7 Search Results for "Turner, Andrew"

Document
DOI: 10.4230/LIPIcs.OPODIS.2025.10
Computing in a Faulty Congested Clique

Authors: Keren Censor-Hillel and Pedro Soto

Published in: LIPIcs, Volume 361, 29th International Conference on Principles of Distributed Systems (OPODIS 2025)

Abstract
We study a Faulty Congested Clique model, in which an adversary may fail nodes in the network throughout the computation. We show that any task of O(nlog{n})-bit input per node can be solved in roughly n rounds, where n is the size of the network. This nearly matches the linear upper bound on the complexity of the non-faulty Congested Clique model for such problems, by learning the entire input, and it holds in the faulty model even with a linear number of faults. Our main contribution is that we establish that one can do much better by looking more closely at the computation. Given a deterministic algorithm 𝒜 for the non-faulty Congested Clique model, we show how to transform it into an algorithm 𝒜' for the faulty model, with an overhead that could be as small as some logarithmic-in-n factor, by considering refined complexity measures of 𝒜. As an exemplifying application of our approach, we show that the O(n^{1/3})-round complexity of semi-ring matrix multiplication [Censor{-}Hillel, Kaski, Korhonen, Lenzen, Paz, Suomela, PODC 2015] remains the same up to polylog factors in the faulty model, even if the adversary can fail 99% of the nodes (or any other constant fraction).
Cite as

Keren Censor-Hillel and Pedro Soto. Computing in a Faulty Congested Clique. In 29th International Conference on Principles of Distributed Systems (OPODIS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 361, pp. 10:1-10:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{censorhillel_et_al:LIPIcs.OPODIS.2025.10,
  author =	{Censor-Hillel, Keren and Soto, Pedro},
  title =	{{Computing in a Faulty Congested Clique}},
  booktitle =	{29th International Conference on Principles of Distributed Systems (OPODIS 2025)},
  pages =	{10:1--10:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-409-3},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{361},
  editor =	{Arusoaie, Andrei and Onica, Emanuel and Spear, Michael and Tucci-Piergiovanni, Sara},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.OPODIS.2025.10},
  URN =		{urn:nbn:de:0030-drops-251833},
  doi =		{10.4230/LIPIcs.OPODIS.2025.10},
  annote =	{Keywords: distributed computing, graph algorithms, computing with faults}
}
Document
RANDOM
DOI: 10.4230/LIPIcs.APPROX/RANDOM.2025.61
A Fast Coloring Oracle for Average Case Hypergraphs

Authors: Cassandra Marcussen, Edward Pyne, Ronitt Rubinfeld, Asaf Shapira, and Shlomo Tauber

Published in: LIPIcs, Volume 353, Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025)

Abstract
Hypergraph 2-colorability is one of the classical NP-hard problems. Person and Schacht [SODA'09] designed a deterministic algorithm whose expected running time is polynomial over a uniformly chosen 2-colorable 3-uniform hypergraph. Lee, Molla, and Nagle recently extended this to k-uniform hypergraphs for all k ≥ 3. Both papers relied heavily on the regularity lemma, hence their analysis was involved and their running time hid tower-type constants. Our first result in this paper is a new simple and elementary deterministic 2-coloring algorithm that reproves the theorems of Person-Schacht and Lee-Molla-Nagle while avoiding the use of the regularity lemma. We also show how to turn our new algorithm into a randomized one with average expected running time of only O(n). Our second and main result gives what we consider to be the ultimate evidence of just how easy it is to find a 2-coloring of an average 2-colorable hypergraph. We define a coloring oracle to be an algorithm which, given vertex v, assigns color red/blue to v while inspecting as few edges as possible, so that the answers to any sequence of queries to the oracle are consistent with a single legal 2-coloring of the input. Surprisingly, we show that there is a coloring oracle that, on average, can answer every vertex query in time O(1).
Cite as

Cassandra Marcussen, Edward Pyne, Ronitt Rubinfeld, Asaf Shapira, and Shlomo Tauber. A Fast Coloring Oracle for Average Case Hypergraphs. In Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 353, pp. 61:1-61:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{marcussen_et_al:LIPIcs.APPROX/RANDOM.2025.61,
  author =	{Marcussen, Cassandra and Pyne, Edward and Rubinfeld, Ronitt and Shapira, Asaf and Tauber, Shlomo},
  title =	{{A Fast Coloring Oracle for Average Case Hypergraphs}},
  booktitle =	{Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025)},
  pages =	{61:1--61:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-397-3},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{353},
  editor =	{Ene, Alina and Chattopadhyay, Eshan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.APPROX/RANDOM.2025.61},
  URN =		{urn:nbn:de:0030-drops-244272},
  doi =		{10.4230/LIPIcs.APPROX/RANDOM.2025.61},
  annote =	{Keywords: average-case algorithms, local computation algorithms, graph coloring}
}
Document
DOI: 10.4230/LIPIcs.WABI.2025.13
Spark: Sparsified Hierarchical Energy Minimization of RNA Pseudoknots

Authors: Mateo Gray, Sebastian Will, and Hosna Jabbari

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

Abstract
Motivation. Determining RNA structure is essential for understanding RNA function and interaction networks. Although experimental techniques yield high‑accuracy structures, they are costly and time‑consuming; thus, computational approaches - especially minimum‑free‑energy (MFE) prediction algorithms - are indispensable. Accurately predicting pseudoknots, however, remains challenging because their inclusion usually leads to prohibitive computational complexity. Recent work demonstrated that sparsification can improve the efficiency of complex pseudoknot prediction algorithms such as Knotty. This finding suggests similar gains are possible for already efficient algorithms like HFold, which targets a complementary class of hierarchically constrained pseudoknots. Results. We introduce Spark, an exact, fully sparsified algorithm for predicting pseudoknotted RNA structures. Like its non‑sparsified predecessor HFold, Spark searches for the minimum‑energy structure under the HotKots 2.0 energy model, a pseudoknot extension of the Turner model. Because the sparsification is non‑heuristic, Spark preserves the asymptotic time‑ and space‑complexity guarantees of HFold while greatly reducing the constant factors. We benchmarked the performance of Spark against HFold and, as a pseudoknot‑free baseline, RNAfold. Compared with HFold, Spark substantially lowers both run time and memory usage, while achieving run‑time figures close to those of RNAfold. Across all tested sequence lengths, Spark used the least memory and consistently ran faster than HFold. Conclusion. By extending non‑heuristic sparsification to hierarchical pseudoknot prediction, Spark delivers an exceptionally fast and memory‑efficient tool accurate prediction of pseudoknotted RNA structures, enabling routine analysis of long sequences. The algorithm broadens the practical scope of computational RNA biology and provides a solid foundation for future advances in structure‑based functional annotation. Availability. Spark’s implementation and detailed results are available at https://github.com/TheCOBRALab/Spark.
Cite as

Mateo Gray, Sebastian Will, and Hosna Jabbari. Spark: Sparsified Hierarchical Energy Minimization of RNA Pseudoknots. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 13:1-13:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{gray_et_al:LIPIcs.WABI.2025.13,
  author =	{Gray, Mateo and Will, Sebastian and Jabbari, Hosna},
  title =	{{Spark: Sparsified Hierarchical Energy Minimization of RNA Pseudoknots}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{13:1--13:18},
  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.2025.13},
  URN =		{urn:nbn:de:0030-drops-239383},
  doi =		{10.4230/LIPIcs.WABI.2025.13},
  annote =	{Keywords: RNA, MFE, Secondary Structure Prediction, Pseudoknot, Sparsification, Space Complexity, Time Complexity}
}
Document
DOI: 10.4230/LIPIcs.FSCD.2025.5
The Cost of Skeletal Call-By-Need, Smoothly

Authors: Beniamino Accattoli, Francesco Magliocca, Loïc Peyrot, and Claudio Sacerdoti Coen

Published in: LIPIcs, Volume 337, 10th International Conference on Formal Structures for Computation and Deduction (FSCD 2025)

Abstract
Skeletal call-by-need is an optimization of call-by-need evaluation also known as "fully lazy sharing": when the duplication of a value has to take place, it is first split into "skeleton", which is then duplicated, and "flesh" which is instead kept shared. Here, we provide two cost analyses of skeletal call-by-need. Firstly, we provide a family of terms showing that skeletal call-by-need can be asymptotically exponentially faster than call-by-need in both time and space; it is the first such evidence, to our knowledge. Secondly, we prove that skeletal call-by-need can be implemented efficiently, that is, with bi-linear overhead. This result is obtained by providing a new smooth presentation of ideas by Shivers and Wand for the reconstruction of skeletons, which is then smoothly plugged into the study of an abstract machine following the distillation technique by Accattoli et al.
Cite as

Beniamino Accattoli, Francesco Magliocca, Loïc Peyrot, and Claudio Sacerdoti Coen. The Cost of Skeletal Call-By-Need, Smoothly. In 10th International Conference on Formal Structures for Computation and Deduction (FSCD 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 337, pp. 5:1-5:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{accattoli_et_al:LIPIcs.FSCD.2025.5,
  author =	{Accattoli, Beniamino and Magliocca, Francesco and Peyrot, Lo\"{i}c and Sacerdoti Coen, Claudio},
  title =	{{The Cost of Skeletal Call-By-Need, Smoothly}},
  booktitle =	{10th International Conference on Formal Structures for Computation and Deduction (FSCD 2025)},
  pages =	{5:1--5:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-374-4},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{337},
  editor =	{Fern\'{a}ndez, Maribel},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FSCD.2025.5},
  URN =		{urn:nbn:de:0030-drops-236206},
  doi =		{10.4230/LIPIcs.FSCD.2025.5},
  annote =	{Keywords: \lambda-calculus, abstract machines, call-by-need, cost models}
}
Document
Track A: Algorithms, Complexity and Games
DOI: 10.4230/LIPIcs.ICALP.2025.130
An Efficient Algorithm to Compute the Minimum Free Energy of Interacting Nucleic Acid Strands

Authors: Ahmed Shalaby and Damien Woods

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

Abstract
The information-encoding molecules RNA and DNA bind via base pairing to form an exponentially large set of secondary structures. Practitioners need algorithms to predict the most favoured structures, called minimum free energy (MFE) structures, or to compute a partition function that allows assigning a probability to any structure. MFE prediction is NP-hard in the presence pseudoknots - base pairings that violate a restricted planarity condition. However, for single-stranded unpseudoknotted structures, there are polynomial time dynamic programming algorithms. For multiple strands, the problem is significantly more complicated: Codon, Hajiaghayi and Thachuk [DNA27, 2021] proved it NP-hard for N bases and 𝒪(N) strands. Dirks, Bois, Schaeffer, Winfree and Pierce [SIAM Review, 2007] gave a polynomial time partition function algorithm for multiple (𝒪(1)) strands, now widely-used, however their technique did not generalise to MFE which they left open. We give an 𝒪(N⁴) time algorithm for unpseudoknotted multiple (𝒪(1)) strand MFE prediction, answering the open problem from Dirks et al. The challenge lies in considering the rotational symmetry of secondary structures, a global feature not immediately amenable to local subproblem decomposition used in dynamic programming. Our proof has two main technical contributions: First, a characterisation of symmetric secondary structures implying only quadratically many need to be considered when computing the rotational symmetry penalty. Second, that bound is leveraged by a backtracking algorithm to efficiently find the MFE in an exponential space of contenders.
Cite as

Ahmed Shalaby and Damien Woods. An Efficient Algorithm to Compute the Minimum Free Energy of Interacting Nucleic Acid Strands. In 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 334, pp. 130:1-130:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{shalaby_et_al:LIPIcs.ICALP.2025.130,
  author =	{Shalaby, Ahmed and Woods, Damien},
  title =	{{An Efficient Algorithm to Compute the Minimum Free Energy of Interacting Nucleic Acid Strands}},
  booktitle =	{52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)},
  pages =	{130:1--130:20},
  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.2025.130},
  URN =		{urn:nbn:de:0030-drops-235071},
  doi =		{10.4230/LIPIcs.ICALP.2025.130},
  annote =	{Keywords: Minimum free energy, MFE, partition function, nucleic acid, DNA, RNA, secondary structure, computational complexity, algorithm analysis and design, dynamic programming}
}
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.GISCIENCE.2018.9
Improving Discovery of Open Civic Data

Authors: Sara Lafia, Andrew Turner, and Werner Kuhn

Published in: LIPIcs, Volume 114, 10th International Conference on Geographic Information Science (GIScience 2018)

Abstract
We describe a method and system design for improved data discovery in an integrated network of open geospatial data that supports collaborative policy development between governments and local constituents. Metadata about civic data (such as thematic categories, user-generated tags, geo-references, or attribute schemata) primarily rely on technical vocabularies that reflect scientific or organizational hierarchies. By contrast, public consumers of data often search for information using colloquial terminology that does not align with official metadata vocabularies. For example, citizens searching for data about bicycle collisions in an area are unlikely to use the search terms with which organizations like Departments of Transportation describe relevant data. Users may also search with broad terms, such as "traffic safety", and will then not discover data tagged with narrower official terms, such as "vehicular crash". This mismatch raises the question of how to bridge the users' ways of talking and searching with the language of technical metadata. In similar situations, it has been beneficial to augment official metadata with semantic annotations that expand the discoverability and relevance recommendations of data, supporting more inclusive access. Adopting this strategy, we develop a method for automated semantic annotation, which aggregates similar thematic and geographic information. A novelty of our approach is the development and application of a crosscutting base vocabulary that supports the description of geospatial themes. The resulting annotation method is integrated into a novel open access collaboration platform (Esri's ArcGIS Hub) that supports public dissemination of civic data and is in use by thousands of government agencies. Our semantic annotation method improves data discovery for users across organizational repositories and has the potential to facilitate the coordination of community and organizational work, improving the transparency and efficacy of government policies.
Cite as

Sara Lafia, Andrew Turner, and Werner Kuhn. Improving Discovery of Open Civic Data. In 10th International Conference on Geographic Information Science (GIScience 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 114, pp. 9:1-9:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@InProceedings{lafia_et_al:LIPIcs.GISCIENCE.2018.9,
  author =	{Lafia, Sara and Turner, Andrew and Kuhn, Werner},
  title =	{{Improving Discovery of Open Civic Data}},
  booktitle =	{10th International Conference on Geographic Information Science (GIScience 2018)},
  pages =	{9:1--9:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-083-5},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{114},
  editor =	{Winter, Stephan and Griffin, Amy and Sester, Monika},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.GISCIENCE.2018.9},
  URN =		{urn:nbn:de:0030-drops-93376},
  doi =		{10.4230/LIPIcs.GISCIENCE.2018.9},
  annote =	{Keywords: data discovery, metadata, query expansion, interoperability}
}
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