13 Search Results for "Pereira, Olivier"

Document
DOI: 10.4230/OASIcs.NINeS.2026.17
Don’t Get Caught, Keep Your Onions in a Vault

Authors: Humza Ikram, Rumaisa Habib, Muaz Ali, and Zartash Afzal Uzmi

Published in: OASIcs, Volume 139, 1st New Ideas in Networked Systems (NINeS 2026)

Abstract
When web applications wish to operate anonymously, they routinely host themselves as "Hidden Services" in the Tor network. However, these services are frequently threatened by deanonymization attacks, whereby their IP address and location may be inferred by the authorities. We present VaulTor, a novel architecture for the Tor network that ensures an extra layer of security for the Hidden Services against deanonymization attacks. In this new architecture, a volunteer (vault) is incentivized to host the web application content on behalf of the Hidden Service. The vault runs the hosted application in a Trusted Execution Environment (TEE) and becomes the point of contact for interested clients. This setup can substantially reduce the uptime requirement of the original Hidden Service provider, thereby significantly decreasing the chance of deanonymization attacks against them. Using a vault node in place of the hidden service node does not cause any noticeable performance degradation when accessing the hosted content.
Cite as

Humza Ikram, Rumaisa Habib, Muaz Ali, and Zartash Afzal Uzmi. Don’t Get Caught, Keep Your Onions in a Vault. In 1st New Ideas in Networked Systems (NINeS 2026). Open Access Series in Informatics (OASIcs), Volume 139, pp. 17:1-17:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{ikram_et_al:OASIcs.NINeS.2026.17,
  author =	{Ikram, Humza and Habib, Rumaisa and Ali, Muaz and Uzmi, Zartash Afzal},
  title =	{{Don’t Get Caught, Keep Your Onions in a Vault}},
  booktitle =	{1st New Ideas in Networked Systems (NINeS 2026)},
  pages =	{17:1--17:24},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-414-7},
  ISSN =	{2190-6807},
  year =	{2026},
  volume =	{139},
  editor =	{Argyraki, Katerina and Panda, Aurojit},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.NINeS.2026.17},
  URN =		{urn:nbn:de:0030-drops-256027},
  doi =		{10.4230/OASIcs.NINeS.2026.17},
  annote =	{Keywords: Tor, anonymity, Hidden Services, Trusted Execution Environments}
}
Document
DOI: 10.4230/LIPIcs.ITP.2025.5
A Mechanized First-Order Theory of Algebraic Data Types with Pattern Matching

Authors: Joshua M. Cohen

Published in: LIPIcs, Volume 352, 16th International Conference on Interactive Theorem Proving (ITP 2025)

Abstract
Algebraic data types (ADTs) and pattern matching are widely used to write elegant functional programs and to specify program behavior. These constructs are critical to most general-purpose interactive theorem provers (e.g. Lean, Rocq/Coq), first-order SMT-based deductive verifiers (e.g. Dafny, VeriFast), and intermediate verification languages (e.g. Why3). Such features require layers of compilation - in Rocq, pattern matches are compiled to remove nesting, while SMT-based tools further axiomatize ADTs with a first-order specification. However, these critical steps have been omitted from prior formalizations of such toolchains (e.g. MetaRocq). We give the first proved-sound sophisticated pattern matching compiler (based on Maranget’s compilation to decision trees) and first-order axiomatization of ADTs, both based on Why3 implementations. We prove the soundness of exhaustiveness checking, extending pen-and-paper proofs from the literature, and formulate a robustness property with which we find an exhaustiveness-related bug in Why3. We show that many of our proofs could be useful for reasoning about any first-order program verifier supporting ADTs.
Cite as

Joshua M. Cohen. A Mechanized First-Order Theory of Algebraic Data Types with Pattern Matching. In 16th International Conference on Interactive Theorem Proving (ITP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 352, pp. 5:1-5:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{cohen:LIPIcs.ITP.2025.5,
  author =	{Cohen, Joshua M.},
  title =	{{A Mechanized First-Order Theory of Algebraic Data Types with Pattern Matching}},
  booktitle =	{16th International Conference on Interactive Theorem Proving (ITP 2025)},
  pages =	{5:1--5:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-396-6},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{352},
  editor =	{Forster, Yannick and Keller, Chantal},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITP.2025.5},
  URN =		{urn:nbn:de:0030-drops-246046},
  doi =		{10.4230/LIPIcs.ITP.2025.5},
  annote =	{Keywords: Pattern Matching Compilation, Algebraic Data Types, First-Order Logic}
}
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.2025.32
Efficient Certified Reasoning for Binarized Neural Networks

Authors: Jiong Yang, Yong Kiam Tan, Mate Soos, Magnus O. Myreen, and Kuldeep S. Meel

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

Abstract
Neural networks have emerged as essential components in safety-critical applications - these use cases demand complex, yet trustworthy computations. Binarized Neural Networks (BNNs) are a type of neural network where each neuron is constrained to a Boolean value; they are particularly well-suited for safety-critical tasks because they retain much of the computational capacities of full-scale (floating-point or quantized) deep neural networks, but remain compatible with satisfiability solvers for qualitative verification and with model counters for quantitative reasoning. However, existing methods for BNN analysis suffer from either limited scalability or susceptibility to soundness errors, which hinders their applicability in real-world scenarios. In this work, we present a scalable and trustworthy approach for both qualitative and quantitative verification of BNNs. Our approach introduces a native representation of BNN constraints in a custom-designed solver for qualitative reasoning, and in an approximate model counter for quantitative reasoning. We further develop specialized proof generation and checking pipelines with native support for BNN constraint reasoning, ensuring trustworthiness for all of our verification results. Empirical evaluations on a BNN robustness verification benchmark suite demonstrate that our certified solving approach achieves a 9× speedup over prior certified CNF and PB-based approaches, and our certified counting approach achieves a 218× speedup over the existing CNF-based baseline. In terms of coverage, our pipeline produces fully certified results for 99% and 86% of the qualitative and quantitative reasoning queries on BNNs, respectively. This is in sharp contrast to the best existing baselines which can fully certify only 62% and 4% of the queries, respectively.
Cite as

Jiong Yang, Yong Kiam Tan, Mate Soos, Magnus O. Myreen, and Kuldeep S. Meel. Efficient Certified Reasoning for Binarized Neural Networks. In 28th International Conference on Theory and Applications of Satisfiability Testing (SAT 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 341, pp. 32:1-32:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{yang_et_al:LIPIcs.SAT.2025.32,
  author =	{Yang, Jiong and Tan, Yong Kiam and Soos, Mate and Myreen, Magnus O. and Meel, Kuldeep S.},
  title =	{{Efficient Certified Reasoning for Binarized Neural Networks}},
  booktitle =	{28th International Conference on Theory and Applications of Satisfiability Testing (SAT 2025)},
  pages =	{32:1--32:22},
  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.2025.32},
  URN =		{urn:nbn:de:0030-drops-237665},
  doi =		{10.4230/LIPIcs.SAT.2025.32},
  annote =	{Keywords: Neural network verification, proof certification, SAT solving, approximate model counting}
}
Document
DOI: 10.4230/LIPIcs.FSCD.2025.34
Monad Translations for Higher-Order Logic

Authors: Thomas Traversié

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

Abstract
Classical logic can be embedded into intuitionistic logic by inserting double negations in formulas. Several translations generalize this idea by using monad operators instead of double negations. They eliminate particular axioms, for instance the principle of excluded middle or the principle of explosion, and therefore can be used to embed classical logic into intuitionistic logic or intuitionistic logic into minimal logic. Such translations have been defined for first-order logic. In this paper, we define a translation, parameterized by monad operators, for higher-order logic. In particular, the property that any formula and its translation are equivalent in the presence of the eliminated axiom holds under functional extensionality and propositional extensionality. We apply this translation to embed higher-order classical (respectively intuitionistic) logic into higher-order intuitionistic (respectively minimal) logic. By adapting Friedman’s trick, we show that coherent formulas correspond to a constructive fragment of higher-order classical logic, meaning that we can transform classical proofs into intuitionistic proofs without modifying the proven statements.
Cite as

Thomas Traversié. Monad Translations for Higher-Order Logic. In 10th International Conference on Formal Structures for Computation and Deduction (FSCD 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 337, pp. 34:1-34:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{traversie:LIPIcs.FSCD.2025.34,
  author =	{Traversi\'{e}, Thomas},
  title =	{{Monad Translations for Higher-Order Logic}},
  booktitle =	{10th International Conference on Formal Structures for Computation and Deduction (FSCD 2025)},
  pages =	{34:1--34:14},
  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.2025.34},
  URN =		{urn:nbn:de:0030-drops-236495},
  doi =		{10.4230/LIPIcs.FSCD.2025.34},
  annote =	{Keywords: Higher-order logic, Intuitionistic logic, Kuroda’s translation, Monad}
}
Document
Track B: Automata, Logic, Semantics, and Theory of Programming
DOI: 10.4230/LIPIcs.ICALP.2025.160
Using Games and Universal Trees to Characterise the Nondeterministic Index of Tree Languages

Authors: Olivier Idir and Karoliina Lehtinen

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

Abstract
The parity index problem of tree automata asks, given a regular tree language L and a set of priorities J, is L J-feasible, that is, recognised by a nondeterministic parity automaton with priorities J? This is a long-standing open problem, of which only a few sub-cases and variations are known to be decidable. In a significant but technically difficult step, Colcombet and Löding reduced the problem to the uniform universality of distance-parity automata. In this article, we revisit the index problem using tools from the parity game literature. We add some counters to Lehtinen’s register game, originally used to solve parity games in quasipolynomial time, and use this novel game to characterise J-feasibility. This provides a alternative proof to Colcombet and Löding’s reduction. We then provide a second characterisation, based on the notion of attractor decompositions and the complexity of their structure, as measured by a parameterised version of their Strahler number, which we call n-Strahler number. Finally, we rephrase this result using the notion of universal tree extended to automata: a guidable automaton recognises a [1,2j]-feasible language if and only if it admits a universal tree with n-Strahler number j, for some n. In particular, a language recognised by a guidable automaton {A} is Büchi-feasible if and only if there is a uniform bound n ∈ ℕ such that all trees in the language admit an accepting run with an attractor decomposition of width bounded by n. Equivalently, the language is Büchi-feasible if and only if {A} admits a finite universal tree. While we do not solve the decidability of the index problem, our work makes the state-of-the-art more accessible and brings to light the deep relationships between the J-feasibility of a language and attractor decompositions, universal trees and Lehtinen’s register game.
Cite as

Olivier Idir and Karoliina Lehtinen. Using Games and Universal Trees to Characterise the Nondeterministic Index of Tree Languages. In 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 334, pp. 160:1-160:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{idir_et_al:LIPIcs.ICALP.2025.160,
  author =	{Idir, Olivier and Lehtinen, Karoliina},
  title =	{{Using Games and Universal Trees to Characterise the Nondeterministic Index of Tree Languages}},
  booktitle =	{52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)},
  pages =	{160:1--160:19},
  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.2025.160},
  URN =		{urn:nbn:de:0030-drops-235377},
  doi =		{10.4230/LIPIcs.ICALP.2025.160},
  annote =	{Keywords: Tree automata, parity automata, Mostowski index, Strahler number, attractor decomposition, universal trees}
}
Document
DOI: 10.4230/LIPIcs.ECOOP.2025.11
Contract Usage and Evolution in Android Mobile Applications

Authors: David R. Ferreira, Alexandra Mendes, João F. Ferreira, and Carolina Carreira

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

Abstract
Contracts and assertions are effective methods to enhance software quality by enforcing preconditions, postconditions, and invariants. Previous research has demonstrated the value of contracts in traditional software development. However, the adoption and impact of contracts in the context of mobile app development, particularly of Android apps, remain unexplored. To address this, we present the first large-scale empirical study on the use of contracts in Android apps, written in Java or Kotlin. We consider contract elements divided into five categories: conditional runtime exceptions, APIs, annotations, assertions, and other. We analyzed 2,390 Android apps from the F-Droid repository and processed 52,977 KLOC to determine 1) how and to what extent contracts are used, 2) which language features are used to denote contracts, 3) how contract usage evolves from the first to the last version, and 4) whether contracts are used safely in the context of program evolution and inheritance. Our findings include: 1) although most apps do not specify contracts, annotation-based approaches are the most popular; 2) apps that use contracts continue to use them in later versions, but the number of methods increases at a higher rate than the number of contracts; and 3) there are potentially unsafe specification changes when apps evolve and in subtyping relationships, which indicates a lack of specification stability. Finally, we present a qualitative study that gathers challenges faced by practitioners when using contracts and that validates our recommendations.
Cite as

David R. Ferreira, Alexandra Mendes, João F. Ferreira, and Carolina Carreira. Contract Usage and Evolution in Android Mobile Applications. In 39th European Conference on Object-Oriented Programming (ECOOP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 333, pp. 11:1-11:30, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{ferreira_et_al:LIPIcs.ECOOP.2025.11,
  author =	{Ferreira, David R. and Mendes, Alexandra and Ferreira, Jo\~{a}o F. and Carreira, Carolina},
  title =	{{Contract Usage and Evolution in Android Mobile Applications}},
  booktitle =	{39th European Conference on Object-Oriented Programming (ECOOP 2025)},
  pages =	{11:1--11:30},
  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.2025.11},
  URN =		{urn:nbn:de:0030-drops-233041},
  doi =		{10.4230/LIPIcs.ECOOP.2025.11},
  annote =	{Keywords: Contracts, Design by Contract, DbC, Android, Java, Kotlin}
}
Document
Tool Paper
DOI: 10.4230/OASIcs.FMBC.2025.13
A Benchmark Framework for Byzantine Fault Tolerance Testing Algorithms (Tool Paper)

Authors: João Miguel Louro Neto and Burcu Kulahcioglu Ozkan

Published in: OASIcs, Volume 129, 6th International Workshop on Formal Methods for Blockchains (FMBC 2025)

Abstract
Recent discoveries of vulnerabilities in the design and implementation of Byzantine fault-tolerant protocols underscore the need for testing and exploration techniques to ensure their correctness. While there has been some recent effort for automated test generation for BFT protocols, there is no benchmark framework available to systematically evaluate their performance. We present ByzzBench, a benchmark framework designed to evaluate the performance of testing algorithms in detecting Byzantine fault tolerance bugs. ByzzBench is designed for a standardized implementation of BFT protocols and their execution in a controlled testing environment. It controls the nondeterminism in the concurrency, network, and process faults in the protocol execution, enabling the functionality to enforce particular execution scenarios and thereby facilitating the implementation of testing algorithms for BFT protocols.
Cite as

João Miguel Louro Neto and Burcu Kulahcioglu Ozkan. A Benchmark Framework for Byzantine Fault Tolerance Testing Algorithms (Tool Paper). In 6th International Workshop on Formal Methods for Blockchains (FMBC 2025). Open Access Series in Informatics (OASIcs), Volume 129, pp. 13:1-13:11, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{louroneto_et_al:OASIcs.FMBC.2025.13,
  author =	{Louro Neto, Jo\~{a}o Miguel and Kulahcioglu Ozkan, Burcu},
  title =	{{A Benchmark Framework for Byzantine Fault Tolerance Testing Algorithms}},
  booktitle =	{6th International Workshop on Formal Methods for Blockchains (FMBC 2025)},
  pages =	{13:1--13:11},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-371-3},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{129},
  editor =	{Marmsoler, Diego and Xu, Meng},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.FMBC.2025.13},
  URN =		{urn:nbn:de:0030-drops-230406},
  doi =		{10.4230/OASIcs.FMBC.2025.13},
  annote =	{Keywords: Byzantine Fault Tolerance, BFT Protocols, Automated Testing}
}
Document
Position
DOI: 10.4230/TGDK.2.1.2
Grounding Stream Reasoning Research

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

Published in: TGDK, Volume 2, Issue 1 (2024): Special Issue on Trends in Graph Data and Knowledge - Part 2. Transactions on Graph Data and Knowledge, Volume 2, Issue 1

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

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@Article{bonte_et_al:TGDK.2.1.2,
  author =	{Bonte, Pieter and Calbimonte, Jean-Paul and de Leng, Daniel and Dell'Aglio, Daniele and Della Valle, Emanuele and Eiter, Thomas and Giannini, Federico and Heintz, Fredrik and Schekotihin, Konstantin and Le-Phuoc, Danh and Mileo, Alessandra and Schneider, Patrik and Tommasini, Riccardo and Urbani, Jacopo and Ziffer, Giacomo},
  title =	{{Grounding Stream Reasoning Research}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{2:1--2:47},
  ISSN =	{2942-7517},
  year =	{2024},
  volume =	{2},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.2.1.2},
  URN =		{urn:nbn:de:0030-drops-198597},
  doi =		{10.4230/TGDK.2.1.2},
  annote =	{Keywords: Stream Reasoning, Stream Processing, RDF streams, Streaming Linked Data, Continuous query processing, Temporal Logics, High-performance computing, Databases}
}
Document
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.FSTTCS.2009.2316
Simulation based security in the applied pi calculus

Authors: Stéphanie Delaune, Steve Kremer, and Olivier Pereira

Published in: LIPIcs, Volume 4, IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (2009)

Abstract
We present a symbolic framework for refinement and composition of security protocols. The framework uses the notion of ideal functionalities. These are abstract systems which are secure by construction and which can be combined into larger systems. They can be separately refined in order to obtain concrete protocols implementing them. Our work builds on ideas from the ``trusted party paradigm'' used in computational cryptography models. The underlying language we use is the applied pi calculus which is a general language for specifying security protocols. In our framework we can express the different standard flavours of simulation-based security which happen to all coincide. We illustrate our framework on an authentication functionality which can be realized using the Needham-Schroeder-Lowe protocol. For this we need to define an ideal functionality for asymmetric encryption and its realization. We show a joint state result for this functionality which allows composition (even though the same key material is reused) using a tagging mechanism.
Cite as

Stéphanie Delaune, Steve Kremer, and Olivier Pereira. Simulation based security in the applied pi calculus. In IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science. Leibniz International Proceedings in Informatics (LIPIcs), Volume 4, pp. 169-180, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2009)

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@InProceedings{delaune_et_al:LIPIcs.FSTTCS.2009.2316,
  author =	{Delaune, St\'{e}phanie and Kremer, Steve and Pereira, Olivier},
  title =	{{Simulation based security in the applied pi calculus}},
  booktitle =	{IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science},
  pages =	{169--180},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-939897-13-2},
  ISSN =	{1868-8969},
  year =	{2009},
  volume =	{4},
  editor =	{Kannan, Ravi and Narayan Kumar, K.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FSTTCS.2009.2316},
  URN =		{urn:nbn:de:0030-drops-23163},
  doi =		{10.4230/LIPIcs.FSTTCS.2009.2316},
  annote =	{Keywords: Simulation based security, applied pi calculus, joint state theorem, authentication protocols}
}
Document
DOI: 10.4230/DagSemProc.08491.3
Modeling Computational Security in Long-Lived Systems

Authors: Ran Canetti, Ling Cheung, Dilsun Kaynar, Nancy Lynch, and Olivier Pereira

Published in: Dagstuhl Seminar Proceedings, Volume 8491, Theoretical Foundations of Practical Information Security (2009)

Abstract
For many cryptographic protocols, security relies on the assumption that adversarial entities have limited computational power. This type of security degrades progressively over the lifetime of a protocol. However, some cryptographic services, such as timestamping services or digital archives, are emph{long-lived} in nature; they are expected to be secure and operational for a very long time (ie super-polynomial). In such cases, security cannot be guaranteed in the traditional sense: a computationally secure protocol may become insecure if the attacker has a super-polynomial number of interactions with the protocol. This paper proposes a new paradigm for the analysis of long-lived security protocols. We allow entities to be active for a potentially unbounded amount of real time, provided they perform only a polynomial amount of work emph{per unit of real time}. Moreover, the space used by these entities is allocated dynamically and must be polynomially bounded. We propose a new notion of emph{long-term implementation}, which is an adaptation of computational indistinguishability to the long-lived setting. We show that long-term implementation is preserved under polynomial parallel composition and exponential sequential composition. We illustrate the use of this new paradigm by analyzing some security properties of the long-lived timestamping protocol of Haber and Kamat.
Cite as

Ran Canetti, Ling Cheung, Dilsun Kaynar, Nancy Lynch, and Olivier Pereira. Modeling Computational Security in Long-Lived Systems. In Theoretical Foundations of Practical Information Security. Dagstuhl Seminar Proceedings, Volume 8491, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2009)

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@InProceedings{canetti_et_al:DagSemProc.08491.3,
  author =	{Canetti, Ran and Cheung, Ling and Kaynar, Dilsun and Lynch, Nancy and Pereira, Olivier},
  title =	{{Modeling Computational Security in Long-Lived Systems}},
  booktitle =	{Theoretical Foundations of Practical Information Security},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2009},
  volume =	{8491},
  editor =	{Ran Canetti and Shafi Goldwasser and G\"{u}nter M\"{u}ller and Rainer Steinwandt},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.08491.3},
  URN =		{urn:nbn:de:0030-drops-18908},
  doi =		{10.4230/DagSemProc.08491.3},
  annote =	{Keywords: Long lived security; universally composable security;}
}
Document
DOI: 10.4230/DagSemProc.07311.8
Simulation-based analysis of E2E voting systems

Authors: Olivier de Marneffe, Olivier Pereira, and Jean-Jacques Quisquater

Published in: Dagstuhl Seminar Proceedings, Volume 7311, Frontiers of Electronic Voting (2008)

Abstract
End-to-end auditable voting systems are expected to guarantee very interesting, and often sophisticated security properties, including correctness, privacy, fairness, receipt-freeness, dots However, for many well-known protocols, these properties have never been analyzed in a systematic way. In this paper, we investigate the use of techniques from the simulation-based security tradition for the analysis of these protocols, through a case-study on the ThreeBallot protocol. Our analysis shows that the ThreeBallot protocol fails to emulate some natural voting functionality, reflecting the lack of election fairness guarantee from this protocol. Guided by the reasons that make our security proof fail, we propose a simple variant of the ThreeBallot protocol and show that this variant emulates our functionality.
Cite as

Olivier de Marneffe, Olivier Pereira, and Jean-Jacques Quisquater. Simulation-based analysis of E2E voting systems. In Frontiers of Electronic Voting. Dagstuhl Seminar Proceedings, Volume 7311, pp. 1-14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2008)

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@InProceedings{demarneffe_et_al:DagSemProc.07311.8,
  author =	{de Marneffe, Olivier and Pereira, Olivier and Quisquater, Jean-Jacques},
  title =	{{Simulation-based analysis of E2E voting systems}},
  booktitle =	{Frontiers of Electronic Voting},
  pages =	{1--14},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2008},
  volume =	{7311},
  editor =	{David Chaum and Miroslaw Kutylowski and Ronald L. Rivest and Peter Y. A. Ryan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.07311.8},
  URN =		{urn:nbn:de:0030-drops-12970},
  doi =		{10.4230/DagSemProc.07311.8},
  annote =	{Keywords: UC framework, simulatability, security proof, ThreeBallot}
}
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