99 Search Results for "Joseph, Michael"

Document
DOI: 10.4230/LIPIcs.ECOOP.2024.7
HOBBIT: Hashed OBject Based InTegrity

Authors: Matthias Bernad and Stefan Brunthaler

Published in: LIPIcs, Volume 313, 38th European Conference on Object-Oriented Programming (ECOOP 2024)

Abstract
C vulnerabilities usually hold verbatim for C++ programs. The counterfeit-object-oriented programming attack demonstrated that this relation is asymmetric, i.e., it only applies to C++. The problem pinpointed by this COOP attack is that C++ does not validate the integrity of its objects. By injecting malicious objects with manipulated virtual function table pointers, attackers can hijack control-flow of programs. The software security community addressed the COOP-problem in the years following its discovery, but together with the emergence of transient-execution attacks, such as Spectre, researchers also shifted their attention. We present Hobbit, a software-only solution to prevent COOP attacks by validating object integrity for virtual function pointer tables. Hobbit does not require any hardware specific features, scales to multi-million lines of C++ source code, and our LLVM-based implementation offers a configurable performance impact between 121.63% and 2.80% on compute-intensive SPEC CPU C++ benchmarks. Hobbit’s security analysis indicates strong resistance to brute forcing attacks and demonstrates additional benefits of using execute-only memory.
Cite as

Matthias Bernad and Stefan Brunthaler. HOBBIT: Hashed OBject Based InTegrity. In 38th European Conference on Object-Oriented Programming (ECOOP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 313, pp. 7:1-7:25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{bernad_et_al:LIPIcs.ECOOP.2024.7,
  author =	{Bernad, Matthias and Brunthaler, Stefan},
  title =	{{HOBBIT: Hashed OBject Based InTegrity}},
  booktitle =	{38th European Conference on Object-Oriented Programming (ECOOP 2024)},
  pages =	{7:1--7:25},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-341-6},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{313},
  editor =	{Aldrich, Jonathan and Salvaneschi, Guido},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECOOP.2024.7},
  URN =		{urn:nbn:de:0030-drops-208566},
  doi =		{10.4230/LIPIcs.ECOOP.2024.7},
  annote =	{Keywords: software security, code-reuse attacks, language-based security, counterfeit-object-oriented programming, object integrity, compiler security}
}
Document
DOI: 10.4230/LIPIcs.ECOOP.2024.17
Fair Join Pattern Matching for Actors

Authors: Philipp Haller, Ayman Hussein, Hernán Melgratti, Alceste Scalas, and Emilio Tuosto

Published in: LIPIcs, Volume 313, 38th European Conference on Object-Oriented Programming (ECOOP 2024)

Abstract
Join patterns provide a promising approach to the development of concurrent and distributed message-passing applications. Several variations and implementations have been presented in the literature - but various aspects remain under-explored: in particular, how to specify a suitable notion of message matching, how to implement it correctly and efficiently, and how to systematically evaluate the implementation performance. In this work we focus on actor-based programming, and study the application of join patterns with conditional guards (i.e., the most expressive and challenging version of join patterns in literature). We formalise a novel specification of fair and deterministic join pattern matching, ensuring that older messages are always consumed if they can be matched. We present a stateful, tree-based join pattern matching algorithm and prove that it correctly implements our fair and deterministic matching specification. We present a novel Scala 3 actor library (called JoinActors) that implements our join pattern formalisation, leveraging macros to provide an intuitive API. Finally, we evaluate the performance of our implementation, by introducing a systematic benchmarking approach that takes into account the nuances of join pattern matching (in particular, its sensitivity to input traffic and complexity of patterns and guards).
Cite as

Philipp Haller, Ayman Hussein, Hernán Melgratti, Alceste Scalas, and Emilio Tuosto. Fair Join Pattern Matching for Actors. In 38th European Conference on Object-Oriented Programming (ECOOP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 313, pp. 17:1-17:28, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{haller_et_al:LIPIcs.ECOOP.2024.17,
  author =	{Haller, Philipp and Hussein, Ayman and Melgratti, Hern\'{a}n and Scalas, Alceste and Tuosto, Emilio},
  title =	{{Fair Join Pattern Matching for Actors}},
  booktitle =	{38th European Conference on Object-Oriented Programming (ECOOP 2024)},
  pages =	{17:1--17:28},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-341-6},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{313},
  editor =	{Aldrich, Jonathan and Salvaneschi, Guido},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECOOP.2024.17},
  URN =		{urn:nbn:de:0030-drops-208663},
  doi =		{10.4230/LIPIcs.ECOOP.2024.17},
  annote =	{Keywords: Concurrency, join patterns, join calculus, actor model}
}
Document
DOI: 10.4230/LIPIcs.ECOOP.2024.20
Taking a Closer Look: An Outlier-Driven Approach to Compilation-Time Optimization

Authors: Florian Huemer, David Leopoldseder, Aleksandar Prokopec, Raphael Mosaner, and Hanspeter Mössenböck

Published in: LIPIcs, Volume 313, 38th European Conference on Object-Oriented Programming (ECOOP 2024)

Abstract
Improving compilation time in optimizing compilers is challenging due to their large number of interconnected components. This includes compiler optimizations, compiler tiers, heuristics, and profiling information. Despite this complexity, research in compilation-time optimization is often guided by analyzing metrics of entire program runs, such as the total compilation time and overall memory footprint. This coarse-grained perspective hides relevant information, such as source program functions for which the compiler allocates a lot of memory or compiler optimizations with a high impact on the total compilation time. This leaves high-level metrics as the only reference point for driving optimization design. Consequently, compilation-time regressions in one program function that are obscured by improvements in other functions stay undetected, while the impacts of compiler changes on untouched parts of the compiler are mainly unknown. Furthermore, developers overlook long-standing compiler defects because their high-level metrics do not change over time. To address these limitations, we propose ICON, a new data-driven approach to compilation-time optimization that breaks up high-level metrics into individual source program functions, compiler optimizations, or even into individual instructions in the compiler source code. Our methodology enables an iterative in-depth compilation-time analysis, focusing on outliers to identify optimization opportunities. We show that outliers, both in terms of time spent in a particular compiler optimization, and in terms of individual compilations that take substantially longer, can reveal potential problems in the compiler implementation. We applied our approach to GraalVM and extracted data for multiple of its language runtimes. We analyzed the resulting data, present the first detailed look into the distribution of compilation time in the GraalVM compiler, a state-of-the-art multi-language compiler, and identified defects that led to regressions in overall compilation time or the compilation time of specific languages. We furthermore designed two optimizations based on the identified outliers that improve compilation time between 2.25% and 9.45%. We believe that our approach can guide compiler developers in finding usually overlooked optimization potential and defects, and focus future research efforts in making compilers more efficient.
Cite as

Florian Huemer, David Leopoldseder, Aleksandar Prokopec, Raphael Mosaner, and Hanspeter Mössenböck. Taking a Closer Look: An Outlier-Driven Approach to Compilation-Time Optimization. In 38th European Conference on Object-Oriented Programming (ECOOP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 313, pp. 20:1-20:28, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{huemer_et_al:LIPIcs.ECOOP.2024.20,
  author =	{Huemer, Florian and Leopoldseder, David and Prokopec, Aleksandar and Mosaner, Raphael and M\"{o}ssenb\"{o}ck, Hanspeter},
  title =	{{Taking a Closer Look: An Outlier-Driven Approach to Compilation-Time Optimization}},
  booktitle =	{38th European Conference on Object-Oriented Programming (ECOOP 2024)},
  pages =	{20:1--20:28},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-341-6},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{313},
  editor =	{Aldrich, Jonathan and Salvaneschi, Guido},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECOOP.2024.20},
  URN =		{urn:nbn:de:0030-drops-208693},
  doi =		{10.4230/LIPIcs.ECOOP.2024.20},
  annote =	{Keywords: Compilation time, outliers, dynamic languages, virtual machines, GraalVM, ICON}
}
Document
DOI: 10.4230/LIPIcs.ECOOP.2024.32
Tenspiler: A Verified-Lifting-Based Compiler for Tensor Operations

Authors: Jie Qiu, Colin Cai, Sahil Bhatia, Niranjan Hasabnis, Sanjit A. Seshia, and Alvin Cheung

Published in: LIPIcs, Volume 313, 38th European Conference on Object-Oriented Programming (ECOOP 2024)

Abstract
Tensor processing infrastructures such as deep learning frameworks and specialized hardware accelerators have revolutionized how computationally intensive code from domains such as deep learning and image processing is executed and optimized. These infrastructures provide powerful and expressive abstractions while ensuring high performance. However, to utilize them, code must be written specifically using the APIs / ISAs of such software frameworks or hardware accelerators. Importantly, given the fast pace of innovation in these domains, code written today quickly becomes legacy as new frameworks and accelerators are developed, and migrating such legacy code manually is a considerable effort. To enable developers in leveraging such DSLs while preserving their current programming paradigm, we present Tenspiler, a verified-lifting-based compiler that uses program synthesis to translate sequential programs written in general-purpose programming languages (e.g., C++ or Python code that does not leverage any specialized framework or accelerator) into tensor operations. Central to Tenspiler is our carefully crafted yet simple intermediate language, named TensIR, that expresses tensor operations. TensIR enables efficient lifting, verification, and code generation. Unlike classical pattern-matching-based compilers, Tenspiler uses program synthesis to translate input code into TensIR, which is then compiled to the target API / ISA. Currently, Tenspiler already supports six DSLs, spanning a broad spectrum of software and hardware environments. Furthermore, we show that new backends can be easily supported by Tenspiler by adding simple pattern-matching rules for TensIR. Using 10 real-world code benchmark suites, our experimental evaluation shows that by translating code to be executed on 6 different software frameworks and hardware devices, Tenspiler offers on average 105× kernel and 9.65× end-to-end execution time improvement over the fully-optimized sequential implementation of the same benchmarks.
Cite as

Jie Qiu, Colin Cai, Sahil Bhatia, Niranjan Hasabnis, Sanjit A. Seshia, and Alvin Cheung. Tenspiler: A Verified-Lifting-Based Compiler for Tensor Operations. In 38th European Conference on Object-Oriented Programming (ECOOP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 313, pp. 32:1-32:28, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{qiu_et_al:LIPIcs.ECOOP.2024.32,
  author =	{Qiu, Jie and Cai, Colin and Bhatia, Sahil and Hasabnis, Niranjan and Seshia, Sanjit A. and Cheung, Alvin},
  title =	{{Tenspiler: A Verified-Lifting-Based Compiler for Tensor Operations}},
  booktitle =	{38th European Conference on Object-Oriented Programming (ECOOP 2024)},
  pages =	{32:1--32:28},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-341-6},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{313},
  editor =	{Aldrich, Jonathan and Salvaneschi, Guido},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECOOP.2024.32},
  URN =		{urn:nbn:de:0030-drops-208817},
  doi =		{10.4230/LIPIcs.ECOOP.2024.32},
  annote =	{Keywords: Program Synthesis, Code Transpilation, Tensor DSLs, Verification}
}
Document
DOI: 10.4230/LIPIcs.ECOOP.2024.38
Optimizing Layout of Recursive Datatypes with Marmoset: Or, Algorithms {+} Data Layouts {=} Efficient Programs

Authors: Vidush Singhal, Chaitanya Koparkar, Joseph Zullo, Artem Pelenitsyn, Michael Vollmer, Mike Rainey, Ryan Newton, and Milind Kulkarni

Published in: LIPIcs, Volume 313, 38th European Conference on Object-Oriented Programming (ECOOP 2024)

Abstract
While programmers know that memory representation of data structures can have significant effects on performance, compiler support to optimize the layout of those structures is an under-explored field. Prior work has optimized the layout of individual, non-recursive structures without considering how collections of those objects in linked or recursive data structures are laid out. This work introduces Marmoset, a compiler that optimizes the layouts of algebraic datatypes, with a special focus on producing highly optimized, packed data layouts where recursive structures can be traversed with minimal pointer chasing. Marmoset performs an analysis of how a recursive ADT is used across functions to choose a global layout that promotes simple, strided access for that ADT in memory. It does so by building and solving a constraint system to minimize an abstract cost model, yielding a predicted efficient layout for the ADT. Marmoset then builds on top of Gibbon, a prior compiler for packed, mostly-serial representations, to synthesize optimized ADTs. We show experimentally that Marmoset is able to choose optimal layouts across a series of microbenchmarks and case studies, outperforming both Gibbon’s baseline approach, as well as MLton, a Standard ML compiler that uses traditional pointer-heavy representations.
Cite as

Vidush Singhal, Chaitanya Koparkar, Joseph Zullo, Artem Pelenitsyn, Michael Vollmer, Mike Rainey, Ryan Newton, and Milind Kulkarni. Optimizing Layout of Recursive Datatypes with Marmoset: Or, Algorithms {+} Data Layouts {=} Efficient Programs. In 38th European Conference on Object-Oriented Programming (ECOOP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 313, pp. 38:1-38:28, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{singhal_et_al:LIPIcs.ECOOP.2024.38,
  author =	{Singhal, Vidush and Koparkar, Chaitanya and Zullo, Joseph and Pelenitsyn, Artem and Vollmer, Michael and Rainey, Mike and Newton, Ryan and Kulkarni, Milind},
  title =	{{Optimizing Layout of Recursive Datatypes with Marmoset: Or, Algorithms \{+\} Data Layouts \{=\} Efficient Programs}},
  booktitle =	{38th European Conference on Object-Oriented Programming (ECOOP 2024)},
  pages =	{38:1--38:28},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-341-6},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{313},
  editor =	{Aldrich, Jonathan and Salvaneschi, Guido},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECOOP.2024.38},
  URN =		{urn:nbn:de:0030-drops-208875},
  doi =		{10.4230/LIPIcs.ECOOP.2024.38},
  annote =	{Keywords: Tree traversals, Compilers, Data layout optimization, Dense data layout}
}
Document
DOI: 10.4230/LIPIcs.ECOOP.2024.42
Failure Transparency in Stateful Dataflow Systems

Authors: Aleksey Veresov, Jonas Spenger, Paris Carbone, and Philipp Haller

Published in: LIPIcs, Volume 313, 38th European Conference on Object-Oriented Programming (ECOOP 2024)

Abstract
Failure transparency enables users to reason about distributed systems at a higher level of abstraction, where complex failure-handling logic is hidden. This is especially true for stateful dataflow systems, which are the backbone of many cloud applications. In particular, this paper focuses on proving failure transparency in Apache Flink, a popular stateful dataflow system. Even though failure transparency is a critical aspect of Apache Flink, to date it has not been formally proven. Showing that the failure transparency mechanism is correct, however, is challenging due to the complexity of the mechanism itself. Nevertheless, this complexity can be effectively hidden behind a failure transparent programming interface. To show that Apache Flink is failure transparent, we model it in small-step operational semantics. Next, we provide a novel definition of failure transparency based on observational explainability, a concept which relates executions according to their observations. Finally, we provide a formal proof of failure transparency for the implementation model; i.e., we prove that the failure-free model correctly abstracts from the failure-related details of the implementation model. We also show liveness of the implementation model under a fair execution assumption. These results are a first step towards a verified stack for stateful dataflow systems.
Cite as

Aleksey Veresov, Jonas Spenger, Paris Carbone, and Philipp Haller. Failure Transparency in Stateful Dataflow Systems. In 38th European Conference on Object-Oriented Programming (ECOOP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 313, pp. 42:1-42:31, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{veresov_et_al:LIPIcs.ECOOP.2024.42,
  author =	{Veresov, Aleksey and Spenger, Jonas and Carbone, Paris and Haller, Philipp},
  title =	{{Failure Transparency in Stateful Dataflow Systems}},
  booktitle =	{38th European Conference on Object-Oriented Programming (ECOOP 2024)},
  pages =	{42:1--42:31},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-341-6},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{313},
  editor =	{Aldrich, Jonathan and Salvaneschi, Guido},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECOOP.2024.42},
  URN =		{urn:nbn:de:0030-drops-208911},
  doi =		{10.4230/LIPIcs.ECOOP.2024.42},
  annote =	{Keywords: Failure transparency, stateful dataflow, operational semantics, checkpoint recovery}
}
Document
DOI: 10.4230/LIPIcs.ECOOP.2024.46
{CtChecker}: A Precise, Sound and Efficient Static Analysis for Constant-Time Programming

Authors: Quan Zhou, Sixuan Dang, and Danfeng Zhang

Published in: LIPIcs, Volume 313, 38th European Conference on Object-Oriented Programming (ECOOP 2024)

Abstract
Timing channel attacks are emerging as real-world threats to computer security. In cryptographic systems, an effective countermeasure against timing attacks is the constant-time programming discipline. However, strictly enforcing the discipline manually is both time-consuming and error-prone. While various tools exist for analyzing/verifying constant-time programs, they sacrifice at least one feature among precision, soundness and efficiency. In this paper, we build CtChecker, a sound static analysis for constant-time programming. Under the hood, CtChecker uses a static information flow analysis to identify violations of constant-time discipline. Despite the common wisdom that sound, static information flow analysis lacks precision for real-world applications, we show that by enabling field-sensitivity, context-sensitivity and partial flow-sensitivity, CtChecker reports fewer false positives compared with existing sound tools. Evaluation on real-world cryptographic systems shows that CtChecker analyzes 24K lines of source code in under one minute. Moreover, CtChecker reveals that some repaired code generated by program rewriters supposedly remove timing channels are still not constant-time.
Cite as

Quan Zhou, Sixuan Dang, and Danfeng Zhang. {CtChecker}: A Precise, Sound and Efficient Static Analysis for Constant-Time Programming. In 38th European Conference on Object-Oriented Programming (ECOOP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 313, pp. 46:1-46:26, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{zhou_et_al:LIPIcs.ECOOP.2024.46,
  author =	{Zhou, Quan and Dang, Sixuan and Zhang, Danfeng},
  title =	{{\{CtChecker\}: A Precise, Sound and Efficient Static Analysis for Constant-Time Programming}},
  booktitle =	{38th European Conference on Object-Oriented Programming (ECOOP 2024)},
  pages =	{46:1--46:26},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-341-6},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{313},
  editor =	{Aldrich, Jonathan and Salvaneschi, Guido},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECOOP.2024.46},
  URN =		{urn:nbn:de:0030-drops-208951},
  doi =		{10.4230/LIPIcs.ECOOP.2024.46},
  annote =	{Keywords: Information flow control, static analysis, side channel, constant-time programming}
}
Document
Artifact
DOI: 10.4230/DARTS.10.2.21
Optimizing Layout of Recursive Datatypes with Marmoset (Artifact)

Authors: Vidush Singhal, Chaitanya Koparkar, Joseph Zullo, Artem Pelenitsyn, Michael Vollmer, Mike Rainey, Ryan Newton, and Milind Kulkarni

Published in: DARTS, Volume 10, Issue 2, Special Issue of the 38th European Conference on Object-Oriented Programming (ECOOP 2024)

Abstract
While programmers know that memory representation of data structures can have significant effects on performance, compiler support to optimize the layout of those structures is an under-explored field. Prior work has optimized the layout of individual, non-recursive structures without considering how collections of those objects in linked or recursive data structures are laid out. This work introduces Marmoset, a compiler that optimizes the layouts of algebraic datatypes, with a special focus on producing highly optimized, packed data layouts where recursive structures can be traversed with minimal pointer chasing. Marmoset performs an analysis of how a recursive ADT is used across functions to choose a global layout that promotes simple, strided access for that ADT in memory. It does so by building and solving a constraint system to minimize an abstract cost model, yielding a predicted efficient layout for the ADT. Marmoset then builds on top of Gibbon, a prior compiler for packed, mostly-serial representations, to synthesize optimized ADTs. We show experimentally that Marmoset is able to choose optimal layouts across a series of microbenchmarks and case studies, outperforming both Gibbon’s baseline approach, as well as MLton, a Standard ML compiler that uses traditional pointer-heavy representations.
Cite as

Vidush Singhal, Chaitanya Koparkar, Joseph Zullo, Artem Pelenitsyn, Michael Vollmer, Mike Rainey, Ryan Newton, and Milind Kulkarni. Optimizing Layout of Recursive Datatypes with Marmoset (Artifact). In Special Issue of the 38th European Conference on Object-Oriented Programming (ECOOP 2024). Dagstuhl Artifacts Series (DARTS), Volume 10, Issue 2, pp. 21:1-21:10, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@Article{singhal_et_al:DARTS.10.2.21,
  author =	{Singhal, Vidush and Koparkar, Chaitanya and Zullo, Joseph and Pelenitsyn, Artem and Vollmer, Michael and Rainey, Mike and Newton, Ryan and Kulkarni, Milind},
  title =	{{Optimizing Layout of Recursive Datatypes with Marmoset (Artifact)}},
  pages =	{21:1--21:10},
  journal =	{Dagstuhl Artifacts Series},
  ISBN =	{978-3-95977-342-3},
  ISSN =	{2509-8195},
  year =	{2024},
  volume =	{10},
  number =	{2},
  editor =	{Singhal, Vidush and Koparkar, Chaitanya and Zullo, Joseph and Pelenitsyn, Artem and Vollmer, Michael and Rainey, Mike and Newton, Ryan and Kulkarni, Milind},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DARTS.10.2.21},
  URN =		{urn:nbn:de:0030-drops-209199},
  doi =		{10.4230/DARTS.10.2.21},
  annote =	{Keywords: Tree traversals, Compilers, Data layout optimization, Dense data layout}
}
Document
DOI: 10.4230/LIPIcs.DNA.30.1
Geometric Enumeration of Localized DNA Strand Displacement Reaction Networks

Authors: Matthew R. Lakin and Sarika Kumar

Published in: LIPIcs, Volume 314, 30th International Conference on DNA Computing and Molecular Programming (DNA 30) (2024)

Abstract
Localized molecular devices are a powerful tool for engineering complex information-processing circuits and molecular robots. Their practical advantages include speed and scalability of interactions between components tethered near to each other on an underlying nanostructure, and the ability to restrict interactions between more distant components. The latter is a critical feature that must be factored into computational tools for the design and simulation of localized molecular devices: unlike in solution-phase systems, the geometries of molecular interactions must be accounted for when attempting to determine the network of possible reactions in a tethered molecular system. This work aims to address that challenge by integrating, for the first time, automated approaches to analysis of molecular geometry with reaction enumeration algorithms for DNA strand displacement reaction networks that can be applied to tethered molecular systems. By adapting a simple approach to solving the biophysical constraints inherent in molecular interactions to be applicable to tethered systems, we produce a localized reaction enumeration system that enhances previous approaches to reaction enumeration in tethered system by not requiring users to explicitly specify the subsets of components that are capable of interacting. This greatly simplifies the user’s task and could also be used as the basis of future systems for automated placement or routing of signal-transmission and logical processing in molecular devices. We apply this system to several published example systems from the literature, including both tethered molecular logic systems and molecular robots.
Cite as

Matthew R. Lakin and Sarika Kumar. Geometric Enumeration of Localized DNA Strand Displacement Reaction Networks. In 30th International Conference on DNA Computing and Molecular Programming (DNA 30). Leibniz International Proceedings in Informatics (LIPIcs), Volume 314, pp. 1:1-1:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{lakin_et_al:LIPIcs.DNA.30.1,
  author =	{Lakin, Matthew R. and Kumar, Sarika},
  title =	{{Geometric Enumeration of Localized DNA Strand Displacement Reaction Networks}},
  booktitle =	{30th International Conference on DNA Computing and Molecular Programming (DNA 30)},
  pages =	{1:1--1:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-344-7},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{314},
  editor =	{Seki, Shinnosuke and Stewart, Jaimie Marie},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.30.1},
  URN =		{urn:nbn:de:0030-drops-209294},
  doi =		{10.4230/LIPIcs.DNA.30.1},
  annote =	{Keywords: Localized circuits, reaction enumeration, DNA strand displacement, geometry, molecular computing}
}
Document
DOI: 10.4230/LIPIcs.DNA.30.2
Domain-Based Nucleic-Acid Minimum Free Energy: Algorithmic Hardness and Parameterized Bounds

Authors: Erik D. Demaine, Timothy Gomez, Elise Grizzell, Markus Hecher, Jayson Lynch, Robert Schweller, Ahmed Shalaby, and Damien Woods

Published in: LIPIcs, Volume 314, 30th International Conference on DNA Computing and Molecular Programming (DNA 30) (2024)

Abstract
Molecular programmers and nanostructure engineers use domain-level design to abstract away messy DNA/RNA sequence, chemical and geometric details. Such domain-level abstractions are enforced by sequence design principles and provide a key principle that allows scaling up of complex multistranded DNA/RNA programs and structures. Determining the most favoured secondary structure, or Minimum Free Energy (MFE), of a set of strands, is typically studied at the sequence level but has seen limited domain-level work. We analyse the computational complexity of MFE for multistranded systems in a simple setting were we allow only 1 or 2 domains per strand. On the one hand, with 2-domain strands, we find that the MFE decision problem is NP-complete, even without pseudoknots, and requires exponential time algorithms assuming SAT does. On the other hand, in the simplest case of 1-domain strands there are efficient MFE algorithms for various binding modes. However, even in this single-domain case, MFE is P-hard for promiscuous binding, where one domain may bind to multiple as experimentally used by Nikitin [Nat Chem., 2023], which in turn implies that strands consisting of a single domain efficiently implement arbitrary Boolean circuits.
Cite as

Erik D. Demaine, Timothy Gomez, Elise Grizzell, Markus Hecher, Jayson Lynch, Robert Schweller, Ahmed Shalaby, and Damien Woods. Domain-Based Nucleic-Acid Minimum Free Energy: Algorithmic Hardness and Parameterized Bounds. In 30th International Conference on DNA Computing and Molecular Programming (DNA 30). Leibniz International Proceedings in Informatics (LIPIcs), Volume 314, pp. 2:1-2:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{demaine_et_al:LIPIcs.DNA.30.2,
  author =	{Demaine, Erik D. and Gomez, Timothy and Grizzell, Elise and Hecher, Markus and Lynch, Jayson and Schweller, Robert and Shalaby, Ahmed and Woods, Damien},
  title =	{{Domain-Based Nucleic-Acid Minimum Free Energy: Algorithmic Hardness and Parameterized Bounds}},
  booktitle =	{30th International Conference on DNA Computing and Molecular Programming (DNA 30)},
  pages =	{2:1--2:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-344-7},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{314},
  editor =	{Seki, Shinnosuke and Stewart, Jaimie Marie},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.30.2},
  URN =		{urn:nbn:de:0030-drops-209304},
  doi =		{10.4230/LIPIcs.DNA.30.2},
  annote =	{Keywords: Domain-based DNA designs, minimum free energy, efficient algorithms, NP-hard, P-hard, NC, fixed-parameter tractable}
}
Document
DOI: 10.4230/LIPIcs.DNA.30.4
Designing 3D RNA Origami Nanostructures with a Minimum Number of Kissing Loops

Authors: Antti Elonen and Pekka Orponen

Published in: LIPIcs, Volume 314, 30th International Conference on DNA Computing and Molecular Programming (DNA 30) (2024)

Abstract
We present a general design technique for rendering any 3D wireframe model, that is any connected graph linearly embedded in 3D space, as an RNA origami nanostructure with a minimum number of kissing loops. The design algorithm, which applies some ideas and methods from topological graph theory, produces renderings that contain at most one kissing-loop pair for many interesting model families, including for instance all fully triangulated wireframes and the wireframes of all Platonic solids. The design method is already implemented and available for use in the design tool DNAforge (https://dnaforge.org).
Cite as

Antti Elonen and Pekka Orponen. Designing 3D RNA Origami Nanostructures with a Minimum Number of Kissing Loops. In 30th International Conference on DNA Computing and Molecular Programming (DNA 30). Leibniz International Proceedings in Informatics (LIPIcs), Volume 314, pp. 4:1-4:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{elonen_et_al:LIPIcs.DNA.30.4,
  author =	{Elonen, Antti and Orponen, Pekka},
  title =	{{Designing 3D RNA Origami Nanostructures with a Minimum Number of Kissing Loops}},
  booktitle =	{30th International Conference on DNA Computing and Molecular Programming (DNA 30)},
  pages =	{4:1--4:12},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-344-7},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{314},
  editor =	{Seki, Shinnosuke and Stewart, Jaimie Marie},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.30.4},
  URN =		{urn:nbn:de:0030-drops-209325},
  doi =		{10.4230/LIPIcs.DNA.30.4},
  annote =	{Keywords: RNA origami, wireframe nanostructures, polyhedra, kissing loops, topological graph embeddings, self-assembly}
}
Document
DOI: 10.4230/LIPIcs.COSIT.2024.1
Wayfinding Stages: The Role of Familiarity, Gaze Events, and Visual Attention

Authors: Negar Alinaghi and Ioannis Giannopoulos

Published in: LIPIcs, Volume 315, 16th International Conference on Spatial Information Theory (COSIT 2024)

Abstract
Understanding the cognitive processes involved in wayfinding is crucial for both theoretical advances and practical applications in navigation systems development. This study explores how gaze behavior and visual attention contribute to our understanding of cognitive states during wayfinding. Based on the model proposed by Downs and Stea, which segments wayfinding into four distinct stages: self-localization, route planning, monitoring, and goal recognition, we conducted an outdoor wayfinding experiment with 56 participants. Given the significant role of spatial familiarity in wayfinding behavior, each participant navigated six different routes in both familiar and unfamiliar environments, with their eye movements being recorded. We provide a detailed examination of participants' gaze behavior and the actual objects of focus. Our findings reveal distinct gaze behavior patterns and visual attention, differentiating wayfinding stages while emphasizing the impact of spatial familiarity. This examination of visual engagement during wayfinding explains adaptive cognitive processes, demonstrating how familiarity influences navigation strategies. The results enhance our theoretical understanding of wayfinding and offer practical insights for developing navigation aids capable of predicting different wayfinding stages.
Cite as

Negar Alinaghi and Ioannis Giannopoulos. Wayfinding Stages: The Role of Familiarity, Gaze Events, and Visual Attention. In 16th International Conference on Spatial Information Theory (COSIT 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 315, pp. 1:1-1:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{alinaghi_et_al:LIPIcs.COSIT.2024.1,
  author =	{Alinaghi, Negar and Giannopoulos, Ioannis},
  title =	{{Wayfinding Stages: The Role of Familiarity, Gaze Events, and Visual Attention}},
  booktitle =	{16th International Conference on Spatial Information Theory (COSIT 2024)},
  pages =	{1:1--1:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-330-0},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{315},
  editor =	{Adams, Benjamin and Griffin, Amy L. and Scheider, Simon and McKenzie, Grant},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.COSIT.2024.1},
  URN =		{urn:nbn:de:0030-drops-208161},
  doi =		{10.4230/LIPIcs.COSIT.2024.1},
  annote =	{Keywords: Eye-tracking, Wayfinding, Spatial Familiarity, Visual Attention, Gaze Behavior}
}
Document
DOI: 10.4230/LIPIcs.COSIT.2024.3
Can You Sketch in 3D? Exploring Perceived Feasibility and Use Cases of 3D Sketch Mapping

Authors: Kevin Gonyop Kim, Tiffany C.K. Kwok, Sailin Zhong, Peter Kiefer, and Martin Raubal

Published in: LIPIcs, Volume 315, 16th International Conference on Spatial Information Theory (COSIT 2024)

Abstract
Sketch mapping is a research technique that has been widely used to study what people think about the spatial layout of an environment. One of the limitations of the current practice of sketch mapping is that the interface (a pen on paper or digital tablets) forces people to draw on 2D surfaces even when the information to be represented is 3D. For the purpose of studying the 3D aspect of spatial understanding, the recent advancements in extended reality (XR) technologies including virtual reality, augmented reality, and mixed reality are interesting as they provide novel ways to create 3D sketches. In this paper, we investigate how the concept of 3D sketch mapping using XR is perceived by users and explore its potential feasibility and use cases. For this, we conducted semi-structured interviews with 27 participants from three domains: aviation, architecture, and wayfinding. Our findings show that the concept is well-perceived as an intuitive way to externalize the 3D aspect of spatial information, and it has the potential to be a research tool for human cognition research as well as a practical tool that can provide added value in different professional activities.
Cite as

Kevin Gonyop Kim, Tiffany C.K. Kwok, Sailin Zhong, Peter Kiefer, and Martin Raubal. Can You Sketch in 3D? Exploring Perceived Feasibility and Use Cases of 3D Sketch Mapping. In 16th International Conference on Spatial Information Theory (COSIT 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 315, pp. 3:1-3:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{kim_et_al:LIPIcs.COSIT.2024.3,
  author =	{Kim, Kevin Gonyop and Kwok, Tiffany C.K. and Zhong, Sailin and Kiefer, Peter and Raubal, Martin},
  title =	{{Can You Sketch in 3D? Exploring Perceived Feasibility and Use Cases of 3D Sketch Mapping}},
  booktitle =	{16th International Conference on Spatial Information Theory (COSIT 2024)},
  pages =	{3:1--3:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-330-0},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{315},
  editor =	{Adams, Benjamin and Griffin, Amy L. and Scheider, Simon and McKenzie, Grant},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.COSIT.2024.3},
  URN =		{urn:nbn:de:0030-drops-208186},
  doi =		{10.4230/LIPIcs.COSIT.2024.3},
  annote =	{Keywords: Sketch maps, spatial understanding, 3D sketching, extended reality, use cases, interviews}
}
Document
DOI: 10.4230/LIPIcs.COSIT.2024.11
Semantic Perspectives on the Lake District Writing: Spatial Ontology Modeling and Relation Extraction for Deeper Insights

Authors: Erum Haris, Anthony G. Cohn, and John G. Stell

Published in: LIPIcs, Volume 315, 16th International Conference on Spatial Information Theory (COSIT 2024)

Abstract
Extracting spatial details from historical texts can be difficult, hindering our understanding of past landscapes. The study addresses this challenge by analyzing the Corpus of the Lake District Writing, focusing on the English Lake District region. We systematically link the theoretical notions from the core concepts of spatial information to provide basis for the problem domain. The conceptual foundation is further complemented with a spatial ontology and a custom gazetteer, allowing a formal and insightful semantic exploration of the massive unstructured corpus. The other contrasting side of the framework is the usage of LLMs for spatial relation extraction. We formulate prompts leveraging understanding of the LLMs of the intended task, curate a list of spatial relations representing the most recurring proximity or vicinity relations terms and extract semantic triples for the top five place names appearing in the corpus. We compare the extraction capabilities of three benchmark LLMs for a scholarly significant historical archive, representing their potential in a challenging and interdisciplinary research problem. Finally, the network comprising the semantic triples is enhanced by incorporating a gazetteer-based classification of the objects involved thus improving their spatial profiling.
Cite as

Erum Haris, Anthony G. Cohn, and John G. Stell. Semantic Perspectives on the Lake District Writing: Spatial Ontology Modeling and Relation Extraction for Deeper Insights. In 16th International Conference on Spatial Information Theory (COSIT 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 315, pp. 11:1-11:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{haris_et_al:LIPIcs.COSIT.2024.11,
  author =	{Haris, Erum and Cohn, Anthony G. and Stell, John G.},
  title =	{{Semantic Perspectives on the Lake District Writing: Spatial Ontology Modeling and Relation Extraction for Deeper Insights}},
  booktitle =	{16th International Conference on Spatial Information Theory (COSIT 2024)},
  pages =	{11:1--11:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-330-0},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{315},
  editor =	{Adams, Benjamin and Griffin, Amy L. and Scheider, Simon and McKenzie, Grant},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.COSIT.2024.11},
  URN =		{urn:nbn:de:0030-drops-208268},
  doi =		{10.4230/LIPIcs.COSIT.2024.11},
  annote =	{Keywords: spatial humanities, spatial narratives, ontology, large language models}
}
Document
Short Paper
DOI: 10.4230/LIPIcs.COSIT.2024.18
Inferring the Origin of Linguistic Features from an Atlas: A Case Study of Swiss-German Dialects. (Short Paper)

Authors: Takuya Takahashi, Elvira Glaser, and Peter Ranacher

Published in: LIPIcs, Volume 315, 16th International Conference on Spatial Information Theory (COSIT 2024)

Abstract
A linguistic atlas is a set of maps which visualize the geographical variation of linguistic features in a single language. We present a novel model for Bayesian statistics which infers when and where the variants of a linguistic feature were invented based on the geographical distribution shown in a linguistic atlas. Based on a spatial network representing the rate of diffusion between locations, our model evaluates the probability (likelihood) that the observed geographical pattern is realized by considering the genealogical relationship between variants at different locations. We apply our model to a linguistic atlas of Swiss-German dialects and infer the origin of three forms of the High-German word "nein" meaning "no".
Cite as

Takuya Takahashi, Elvira Glaser, and Peter Ranacher. Inferring the Origin of Linguistic Features from an Atlas: A Case Study of Swiss-German Dialects. (Short Paper). In 16th International Conference on Spatial Information Theory (COSIT 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 315, pp. 18:1-18:9, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{takahashi_et_al:LIPIcs.COSIT.2024.18,
  author =	{Takahashi, Takuya and Glaser, Elvira and Ranacher, Peter},
  title =	{{Inferring the Origin of Linguistic Features from an Atlas: A Case Study of Swiss-German Dialects.}},
  booktitle =	{16th International Conference on Spatial Information Theory (COSIT 2024)},
  pages =	{18:1--18:9},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-330-0},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{315},
  editor =	{Adams, Benjamin and Griffin, Amy L. and Scheider, Simon and McKenzie, Grant},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.COSIT.2024.18},
  URN =		{urn:nbn:de:0030-drops-208331},
  doi =		{10.4230/LIPIcs.COSIT.2024.18},
  annote =	{Keywords: Dialectology, Linguistic geography, Geographic information science, Bayesian inference}
}
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