and efficient systems is desired. We study the overlay reconstruction problem in a network of n nodes in two models: GOSSIP-reply and HYBRID. In the GOSSIP-reply model, each node can send a message and receive a corresponding reply message in one round. In the HYBRID model, a node can send O(1) messages to each neighbor in the local channel and a total of O(log n) messages in the global channel. In both models, we propose protocols for WFT construction with O (n log n) message complexities using messages of O(log n) bits. In the GOSSIP-reply model, our protocol takes O(log n) rounds while in the HYBRID model, our protocol takes O(log² n) rounds. Both protocols use O (n log² n) bits of communication. We obtain improved bounds over prior work: GOSSIP-reply: A recent result by Dufoulon et al. (ITCS 2024) achieved O(log⁵ n) round complexity and O (n log⁵ n) message complexity using messages of at least Ω(log² n) bits in GOSSIP-reply. With messages of size O(log n), our protocol achieves an optimal round complexity of O(log n) and an improved message complexity of O(n log n). HYBRID: Götte et al. (Distributed Computing 2023) showed an optimal O(log n)-round algorithm with O(log² n) global messages per round which incurs a message complexity of Ω(m), where m is the number of edges in the initial topology. At the cost of increasing the round complexity to O(log² n) while using only O(log n) messages globally, our protocol achieves a message complexity that is independent of m. Our approach ensures that the total number of messages for node v, with degree deg(v) in the initial topology, is bounded by O(deg(v) + log n), while the algorithm of Götte et al. requires O(deg(v) + (log⁴ n)/(log log n)) messages per node.
Cite as

Yi-Jun Chang, Yanyu Chen, and Gopinath Mishra. Overlay Network Construction: Improved Overall and Node-Wise Message Complexity. In 45th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 360, pp. 21:1-21:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{chang_et_al:LIPIcs.FSTTCS.2025.21,
  author =	{Chang, Yi-Jun and Chen, Yanyu and Mishra, Gopinath},
  title =	{{Overlay Network Construction: Improved Overall and Node-Wise Message Complexity}},
  booktitle =	{45th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2025)},
  pages =	{21:1--21:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-406-2},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{360},
  editor =	{Aiswarya, C. and Mehta, Ruta and Roy, Subhajit},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FSTTCS.2025.21},
  URN =		{urn:nbn:de:0030-drops-251025},
  doi =		{10.4230/LIPIcs.FSTTCS.2025.21},
  annote =	{Keywords: Distributed algorithms, Overlay networks, Expander graphs}
}
Document
DOI: 10.4230/LIPIcs.TQC.2025.9
Efficient Quantum Pseudorandomness from Hamiltonian Phase States

Authors: John Bostanci, Jonas Haferkamp, Dominik Hangleiter, and Alexander Poremba

Published in: LIPIcs, Volume 350, 20th Conference on the Theory of Quantum Computation, Communication and Cryptography (TQC 2025)

Abstract
Quantum pseudorandomness has found applications in many areas of quantum information, ranging from entanglement theory, to models of scrambling phenomena in chaotic quantum systems, and, more recently, in the foundations of quantum cryptography. Kretschmer (TQC '21) showed that both pseudorandom states and pseudorandom unitaries exist even in a world without classical one-way functions. To this day, however, all known constructions require classical cryptographic building blocks which are themselves synonymous with the existence of one-way functions, and which are also challenging to implement on realistic quantum hardware. In this work, we seek to make progress on both of these fronts simultaneously - by decoupling quantum pseudorandomness from classical cryptography altogether. We introduce a quantum hardness assumption called the Hamiltonian Phase State (HPS) problem, which is the task of decoding output states of a random instantaneous quantum polynomial-time (IQP) circuit. Hamiltonian phase states can be generated very efficiently using only Hadamard gates, single-qubit Z rotations and CNOT circuits. We show that the hardness of our problem reduces to a worst-case version of the problem, and we provide evidence that our assumption is plausibly fully quantum; meaning, it cannot be used to construct one-way functions. We also show information-theoretic hardness when only few copies of HPS are available by proving an approximate t-design property of our ensemble. Finally, we show that our HPS assumption and its variants allow us to efficiently construct many pseudorandom quantum primitives, ranging from pseudorandom states, to quantum pseudoentanglement, to pseudorandom unitaries, and even primitives such as public-key encryption with quantum keys.
Cite as

John Bostanci, Jonas Haferkamp, Dominik Hangleiter, and Alexander Poremba. Efficient Quantum Pseudorandomness from Hamiltonian Phase States. In 20th Conference on the Theory of Quantum Computation, Communication and Cryptography (TQC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 350, pp. 9:1-9:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{bostanci_et_al:LIPIcs.TQC.2025.9,
  author =	{Bostanci, John and Haferkamp, Jonas and Hangleiter, Dominik and Poremba, Alexander},
  title =	{{Efficient Quantum Pseudorandomness from Hamiltonian Phase States}},
  booktitle =	{20th Conference on the Theory of Quantum Computation, Communication and Cryptography (TQC 2025)},
  pages =	{9:1--9:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-392-8},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{350},
  editor =	{Fefferman, Bill},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.TQC.2025.9},
  URN =		{urn:nbn:de:0030-drops-240586},
  doi =		{10.4230/LIPIcs.TQC.2025.9},
  annote =	{Keywords: Quantum pseudorandomness, quantum phase states, quantum cryptography}
}
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
Track A: Algorithms, Complexity and Games
DOI: 10.4230/LIPIcs.ICALP.2025.24
Counting Permutation Patterns with Multidimensional Trees

Authors: Gal Beniamini and Nir Lavee

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

Abstract
We consider the well-studied pattern-counting problem: given a permutation π ∈ 𝕊_n and an integer k > 1, count the number of order-isomorphic occurrences of every pattern τ ∈ 𝕊_k in π. Our first result is an 𝒪̃(n²)-time algorithm for k = 6 and k = 7. The proof relies heavily on a new family of graphs that we introduce, called pattern-trees. Every such tree corresponds to an integer linear combination of permutations in 𝕊_k, and is associated with linear extensions of partially ordered sets. We design an evaluation algorithm for these combinations, and apply it to a family of linearly-independent trees. For k = 8, we show a barrier: the subspace spanned by trees in the previous family has dimension exactly |𝕊₈| - 1, one less than required. Our second result is an 𝒪̃(n^{7/4})-time algorithm for k = 5. This algorithm extends the framework of pattern-trees by speeding-up their evaluation in certain cases. A key component of the proof is the introduction of pair-rectangle-trees, a data structure for dominance counting.
Cite as

Gal Beniamini and Nir Lavee. Counting Permutation Patterns with Multidimensional Trees. In 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 334, pp. 24:1-24:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{beniamini_et_al:LIPIcs.ICALP.2025.24,
  author =	{Beniamini, Gal and Lavee, Nir},
  title =	{{Counting Permutation Patterns with Multidimensional Trees}},
  booktitle =	{52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)},
  pages =	{24:1--24:18},
  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.2025.24},
  URN =		{urn:nbn:de:0030-drops-234018},
  doi =		{10.4230/LIPIcs.ICALP.2025.24},
  annote =	{Keywords: Pattern counting, patterns, permutations}
}
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.2.1.2
Grounding Stream Reasoning Research

Authors: Pieter Bonte, Jean-Paul Calbimonte, Daniel de Leng, Daniele Dell'Aglio, Emanuele Della Valle, Thomas Eiter, Federico Giannini, Fredrik Heintz, Konstantin Schekotihin, Danh Le-Phuoc, Alessandra Mileo, Patrik Schneider, Riccardo Tommasini, Jacopo Urbani, and Giacomo Ziffer

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
In the last decade, there has been a growing interest in applying AI technologies to implement complex data analytics over data streams. To this end, researchers in various fields have been organising a yearly event called the "Stream Reasoning Workshop" to share perspectives, challenges, and experiences around this topic. In this paper, the previous organisers of the workshops and other community members provide a summary of the main research results that have been discussed during the first six editions of the event. These results can be categorised into four main research areas: The first is concerned with the technological challenges related to handling large data streams. The second area aims at adapting and extending existing semantic technologies to data streams. The third and fourth areas focus on how to implement reasoning techniques, either considering deductive or inductive techniques, to extract new and valuable knowledge from the data in the stream. This summary is written not only to provide a crystallisation of the field, but also to point out distinctive traits of the stream reasoning community. Moreover, it also provides a foundation for future research by enumerating a list of use cases and open challenges, to stimulate others to join this exciting research area.
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Pieter Bonte, Jean-Paul Calbimonte, Daniel de Leng, Daniele Dell'Aglio, Emanuele Della Valle, Thomas Eiter, Federico Giannini, Fredrik Heintz, Konstantin Schekotihin, Danh Le-Phuoc, Alessandra Mileo, Patrik Schneider, Riccardo Tommasini, Jacopo Urbani, and Giacomo Ziffer. Grounding Stream Reasoning Research. In Special Issue on Trends in Graph Data and Knowledge - Part 2. Transactions on Graph Data and Knowledge (TGDK), Volume 2, Issue 1, pp. 2:1-2:47, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@Article{bonte_et_al:TGDK.2.1.2,
  author =	{Bonte, Pieter and Calbimonte, Jean-Paul and de Leng, Daniel and Dell'Aglio, Daniele and Della Valle, Emanuele and Eiter, Thomas and Giannini, Federico and Heintz, Fredrik and Schekotihin, Konstantin and Le-Phuoc, Danh and Mileo, Alessandra and Schneider, Patrik and Tommasini, Riccardo and Urbani, Jacopo and Ziffer, Giacomo},
  title =	{{Grounding Stream Reasoning Research}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{2:1--2:47},
  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.2.1.2},
  URN =		{urn:nbn:de:0030-drops-198597},
  doi =		{10.4230/TGDK.2.1.2},
  annote =	{Keywords: Stream Reasoning, Stream Processing, RDF streams, Streaming Linked Data, Continuous query processing, Temporal Logics, High-performance computing, Databases}
}
Document
Vision
DOI: 10.4230/TGDK.1.1.9
Trust, Accountability, and Autonomy in Knowledge Graph-Based AI for Self-Determination

Authors: Luis-Daniel Ibáñez, John Domingue, Sabrina Kirrane, Oshani Seneviratne, Aisling Third, and Maria-Esther Vidal

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
Knowledge Graphs (KGs) have emerged as fundamental platforms for powering intelligent decision-making and a wide range of Artificial Intelligence (AI) services across major corporations such as Google, Walmart, and AirBnb. KGs complement Machine Learning (ML) algorithms by providing data context and semantics, thereby enabling further inference and question-answering capabilities. The integration of KGs with neuronal learning (e.g., Large Language Models (LLMs)) is currently a topic of active research, commonly named neuro-symbolic AI. Despite the numerous benefits that can be accomplished with KG-based AI, its growing ubiquity within online services may result in the loss of self-determination for citizens as a fundamental societal issue. The more we rely on these technologies, which are often centralised, the less citizens will be able to determine their own destinies. To counter this threat, AI regulation, such as the European Union (EU) AI Act, is being proposed in certain regions. The regulation sets what technologists need to do, leading to questions concerning How the output of AI systems can be trusted? What is needed to ensure that the data fuelling and the inner workings of these artefacts are transparent? How can AI be made accountable for its decision-making? This paper conceptualises the foundational topics and research pillars to support KG-based AI for self-determination. Drawing upon this conceptual framework, challenges and opportunities for citizen self-determination are illustrated and analysed in a real-world scenario. As a result, we propose a research agenda aimed at accomplishing the recommended objectives.
Cite as

Luis-Daniel Ibáñez, John Domingue, Sabrina Kirrane, Oshani Seneviratne, Aisling Third, and Maria-Esther Vidal. Trust, Accountability, and Autonomy in Knowledge Graph-Based AI for Self-Determination. In Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge (TGDK), Volume 1, Issue 1, pp. 9:1-9:32, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@Article{ibanez_et_al:TGDK.1.1.9,
  author =	{Ib\'{a}\~{n}ez, Luis-Daniel and Domingue, John and Kirrane, Sabrina and Seneviratne, Oshani and Third, Aisling and Vidal, Maria-Esther},
  title =	{{Trust, Accountability, and Autonomy in Knowledge Graph-Based AI for Self-Determination}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{9:1--9:32},
  ISSN =	{2942-7517},
  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.1.1.9},
  URN =		{urn:nbn:de:0030-drops-194839},
  doi =		{10.4230/TGDK.1.1.9},
  annote =	{Keywords: Trust, Accountability, Autonomy, AI, Knowledge Graphs}
}
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)

Copy BibTex To Clipboard

@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
Track A: Algorithms, Complexity and Games
DOI: 10.4230/LIPIcs.ICALP.2020.26
Matrices of Optimal Tree-Depth and Row-Invariant Parameterized Algorithm for Integer Programming

Authors: Timothy F. N. Chan, Jacob W. Cooper, Martin Koutecký, Daniel Král', and Kristýna Pekárková

Published in: LIPIcs, Volume 168, 47th International Colloquium on Automata, Languages, and Programming (ICALP 2020)

Abstract
A long line of research on fixed parameter tractability of integer programming culminated with showing that integer programs with n variables and a constraint matrix with tree-depth d and largest entry Δ are solvable in time g(d,Δ) poly(n) for some function g, i.e., fixed parameter tractable when parameterized by tree-depth d and Δ. However, the tree-depth of a constraint matrix depends on the positions of its non-zero entries and thus does not reflect its geometric structure. In particular, tree-depth of a constraint matrix is not preserved by row operations, i.e., a given integer program can be equivalent to another with a smaller dual tree-depth. We prove that the branch-depth of the matroid defined by the columns of the constraint matrix is equal to the minimum tree-depth of a row-equivalent matrix. We also design a fixed parameter algorithm parameterized by an integer d and the entry complexity of an input matrix that either outputs a matrix with the smallest dual tree-depth that is row-equivalent to the input matrix or outputs that there is no matrix with dual tree-depth at most d that is row-equivalent to the input matrix. Finally, we use these results to obtain a fixed parameter algorithm for integer programming parameterized by the branch-depth of the input constraint matrix and the entry complexity. The parameterization by branch-depth cannot be replaced by the more permissive notion of branch-width.
Cite as

Timothy F. N. Chan, Jacob W. Cooper, Martin Koutecký, Daniel Král', and Kristýna Pekárková. Matrices of Optimal Tree-Depth and Row-Invariant Parameterized Algorithm for Integer Programming. In 47th International Colloquium on Automata, Languages, and Programming (ICALP 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 168, pp. 26:1-26:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@InProceedings{chan_et_al:LIPIcs.ICALP.2020.26,
  author =	{Chan, Timothy F. N. and Cooper, Jacob W. and Kouteck\'{y}, Martin and Kr\'{a}l', Daniel and Pek\'{a}rkov\'{a}, Krist\'{y}na},
  title =	{{Matrices of Optimal Tree-Depth and Row-Invariant Parameterized Algorithm for Integer Programming}},
  booktitle =	{47th International Colloquium on Automata, Languages, and Programming (ICALP 2020)},
  pages =	{26:1--26:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-138-2},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{168},
  editor =	{Czumaj, Artur and Dawar, Anuj and Merelli, Emanuela},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2020.26},
  URN =		{urn:nbn:de:0030-drops-124339},
  doi =		{10.4230/LIPIcs.ICALP.2020.26},
  annote =	{Keywords: Matroid algorithms, width parameters, integer programming, fixed parameter tractability, branch-width, branch-depth}
}
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