23 Search Results for "Evans, William S."

Document
Invited Paper
DOI: 10.4230/OASIcs.RW.2024/2025.1
Rule-Based Knowledge Graph Completion (Invited Paper)

Authors: Patrick Betz, Christian Meilicke, and Heiner Stuckenschmidt

Published in: OASIcs, Volume 138, Joint Proceedings of the 20th and 21st Reasoning Web Summer Schools (RW 2024 & RW 2025)

Abstract
The field of knowledge graph completion is concerned with augmenting knowledge graphs with missing information. Symbolic rule-based approaches are not only efficient and interpretable but also competitive with embedding-based methods in regard to predictive quality. Rule-based knowledge graph completion can be separated into two stages, the learning stage and the application stage, which are both individually challenging. In the learning stage, horn rules are mined from a given knowledge graph. Given the vast size of the space of all possible rules, the mining approach must select relevant rules effectively. In the application stage, the mined rules are used to make new predictions which are assigned with plausibility scores. These scores need to be set by aggregating individual confidence values of rules that have the same consequence. This tutorial covers the fundamental aspects required to build a symbolic rule-based approach for knowledge graph completion. It will discuss the different rule types, mining strategies, and how to effectively apply the rules in different scenarios. Finally, we discuss practical examples for rule application by using the Python-based PyClause library.
Cite as

Patrick Betz, Christian Meilicke, and Heiner Stuckenschmidt. Rule-Based Knowledge Graph Completion (Invited Paper). In Joint Proceedings of the 20th and 21st Reasoning Web Summer Schools (RW 2024 & RW 2025). Open Access Series in Informatics (OASIcs), Volume 138, pp. 1:1-1:45, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{betz_et_al:OASIcs.RW.2024/2025.1,
  author =	{Betz, Patrick and Meilicke, Christian and Stuckenschmidt, Heiner},
  title =	{{Rule-Based Knowledge Graph Completion}},
  booktitle =	{Joint Proceedings of the 20th and 21st Reasoning Web Summer Schools (RW 2024 \& RW 2025)},
  pages =	{1:1--1:45},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-405-5},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{138},
  editor =	{Artale, Alessandro and Bienvenu, Meghyn and Garc{\'\i}a, Yazm{\'\i}n Ib\'{a}\~{n}ez and Murlak, Filip},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.RW.2024/2025.1},
  URN =		{urn:nbn:de:0030-drops-250461},
  doi =		{10.4230/OASIcs.RW.2024/2025.1},
  annote =	{Keywords: Knowledge Graph Completion, Rule Learning, Symbolic AI}
}
Document
Survey
DOI: 10.4230/TGDK.3.2.1
Resilience in Knowledge Graph Embeddings

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

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

Abstract
In recent years, knowledge graphs have gained interest and witnessed widespread applications in various domains, such as information retrieval, question-answering, recommendation systems, amongst others. Large-scale knowledge graphs to this end have demonstrated their utility in effectively representing structured knowledge. To further facilitate the application of machine learning techniques, knowledge graph embedding models have been developed. Such models can transform entities and relationships within knowledge graphs into vectors. However, these embedding models often face challenges related to noise, missing information, distribution shift, adversarial attacks, etc. This can lead to sub-optimal embeddings and incorrect inferences, thereby negatively impacting downstream applications. While the existing literature has focused so far on adversarial attacks on KGE models, the challenges related to the other critical aspects remain unexplored. In this paper, we, first of all, give a unified definition of resilience, encompassing several factors such as generalisation, in-distribution generalization, distribution adaption, and robustness. After formalizing these concepts for machine learning in general, we define them in the context of knowledge graphs. To find the gap in the existing works on resilience in the context of knowledge graphs, we perform a systematic survey, taking into account all these aspects mentioned previously. Our survey results show that most of the existing works focus on a specific aspect of resilience, namely robustness. After categorizing such works based on their respective aspects of resilience, we discuss the challenges and future research directions.
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Arnab Sharma, N'Dah Jean Kouagou, and Axel-Cyrille Ngonga Ngomo. Resilience in Knowledge Graph Embeddings. In Transactions on Graph Data and Knowledge (TGDK), Volume 3, Issue 2, pp. 1:1-1:38, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@Article{sharma_et_al:TGDK.3.2.1,
  author =	{Sharma, Arnab and Kouagou, N'Dah Jean and Ngomo, Axel-Cyrille Ngonga},
  title =	{{Resilience in Knowledge Graph Embeddings}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{1:1--1:38},
  ISSN =	{2942-7517},
  year =	{2025},
  volume =	{3},
  number =	{2},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.3.2.1},
  URN =		{urn:nbn:de:0030-drops-248117},
  doi =		{10.4230/TGDK.3.2.1},
  annote =	{Keywords: Knowledge graphs, Resilience, Robustness}
}
Document
DOI: 10.4230/LIPIcs.AFT.2025.1
Cache Timing Leakages in Zero-Knowledge Protocols

Authors: Shibam Mukherjee, Christian Rechberger, and Markus Schofnegger

Published in: LIPIcs, Volume 354, 7th Conference on Advances in Financial Technologies (AFT 2025)

Abstract
The area of modern zero-knowledge proof systems has seen a significant rise in popularity over the last couple of years, with new techniques and optimized constructions emerging on a regular basis. As the field matures, the aspect of implementation attacks becomes more relevant, however side-channel attacks on zero-knowledge proof systems have seen surprisingly little treatment so far. In this paper, we give an overview of potential attack vectors and show that some of the underlying finite field libraries, and implementations of heavily used components like hash functions using them, are vulnerable w.r.t. cache attacks on CPUs. On the positive side, we demonstrate that the computational overhead to protect against these attacks is relatively small.
Cite as

Shibam Mukherjee, Christian Rechberger, and Markus Schofnegger. Cache Timing Leakages in Zero-Knowledge Protocols. In 7th Conference on Advances in Financial Technologies (AFT 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 354, pp. 1:1-1:26, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{mukherjee_et_al:LIPIcs.AFT.2025.1,
  author =	{Mukherjee, Shibam and Rechberger, Christian and Schofnegger, Markus},
  title =	{{Cache Timing Leakages in Zero-Knowledge Protocols}},
  booktitle =	{7th Conference on Advances in Financial Technologies (AFT 2025)},
  pages =	{1:1--1:26},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-400-0},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{354},
  editor =	{Avarikioti, Zeta and Christin, Nicolas},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.AFT.2025.1},
  URN =		{urn:nbn:de:0030-drops-247201},
  doi =		{10.4230/LIPIcs.AFT.2025.1},
  annote =	{Keywords: zero-knowledge, protocol, cache timing, side-channel, leakage}
}
Document
DOI: 10.4230/LIPIcs.ESA.2025.79
Semi-Streaming Algorithms for Hypergraph Matching

Authors: Henrik Reinstädtler, S M Ferdous, Alex Pothen, Bora Uçar, and Christian Schulz

Published in: LIPIcs, Volume 351, 33rd Annual European Symposium on Algorithms (ESA 2025)

Abstract
We propose two one-pass streaming algorithms for the NP-hard hypergraph matching problem. The first algorithm stores a small subset of potential matching edges in a stack using dual variables to select edges. It has an approximation guarantee of 1/(d(1+ε)) and requires 𝒪((n/ε)log²n) bits of memory, where n is the number of vertices in the hypergraph, d is the maximum number of vertices in a hyperedge, and ε > 0 is a parameter to be chosen. The second algorithm computes, stores, and updates a single matching as the edges stream, with an approximation ratio dependent on a parameter α. Its best approximation guarantee is 1/((2d-1) + 2 √{d(d-1)}), and it requires only 𝒪(n) memory. We have implemented both algorithms and compared them with respect to solution quality, memory consumption, and running times on two diverse sets of hypergraphs with a non-streaming greedy and a naive streaming algorithm. Our results show that the streaming algorithms achieve much better solution quality than naive algorithms when facing adverse orderings. Furthermore, these algorithms reduce the memory required by a factor of 13 in the geometric mean on our test problems, and also outperform the offline Greedy algorithm in running time.
Cite as

Henrik Reinstädtler, S M Ferdous, Alex Pothen, Bora Uçar, and Christian Schulz. Semi-Streaming Algorithms for Hypergraph Matching. In 33rd Annual European Symposium on Algorithms (ESA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 351, pp. 79:1-79:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{reinstadtler_et_al:LIPIcs.ESA.2025.79,
  author =	{Reinst\"{a}dtler, Henrik and Ferdous, S M and Pothen, Alex and U\c{c}ar, Bora and Schulz, Christian},
  title =	{{Semi-Streaming Algorithms for Hypergraph Matching}},
  booktitle =	{33rd Annual European Symposium on Algorithms (ESA 2025)},
  pages =	{79:1--79:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-395-9},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{351},
  editor =	{Benoit, Anne and Kaplan, Haim and Wild, Sebastian 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.2025.79},
  URN =		{urn:nbn:de:0030-drops-245478},
  doi =		{10.4230/LIPIcs.ESA.2025.79},
  annote =	{Keywords: hypergraph, matching, semi-streaming}
}
Document
DOI: 10.4230/LIPIcs.ESA.2025.67
Compact Representation of Semilinear and Terrain-Like Graphs

Authors: Jean Cardinal and Yelena Yuditsky

Published in: LIPIcs, Volume 351, 33rd Annual European Symposium on Algorithms (ESA 2025)

Abstract
We consider the existence and construction of biclique covers of graphs, consisting of coverings of their edge sets by complete bipartite graphs. The size of such a cover is the sum of the sizes of the bicliques. Small-size biclique covers of graphs are ubiquitous in computational geometry, and have been shown to be useful compact representations of graphs. We give a brief survey of classical and recent results on biclique covers and their applications, and give new families of graphs having biclique covers of near-linear size. In particular, we show that semilinear graphs, whose edges are defined by linear relations in bounded dimensional space, always have biclique covers of size O(npolylog n). This generalizes many previously known results on special classes of graphs including interval graphs, permutation graphs, and graphs of bounded boxicity, but also new classes such as intersection graphs of L-shapes in the plane. It also directly implies the bounds for Zarankiewicz’s problem derived by Basit, Chernikov, Starchenko, Tao, and Tran (Forum Math. Sigma, 2021). We also consider capped graphs, also known as terrain-like graphs, defined as ordered graphs forbidding a certain ordered pattern on four vertices. Terrain-like graphs contain the induced subgraphs of terrain visibility graphs. We give an elementary proof that these graphs admit biclique partitions of size O(nlog³ n). This provides a simple combinatorial analogue of a classical result from Agarwal, Alon, Aronov, and Suri on polygon visibility graphs (Discrete Comput. Geom. 1994). Finally, we prove that there exists families of unit disk graphs on n vertices that do not admit biclique coverings of size o(n^{4/3}), showing that we are unlikely to improve on Szemerédi-Trotter type incidence bounds for higher-degree semialgebraic graphs.
Cite as

Jean Cardinal and Yelena Yuditsky. Compact Representation of Semilinear and Terrain-Like Graphs. In 33rd Annual European Symposium on Algorithms (ESA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 351, pp. 67:1-67:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{cardinal_et_al:LIPIcs.ESA.2025.67,
  author =	{Cardinal, Jean and Yuditsky, Yelena},
  title =	{{Compact Representation of Semilinear and Terrain-Like Graphs}},
  booktitle =	{33rd Annual European Symposium on Algorithms (ESA 2025)},
  pages =	{67:1--67:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-395-9},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{351},
  editor =	{Benoit, Anne and Kaplan, Haim and Wild, Sebastian 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.2025.67},
  URN =		{urn:nbn:de:0030-drops-245359},
  doi =		{10.4230/LIPIcs.ESA.2025.67},
  annote =	{Keywords: Biclique covers, intersection graphs, visibility graphs, Zarankiewicz’s problem}
}
Document
DOI: 10.4230/LIPIcs.ESA.2025.37
Hardness of Computation of Quantum Invariants on 3-Manifolds with Restricted Topology

Authors: Henrique Ennes and Clément Maria

Published in: LIPIcs, Volume 351, 33rd Annual European Symposium on Algorithms (ESA 2025)

Abstract
Quantum invariants in low-dimensional topology offer a wide variety of valuable invariants about knots and 3-manifolds, presented by explicit formulas that are readily computable. Their computational complexity has been actively studied and is tightly connected to topological quantum computing. In this article, we prove that for any 3-manifold quantum invariant in the Reshetikhin-Turaev model, there is a deterministic polynomial time algorithm that, given as input an arbitrary closed 3-manifold M, outputs a closed 3-manifold M' with the same quantum invariant, such that M' is hyperbolic, contains no low genus embedded incompressible surface, and is presented by a strongly irreducible Heegaard diagram. Our construction relies on properties of Heegaard splittings and the Hempel distance. At the level of computational complexity, this proves that the hardness of computing a given quantum invariant of 3-manifolds is preserved even when severely restricting the topology and the combinatorics of the input. This positively answers a question raised by Samperton [Samperton, 2023].
Cite as

Henrique Ennes and Clément Maria. Hardness of Computation of Quantum Invariants on 3-Manifolds with Restricted Topology. In 33rd Annual European Symposium on Algorithms (ESA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 351, pp. 37:1-37:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{ennes_et_al:LIPIcs.ESA.2025.37,
  author =	{Ennes, Henrique and Maria, Cl\'{e}ment},
  title =	{{Hardness of Computation of Quantum Invariants on 3-Manifolds with Restricted Topology}},
  booktitle =	{33rd Annual European Symposium on Algorithms (ESA 2025)},
  pages =	{37:1--37:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-395-9},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{351},
  editor =	{Benoit, Anne and Kaplan, Haim and Wild, Sebastian 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.2025.37},
  URN =		{urn:nbn:de:0030-drops-245057},
  doi =		{10.4230/LIPIcs.ESA.2025.37},
  annote =	{Keywords: 3-manifold, Heegaard splitting, Hempel distance, Quantum invariant, polynomial time reduction}
}
Document
DOI: 10.4230/OASIcs.SpaceCHI.2025.1
Human-AI Interaction in Space: Insights from a Mars Analog Mission with the Harmony Large Language Model

Authors: Hippolyte Hilgers, Jean Vanderdonckt, and Radu-Daniel Vatavu

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

Abstract
The operational complexities of space missions require reliable, context-aware technical assistance for astronauts, especially when technical expertise is not available onboard and communication with Earth is delayed or limited. In this context, Large Language Models present a promising opportunity to augment human capabilities. To this end, we present Harmony, a model designed to provide astronauts with real-time technical assistance, fostering human-AI collaboration during analog missions. We report empirical results from an experiment involving seven analog astronauts that evaluated their user experience with Harmony in both a conventional environment and an isolated, confined, and extreme physical setting at the Mars Desert Research Station over four sessions, and discuss how the Mars analog environment impacted their experience. Our findings reveal the extent to which human-AI interactions evolve across various user experience dimensions and suggest how Harmony can be further adapted to suit extreme environments, with a focus on SpaceCHI.
Cite as

Hippolyte Hilgers, Jean Vanderdonckt, and Radu-Daniel Vatavu. Human-AI Interaction in Space: Insights from a Mars Analog Mission with the Harmony Large Language Model. In Advancing Human-Computer Interaction for Space Exploration (SpaceCHI 2025). Open Access Series in Informatics (OASIcs), Volume 130, pp. 1:1-1:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{hilgers_et_al:OASIcs.SpaceCHI.2025.1,
  author =	{Hilgers, Hippolyte and Vanderdonckt, Jean and Vatavu, Radu-Daniel},
  title =	{{Human-AI Interaction in Space: Insights from a Mars Analog Mission with the Harmony Large Language Model}},
  booktitle =	{Advancing Human-Computer Interaction for Space Exploration (SpaceCHI 2025)},
  pages =	{1:1--1:20},
  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.2025.1},
  URN =		{urn:nbn:de:0030-drops-239912},
  doi =		{10.4230/OASIcs.SpaceCHI.2025.1},
  annote =	{Keywords: Extreme user experience, Human-AI interaction, Isolated-confined-extreme environment, Interaction design, Large Language Models, Mars Desert Research Station, Space mission, Technical assistance, Technical documentation, User experience}
}
Document
DOI: 10.4230/OASIcs.Programming.2025.11
Renkon-Pad: A Live and Self-Sustaining Programming Environment Based on Functional Reactive Programming

Authors: Yoshiki Ohshima, Adam Bouhenguel, and Matthew Good

Published in: OASIcs, Volume 134, Companion Proceedings of the 9th International Conference on the Art, Science, and Engineering of Programming (Programming 2025)

Abstract
Renkon-pad is a live programming environment based on a Functional Reactive Programming language called Renkon. In Renkon-pad, the user creates text boxes to write reactive expressions. The user can also create any number of "runner" windows (separate execution environments) to run the program. The user can modify the program and update a running runner or create a new one to experiment quickly. The FRP-based model of the Renkon language is conducive to programming in node-and-wire dataflow diagrams. However, Renkon-pad does not employ a typical node-and-wire visual representation. The dependency relationships are expressed in code as text rather than by connecting boxes with wires. Additionally, a text box can contain any number of expressions. This design helps scale the size of a program that the user can handle in the environment. In other words, the programmer has greater flexibility in organizing their program in a logically meaningful way. The application analyzes the dependencies among expressions and visualizes the dependencies in the program to aid comprehension. Renkon-pad is powerful enough to create and live-edit non-trivial applications, including itself. The bootstrapping version of Renkon-pad, with text box and runner window management, user interaction, interfacing with a virtual DOM library, the file save and load feature, and dependency visualization, is implemented in about 700 lines of Renkon and CSS definitions.
Cite as

Yoshiki Ohshima, Adam Bouhenguel, and Matthew Good. Renkon-Pad: A Live and Self-Sustaining Programming Environment Based on Functional Reactive Programming. In Companion Proceedings of the 9th International Conference on the Art, Science, and Engineering of Programming (Programming 2025). Open Access Series in Informatics (OASIcs), Volume 134, pp. 11:1-11:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{ohshima_et_al:OASIcs.Programming.2025.11,
  author =	{Ohshima, Yoshiki and Bouhenguel, Adam and Good, Matthew},
  title =	{{Renkon-Pad: A Live and Self-Sustaining Programming Environment Based on Functional Reactive Programming}},
  booktitle =	{Companion Proceedings of the 9th International Conference on the Art, Science, and Engineering of Programming (Programming 2025)},
  pages =	{11:1--11:20},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-382-9},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{134},
  editor =	{Edwards, Jonathan and Perera, Roly and Petricek, Tomas},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.Programming.2025.11},
  URN =		{urn:nbn:de:0030-drops-242956},
  doi =		{10.4230/OASIcs.Programming.2025.11},
  annote =	{Keywords: Live Programming, Functional Reactive Programming, Live Development Environment}
}
Document
RANDOM
DOI: 10.4230/LIPIcs.APPROX/RANDOM.2025.39
Consumable Data via Quantum Communication

Authors: Dar Gilboa, Siddhartha Jain, and Jarrod R. McClean

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

Abstract
Classical data can be copied and re-used for computation, with adverse consequences economically and in terms of data privacy. Motivated by this, we formulate problems in one-way communication complexity where Alice holds some data x and Bob holds m inputs y_1, …, y_m. They want to compute m instances of a bipartite relation R(⋅,⋅) on every pair (x, y_1), …, (x, y_m). We call this the asymmetric direct sum question for one-way communication. We give examples where the quantum communication complexity of such problems scales polynomially with m, while the classical communication complexity depends at most logarithmically on m. Thus, for such problems, data behaves like a consumable resource that is effectively destroyed upon use when the owner stores and transmits it as quantum states, but not when transmitted classically. We show an application to a strategic data-selling game, and discuss other potential economic implications.
Cite as

Dar Gilboa, Siddhartha Jain, and Jarrod R. McClean. Consumable Data via Quantum Communication. In Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 353, pp. 39:1-39:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{gilboa_et_al:LIPIcs.APPROX/RANDOM.2025.39,
  author =	{Gilboa, Dar and Jain, Siddhartha and McClean, Jarrod R.},
  title =	{{Consumable Data via Quantum Communication}},
  booktitle =	{Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025)},
  pages =	{39:1--39:23},
  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.2025.39},
  URN =		{urn:nbn:de:0030-drops-244059},
  doi =		{10.4230/LIPIcs.APPROX/RANDOM.2025.39},
  annote =	{Keywords: quantum communication, one-time programs, data markets}
}
Document
DOI: 10.4230/LIPIcs.DNA.31.4
Differentiable Programming of Indexed Chemical Reaction Networks and Reaction-Diffusion Systems

Authors: Inhoo Lee, Salvador Buse, and Erik Winfree

Published in: LIPIcs, Volume 347, 31st International Conference on DNA Computing and Molecular Programming (DNA 31) (2025)

Abstract
Many molecular systems are best understood in terms of prototypical species and reactions. The central dogma and related biochemistry are rife with examples: gene i is transcribed into RNA i, which is translated into protein i; kinase n phosphorylates substrate m; protein p dimerizes with protein q. Engineered nucleic acid systems also often have this form: oligonucleotide i hybridizes to complementary oligonucleotide j; signal strand n displaces the output of seesaw gate m; hairpin p triggers the opening of target q. When there are many variants of a small number of prototypes, it can be conceptually cleaner and computationally more efficient to represent the full system in terms of indexed species (e.g. for dimerization, M_p, D_pq) and indexed reactions (M_p + M_q → D_pq). Here, we formalize the Indexed Chemical Reaction Network (ICRN) model and describe a Python software package designed to simulate such systems in the well-mixed and reaction-diffusion settings, using a differentiable programming framework originally developed for large-scale neural network models, taking advantage of GPU acceleration when available. Notably, this framework makes it straightforward to train the models’ initial conditions and rate constants to optimize a target behavior, such as matching experimental data, performing a computation, or exhibiting spatial pattern formation. The natural map of indexed chemical reaction networks onto neural network formalisms provides a tangible yet general perspective for translating concepts and techniques from the theory and practice of neural computation into the design of biomolecular systems.
Cite as

Inhoo Lee, Salvador Buse, and Erik Winfree. Differentiable Programming of Indexed Chemical Reaction Networks and Reaction-Diffusion Systems. In 31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 4:1-4:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{lee_et_al:LIPIcs.DNA.31.4,
  author =	{Lee, Inhoo and Buse, Salvador and Winfree, Erik},
  title =	{{Differentiable Programming of Indexed Chemical Reaction Networks and Reaction-Diffusion Systems}},
  booktitle =	{31st International Conference on DNA Computing and Molecular Programming (DNA 31)},
  pages =	{4:1--4:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-399-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{347},
  editor =	{Schaeffer, Josie and Zhang, Fei},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.31.4},
  URN =		{urn:nbn:de:0030-drops-238534},
  doi =		{10.4230/LIPIcs.DNA.31.4},
  annote =	{Keywords: Differentiable Programming, Chemical Reaction Networks, Reaction-Diffusion Systems}
}
Document
DOI: 10.4230/LIPIcs.DNA.31.7
Tile Blockers as a Simple Motif to Control Self-Assembly: Kinetics and Thermodynamics

Authors: Constantine G. Evans, Angel Cervera Roldan, Trent Rogers, and Damien Woods

Published in: LIPIcs, Volume 347, 31st International Conference on DNA Computing and Molecular Programming (DNA 31) (2025)

Abstract
A fundamental problem in crystallisation, and in molecular tile-based self-assembly in particular, is how to simultaneously control its two main constituent processes: seeded growth and spontaneous nucleation. Often, we desire out-of-equilibrium growth without spontaneous nucleation, which can be achieved through careful calibration of temperature, concentration and experimental time-scale a laborious and overly-sensitive approach. Another technique is to find alternative nucleation-resistant tile designs [Minev et al, 2001]. Rogers, Evans and Woods [In prep] propose blockers: short DNA strands designed to dynamically block DNA tile sides, altering self-assembly dynamics. Experiments showed independent and tunable control on nucleation and growth rates. Here, we provide a theoretical explanation for these surprising results. We formally define the kBlock model where blockers bind to tiles at thermodynamic equilibrium in solution and stochastic kinetics allow self-assembly of a tiled structure. In an intentionally simplified mathematical setting we show that blockers permit reasonable seeded growth rates, akin to a non-blocked tile system at lower tile concentration, crucially giving nucleation rates that are exponentially suppressed. We then implement the kBlock model in a stochastic simulator, with results showing remarkable alignment with oversimplified theory. We provide evidence of blocker-induced tile buffering, where a large reservoir of blocked tiles slowly feeds a small unblocked tile subpopulation which acts like a regular, non-blocked, low tile concentration system, yet is capable of long-term buffered assembly. Finally, and perhaps most satisfyingly, theory and simulations align remarkably well with DNA self-assembly experiments over a wide range of concentrations and temperatures, matching the size of growth temperature windows to within 12%. Blockers are a straightforward solution to the challenging problem of simultaneously and independently controlling growth and nucleation, using a motif compatible with many DNA tile systems.
Cite as

Constantine G. Evans, Angel Cervera Roldan, Trent Rogers, and Damien Woods. Tile Blockers as a Simple Motif to Control Self-Assembly: Kinetics and Thermodynamics. In 31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 7:1-7:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{evans_et_al:LIPIcs.DNA.31.7,
  author =	{Evans, Constantine G. and Cervera Roldan, Angel and Rogers, Trent and Woods, Damien},
  title =	{{Tile Blockers as a Simple Motif to Control Self-Assembly: Kinetics and Thermodynamics}},
  booktitle =	{31st International Conference on DNA Computing and Molecular Programming (DNA 31)},
  pages =	{7:1--7:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-399-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{347},
  editor =	{Schaeffer, Josie and Zhang, Fei},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.31.7},
  URN =		{urn:nbn:de:0030-drops-238564},
  doi =		{10.4230/LIPIcs.DNA.31.7},
  annote =	{Keywords: Self-assembly, kinetic model, kinetic simulation, thermodynamic prediction}
}
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
DOI: 10.4230/LIPIcs.ECOOP.2025.22
Quantifying Cache Side-Channel Leakage by Refining Set-Based Abstractions

Authors: Jacqueline L. Mitchell and Chao Wang

Published in: LIPIcs, Volume 333, 39th European Conference on Object-Oriented Programming (ECOOP 2025)

Abstract
We propose an improved abstract interpretation based method for quantifying cache side-channel leakage by addressing two key components of precision loss in existing set-based cache abstractions. Our method targets two key sources of imprecision: (1) imprecision in the abstract transfer function used to update the abstract cache state when interpreting a memory access and (2) imprecision due to the incompleteness of the set-based domain. At the center of our method are two key improvements: (1) the introduction of a new transfer function for updating the abstract cache state which carefully leverages information in the abstract state to prevent the spurious aging of memory blocks and (2) a refinement of the set-based domain based on the finite powerset construction. We show that both the new abstract transformer and the domain refinement enjoy certain enhanced precision properties. We have implemented the method and compared it against the state-of-the-art technique on a suite of benchmark programs implementing both sorting algorithms and cryptographic algorithms. The experimental results show that our method is effective in improving the precision of cache side-channel leakage quantification.
Cite as

Jacqueline L. Mitchell and Chao Wang. Quantifying Cache Side-Channel Leakage by Refining Set-Based Abstractions. In 39th European Conference on Object-Oriented Programming (ECOOP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 333, pp. 22:1-22:28, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{mitchell_et_al:LIPIcs.ECOOP.2025.22,
  author =	{Mitchell, Jacqueline L. and Wang, Chao},
  title =	{{Quantifying Cache Side-Channel Leakage by Refining Set-Based Abstractions}},
  booktitle =	{39th European Conference on Object-Oriented Programming (ECOOP 2025)},
  pages =	{22:1--22:28},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-373-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{333},
  editor =	{Aldrich, Jonathan and Silva, Alexandra},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECOOP.2025.22},
  URN =		{urn:nbn:de:0030-drops-233140},
  doi =		{10.4230/LIPIcs.ECOOP.2025.22},
  annote =	{Keywords: Abstract interpretation, side-channel, leakage quantification, cache}
}
Document
DOI: 10.4230/LIPIcs.SoCG.2025.47
Shelling and Sinking Graphs on the Sphere

Authors: Jeff Erickson and Christian Howard

Published in: LIPIcs, Volume 332, 41st International Symposium on Computational Geometry (SoCG 2025)

Abstract
We describe a promising approach to efficiently morph spherical graphs, extending earlier approaches of Awartani and Henderson [Trans. AMS 1987] and Kobourov and Landis [JGAA 2006]. Specifically, we describe two methods to morph shortest-path triangulations of the sphere by moving their vertices along longitudes into the southern hemisphere; we call a triangulation sinkable if such a morph exists. Our first method generalizes a longitudinal shelling construction of Awartani and Henderson; a triangulation is sinkable if a specific orientation of its dual graph is acyclic. We describe a simple polynomial-time algorithm to find a longitudinally shellable rotation of a given spherical triangulation, if one exists; we also construct a spherical triangulation that has no longitudinally shellable rotation. Our second method is based on a linear-programming characterization of sinkability. By identifying its optimal basis, we show that this linear program can be solved in O(n^{ω/2}) time, where ω is the matrix-multiplication exponent, assuming the underlying linear system is non-singular. Finally, we pose several conjectures and describe experimental results that support them.
Cite as

Jeff Erickson and Christian Howard. Shelling and Sinking Graphs on the Sphere. In 41st International Symposium on Computational Geometry (SoCG 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 332, pp. 47:1-47:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{erickson_et_al:LIPIcs.SoCG.2025.47,
  author =	{Erickson, Jeff and Howard, Christian},
  title =	{{Shelling and Sinking Graphs on the Sphere}},
  booktitle =	{41st International Symposium on Computational Geometry (SoCG 2025)},
  pages =	{47:1--47:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-370-6},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{332},
  editor =	{Aichholzer, Oswin and Wang, Haitao},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SoCG.2025.47},
  URN =		{urn:nbn:de:0030-drops-231996},
  doi =		{10.4230/LIPIcs.SoCG.2025.47},
  annote =	{Keywords: morphing, planar graphs, spherical graph drawing, longitudinal shelling}
}
Document
Survey
DOI: 10.4230/TGDK.3.1.3
Uncertainty Management in the Construction of Knowledge Graphs: A Survey

Authors: Lucas Jarnac, Yoan Chabot, and Miguel Couceiro

Published in: TGDK, Volume 3, Issue 1 (2025). Transactions on Graph Data and Knowledge, Volume 3, Issue 1

Abstract
Knowledge Graphs (KGs) are a major asset for companies thanks to their great flexibility in data representation and their numerous applications, e.g., vocabulary sharing, Q&A or recommendation systems. To build a KG, it is a common practice to rely on automatic methods for extracting knowledge from various heterogeneous sources. However, in a noisy and uncertain world, knowledge may not be reliable and conflicts between data sources may occur. Integrating unreliable data would directly impact the use of the KG, therefore such conflicts must be resolved. This could be done manually by selecting the best data to integrate. This first approach is highly accurate, but costly and time-consuming. That is why recent efforts focus on automatic approaches, which represent a challenging task since it requires handling the uncertainty of extracted knowledge throughout its integration into the KG. We survey state-of-the-art approaches in this direction and present constructions of both open and enterprise KGs. We then describe different knowledge extraction methods and discuss downstream tasks after knowledge acquisition, including KG completion using embedding models, knowledge alignment, and knowledge fusion in order to address the problem of knowledge uncertainty in KG construction. We conclude with a discussion on the remaining challenges and perspectives when constructing a KG taking into account uncertainty.
Cite as

Lucas Jarnac, Yoan Chabot, and Miguel Couceiro. Uncertainty Management in the Construction of Knowledge Graphs: A Survey. In Transactions on Graph Data and Knowledge (TGDK), Volume 3, Issue 1, pp. 3:1-3:48, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@Article{jarnac_et_al:TGDK.3.1.3,
  author =	{Jarnac, Lucas and Chabot, Yoan and Couceiro, Miguel},
  title =	{{Uncertainty Management in the Construction of Knowledge Graphs: A Survey}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{3:1--3:48},
  ISSN =	{2942-7517},
  year =	{2025},
  volume =	{3},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.3.1.3},
  URN =		{urn:nbn:de:0030-drops-233733},
  doi =		{10.4230/TGDK.3.1.3},
  annote =	{Keywords: Knowledge reconciliation, Uncertainty, Heterogeneous sources, Knowledge graph construction}
}
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