5 Search Results for "Caires, Luís"


Document
A Generalised Union of Rely-Guarantee and Separation Logic Using Permission Algebras

Authors: Vincent Jackson, Toby Murray, and Christine Rizkallah

Published in: LIPIcs, Volume 309, 15th International Conference on Interactive Theorem Proving (ITP 2024)


Abstract
This paper describes GenRGSep, an Isabelle/HOL library for the development of RGSep logics using a general algebraic state model. In particular, we develop an algebraic state models based on resource algebras that assume neither the presence of unit resources or the cancellativity law. If a new resource model is required, its components need only be proven an instance of a permission algebra, and then they can be composed together using tuples and functions. The proof of soundness is performed by Vafeiadis' operational soundness method. This method was originally formulated with respect to a concrete heap model. This paper adapts it to account for the absence of both units as well as the cancellativity law.

Cite as

Vincent Jackson, Toby Murray, and Christine Rizkallah. A Generalised Union of Rely-Guarantee and Separation Logic Using Permission Algebras. In 15th International Conference on Interactive Theorem Proving (ITP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 309, pp. 23:1-23:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)


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@InProceedings{jackson_et_al:LIPIcs.ITP.2024.23,
  author =	{Jackson, Vincent and Murray, Toby and Rizkallah, Christine},
  title =	{{A Generalised Union of Rely-Guarantee and Separation Logic Using Permission Algebras}},
  booktitle =	{15th International Conference on Interactive Theorem Proving (ITP 2024)},
  pages =	{23:1--23:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-337-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{309},
  editor =	{Bertot, Yves and Kutsia, Temur and Norrish, Michael},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITP.2024.23},
  URN =		{urn:nbn:de:0030-drops-207510},
  doi =		{10.4230/LIPIcs.ITP.2024.23},
  annote =	{Keywords: verification, concurrency, rely-guarantee, separation logic, resource algebras}
}
Document
Memoization on Shared Subtrees Accelerates Computations on Genealogical Forests

Authors: Lukas Hübner and Alexandros Stamatakis

Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)


Abstract
The field of population genetics attempts to advance our understanding of evolutionary processes. It has applications, for example, in medical research, wildlife conservation, and - in conjunction with recent advances in ancient DNA sequencing technology - studying human migration patterns over the past few thousand years. The basic toolbox of population genetics includes genealogical trees, which describe the shared evolutionary history among individuals of the same species. They are calculated on the basis of genetic variations. However, in recombining organisms, a single tree is insufficient to describe the evolutionary history of the whole genome. Instead, a collection of correlated trees can be used, where each describes the evolutionary history of a consecutive region of the genome. The current corresponding state of-the-art data structure, tree sequences, compresses these genealogical trees via edit operations when moving from one tree to the next along the genome instead of storing the full, often redundant, description for each tree. We propose a new data structure, genealogical forests, which compresses the set of genealogical trees into a DAG. In this DAG identical subtrees that are shared across the input trees are encoded only once, thereby allowing for straight-forward memoization of intermediate results. Additionally, we provide a C++ implementation of our proposed data structure, called gfkit, which is 2.1 to 11.2 (median 4.0) times faster than the state-of-the-art tool on empirical and simulated datasets at computing important population genetics statistics such as the Allele Frequency Spectrum, Patterson’s f, the Fixation Index, Tajima’s D, pairwise Lowest Common Ancestors, and others. On Lowest Common Ancestor queries with more than two samples as input, gfkit scales asymptotically better than the state-of-the-art, and is thus up to 990 times faster. In conclusion, our proposed data structure compresses genealogical trees by storing shared subtrees only once, thereby enabling straight-forward memoization of intermediate results, yielding a substantial runtime reduction and a potentially more intuitive data representation over the state-of-the-art. Our improvements will boost the development of novel analyses and models in the field of population genetics and increases scalability to ever-growing genomic datasets.

Cite as

Lukas Hübner and Alexandros Stamatakis. Memoization on Shared Subtrees Accelerates Computations on Genealogical Forests. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 5:1-5:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)


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@InProceedings{hubner_et_al:LIPIcs.WABI.2024.5,
  author =	{H\"{u}bner, Lukas and Stamatakis, Alexandros},
  title =	{{Memoization on Shared Subtrees Accelerates Computations on Genealogical Forests}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{5:1--5:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-340-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{312},
  editor =	{Pissis, Solon P. and Sung, Wing-Kin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2024.5},
  URN =		{urn:nbn:de:0030-drops-206499},
  doi =		{10.4230/LIPIcs.WABI.2024.5},
  annote =	{Keywords: bioinformatics, population genetics, algorithms}
}
Document
Domain-Aware Session Types

Authors: Luís Caires, Jorge A. Pérez, Frank Pfenning, and Bernardo Toninho

Published in: LIPIcs, Volume 140, 30th International Conference on Concurrency Theory (CONCUR 2019)


Abstract
We develop a generalization of existing Curry-Howard interpretations of (binary) session types by relying on an extension of linear logic with features from hybrid logic, in particular modal worlds that indicate domains. These worlds govern domain migration, subject to a parametric accessibility relation familiar from the Kripke semantics of modal logic. The result is an expressive new typed process framework for domain-aware, message-passing concurrency. Its logical foundations ensure that well-typed processes enjoy session fidelity, global progress, and termination. Typing also ensures that processes only communicate with accessible domains and so respect the accessibility relation. Remarkably, our domain-aware framework can specify scenarios in which domain information is available only at runtime; flexible accessibility relations can be cleanly defined and statically enforced. As a specific application, we introduce domain-aware multiparty session types, in which global protocols can express arbitrarily nested sub-protocols via domain migration. We develop a precise analysis of these multiparty protocols by reduction to our binary domain-aware framework: complex domain-aware protocols can be reasoned about at the right level of abstraction, ensuring also the principled transfer of key correctness properties from the binary to the multiparty setting.

Cite as

Luís Caires, Jorge A. Pérez, Frank Pfenning, and Bernardo Toninho. Domain-Aware Session Types. In 30th International Conference on Concurrency Theory (CONCUR 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 140, pp. 39:1-39:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@InProceedings{caires_et_al:LIPIcs.CONCUR.2019.39,
  author =	{Caires, Lu{\'\i}s and P\'{e}rez, Jorge A. and Pfenning, Frank and Toninho, Bernardo},
  title =	{{Domain-Aware Session Types}},
  booktitle =	{30th International Conference on Concurrency Theory (CONCUR 2019)},
  pages =	{39:1--39:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-121-4},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{140},
  editor =	{Fokkink, Wan and van Glabbeek, Rob},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CONCUR.2019.39},
  URN =		{urn:nbn:de:0030-drops-109417},
  doi =		{10.4230/LIPIcs.CONCUR.2019.39},
  annote =	{Keywords: Session Types, Linear Logic, Process Calculi, Hybrid Logic}
}
Document
Composing Interfering Abstract Protocols

Authors: Filipe Militão, Jonathan Aldrich, and Luís Caires

Published in: LIPIcs, Volume 56, 30th European Conference on Object-Oriented Programming (ECOOP 2016)


Abstract
The undisciplined use of shared mutable state can be a source of program errors when aliases unsafely interfere with each other. While protocol-based techniques to reason about interference abound, they do not address two practical concerns: the decidability of protocol composition and its integration with protocol abstraction. We show that our composition procedure is decidable and that it ensures safe interference even when composing abstract protocols. To evaluate the expressiveness of our protocol framework for safe shared memory interference, we show how this same protocol framework can be used to model safe, typeful message-passing concurrency idioms.

Cite as

Filipe Militão, Jonathan Aldrich, and Luís Caires. Composing Interfering Abstract Protocols. In 30th European Conference on Object-Oriented Programming (ECOOP 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 56, pp. 16:1-16:26, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)


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@InProceedings{militao_et_al:LIPIcs.ECOOP.2016.16,
  author =	{Milit\~{a}o, Filipe and Aldrich, Jonathan and Caires, Lu{\'\i}s},
  title =	{{Composing Interfering Abstract Protocols}},
  booktitle =	{30th European Conference on Object-Oriented Programming (ECOOP 2016)},
  pages =	{16:1--16:26},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-014-9},
  ISSN =	{1868-8969},
  year =	{2016},
  volume =	{56},
  editor =	{Krishnamurthi, Shriram and Lerner, Benjamin S.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECOOP.2016.16},
  URN =		{urn:nbn:de:0030-drops-61108},
  doi =		{10.4230/LIPIcs.ECOOP.2016.16},
  annote =	{Keywords: shared memory interference, protocol composition, aliasing, linearity}
}
Document
Cut Reduction in Linear Logic as Asynchronous Session-Typed Communication

Authors: Henry DeYoung, Luís Caires, Frank Pfenning, and Bernardo Toninho

Published in: LIPIcs, Volume 16, Computer Science Logic (CSL'12) - 26th International Workshop/21st Annual Conference of the EACSL (2012)


Abstract
Prior work has shown that intuitionistic linear logic can be seen as a session-type discipline for the pi-calculus, where cut reduction in the sequent calculus corresponds to synchronous process reduction. In this paper, we exhibit a new process assignment from the asynchronous, polyadic pi-calculus to exactly the same proof rules. Proof-theoretically, the difference between these interpretations can be understood through permutations of inference rules that preserve observational equivalence of closed processes in the synchronous case. We also show that, under this new asynchronous interpretation, cut reductions correspond to a natural asynchronous buffered session semantics, where each session is allocated a separate communication buffer.

Cite as

Henry DeYoung, Luís Caires, Frank Pfenning, and Bernardo Toninho. Cut Reduction in Linear Logic as Asynchronous Session-Typed Communication. In Computer Science Logic (CSL'12) - 26th International Workshop/21st Annual Conference of the EACSL. Leibniz International Proceedings in Informatics (LIPIcs), Volume 16, pp. 228-242, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2012)


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@InProceedings{deyoung_et_al:LIPIcs.CSL.2012.228,
  author =	{DeYoung, Henry and Caires, Lu{\'\i}s and Pfenning, Frank and Toninho, Bernardo},
  title =	{{Cut Reduction in Linear Logic as Asynchronous Session-Typed Communication}},
  booktitle =	{Computer Science Logic (CSL'12) - 26th International Workshop/21st Annual Conference of the EACSL},
  pages =	{228--242},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-939897-42-2},
  ISSN =	{1868-8969},
  year =	{2012},
  volume =	{16},
  editor =	{C\'{e}gielski, Patrick and Durand, Arnaud},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CSL.2012.228},
  URN =		{urn:nbn:de:0030-drops-36753},
  doi =		{10.4230/LIPIcs.CSL.2012.228},
  annote =	{Keywords: linear logic, cut reduction, asynchronous pi-calculus, session types}
}
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