26 Search Results for "Hao, Yu"

Document
APPROX
DOI: 10.4230/LIPIcs.APPROX/RANDOM.2024.2
Online Time-Windows TSP with Predictions

Authors: Shuchi Chawla and Dimitris Christou

Published in: LIPIcs, Volume 317, Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2024)

Abstract
In the Time-Windows TSP (TW-TSP) we are given requests at different locations on a network; each request is endowed with a reward and an interval of time; the goal is to find a tour that visits as much reward as possible during the corresponding time window. For the online version of this problem, where each request is revealed at the start of its time window, no finite competitive ratio can be obtained. We consider a version of the problem where the algorithm is presented with predictions of where and when the online requests will appear, without any knowledge of the quality of this side information. Vehicle routing problems such as the TW-TSP can be very sensitive to errors or changes in the input due to the hard time-window constraints, and it is unclear whether imperfect predictions can be used to obtain a finite competitive ratio. We show that good performance can be achieved by explicitly building slack into the solution. Our main result is an online algorithm that achieves a competitive ratio logarithmic in the diameter of the underlying network, matching the performance of the best offline algorithm to within factors that depend on the quality of the provided predictions. The competitive ratio degrades smoothly as a function of the quality and we show that this dependence is tight within constant factors.
Cite as

Shuchi Chawla and Dimitris Christou. Online Time-Windows TSP with Predictions. In Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 317, pp. 2:1-2:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{chawla_et_al:LIPIcs.APPROX/RANDOM.2024.2,
  author =	{Chawla, Shuchi and Christou, Dimitris},
  title =	{{Online Time-Windows TSP with Predictions}},
  booktitle =	{Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2024)},
  pages =	{2:1--2:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-348-5},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{317},
  editor =	{Kumar, Amit and Ron-Zewi, Noga},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.APPROX/RANDOM.2024.2},
  URN =		{urn:nbn:de:0030-drops-209954},
  doi =		{10.4230/LIPIcs.APPROX/RANDOM.2024.2},
  annote =	{Keywords: Travelling Salesman Problem, Predictions, Learning-Augmented Algorithms, Approximation}
}
Document
APPROX
DOI: 10.4230/LIPIcs.APPROX/RANDOM.2024.16
Weighted Matching in the Random-Order Streaming and Robust Communication Models

Authors: Diba Hashemi and Weronika Wrzos-Kaminska

Published in: LIPIcs, Volume 317, Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2024)

Abstract
We study the maximum weight matching problem in the random-order semi-streaming model and in the robust communication model. Unlike many other sublinear models, in these two frameworks, there is a large gap between the guarantees of the best known algorithms for the unweighted and weighted versions of the problem. In the random-order semi-streaming setting, the edges of an n-vertex graph arrive in a stream in a random order. The goal is to compute an approximate maximum weight matching with a single pass over the stream using O(npolylog n) space. Our main result is a (2/3-ε)-approximation algorithm for maximum weight matching in random-order streams, using space O(n log n log R), where R is the ratio between the heaviest and the lightest edge in the graph. Our result nearly matches the best known unweighted (2/3+ε₀)-approximation (where ε₀ ∼ 10^{-14} is a small constant) achieved by Assadi and Behnezhad [Assadi and Behnezhad, 2021], and significantly improves upon previous weighted results. Our techniques also extend to the related robust communication model, in which the edges of a graph are partitioned randomly between Alice and Bob. Alice sends a single message of size O(npolylog n) to Bob, who must compute an approximate maximum weight matching. We achieve a (5/6-ε)-approximation using O(n log n log R) words of communication, matching the results of Azarmehr and Behnezhad [Azarmehr and Behnezhad, 2023] for unweighted graphs.
Cite as

Diba Hashemi and Weronika Wrzos-Kaminska. Weighted Matching in the Random-Order Streaming and Robust Communication Models. In Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 317, pp. 16:1-16:26, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{hashemi_et_al:LIPIcs.APPROX/RANDOM.2024.16,
  author =	{Hashemi, Diba and Wrzos-Kaminska, Weronika},
  title =	{{Weighted Matching in the Random-Order Streaming and Robust Communication Models}},
  booktitle =	{Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2024)},
  pages =	{16:1--16:26},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-348-5},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{317},
  editor =	{Kumar, Amit and Ron-Zewi, Noga},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.APPROX/RANDOM.2024.16},
  URN =		{urn:nbn:de:0030-drops-210097},
  doi =		{10.4230/LIPIcs.APPROX/RANDOM.2024.16},
  annote =	{Keywords: Maximum Weight Matching, Streaming, Random-Order Streaming, Robust Communication Complexity}
}
Document
APPROX
DOI: 10.4230/LIPIcs.APPROX/RANDOM.2024.24
Learning-Augmented Maximum Independent Set

Authors: Vladimir Braverman, Prathamesh Dharangutte, Vihan Shah, and Chen Wang

Published in: LIPIcs, Volume 317, Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2024)

Abstract
We study the Maximum Independent Set (MIS) problem on general graphs within the framework of learning-augmented algorithms. The MIS problem is known to be NP-hard and is also NP-hard to approximate to within a factor of n^(1-δ) for any δ > 0. We show that we can break this barrier in the presence of an oracle obtained through predictions from a machine learning model that answers vertex membership queries for a fixed MIS with probability 1/2+ε. In the first setting we consider, the oracle can be queried once per vertex to know if a vertex belongs to a fixed MIS, and the oracle returns the correct answer with probability 1/2 + ε. Under this setting, we show an algorithm that obtains an Õ((√Δ)/ε)-approximation in O(m) time where Δ is the maximum degree of the graph. In the second setting, we allow multiple queries to the oracle for a vertex, each of which is correct with probability 1/2 + ε. For this setting, we show an O(1)-approximation algorithm using O(n/ε²) total queries and Õ(m) runtime.
Cite as

Vladimir Braverman, Prathamesh Dharangutte, Vihan Shah, and Chen Wang. Learning-Augmented Maximum Independent Set. In Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 317, pp. 24:1-24:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{braverman_et_al:LIPIcs.APPROX/RANDOM.2024.24,
  author =	{Braverman, Vladimir and Dharangutte, Prathamesh and Shah, Vihan and Wang, Chen},
  title =	{{Learning-Augmented Maximum Independent Set}},
  booktitle =	{Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2024)},
  pages =	{24:1--24:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-348-5},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{317},
  editor =	{Kumar, Amit and Ron-Zewi, Noga},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.APPROX/RANDOM.2024.24},
  URN =		{urn:nbn:de:0030-drops-210179},
  doi =		{10.4230/LIPIcs.APPROX/RANDOM.2024.24},
  annote =	{Keywords: Learning-augmented algorithms, maximum independent set, graph algorithms}
}
Document
DOI: 10.4230/LIPIcs.ECOOP.2024.8
Understanding Concurrency Bugs in Real-World Programs with Kotlin Coroutines

Authors: Bob Brockbernd, Nikita Koval, Arie van Deursen, and Burcu Kulahcioglu Ozkan

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

Abstract
Kotlin language has recently become prominent for developing both Android and server-side applications. These programs are typically designed to be fast and responsive, with asynchrony and concurrency at their core. To enable developers to write asynchronous and concurrent code safely and concisely, Kotlin provides built-in coroutines support. However, developers unfamiliar with the coroutines concept may write programs with subtle concurrency bugs and face unexpected program behaviors. Besides the traditional concurrency bug patterns, such as data races and deadlocks, these bugs may exhibit patterns related to the coroutine semantics. Understanding these coroutine-specific bug patterns in real-world Kotlin applications is essential in avoiding common mistakes and writing correct programs. In this paper, we present the first study of real-world concurrency bugs related to Kotlin coroutines. We examined 55 concurrency bug cases selected from 7 popular open-source repositories that use Kotlin coroutines, including IntelliJ IDEA, Firefox, and Ktor, and analyzed their bug characteristics and root causes. We identified common bug patterns related to asynchrony and Kotlin’s coroutine semantics, presenting them with their root causes, misconceptions that led to the bugs, and strategies for their automated detection. Overall, this study provides insight into programming with Kotlin coroutines concurrency and its pitfalls, aiming to shed light on common bug patterns and foster further research and development of concurrency analysis tools for Kotlin programs.
Cite as

Bob Brockbernd, Nikita Koval, Arie van Deursen, and Burcu Kulahcioglu Ozkan. Understanding Concurrency Bugs in Real-World Programs with Kotlin Coroutines. In 38th European Conference on Object-Oriented Programming (ECOOP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 313, pp. 8:1-8:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{brockbernd_et_al:LIPIcs.ECOOP.2024.8,
  author =	{Brockbernd, Bob and Koval, Nikita and van Deursen, Arie and Ozkan, Burcu Kulahcioglu},
  title =	{{Understanding Concurrency Bugs in Real-World Programs with Kotlin Coroutines}},
  booktitle =	{38th European Conference on Object-Oriented Programming (ECOOP 2024)},
  pages =	{8:1--8:20},
  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.2024.8},
  URN =		{urn:nbn:de:0030-drops-208579},
  doi =		{10.4230/LIPIcs.ECOOP.2024.8},
  annote =	{Keywords: Kotlin, coroutines, concurrency, asynchrony, software bugs}
}
Document
DOI: 10.4230/LIPIcs.ECOOP.2024.18
A CFL-Reachability Formulation of Callsite-Sensitive Pointer Analysis with Built-In On-The-Fly Call Graph Construction

Authors: Dongjie He, Jingbo Lu, and Jingling Xue

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

Abstract
In object-oriented languages, the traditional CFL-reachability formulation for k-callsite-sensitive pointer analysis (kCFA) focuses on modeling field accesses and calling contexts, but it relies on a separate algorithm for call graph construction. This division can result in a loss of precision in kCFA, a problem that persists even when using the most precise call graphs, whether pre-constructed or generated on the fly. Moreover, pre-analyses based on this framework aiming to improve the efficiency of kCFA may inadvertently reduce its precision, due to the framework’s lack of native call graph construction, essential for precise analysis. Addressing this gap, this paper introduces a novel CFL-reachability formulation of kCFA for Java, uniquely integrating on-the-fly call graph construction. This advancement not only addresses the precision loss inherent in the traditional CFL-reachability-based approach but also enhances its overall applicability. In a significant secondary contribution, we present the first precision-preserving pre-analysis to accelerate kCFA. This pre-analysis leverages selective context sensitivity to improve the efficiency of kCFA without sacrificing its precision. Collectively, these contributions represent a substantial step forward in pointer analysis, offering both theoretical and practical advancements that could benefit future developments in the field.
Cite as

Dongjie He, Jingbo Lu, and Jingling Xue. A CFL-Reachability Formulation of Callsite-Sensitive Pointer Analysis with Built-In On-The-Fly Call Graph Construction. In 38th European Conference on Object-Oriented Programming (ECOOP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 313, pp. 18:1-18:29, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{he_et_al:LIPIcs.ECOOP.2024.18,
  author =	{He, Dongjie and Lu, Jingbo and Xue, Jingling},
  title =	{{A CFL-Reachability Formulation of Callsite-Sensitive Pointer Analysis with Built-In On-The-Fly Call Graph Construction}},
  booktitle =	{38th European Conference on Object-Oriented Programming (ECOOP 2024)},
  pages =	{18:1--18:29},
  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.2024.18},
  URN =		{urn:nbn:de:0030-drops-208674},
  doi =		{10.4230/LIPIcs.ECOOP.2024.18},
  annote =	{Keywords: Pointer Analysis, CFL Reachability, Call Graph Construction}
}
Document
DOI: 10.4230/LIPIcs.ECOOP.2024.24
Qafny: A Quantum-Program Verifier

Authors: Liyi Li, Mingwei Zhu, Rance Cleaveland, Alexander Nicolellis, Yi Lee, Le Chang, and Xiaodi Wu

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

Abstract
Because of the probabilistic/nondeterministic behavior of quantum programs, it is highly advisable to verify them formally to ensure that they correctly implement their specifications. Formal verification, however, also traditionally requires significant effort. To address this challenge, we present Qafny, an automated proof system based on the program verifier Dafny and designed for verifying quantum programs. At its core, Qafny uses a type-guided quantum proof system that translates quantum operations to classical array operations modeled within a classical separation logic framework. We prove the soundness and completeness of our proof system and implement a prototype compiler that transforms Qafny programs and specifications into Dafny for automated verification purposes. We then illustrate the utility of Qafny’s automated capabilities in efficiently verifying important quantum algorithms, including quantum-walk algorithms, Grover’s algorithm, and Shor’s algorithm.
Cite as

Liyi Li, Mingwei Zhu, Rance Cleaveland, Alexander Nicolellis, Yi Lee, Le Chang, and Xiaodi Wu. Qafny: A Quantum-Program Verifier. In 38th European Conference on Object-Oriented Programming (ECOOP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 313, pp. 24:1-24:31, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{li_et_al:LIPIcs.ECOOP.2024.24,
  author =	{Li, Liyi and Zhu, Mingwei and Cleaveland, Rance and Nicolellis, Alexander and Lee, Yi and Chang, Le and Wu, Xiaodi},
  title =	{{Qafny: A Quantum-Program Verifier}},
  booktitle =	{38th European Conference on Object-Oriented Programming (ECOOP 2024)},
  pages =	{24:1--24:31},
  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.2024.24},
  URN =		{urn:nbn:de:0030-drops-208735},
  doi =		{10.4230/LIPIcs.ECOOP.2024.24},
  annote =	{Keywords: Quantum Computing, Automated Verification, Separation Logic}
}
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.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.30.3
Simulation of the Abstract Tile Assembly Model Using Crisscross Slats

Authors: Phillip Drake, Daniel Hader, and Matthew J. Patitz

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

Abstract
The abstract Tile Assembly Model (aTAM) provides an excellent foundation for the mathematical study of DNA-tile-based self-assembling systems, especially those wherein logic is embedded within the designs of the tiles so that they follow prescribed algorithms. While such algorithmic self-assembling systems are theoretically powerful, being computationally universal and capable of building complex shapes using information-theoretically optimal numbers of tiles, physical DNA-based implementations of these systems still encounter formidable error rates and undesired nucleation that hinder this theoretical potential. Slat-based self-assembly is a recent development wherein DNA forms long slats that combine together in 2 layers, rather than square tiles in a plane. In this approach, the length of the slats is key; while tiles typically only bind to 2 neighboring tiles at a time, slats may bind to dozens of other slats. This increased coordination between slats means that several mismatched slats must coincidentally meet in just the right way for errors to persist, unlike tiles where only a few are required. Consequently, while still a novel technology, large slat-based DNA constructions have been successfully implemented in the lab with resilience to many tile-based construction problems. These improved error characteristics come at a cost however, as slat-based systems are often more difficult to design and simulate than tile-based ones. Moreover, it has not been clear whether slats, with their larger sizes and different geometries, have the same theoretical capabilities as tiles. In this paper, we show that slats are capable of doing anything that tiles can, at least at scale. We demonstrate that any aTAM system may be converted to and simulated by an effectively equivalent system of slats. Furthermore, we show that these simulating slat systems can be made more efficiently, using shorter slats and a smaller scale factor, if the simulated tile system avoids certain uncommon growth patterns. Specifically, we consider 5 classes of aTAM systems with increasing complexity, from zig-zag systems which grow in a rigid pattern to the full class of all aTAM systems, and show how they may be converted to equivalent slat systems. We show that the simplest class may be simulated by slats at only a 2c × 2c scale, where c is the freely chosen coordination number of the slats, and further show that the full class of aTAM systems can be simulated at only a 5c × 5c scale. These results prove that slats have the full theoretical power of aTAM tiles while also providing constructions that are compact enough for potential DNA-based implementations of slat systems that are both capable of powerful algorithmic self-assembly and possessing of the strong error resilience of slats.
Cite as

Phillip Drake, Daniel Hader, and Matthew J. Patitz. Simulation of the Abstract Tile Assembly Model Using Crisscross Slats. In 30th International Conference on DNA Computing and Molecular Programming (DNA 30). Leibniz International Proceedings in Informatics (LIPIcs), Volume 314, pp. 3:1-3:25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{drake_et_al:LIPIcs.DNA.30.3,
  author =	{Drake, Phillip and Hader, Daniel and Patitz, Matthew J.},
  title =	{{Simulation of the Abstract Tile Assembly Model Using Crisscross Slats}},
  booktitle =	{30th International Conference on DNA Computing and Molecular Programming (DNA 30)},
  pages =	{3:1--3:25},
  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.30.3},
  URN =		{urn:nbn:de:0030-drops-209315},
  doi =		{10.4230/LIPIcs.DNA.30.3},
  annote =	{Keywords: DNA origami, tile-assembly, self-assembly, aTAM, kinetic modeling, computational modeling}
}
Document
DOI: 10.4230/LIPIcs.ITP.2024.17
Verifying Software Emulation of an Unsupported Hardware Instruction

Authors: Samuel Gruetter, Thomas Bourgeat, and Adam Chlipala

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

Abstract
Some processors, especially embedded ones, do not implement all instructions in hardware. Instead, if the processor encounters an unimplemented instruction, an unsupported-instruction exception is raised, and an exception handler is run that implements the missing instruction in software. Getting such a system to work correctly is tricky: The exception-handler code must not destroy any state of the user program and must use the control and status registers (CSRs) of the processor correctly. Moreover, parts of the handler are typically implemented in assembly, while other parts are implemented in a language like C, and one must make sure that when jumping from the user program into the handler assembly, from the handler assembly into C, back to assembly and finally back to the user program, all the assumptions made by the different pieces of code, hardware, and the compiler are satisfied. Despite all these tricky details, there is a concise and intuitive way of stating the correctness of such a system: User programs running on a system where some instructions are implemented in software behave the same as if they were running on a system where all instructions are implemented in hardware. We formalize and prove such a statement in the Coq proof assistant, for the case of a simple exception handler implementing the multiplication instruction on a RISC-V processor.
Cite as

Samuel Gruetter, Thomas Bourgeat, and Adam Chlipala. Verifying Software Emulation of an Unsupported Hardware Instruction. In 15th International Conference on Interactive Theorem Proving (ITP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 309, pp. 17:1-17:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{gruetter_et_al:LIPIcs.ITP.2024.17,
  author =	{Gruetter, Samuel and Bourgeat, Thomas and Chlipala, Adam},
  title =	{{Verifying Software Emulation of an Unsupported Hardware Instruction}},
  booktitle =	{15th International Conference on Interactive Theorem Proving (ITP 2024)},
  pages =	{17:1--17:16},
  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.2024.17},
  URN =		{urn:nbn:de:0030-drops-207452},
  doi =		{10.4230/LIPIcs.ITP.2024.17},
  annote =	{Keywords: Software verification, Software-hardware boundary, Coq}
}
Document
DOI: 10.4230/LIPIcs.CP.2024.5
ParLS-PBO: A Parallel Local Search Solver for Pseudo Boolean Optimization

Authors: Zhihan Chen, Peng Lin, Hao Hu, and Shaowei Cai

Published in: LIPIcs, Volume 307, 30th International Conference on Principles and Practice of Constraint Programming (CP 2024)

Abstract
As a broadly applied technique in numerous optimization problems, recently, local search has been employed to solve Pseudo-Boolean Optimization (PBO) problem. A representative local search solver for PBO is LS-PBO. In this paper, firstly, we improve LS-PBO by a dynamic scoring mechanism, which dynamically strikes a balance between score on hard constraints and score on the objective function. Moreover, on top of this improved LS-PBO, we develop the first parallel local search PBO solver. The main idea is to share good solutions among different threads to guide the search, by maintaining a pool of feasible solutions. For evaluating solutions when updating the pool, we propose a function that considers both the solution quality and the diversity of the pool. Furthermore, we calculate the polarity density in the pool to enhance the scoring function of local search. Our empirical experiments show clear benefits of the proposed parallel approach, making it competitive with the parallel version of the famous commercial solver Gurobi.
Cite as

Zhihan Chen, Peng Lin, Hao Hu, and Shaowei Cai. ParLS-PBO: A Parallel Local Search Solver for Pseudo Boolean Optimization. In 30th International Conference on Principles and Practice of Constraint Programming (CP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 307, pp. 5:1-5:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{chen_et_al:LIPIcs.CP.2024.5,
  author =	{Chen, Zhihan and Lin, Peng and Hu, Hao and Cai, Shaowei},
  title =	{{ParLS-PBO: A Parallel Local Search Solver for Pseudo Boolean Optimization}},
  booktitle =	{30th International Conference on Principles and Practice of Constraint Programming (CP 2024)},
  pages =	{5:1--5:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-336-2},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{307},
  editor =	{Shaw, Paul},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CP.2024.5},
  URN =		{urn:nbn:de:0030-drops-206900},
  doi =		{10.4230/LIPIcs.CP.2024.5},
  annote =	{Keywords: Pseudo-Boolean Optimization, Parallel Solving, Local Search, Scoring Function, Solution Pool}
}
Document
DOI: 10.4230/LIPIcs.CP.2024.25
Combining Constraint Programming Reasoning with Large Language Model Predictions

Authors: Florian Régin, Elisabetta De Maria, and Alexandre Bonlarron

Published in: LIPIcs, Volume 307, 30th International Conference on Principles and Practice of Constraint Programming (CP 2024)

Abstract
Constraint Programming (CP) and Machine Learning (ML) face challenges in text generation due to CP’s struggle with implementing "meaning" and ML’s difficulty with structural constraints. This paper proposes a solution by combining both approaches and embedding a Large Language Model (LLM) in CP. The LLM handles word generation and meaning, while CP manages structural constraints. This approach builds on GenCP, an improved version of On-the-fly Constraint Programming Search (OTFS) using LLM-generated domains. Compared to Beam Search (BS), a standard NLP method, this combined approach (GenCP with LLM) is faster and produces better results, ensuring all constraints are satisfied. This fusion of CP and ML presents new possibilities for enhancing text generation under constraints.
Cite as

Florian Régin, Elisabetta De Maria, and Alexandre Bonlarron. Combining Constraint Programming Reasoning with Large Language Model Predictions. In 30th International Conference on Principles and Practice of Constraint Programming (CP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 307, pp. 25:1-25:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{regin_et_al:LIPIcs.CP.2024.25,
  author =	{R\'{e}gin, Florian and De Maria, Elisabetta and Bonlarron, Alexandre},
  title =	{{Combining Constraint Programming Reasoning with Large Language Model Predictions}},
  booktitle =	{30th International Conference on Principles and Practice of Constraint Programming (CP 2024)},
  pages =	{25:1--25:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-336-2},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{307},
  editor =	{Shaw, Paul},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CP.2024.25},
  URN =		{urn:nbn:de:0030-drops-207109},
  doi =		{10.4230/LIPIcs.CP.2024.25},
  annote =	{Keywords: Solver and Tools, ML-augmented CP, Constrained Text Generation, ML alongside CO}
}
Document
DOI: 10.4230/LIPIcs.WABI.2024.23
AlfaPang: Alignment Free Algorithm for Pangenome Graph Construction

Authors: Adam Cicherski, Anna Lisiecka, and Norbert Dojer

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

Abstract
The success of pangenome-based approaches to genomics analysis depends largely on the existence of efficient methods for constructing pangenome graphs that are applicable to large genome collections. In the current paper we present AlfaPang, a new pangenome graph building algorithm. AlfaPang is based on a novel alignment-free approach that allows to construct pangenome graphs using significantly less computational resources than state-of-the-art tools. The code of AlfaPang is freely available at https://github.com/AdamCicherski/AlfaPang.
Cite as

Adam Cicherski, Anna Lisiecka, and Norbert Dojer. AlfaPang: Alignment Free Algorithm for Pangenome Graph Construction. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 23:1-23:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{cicherski_et_al:LIPIcs.WABI.2024.23,
  author =	{Cicherski, Adam and Lisiecka, Anna and Dojer, Norbert},
  title =	{{AlfaPang: Alignment Free Algorithm for Pangenome Graph Construction}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{23:1--23:18},
  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.2024.23},
  URN =		{urn:nbn:de:0030-drops-206673},
  doi =		{10.4230/LIPIcs.WABI.2024.23},
  annote =	{Keywords: pangenome, variation graph, genome alignment, population genomics}
}
Document
DOI: 10.4230/LIPIcs.TQC.2024.3
Efficient Optimal Control of Open Quantum Systems

Authors: Wenhao He, Tongyang Li, Xiantao Li, Zecheng Li, Chunhao Wang, and Ke Wang

Published in: LIPIcs, Volume 310, 19th Conference on the Theory of Quantum Computation, Communication and Cryptography (TQC 2024)

Abstract
The optimal control problem for open quantum systems can be formulated as a time-dependent Lindbladian that is parameterized by a number of time-dependent control variables. Given an observable and an initial state, the goal is to tune the control variables so that the expected value of some observable with respect to the final state is maximized. In this paper, we present algorithms for solving this optimal control problem efficiently, i.e., having a poly-logarithmic dependency on the system dimension, which is exponentially faster than best-known classical algorithms. Our algorithms are hybrid, consisting of both quantum and classical components. The quantum procedure simulates time-dependent Lindblad evolution that drives the initial state to the final state, and it also provides access to the gradients of the objective function via quantum gradient estimation. The classical procedure uses the gradient information to update the control variables. At the technical level, we provide the first (to the best of our knowledge) simulation algorithm for time-dependent Lindbladians with an 𝓁₁-norm dependence. As an alternative, we also present a simulation algorithm in the interaction picture to improve the algorithm for the cases where the time-independent component of a Lindbladian dominates the time-dependent part. On the classical side, we heavily adapt the state-of-the-art classical optimization analysis to interface with the quantum part of our algorithms. Both the quantum simulation techniques and the classical optimization analyses might be of independent interest.
Cite as

Wenhao He, Tongyang Li, Xiantao Li, Zecheng Li, Chunhao Wang, and Ke Wang. Efficient Optimal Control of Open Quantum Systems. In 19th Conference on the Theory of Quantum Computation, Communication and Cryptography (TQC 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 310, pp. 3:1-3:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{he_et_al:LIPIcs.TQC.2024.3,
  author =	{He, Wenhao and Li, Tongyang and Li, Xiantao and Li, Zecheng and Wang, Chunhao and Wang, Ke},
  title =	{{Efficient Optimal Control of Open Quantum Systems}},
  booktitle =	{19th Conference on the Theory of Quantum Computation, Communication and Cryptography (TQC 2024)},
  pages =	{3:1--3:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-328-7},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{310},
  editor =	{Magniez, Fr\'{e}d\'{e}ric and Grilo, Alex Bredariol},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.TQC.2024.3},
  URN =		{urn:nbn:de:0030-drops-206733},
  doi =		{10.4230/LIPIcs.TQC.2024.3},
  annote =	{Keywords: Quantum algorithm, quantum optimal control, Lindbladian simulation, accelerated gradient descent}
}
Document
DOI: 10.4230/LIPIcs.TQC.2024.10
Guidable Local Hamiltonian Problems with Implications to Heuristic Ansatz State Preparation and the Quantum PCP Conjecture

Authors: Jordi Weggemans, Marten Folkertsma, and Chris Cade

Published in: LIPIcs, Volume 310, 19th Conference on the Theory of Quantum Computation, Communication and Cryptography (TQC 2024)

Abstract
We study "Merlinized" versions of the recently defined Guided Local Hamiltonian problem, which we call "Guidable Local Hamiltonian" problems. Unlike their guided counterparts, these problems do not have a guiding state provided as a part of the input, but merely come with the promise that one exists. We consider in particular two classes of guiding states: those that can be prepared efficiently by a quantum circuit; and those belonging to a class of quantum states we call classically evaluatable, for which it is possible to efficiently compute expectation values of local observables classically. We show that guidable local Hamiltonian problems for both classes of guiding states are QCMA-complete in the inverse-polynomial precision setting, but lie within NP (or NqP) in the constant precision regime when the guiding state is classically evaluatable. Our completeness results show that, from a complexity-theoretic perspective, classical Ansätze selected by classical heuristics are just as powerful as quantum Ansätze prepared by quantum heuristics, as long as one has access to quantum phase estimation. In relation to the quantum PCP conjecture, we (i) define a complexity class capturing quantum-classical probabilistically checkable proof systems and show that it is contained in BQP^NP[1] for constant proof queries; (ii) give a no-go result on "dequantizing" the known quantum reduction which maps a QPCP-verification circuit to a local Hamiltonian with constant promise gap; (iii) give several no-go results for the existence of quantum gap amplification procedures that preserve certain ground state properties; and (iv) propose two conjectures that can be viewed as stronger versions of the NLTS theorem. Finally, we show that many of our results can be directly modified to obtain similar results for the class MA.
Cite as

Jordi Weggemans, Marten Folkertsma, and Chris Cade. Guidable Local Hamiltonian Problems with Implications to Heuristic Ansatz State Preparation and the Quantum PCP Conjecture. In 19th Conference on the Theory of Quantum Computation, Communication and Cryptography (TQC 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 310, pp. 10:1-10:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{weggemans_et_al:LIPIcs.TQC.2024.10,
  author =	{Weggemans, Jordi and Folkertsma, Marten and Cade, Chris},
  title =	{{Guidable Local Hamiltonian Problems with Implications to Heuristic Ansatz State Preparation and the Quantum PCP Conjecture}},
  booktitle =	{19th Conference on the Theory of Quantum Computation, Communication and Cryptography (TQC 2024)},
  pages =	{10:1--10:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-328-7},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{310},
  editor =	{Magniez, Fr\'{e}d\'{e}ric and Grilo, Alex Bredariol},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.TQC.2024.10},
  URN =		{urn:nbn:de:0030-drops-206804},
  doi =		{10.4230/LIPIcs.TQC.2024.10},
  annote =	{Keywords: Quantum complexity theory, local Hamiltonian problem, quantum state ansatzes, QCMA, quantum PCP conjecture}
}
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