9 Search Results for "Fisher, Kathleen"

Document
DOI: 10.4230/LIPIcs.ITP.2025.16
Finiteness of Symbolic Derivatives in Lean

Authors: Ekaterina Zhuchko, Hendrik Maarand, Margus Veanes, and Gabriel Ebner

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

Abstract
Brzozowski proved that the set of derivatives of any regular expression is finite modulo associativity, idempotence and, notably, commutativity of the union operator. We extend this result to the case of symbolic location based derivatives, for which we prove finiteness of the state space by quotienting only by associativity, deduplication and idempotence (ADI); the fact that we don't use commutativity allows for this result to carry over to the derivative based backtracking (PCRE) match semantics, where the union operator is noncommutative. Furthermore, we consider regular expressions extended with lookarounds, intersection, and negation. We also show that our method for proving finiteness allows us to include certain simplification rules in the derivative operation while preserving finiteness. The finiteness proof is constructive: given an expression R, we construct a finite set that is an overapproximation (modulo ADI) of the set of derivatives of R. We reuse some of the infrastructure provided in previous formalization efforts for regular expressions in Lean 4, showing the flexibility and reusability of the framework.
Cite as

Ekaterina Zhuchko, Hendrik Maarand, Margus Veanes, and Gabriel Ebner. Finiteness of Symbolic Derivatives in Lean. In 16th International Conference on Interactive Theorem Proving (ITP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 352, pp. 16:1-16:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{zhuchko_et_al:LIPIcs.ITP.2025.16,
  author =	{Zhuchko, Ekaterina and Maarand, Hendrik and Veanes, Margus and Ebner, Gabriel},
  title =	{{Finiteness of Symbolic Derivatives in Lean}},
  booktitle =	{16th International Conference on Interactive Theorem Proving (ITP 2025)},
  pages =	{16:1--16:19},
  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.2025.16},
  URN =		{urn:nbn:de:0030-drops-246144},
  doi =		{10.4230/LIPIcs.ITP.2025.16},
  annote =	{Keywords: Lean, regular languages, lookarounds, derivatives, finiteness}
}
Document
DOI: 10.4230/OASIcs.Programming.2025.23
The Pyttern Program Query Language

Authors: Julien Liénard, Kim Mens, and Siegfried Nijssen

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

Abstract
Despite the availability of numerous tools and languages for detecting structural patterns in programs, their complexity often presents a steep learning curve. This highlights the need for a program query language that is easier to learn, use, and read while remaining sufficiently expressive for defining and detecting relevant structural coding patterns in program code. To address this challenge, we present Pyttern, a query language that extends Python syntax with regular-expression-inspired wildcards, enabling intuitive pattern-based querying of Python code. Its implementation relies upon a custom pushdown automaton describing how to match patterns over program parse trees, thus providing a robust foundation for structural code analysis. We evaluate Pyttern’s usability and effectiveness through a study involving 35 master’s students, who were asked to write seven different patterns to identify known programming misconceptions. The results demonstrate that Pyttern is both easy to learn and practical to use, at least for analysing small-scale programs.
Cite as

Julien Liénard, Kim Mens, and Siegfried Nijssen. The Pyttern Program Query Language. In Companion Proceedings of the 9th International Conference on the Art, Science, and Engineering of Programming (Programming 2025). Open Access Series in Informatics (OASIcs), Volume 134, pp. 23:1-23:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{lienard_et_al:OASIcs.Programming.2025.23,
  author =	{Li\'{e}nard, Julien and Mens, Kim and Nijssen, Siegfried},
  title =	{{The Pyttern Program Query Language}},
  booktitle =	{Companion Proceedings of the 9th International Conference on the Art, Science, and Engineering of Programming (Programming 2025)},
  pages =	{23:1--23:15},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-382-9},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{134},
  editor =	{Edwards, Jonathan and Perera, Roly and Petricek, Tomas},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.Programming.2025.23},
  URN =		{urn:nbn:de:0030-drops-243075},
  doi =		{10.4230/OASIcs.Programming.2025.23},
  annote =	{Keywords: Pyttern, Program Query Languages, Python, Pattern Matching, Parse Tree, Pushdown Automaton, Static Code Analysis, Wildcards, Tree Pattern Matching}
}
Document
DOI: 10.4230/LIPIcs.CALCO.2025.7
A Coinductive Representation of Computable Functions

Authors: Alvin Tang and Dirk Pattinson

Published in: LIPIcs, Volume 342, 11th Conference on Algebra and Coalgebra in Computer Science (CALCO 2025)

Abstract
We investigate a representation of computable functions as total functions over 2^∞, the set of finite and infinite sequences over {0,1}. In this model, infinite sequences are interpreted as non-terminating computations whilst finite sequences represent the sum of their digits. We introduce a new definition principle, function space corecursion, that simultaneously generalises minimisation and primitive recursion. This defines the class of computable corecursive functions that is closed under composition and function space corecursion. We prove computable corecursive functions represent all partial recursive functions, and show that all computable corecursive functions are indeed computable by translation into the untyped λ-calculus.
Cite as

Alvin Tang and Dirk Pattinson. A Coinductive Representation of Computable Functions. In 11th Conference on Algebra and Coalgebra in Computer Science (CALCO 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 342, pp. 7:1-7:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{tang_et_al:LIPIcs.CALCO.2025.7,
  author =	{Tang, Alvin and Pattinson, Dirk},
  title =	{{A Coinductive Representation of Computable Functions}},
  booktitle =	{11th Conference on Algebra and Coalgebra in Computer Science (CALCO 2025)},
  pages =	{7:1--7:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-383-6},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{342},
  editor =	{C\^{i}rstea, Corina and Knapp, Alexander},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CALCO.2025.7},
  URN =		{urn:nbn:de:0030-drops-235662},
  doi =		{10.4230/LIPIcs.CALCO.2025.7},
  annote =	{Keywords: Computability, Coinduction}
}
Document
Experience Paper
DOI: 10.4230/LIPIcs.ECOOP.2025.38
Type-Safe and Portable Support for Packed Data (Experience Paper)

Authors: Arthur Jamet and Michael Vollmer

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

Abstract
When components of a system exchange data, they need to serialise the data so that it can be sent over the network. Then, the recipient has to deserialise the data in order to be able to process it. These steps take time and have an impact on the overall system’s performance. A solution to this is to use packed data, which has a unified representation between the memory and the network, removing the need for any marshalling steps. Additionally, using this data representation can improve the program’s performance thanks to the data locality enabled by the compact representation of the data in memory. Unfortunately, no mainstream programming languages support packed data, whether it’s out-of-the-box or through a compiler extension. We present packed-data, a Haskell library that allows for type safe building and reading of packed data in a functional style. The library does not rely on compiler modifications, making it portable, and leverages meta-programming to allow programmers to pack their own data types effortlessly. We evaluate the usability and performance of the library, and conclude that it allows traversing packed data up to 60% faster than unpacked data. We also reflect on how to enhance the performance of library-based support for packed data. Our implementation approach is general and can easily be used with any programming languages that support higher-kinded types.
Cite as

Arthur Jamet and Michael Vollmer. Type-Safe and Portable Support for Packed Data (Experience Paper). In 39th European Conference on Object-Oriented Programming (ECOOP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 333, pp. 38:1-38:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{jamet_et_al:LIPIcs.ECOOP.2025.38,
  author =	{Jamet, Arthur and Vollmer, Michael},
  title =	{{Type-Safe and Portable Support for Packed Data}},
  booktitle =	{39th European Conference on Object-Oriented Programming (ECOOP 2025)},
  pages =	{38:1--38:19},
  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.2025.38},
  URN =		{urn:nbn:de:0030-drops-233301},
  doi =		{10.4230/LIPIcs.ECOOP.2025.38},
  annote =	{Keywords: program optimisation, data structures, data layout, packed data}
}
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
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
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.ITP.2019.24
A Verified LL(1) Parser Generator

Authors: Sam Lasser, Chris Casinghino, Kathleen Fisher, and Cody Roux

Published in: LIPIcs, Volume 141, 10th International Conference on Interactive Theorem Proving (ITP 2019)

Abstract
An LL(1) parser is a recursive descent algorithm that uses a single token of lookahead to build a grammatical derivation for an input sequence. We present an LL(1) parser generator that, when applied to grammar G, produces an LL(1) parser for G if such a parser exists. We use the Coq Proof Assistant to verify that the generator and the parsers that it produces are sound and complete, and that they terminate on all inputs without using fuel parameters. As a case study, we extract the tool’s source code and use it to generate a JSON parser. The generated parser runs in linear time; it is two to four times slower than an unverified parser for the same grammar.
Cite as

Sam Lasser, Chris Casinghino, Kathleen Fisher, and Cody Roux. A Verified LL(1) Parser Generator. In 10th International Conference on Interactive Theorem Proving (ITP 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 141, pp. 24:1-24:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)

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@InProceedings{lasser_et_al:LIPIcs.ITP.2019.24,
  author =	{Lasser, Sam and Casinghino, Chris and Fisher, Kathleen and Roux, Cody},
  title =	{{A Verified LL(1) Parser Generator}},
  booktitle =	{10th International Conference on Interactive Theorem Proving (ITP 2019)},
  pages =	{24:1--24:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-122-1},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{141},
  editor =	{Harrison, John and O'Leary, John and Tolmach, Andrew},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITP.2019.24},
  URN =		{urn:nbn:de:0030-drops-110794},
  doi =		{10.4230/LIPIcs.ITP.2019.24},
  annote =	{Keywords: interactive theorem proving, top-down parsing}
}
Document
DOI: 10.4230/LIPIcs.SNAPL.2015.140
Tracking the Flow of Ideas through the Programming Languages Literature

Authors: Michael Greenberg, Kathleen Fisher, and David Walker

Published in: LIPIcs, Volume 32, 1st Summit on Advances in Programming Languages (SNAPL 2015)

Abstract
How have conferences like ICFP, OOPSLA, PLDI, and POPL evolved over the last 20 years? Did generalizing the Call for Papers for OOPSLA in 2007 or changing the name of the umbrella conference to SPLASH in 2010 have any effect on the kinds of papers published there? How do POPL and PLDI papers compare, topic-wise? Is there related work that I am missing? Have the ideas in O'Hearn's classic paper on separation logic shifted the kinds of papers that appear in POPL? Does a proposed program committee cover the range of submissions expected for the conference? If we had better tools for analyzing the programming language literature, we might be able to answer these questions and others like them in a data-driven way. In this paper, we explore how topic modeling, a branch of machine learning, might help the programming language community better understand our literature.
Cite as

Michael Greenberg, Kathleen Fisher, and David Walker. Tracking the Flow of Ideas through the Programming Languages Literature. In 1st Summit on Advances in Programming Languages (SNAPL 2015). Leibniz International Proceedings in Informatics (LIPIcs), Volume 32, pp. 140-155, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2015)

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@InProceedings{greenberg_et_al:LIPIcs.SNAPL.2015.140,
  author =	{Greenberg, Michael and Fisher, Kathleen and Walker, David},
  title =	{{Tracking the Flow of Ideas through the Programming Languages Literature}},
  booktitle =	{1st Summit on Advances in Programming Languages (SNAPL 2015)},
  pages =	{140--155},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-939897-80-4},
  ISSN =	{1868-8969},
  year =	{2015},
  volume =	{32},
  editor =	{Ball, Thomas and Bodík, Rastislav and Krishnamurthi, Shriram and Lerner, Benjamin S. and Morriset, Greg},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SNAPL.2015.140},
  URN =		{urn:nbn:de:0030-drops-50232},
  doi =		{10.4230/LIPIcs.SNAPL.2015.140},
  annote =	{Keywords: programming languages literature, topic models, irony}
}
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