17 Search Results for "Jackson, Paul B."

Document
DOI: 10.4230/LIPIcs.STACS.2026.49
2D Minimal Graph Rigidity is in NC for One-Crossing-Minor-Free Graphs

Authors: Rohit Gurjar, Kilian Rothmund, and Thomas Thierauf

Published in: LIPIcs, Volume 364, 43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026)

Abstract
Minimally rigid graphs can be decided and embedded in the plane efficiently, i.e. in polynomial time. There is also an efficient randomized parallel algorithm, i.e. in RNC. We present an NC-algorithm to decide whether one-crossing-minor-free graphs are minimally rigid. In the special case of K_{3,3}-free graphs, we also compute an infinitesimally rigid embedding in NC.
Cite as

Rohit Gurjar, Kilian Rothmund, and Thomas Thierauf. 2D Minimal Graph Rigidity is in NC for One-Crossing-Minor-Free Graphs. In 43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 364, pp. 49:1-49:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{gurjar_et_al:LIPIcs.STACS.2026.49,
  author =	{Gurjar, Rohit and Rothmund, Kilian and Thierauf, Thomas},
  title =	{{2D Minimal Graph Rigidity is in NC for One-Crossing-Minor-Free Graphs}},
  booktitle =	{43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026)},
  pages =	{49:1--49:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-412-3},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{364},
  editor =	{Mahajan, Meena and Manea, Florin and McIver, Annabelle and Thắng, Nguy\~{ê}n Kim},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.STACS.2026.49},
  URN =		{urn:nbn:de:0030-drops-255385},
  doi =		{10.4230/LIPIcs.STACS.2026.49},
  annote =	{Keywords: Graph Rigidity, Parallel Algorithms, Polynomial Identity Testing, Derandomization}
}
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.
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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
DOI: 10.4230/LIPIcs.ISAAC.2025.35
Anonymous Self-Stabilising Localisation via Spatial Population Protocols

Authors: Leszek Gąsieniec, Łukasz Kuszner, Ehsan Latif, Ramviyas Parasuraman, Paul Spirakis, and Grzegorz Stachowiak

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

Abstract
In the distributed localisation problem (DLP), n anonymous robots (agents) A_0, ..., A_{n-1} are located at arbitrary points p_0, ..., p_{n-1} ∈ S, where S is a Euclidean space. Initially, each agent A_i operates within its own coordinate system in S, which may be inconsistent with those of other agents. The primary goal in DLP is for agents to reach a consensus on a unified (jointly agreed) coordinate system, in which all agents receive unique labels (coordinates) that accurately reflect the relative distances between all points p_0, ..., p_{n-1} in S. Extensive research on DLP has primarily focus on the feasibility and complexity of achieving consensus when agents have limited access to inter-agent distances, often due to missing or imprecise data. In contrast, this paper proposes a minimalist, computationally efficient distributed computing model where agents can query any pairwise relative positions, if needed. Specifically, we introduce a novel variant of population protocols, referred to as the spatial population protocols model. In this variant each agent can memorise one or a fixed number of coordinates, and when agents A_i and A_j interact, they can not only exchange their current knowledge but also either determine the distance d_{ij} between them in S (distance query model) or obtain the vector v_{ij} spanning points p_i and p_j (vector query model). We propose and analyse several distributed localisation protocols, including: 1) Leader-based localisation protocol with distance queries We propose and analyse two leader-based localisation protocols that stabilise silently in o(n) time. These protocols leverage an efficient solution to the novel concept of multi-contact epidemic, a natural generalisation of the core communication tool in population protocols, known as the one-way epidemic. 2) Self-stabilising leader localisation protocol with distance queries We show how to effectively utilise a leader election mechanism within the leader-based localisation protocol to get a DLP protocol that self-stabilises silently in time O(n(log n/n)^{1/(k+1)}log n) in k-dimensions. 3) Self-stabilising localisation protocol with vector queries We propose and analyse an optimally fast DLP protocol which self-stabilises silently in O(log n) time.
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Leszek Gąsieniec, Łukasz Kuszner, Ehsan Latif, Ramviyas Parasuraman, Paul Spirakis, and Grzegorz Stachowiak. Anonymous Self-Stabilising Localisation via Spatial Population Protocols. In 36th International Symposium on Algorithms and Computation (ISAAC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 359, pp. 35:1-35:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{gasieniec_et_al:LIPIcs.ISAAC.2025.35,
  author =	{G\k{a}sieniec, Leszek and Kuszner, {\L}ukasz and Latif, Ehsan and Parasuraman, Ramviyas and Spirakis, Paul and Stachowiak, Grzegorz},
  title =	{{Anonymous Self-Stabilising Localisation via Spatial Population Protocols}},
  booktitle =	{36th International Symposium on Algorithms and Computation (ISAAC 2025)},
  pages =	{35:1--35:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-408-6},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{359},
  editor =	{Chen, Ho-Lin and Hon, Wing-Kai and Tsai, Meng-Tsung},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ISAAC.2025.35},
  URN =		{urn:nbn:de:0030-drops-249433},
  doi =		{10.4230/LIPIcs.ISAAC.2025.35},
  annote =	{Keywords: Population Protocols, Distributed Localisation, Spacial Queries, Self-Stabilisation}
}
Document
Brief Announcement
DOI: 10.4230/LIPIcs.DISC.2025.62
Brief Announcement: Time, Fences and the Ordering of Events in TSO

Authors: Raïssa Nataf and Yoram Moses

Published in: LIPIcs, Volume 356, 39th International Symposium on Distributed Computing (DISC 2025)

Abstract
Total Store Order (TSO) is one of the most popular relaxed memory model in multiprocessor architectures, widely implemented, for example, in Intel’s x86 and x64 platforms. It delays write visibility via store buffers, thereby allowing a significant improvement in efficiency. This, however, complicates reasoning about correctness, as executions may violate sequential consistency. We present a semantic framework that provides effective tools that can pinpoint when such synchronization is necessary under TSO. We define a TSO-specific occurs-before relation, adapting Lamport’s happens-before to TSO, and prove that events at different sites can be temporally ordered only via an occurs-before chain. Analyzing how fences and RMWs create these chains lets us identify when they are unavoidable. We present in this BA how these results impact linearizable implementations of registers, capturing information flow and causality in TSO. The full version of this work provides details as well as results regarding the need for synchronization in linearizable implementations of additional objects.
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Raïssa Nataf and Yoram Moses. Brief Announcement: Time, Fences and the Ordering of Events in TSO. In 39th International Symposium on Distributed Computing (DISC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 356, pp. 62:1-62:7, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{nataf_et_al:LIPIcs.DISC.2025.62,
  author =	{Nataf, Ra\"{i}ssa and Moses, Yoram},
  title =	{{Brief Announcement: Time, Fences and the Ordering of Events in TSO}},
  booktitle =	{39th International Symposium on Distributed Computing (DISC 2025)},
  pages =	{62:1--62:7},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-402-4},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{356},
  editor =	{Kowalski, Dariusz R.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DISC.2025.62},
  URN =		{urn:nbn:de:0030-drops-248784},
  doi =		{10.4230/LIPIcs.DISC.2025.62},
  annote =	{Keywords: TSO, linearizability, happens before, fences, synchronization actions}
}
Document
DOI: 10.4230/LIPIcs.MFCS.2025.15
Symmetry Classes of Hamiltonian Cycles

Authors: Júlia Baligács, Sofia Brenner, Annette Lutz, and Lena Volk

Published in: LIPIcs, Volume 345, 50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025)

Abstract
We initiate the study of Hamiltonian cycles up to symmetries of the underlying graph. Our focus lies on the extremal case of Hamiltonian-transitive graphs, i.e., Hamiltonian graphs where, for every pair of Hamiltonian cycles, there is a graph automorphism mapping one cycle to the other. This generalizes the extensively studied uniquely Hamiltonian graphs. In this paper, we show that Cayley graphs of abelian groups are not Hamiltonian-transitive (under some mild conditions and some non-surprising exceptions), i.e., they contain at least two structurally different Hamiltonian cycles. To show this, we reduce Hamiltonian-transitivity to properties of the prime factors of a Cartesian product decomposition, which we believe is interesting in its own right. We complement our results by constructing infinite families of regular Hamiltonian-transitive graphs and take a look at the opposite extremal case by constructing a family with many different Hamiltonian cycles up to symmetry.
Cite as

Júlia Baligács, Sofia Brenner, Annette Lutz, and Lena Volk. Symmetry Classes of Hamiltonian Cycles. In 50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 345, pp. 15:1-15:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{baligacs_et_al:LIPIcs.MFCS.2025.15,
  author =	{Balig\'{a}cs, J\'{u}lia and Brenner, Sofia and Lutz, Annette and Volk, Lena},
  title =	{{Symmetry Classes of Hamiltonian Cycles}},
  booktitle =	{50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025)},
  pages =	{15:1--15:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-388-1},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{345},
  editor =	{Gawrychowski, Pawe{\l} and Mazowiecki, Filip and Skrzypczak, Micha{\l}},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2025.15},
  URN =		{urn:nbn:de:0030-drops-241221},
  doi =		{10.4230/LIPIcs.MFCS.2025.15},
  annote =	{Keywords: Hamiltonian cycles, graph automorphisms, Cayley graphs, abelian groups, Cartesian product of graphs}
}
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.
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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.CONCUR.2025.4
Monitorability for the Modal Mu-Calculus over Systems with Data: From Practice to Theory

Authors: Luca Aceto, Antonis Achilleos, Duncan Paul Attard, Léo Exibard, Adrian Francalanza, Anna Ingólfsdóttir, and Karoliina Lehtinen

Published in: LIPIcs, Volume 348, 36th International Conference on Concurrency Theory (CONCUR 2025)

Abstract
Runtime verification consists in checking whether a system satisfies a given specification by observing the execution trace it produces. In the regular setting, the modal μ-calculus provides a versatile formalism for expressing specifications of the control flow of the system. This paper focuses on the data flow and studies an extension of that logic that allows it to express data-dependent properties, identifying fragments that can be verified at runtime and with what correctness guarantees. The logic studied here is closely related with register automata with guessing. That correspondence yields a monitor synthesis algorithm, and a strict hierarchy among the various fragments of the logic, in contrast to the regular setting. We then exhibit a fragment of the logic that can express all monitorable formulae in the logic without greatest fixed-points but not in the full logic, and show this is the best we can get.
Cite as

Luca Aceto, Antonis Achilleos, Duncan Paul Attard, Léo Exibard, Adrian Francalanza, Anna Ingólfsdóttir, and Karoliina Lehtinen. Monitorability for the Modal Mu-Calculus over Systems with Data: From Practice to Theory. In 36th International Conference on Concurrency Theory (CONCUR 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 348, pp. 4:1-4:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{aceto_et_al:LIPIcs.CONCUR.2025.4,
  author =	{Aceto, Luca and Achilleos, Antonis and Attard, Duncan Paul and Exibard, L\'{e}o and Francalanza, Adrian and Ing\'{o}lfsd\'{o}ttir, Anna and Lehtinen, Karoliina},
  title =	{{Monitorability for the Modal Mu-Calculus over Systems with Data: From Practice to Theory}},
  booktitle =	{36th International Conference on Concurrency Theory (CONCUR 2025)},
  pages =	{4:1--4:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-389-8},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{348},
  editor =	{Bouyer, Patricia and van de Pol, Jaco},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CONCUR.2025.4},
  URN =		{urn:nbn:de:0030-drops-239546},
  doi =		{10.4230/LIPIcs.CONCUR.2025.4},
  annote =	{Keywords: Runtime verification, monitorability, \muHML with data, register automata}
}
Document
DOI: 10.4230/LIPIcs.WABI.2025.11
Mutational Signature Refitting on Sparse Pan-Cancer Data

Authors: Gal Gilad, Teresa M. Przytycka, and Roded Sharan

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

Abstract
Mutational processes shape cancer genomes, leaving characteristic marks that are termed signatures. The level of activity of each such process, or its signature exposure, provides important information on the disease, improving patient stratification and the prediction of drug response. Thus, there is growing interest in developing refitting methods that decipher those exposures. Previous work in this domain was unsupervised in nature, employing algebraic decomposition and probabilistic inference methods. Here we provide a supervised approach to the problem of signature refitting and show its superiority over current methods. Our method, SuRe, leverages a neural network model to capture correlations between signature exposures in real data. We show that SuRe outperforms previous methods on sparse mutation data from tumor type specific data sets, as well as pan-cancer data sets, with an increasing advantage as the data become sparser. We further demonstrate its utility in clinical settings.
Cite as

Gal Gilad, Teresa M. Przytycka, and Roded Sharan. Mutational Signature Refitting on Sparse Pan-Cancer Data. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 11:1-11:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{gilad_et_al:LIPIcs.WABI.2025.11,
  author =	{Gilad, Gal and Przytycka, Teresa M. and Sharan, Roded},
  title =	{{Mutational Signature Refitting on Sparse Pan-Cancer Data}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{11:1--11:23},
  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.2025.11},
  URN =		{urn:nbn:de:0030-drops-239374},
  doi =		{10.4230/LIPIcs.WABI.2025.11},
  annote =	{Keywords: mutational signatures, signature refitting, cancer genomics, genomic data analysis, somatic mutations}
}
Document
DOI: 10.4230/LIPIcs.SAT.2025.22
Enumerating All Boolean Matches

Authors: Alexander Nadel and Yogev Shalmon

Published in: LIPIcs, Volume 341, 28th International Conference on Theory and Applications of Satisfiability Testing (SAT 2025)

Abstract
Boolean matching, a fundamental problem in circuit design, determines whether two Boolean circuits are equivalent under input/output permutations and negations. While most works focus on finding a single match or proving its absence, the problem of enumerating all matches remains largely unexplored, with BooM being a notable exception. Motivated by timing challenges in Intel’s library mapping flow, we introduce EBat - an open-source tool for enumerating all matches between single-output circuits. Built from scratch, EBat reuses BooM’s SAT encoding and introduces novel high-level algorithms and performance-critical subroutines to efficiently identify and block multiple mismatches and matches simultaneously. Experiments demonstrate that EBat substantially outperforms BooM’s baseline algorithm, solving 3 to 4 times more benchmarks within a given time limit. EBat has been productized as part of Intel’s library mapping flow, effectively addressing the timing challenges.
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Alexander Nadel and Yogev Shalmon. Enumerating All Boolean Matches. In 28th International Conference on Theory and Applications of Satisfiability Testing (SAT 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 341, pp. 22:1-22:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{nadel_et_al:LIPIcs.SAT.2025.22,
  author =	{Nadel, Alexander and Shalmon, Yogev},
  title =	{{Enumerating All Boolean Matches}},
  booktitle =	{28th International Conference on Theory and Applications of Satisfiability Testing (SAT 2025)},
  pages =	{22:1--22:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-381-2},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{341},
  editor =	{Berg, Jeremias and Nordstr\"{o}m, Jakob},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SAT.2025.22},
  URN =		{urn:nbn:de:0030-drops-237568},
  doi =		{10.4230/LIPIcs.SAT.2025.22},
  annote =	{Keywords: Boolean Matching, All-Boolean-Matching, Enumeration, SAT, Generalization}
}
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
Brief Announcement
DOI: 10.4230/LIPIcs.SAND.2025.19
Brief Announcement: Anonymous Distributed Localisation via Spatial Population Protocols

Authors: Leszek Gąsieniec, Łukasz Kuszner, Ehsan Latif, Ramviyas Parasuraman, Paul Spirakis, and Grzegorz Stachowiak

Published in: LIPIcs, Volume 330, 4th Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2025)

Abstract
In the distributed localization problem (DLP), n anonymous robots (agents) A₀, …, A_{n-1} begin at arbitrary positions p₀, …, p_{n-1} ∈ S, where S is a Euclidean space. Initially, each agent A_i operates within its own coordinate system in S, which may be inconsistent with those of other agents. The primary goal in DLP is for agents to reach a consensus on a unified coordinate system that accurately reflects the relative positions of all points, p₀, …, p_{n-1}, in S. Extensive research on DLP has primarily focused on the feasibility and complexity of achieving consensus when agents have limited access to inter-agent distances, often due to missing or imprecise data. In this paper, however, we examine a minimalist, computationally efficient model of distributed computing in which agents have access to all pairwise distances, if needed. Specifically, we introduce a novel variant of population protocols, referred to as the spatial population protocols model. In this variant each agent can memorise one or a fixed number of coordinates, and when agents A_i and A_j interact, they can not only exchange their current knowledge but also either determine the distance d_{ij} between them in S (distance query model) or obtain the vector v→_{ij} spanning points p_i and p_j (vector query model). We present here a leader-based localisation protocol with distance queries.
Cite as

Leszek Gąsieniec, Łukasz Kuszner, Ehsan Latif, Ramviyas Parasuraman, Paul Spirakis, and Grzegorz Stachowiak. Brief Announcement: Anonymous Distributed Localisation via Spatial Population Protocols. In 4th Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 330, pp. 19:1-19:5, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{gasieniec_et_al:LIPIcs.SAND.2025.19,
  author =	{G\k{a}sieniec, Leszek and Kuszner, {\L}ukasz and Latif, Ehsan and Parasuraman, Ramviyas and Spirakis, Paul and Stachowiak, Grzegorz},
  title =	{{Brief Announcement: Anonymous Distributed Localisation via Spatial Population Protocols}},
  booktitle =	{4th Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2025)},
  pages =	{19:1--19:5},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-368-3},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{330},
  editor =	{Meeks, Kitty and Scheideler, Christian},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SAND.2025.19},
  URN =		{urn:nbn:de:0030-drops-230726},
  doi =		{10.4230/LIPIcs.SAND.2025.19},
  annote =	{Keywords: Population Protocols, Distributed Localisation}
}
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
DOI: 10.4230/TGDK.2.3.1
Unified Multimedia Segmentation - A Comprehensive Model for URI-based Media Segment Representation

Authors: Jan Willi, Abraham Bernstein, and Luca Rossetto

Published in: TGDK, Volume 2, Issue 3 (2024). Transactions on Graph Data and Knowledge, Volume 2, Issue 3

Abstract
In multimedia annotation, referencing specific segments of a document is often desired due to its richness and multimodality, but no universal representation for such references exists. This significantly hampers the usage of multimedia content in knowledge graphs, as it is modeled as one large atomic information container. Unstructured data - such as text, audio, images, and video - can commonly be decomposed into its constituent parts, as such documents rarely contain only one semantic concept. Hence, it is reasonable to assume that these advances will make it possible to decompose these previous atomic components into logical segments. To be processable by the knowledge graph stack, however, one needs to break the atomic nature of multimedia content, providing a mechanism to address media segments. This paper proposes a Unified Segmentation Model capable of depicting arbitrary segmentations on any media document type. The work begins with a formal analysis of multimedia and segmentation, exploring segmentation operations and how to describe them. Building on this analysis, it then develops a practical scheme for expressing segmentation in Uniform Resource Identifiers (URIs). Given that this approach makes segments of multimedia content referencable, it breaks their atomic nature and makes them first-class citizens within knowledge graphs. The proposed model is implemented as a proof of concept in the MediaGraph Store, a multimedia knowledge graph storage and querying engine.
Cite as

Jan Willi, Abraham Bernstein, and Luca Rossetto. Unified Multimedia Segmentation - A Comprehensive Model for URI-based Media Segment Representation. In Transactions on Graph Data and Knowledge (TGDK), Volume 2, Issue 3, pp. 1:1-1:34, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@Article{willi_et_al:TGDK.2.3.1,
  author =	{Willi, Jan and Bernstein, Abraham and Rossetto, Luca},
  title =	{{Unified Multimedia Segmentation - A Comprehensive Model for URI-based Media Segment Representation}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{1:1--1:34},
  ISSN =	{2942-7517},
  year =	{2024},
  volume =	{2},
  number =	{3},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.2.3.1},
  URN =		{urn:nbn:de:0030-drops-225953},
  doi =		{10.4230/TGDK.2.3.1},
  annote =	{Keywords: Multimodal Knowledge Graphs, Multimedia Segmentation, Multimedia Representation}
}
Document
Survey
DOI: 10.4230/TGDK.1.1.11
How Does Knowledge Evolve in Open Knowledge Graphs?

Authors: Axel Polleres, Romana Pernisch, Angela Bonifati, Daniele Dell'Aglio, Daniil Dobriy, Stefania Dumbrava, Lorena Etcheverry, Nicolas Ferranti, Katja Hose, Ernesto Jiménez-Ruiz, Matteo Lissandrini, Ansgar Scherp, Riccardo Tommasini, and Johannes Wachs

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
Openly available, collaboratively edited Knowledge Graphs (KGs) are key platforms for the collective management of evolving knowledge. The present work aims t o provide an analysis of the obstacles related to investigating and processing specifically this central aspect of evolution in KGs. To this end, we discuss (i) the dimensions of evolution in KGs, (ii) the observability of evolution in existing, open, collaboratively constructed Knowledge Graphs over time, and (iii) possible metrics to analyse this evolution. We provide an overview of relevant state-of-the-art research, ranging from metrics developed for Knowledge Graphs specifically to potential methods from related fields such as network science. Additionally, we discuss technical approaches - and their current limitations - related to storing, analysing and processing large and evolving KGs in terms of handling typical KG downstream tasks.
Cite as

Axel Polleres, Romana Pernisch, Angela Bonifati, Daniele Dell'Aglio, Daniil Dobriy, Stefania Dumbrava, Lorena Etcheverry, Nicolas Ferranti, Katja Hose, Ernesto Jiménez-Ruiz, Matteo Lissandrini, Ansgar Scherp, Riccardo Tommasini, and Johannes Wachs. How Does Knowledge Evolve in Open Knowledge Graphs?. In Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge (TGDK), Volume 1, Issue 1, pp. 11:1-11:59, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@Article{polleres_et_al:TGDK.1.1.11,
  author =	{Polleres, Axel and Pernisch, Romana and Bonifati, Angela and Dell'Aglio, Daniele and Dobriy, Daniil and Dumbrava, Stefania and Etcheverry, Lorena and Ferranti, Nicolas and Hose, Katja and Jim\'{e}nez-Ruiz, Ernesto and Lissandrini, Matteo and Scherp, Ansgar and Tommasini, Riccardo and Wachs, Johannes},
  title =	{{How Does Knowledge Evolve in Open Knowledge Graphs?}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{11:1--11:59},
  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.1.1.11},
  URN =		{urn:nbn:de:0030-drops-194855},
  doi =		{10.4230/TGDK.1.1.11},
  annote =	{Keywords: KG evolution, temporal KG, versioned KG, dynamic KG}
}
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}
}
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