29 Search Results for "Li, Yi"

Document
DOI: 10.4230/OASIcs.DX.2024.2
A Model-Based Approach for Monitoring and Diagnosing Digital Twin Discrepancies

Authors: Elaheh Hosseinkhani, Martin Leucker, Martin Sachenbacher, Hendrik Streichhahn, and Lars B. Vosteen

Published in: OASIcs, Volume 125, 35th International Conference on Principles of Diagnosis and Resilient Systems (DX 2024)

Abstract
Recent decades have seen the increasing use of Digital Twins (DTs) - that is, digital models used over the lifetime of a physical product or system for tasks such as predictive maintenance or optimization - in a number of domains such as buildings, manufacturing, or design. DTs face a challenge known as the DT synchronization problem; a DT, often based on machine-learned, or complex simulation models, needs to adequately mirror the physical product or system at all times, as any deviations might affect the quality of predictions or control actions. In this paper, we present a model-based approach that aims to add a level of awareness to DT models by supervising if they are in sync with the physical counterpart. The approach is agnostic to the type of models used in the DT, as long as they are compositional, and based on monitoring critical properties (behavioral or functional aspects) of the system at run-time. In the case violations are detected, it reasons on the DT’s structure to localize and identify parts of the model that cause deviations and need to be adapted. We give a formal description and an implementation of this approach, and illustrate it with an example from building climatisation.
Cite as

Elaheh Hosseinkhani, Martin Leucker, Martin Sachenbacher, Hendrik Streichhahn, and Lars B. Vosteen. A Model-Based Approach for Monitoring and Diagnosing Digital Twin Discrepancies. In 35th International Conference on Principles of Diagnosis and Resilient Systems (DX 2024). Open Access Series in Informatics (OASIcs), Volume 125, pp. 2:1-2:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{hosseinkhani_et_al:OASIcs.DX.2024.2,
  author =	{Hosseinkhani, Elaheh and Leucker, Martin and Sachenbacher, Martin and Streichhahn, Hendrik and Vosteen, Lars B.},
  title =	{{A Model-Based Approach for Monitoring and Diagnosing Digital Twin Discrepancies}},
  booktitle =	{35th International Conference on Principles of Diagnosis and Resilient Systems (DX 2024)},
  pages =	{2:1--2:15},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-356-0},
  ISSN =	{2190-6807},
  year =	{2024},
  volume =	{125},
  editor =	{Pill, Ingo and Natan, Avraham and Wotawa, Franz},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.DX.2024.2},
  URN =		{urn:nbn:de:0030-drops-220944},
  doi =		{10.4230/OASIcs.DX.2024.2},
  annote =	{Keywords: Digital Twins, Runtime Verification, Diagnosis, FDIR, TeSSLa}
}
Document
DOI: 10.4230/LIPIcs.AFT.2024.7
DeFiAligner: Leveraging Symbolic Analysis and Large Language Models for Inconsistency Detection in Decentralized Finance

Authors: Rundong Gan, Liyi Zhou, Le Wang, Kaihua Qin, and Xiaodong Lin

Published in: LIPIcs, Volume 316, 6th Conference on Advances in Financial Technologies (AFT 2024)

Abstract
Decentralized Finance (DeFi) has witnessed a monumental surge, reaching 53.039 billion USD in total value locked. As this sector continues to expand, ensuring the reliability of DeFi smart contracts becomes increasingly crucial. While some users are adept at reading code or the compiled bytecode to understand smart contracts, many rely on documentation. Therefore, discrepancies between the documentation and the deployed code can pose significant risks, whether these discrepancies are due to errors or intentional fraud. To tackle these challenges, we developed DeFiAligner, an end-to-end system to identify inconsistencies between documentation and smart contracts. DeFiAligner incorporates a symbolic execution tool, SEVM, which explores execution paths of on-chain binary code, recording memory and stack states. It automatically generates symbolic expressions for token balance changes and branch conditions, which, along with related project documents, are processed by LLMs. Using structured prompts, the LLMs evaluate the alignment between the symbolic expressions and the documentation. Our tests across three distinct scenarios demonstrate DeFiAligner’s capability to automate inconsistency detection in DeFi, achieving recall rates of 92% and 90% on two public datasets respectively.
Cite as

Rundong Gan, Liyi Zhou, Le Wang, Kaihua Qin, and Xiaodong Lin. DeFiAligner: Leveraging Symbolic Analysis and Large Language Models for Inconsistency Detection in Decentralized Finance. In 6th Conference on Advances in Financial Technologies (AFT 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 316, pp. 7:1-7:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{gan_et_al:LIPIcs.AFT.2024.7,
  author =	{Gan, Rundong and Zhou, Liyi and Wang, Le and Qin, Kaihua and Lin, Xiaodong},
  title =	{{DeFiAligner: Leveraging Symbolic Analysis and Large Language Models for Inconsistency Detection in Decentralized Finance}},
  booktitle =	{6th Conference on Advances in Financial Technologies (AFT 2024)},
  pages =	{7:1--7:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-345-4},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{316},
  editor =	{B\"{o}hme, Rainer and Kiffer, Lucianna},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.AFT.2024.7},
  URN =		{urn:nbn:de:0030-drops-209431},
  doi =		{10.4230/LIPIcs.AFT.2024.7},
  annote =	{Keywords: Decentralized Finance Security, Large Language Models, Project Review, Symbolic Analysis, Smart Contracts}
}
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
Artifact
DOI: 10.4230/DARTS.10.2.12
Qafny: A Quantum-Program Verifier (Artifact)

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

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

Abstract
This artifact contains the Coq theory files for the Qafny proof system, including the formalism of the Qafny syntax, semantics, type system, and proof system, with the theorem proofs of type soundness, proof system soundness and completeness. It also contains a the compiled Dafny example programs generated from our Qafny-to-Dafny prototype compiler. These example programs serve as the validations of our Qafny-to-Dafny prototype compiler mechanism. The main work is introduced in the Qafny paper, which develops a separation logic style verification framework for quantum programs.
Cite as

Liyi Li, Mingwei Zhu, Rance Cleaveland, Alexander Nicolellis, Yi Lee, Le Chang, and Xiaodi Wu. Qafny: A Quantum-Program Verifier (Artifact). In Special Issue of the 38th European Conference on Object-Oriented Programming (ECOOP 2024). Dagstuhl Artifacts Series (DARTS), Volume 10, Issue 2, pp. 12:1-12:2, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@Article{li_et_al:DARTS.10.2.12,
  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 (Artifact)}},
  pages =	{12:1--12:2},
  journal =	{Dagstuhl Artifacts Series},
  ISBN =	{978-3-95977-342-3},
  ISSN =	{2509-8195},
  year =	{2024},
  volume =	{10},
  number =	{2},
  editor =	{Li, Liyi and Zhu, Mingwei and Cleaveland, Rance and Nicolellis, Alexander and Lee, Yi and Chang, Le and Wu, Xiaodi},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DARTS.10.2.12},
  URN =		{urn:nbn:de:0030-drops-209104},
  doi =		{10.4230/DARTS.10.2.12},
  annote =	{Keywords: Quantum Computing, Automated Verification, Separation Logic}
}
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
Short Paper
DOI: 10.4230/LIPIcs.COSIT.2024.21
An Ontology and Geospatial Knowledge Graph for Reasoning About Cascading Failures (Short Paper)

Authors: Torsten Hahmann and David K. Kedrowski

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

Abstract
During a natural disaster such as flooding, the failure of a single asset in the complex and interconnected web of critical urban infrastructure can trigger a cascade of failures within and across multiple systems with potentially life-threatening consequences. To help emergency management effectively and efficiently assess such failures, we design the Utility Connection Ontology Design Pattern to represent utility services and model connections within and across those services. The pattern is encoded as an OWL ontology and instantiated with utility data in a geospatial knowledge graph. We demonstrate how it facilitates reasoning to identify cascading service failures due to flooding for producing maps and other summaries for situational awareness.
Cite as

Torsten Hahmann and David K. Kedrowski. An Ontology and Geospatial Knowledge Graph for Reasoning About Cascading Failures (Short Paper). In 16th International Conference on Spatial Information Theory (COSIT 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 315, pp. 21:1-21:9, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{hahmann_et_al:LIPIcs.COSIT.2024.21,
  author =	{Hahmann, Torsten and Kedrowski, David K.},
  title =	{{An Ontology and Geospatial Knowledge Graph for Reasoning About Cascading Failures}},
  booktitle =	{16th International Conference on Spatial Information Theory (COSIT 2024)},
  pages =	{21:1--21:9},
  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.2024.21},
  URN =		{urn:nbn:de:0030-drops-208364},
  doi =		{10.4230/LIPIcs.COSIT.2024.21},
  annote =	{Keywords: knowledge graph, ontology, OWL, spatial reasoning, cascading failures, urban infrastructure}
}
Document
Short Paper
DOI: 10.4230/LIPIcs.COSIT.2024.28
Evaluating the Ability of Large Language Models to Reason About Cardinal Directions (Short Paper)

Authors: Anthony G Cohn and Robert E Blackwell

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

Abstract
We investigate the abilities of a representative set of Large language Models (LLMs) to reason about cardinal directions (CDs). To do so, we create two datasets: the first, co-created with ChatGPT, focuses largely on recall of world knowledge about CDs; the second is generated from a set of templates, comprehensively testing an LLM’s ability to determine the correct CD given a particular scenario. The templates allow for a number of degrees of variation such as means of locomotion of the agent involved, and whether set in the first , second or third person. Even with a temperature setting of zero, Our experiments show that although LLMs are able to perform well in the simpler dataset, in the second more complex dataset no LLM is able to reliably determine the correct CD, even with a temperature setting of zero.
Cite as

Anthony G Cohn and Robert E Blackwell. Evaluating the Ability of Large Language Models to Reason About Cardinal Directions (Short Paper). In 16th International Conference on Spatial Information Theory (COSIT 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 315, pp. 28:1-28:9, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{cohn_et_al:LIPIcs.COSIT.2024.28,
  author =	{Cohn, Anthony G and Blackwell, Robert E},
  title =	{{Evaluating the Ability of Large Language Models to Reason About Cardinal Directions}},
  booktitle =	{16th International Conference on Spatial Information Theory (COSIT 2024)},
  pages =	{28:1--28:9},
  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.2024.28},
  URN =		{urn:nbn:de:0030-drops-208432},
  doi =		{10.4230/LIPIcs.COSIT.2024.28},
  annote =	{Keywords: Large Language Models, Spatial Reasoning, Cardinal Directions}
}
Document
DOI: 10.4230/LIPIcs.CP.2024.19
An Efficient Local Search Solver for Mixed Integer Programming

Authors: Peng Lin, Mengchuan Zou, and Shaowei Cai

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

Abstract
Mixed integer programming (MIP) is a fundamental model in operations research. Local search is a powerful method for solving hard problems, but the development of local search solvers for MIP still needs to be explored. This work develops an efficient local search solver for solving MIP, called Local-MIP. We propose two new operators for MIP to adaptively modify variables for optimizing the objective function and satisfying constraints, respectively. Furthermore, we design a new weighting scheme to dynamically balance the priority between the objective function and each constraint, and propose a two-level scoring function structure to hierarchically guide the search for high-quality feasible solutions. Experiments are conducted on seven public benchmarks to compare Local-MIP with state-of-the-art MIP solvers, which demonstrate that Local-MIP significantly outperforms CPLEX, HiGHS, SCIP and Feasibility Jump, and is competitive with the most powerful commercial solver Gurobi. Moreover, Local-MIP establishes 4 new records for MIPLIB open instances.
Cite as

Peng Lin, Mengchuan Zou, and Shaowei Cai. An Efficient Local Search Solver for Mixed Integer Programming. In 30th International Conference on Principles and Practice of Constraint Programming (CP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 307, pp. 19:1-19:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{lin_et_al:LIPIcs.CP.2024.19,
  author =	{Lin, Peng and Zou, Mengchuan and Cai, Shaowei},
  title =	{{An Efficient Local Search Solver for Mixed Integer Programming}},
  booktitle =	{30th International Conference on Principles and Practice of Constraint Programming (CP 2024)},
  pages =	{19:1--19:19},
  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.2024.19},
  URN =		{urn:nbn:de:0030-drops-207041},
  doi =		{10.4230/LIPIcs.CP.2024.19},
  annote =	{Keywords: Mixed Integer Programming, Local Search, Operator, Scoring Function}
}
Document
DOI: 10.4230/LIPIcs.CP.2024.20
Constraint Modelling with LLMs Using In-Context Learning

Authors: Kostis Michailidis, Dimos Tsouros, and Tias Guns

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

Abstract
Constraint Programming (CP) allows for the modelling and solving of a wide range of combinatorial problems. However, modelling such problems using constraints over decision variables still requires significant expertise, both in conceptual thinking and syntactic use of modelling languages. In this work, we explore the potential of using pre-trained Large Language Models (LLMs) as coding assistants, to transform textual problem descriptions into concrete and executable CP specifications. We present different transformation pipelines with explicit intermediate representations, and we investigate the potential benefit of various retrieval-augmented example selection strategies for in-context learning. We evaluate our approach on 2 datasets from the literature, namely NL4Opt (optimisation) and Logic Grid Puzzles (satisfaction), and a heterogeneous set of exercises from a CP course. The results show that pre-trained LLMs have promising potential for initialising the modelling process, with retrieval-augmented in-context learning significantly enhancing their modelling capabilities.
Cite as

Kostis Michailidis, Dimos Tsouros, and Tias Guns. Constraint Modelling with LLMs Using In-Context Learning. In 30th International Conference on Principles and Practice of Constraint Programming (CP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 307, pp. 20:1-20:27, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{michailidis_et_al:LIPIcs.CP.2024.20,
  author =	{Michailidis, Kostis and Tsouros, Dimos and Guns, Tias},
  title =	{{Constraint Modelling with LLMs Using In-Context Learning}},
  booktitle =	{30th International Conference on Principles and Practice of Constraint Programming (CP 2024)},
  pages =	{20:1--20:27},
  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.2024.20},
  URN =		{urn:nbn:de:0030-drops-207053},
  doi =		{10.4230/LIPIcs.CP.2024.20},
  annote =	{Keywords: Constraint Modelling, Constraint Acquisition, Constraint Programming, Large Language Models, In-Context Learning, Natural Language Processing, Named Entity Recognition, Retrieval-Augmented Generation, Optimisation}
}
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.SAT.2024.8
Enhancing MaxSAT Local Search via a Unified Soft Clause Weighting Scheme

Authors: Yi Chu, Chu-Min Li, Furong Ye, and Shaowei Cai

Published in: LIPIcs, Volume 305, 27th International Conference on Theory and Applications of Satisfiability Testing (SAT 2024)

Abstract
Local search has been widely applied to solve the well-known (weighted) partial MaxSAT problem, significantly influencing many real-world applications. The main difficulty to overcome when designing a local search algorithm is that it can easily fall into local optima. Clause weighting is a beneficial technique that dynamically adjusts the landscape of search space to help the algorithm escape from local optima. Existing works tend to increase the weights of falsified clauses, and such strategies may result in an unpredictable landscape of search space during the optimization process. Therefore, in this paper, we propose a Unified Soft Clause Weighting Scheme called Unified-SW, which increases the weights of all soft clauses in feasible local optima, whether they are satisfied or not, while preserving the hierarchy among them. We implemented Unified-SW in a new local search solver called USW-LS. Experimental results demonstrate that USW-LS, outperforms the state-of-the-art local search solvers across benchmarks from anytime tracks of recent MaxSAT Evaluations. More promisingly, a hybrid solver combining USW-LS and TT-Open-WBO-Inc won all four categories in the anytime track of MaxSAT Evaluation 2023.
Cite as

Yi Chu, Chu-Min Li, Furong Ye, and Shaowei Cai. Enhancing MaxSAT Local Search via a Unified Soft Clause Weighting Scheme. In 27th International Conference on Theory and Applications of Satisfiability Testing (SAT 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 305, pp. 8:1-8:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{chu_et_al:LIPIcs.SAT.2024.8,
  author =	{Chu, Yi and Li, Chu-Min and Ye, Furong and Cai, Shaowei},
  title =	{{Enhancing MaxSAT Local Search via a Unified Soft Clause Weighting Scheme}},
  booktitle =	{27th International Conference on Theory and Applications of Satisfiability Testing (SAT 2024)},
  pages =	{8:1--8:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-334-8},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{305},
  editor =	{Chakraborty, Supratik and Jiang, Jie-Hong Roland},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SAT.2024.8},
  URN =		{urn:nbn:de:0030-drops-205301},
  doi =		{10.4230/LIPIcs.SAT.2024.8},
  annote =	{Keywords: Weighted Partial MaxSAT, Local Search Method, Weighting Scheme}
}
Document
DOI: 10.4230/DagMan.10.1.1
Current and Future Challenges in Knowledge Representation and Reasoning (Dagstuhl Perspectives Workshop 22282)

Authors: James P. Delgrande, Birte Glimm, Thomas Meyer, Miroslaw Truszczynski, and Frank Wolter

Published in: Dagstuhl Manifestos, Volume 10, Issue 1 (2024)

Abstract
Knowledge Representation and Reasoning is a central, longstanding, and active area of Artificial Intelligence. Over the years it has evolved significantly; more recently it has been challenged and complemented by research in areas such as machine learning and reasoning under uncertainty. In July 2022,sser a Dagstuhl Perspectives workshop was held on Knowledge Representation and Reasoning. The goal of the workshop was to describe the state of the art in the field, including its relation with other areas, its shortcomings and strengths, together with recommendations for future progress. We developed this manifesto based on the presentations, panels, working groups, and discussions that took place at the Dagstuhl Workshop. It is a declaration of our views on Knowledge Representation: its origins, goals, milestones, and current foci; its relation to other disciplines, especially to Artificial Intelligence; and on its challenges, along with key priorities for the next decade.
Cite as

James P. Delgrande, Birte Glimm, Thomas Meyer, Miroslaw Truszczynski, and Frank Wolter. Current and Future Challenges in Knowledge Representation and Reasoning (Dagstuhl Perspectives Workshop 22282). In Dagstuhl Manifestos, Volume 10, Issue 1, pp. 1-61, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@Article{delgrande_et_al:DagMan.10.1.1,
  author =	{Delgrande, James P. and Glimm, Birte and Meyer, Thomas and Truszczynski, Miroslaw and Wolter, Frank},
  title =	{{Current and Future Challenges in Knowledge Representation and Reasoning (Dagstuhl Perspectives Workshop 22282)}},
  pages =	{1--61},
  journal =	{Dagstuhl Manifestos},
  ISSN =	{2193-2433},
  year =	{2024},
  volume =	{10},
  number =	{1},
  editor =	{Delgrande, James P. and Glimm, Birte and Meyer, Thomas and Truszczynski, Miroslaw and Wolter, Frank},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagMan.10.1.1},
  URN =		{urn:nbn:de:0030-drops-201403},
  doi =		{10.4230/DagMan.10.1.1},
  annote =	{Keywords: Knowledge representation and reasoning, Applications of logics, Declarative representations, Formal logic}
}
Document
RANDOM
DOI: 10.4230/LIPIcs.APPROX/RANDOM.2022.13
Streaming Algorithms with Large Approximation Factors

Authors: Yi Li, Honghao Lin, David P. Woodruff, and Yuheng Zhang

Published in: LIPIcs, Volume 245, Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2022)

Abstract
We initiate a broad study of classical problems in the streaming model with insertions and deletions in the setting where we allow the approximation factor α to be much larger than 1. Such algorithms can use significantly less memory than the usual setting for which α = 1+ε for an ε ∈ (0,1). We study large approximations for a number of problems in sketching and streaming, assuming that the underlying n-dimensional vector has all coordinates bounded by M throughout the data stream: 1) For the 𝓁_p norm/quasi-norm, 0 < p ≤ 2, we show that obtaining a poly(n)-approximation requires the same amount of memory as obtaining an O(1)-approximation for any M = n^Θ(1), which holds even for randomly ordered streams or for streams in the bounded deletion model. 2) For estimating the 𝓁_p norm, p > 2, we show an upper bound of O(n^{1-2/p} (log n log M)/α²) bits for an α-approximation, and give a matching lower bound for linear sketches. 3) For the 𝓁₂-heavy hitters problem, we show that the known lower bound of Ω(k log nlog M) bits for identifying (1/k)-heavy hitters holds even if we are allowed to output items that are 1/(α k)-heavy, provided the algorithm succeeds with probability 1-O(1/n). We also obtain a lower bound for linear sketches that is tight even for constant failure probability algorithms. 4) For estimating the number 𝓁₀ of distinct elements, we give an n^{1/t}-approximation algorithm using O(tlog log M) bits of space, as well as a lower bound of Ω(t) bits, both excluding the storage of random bits, where n is the dimension of the underlying frequency vector and M is an upper bound on the magnitude of its coordinates. 5) For α-approximation to the Schatten-p norm, we give near-optimal Õ(n^{2-4/p}/α⁴) sketching dimension for every even integer p and every α ≥ 1, while for p not an even integer we obtain near-optimal sketching dimension once α = Ω(n^{1/q-1/p}), where q is the largest even integer less than p. The latter is surprising as it is unknown what the complexity of Schatten-p norm estimation is for constant approximation; we show once the approximation factor is at least n^{1/q-1/p}, we can obtain near-optimal sketching bounds.
Cite as

Yi Li, Honghao Lin, David P. Woodruff, and Yuheng Zhang. Streaming Algorithms with Large Approximation Factors. In Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 245, pp. 13:1-13:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{li_et_al:LIPIcs.APPROX/RANDOM.2022.13,
  author =	{Li, Yi and Lin, Honghao and Woodruff, David P. and Zhang, Yuheng},
  title =	{{Streaming Algorithms with Large Approximation Factors}},
  booktitle =	{Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2022)},
  pages =	{13:1--13:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-249-5},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{245},
  editor =	{Chakrabarti, Amit and Swamy, Chaitanya},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.APPROX/RANDOM.2022.13},
  URN =		{urn:nbn:de:0030-drops-171354},
  doi =		{10.4230/LIPIcs.APPROX/RANDOM.2022.13},
  annote =	{Keywords: streaming algorithms, 𝓁\underlinep norm, heavy hitters, distinct elements}
}
Document
RANDOM
DOI: 10.4230/LIPIcs.APPROX/RANDOM.2021.35
The Product of Gaussian Matrices Is Close to Gaussian

Authors: Yi Li and David P. Woodruff

Published in: LIPIcs, Volume 207, Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2021)

Abstract
We study the distribution of the matrix product G₁ G₂ ⋯ G_r of r independent Gaussian matrices of various sizes, where G_i is d_{i-1} × d_i, and we denote p = d₀, q = d_r, and require d₁ = d_{r-1}. Here the entries in each G_i are standard normal random variables with mean 0 and variance 1. Such products arise in the study of wireless communication, dynamical systems, and quantum transport, among other places. We show that, provided each d_i, i = 1, …, r, satisfies d_i ≥ C p ⋅ q, where C ≥ C₀ for a constant C₀ > 0 depending on r, then the matrix product G₁ G₂ ⋯ G_r has variation distance at most δ to a p × q matrix G of i.i.d. standard normal random variables with mean 0 and variance ∏_{i = 1}^{r-1} d_i. Here δ → 0 as C → ∞. Moreover, we show a converse for constant r that if d_i < C' max{p,q}^{1/2}min{p,q}^{3/2} for some i, then this total variation distance is at least δ', for an absolute constant δ' > 0 depending on C' and r. This converse is best possible when p = Θ(q).
Cite as

Yi Li and David P. Woodruff. The Product of Gaussian Matrices Is Close to Gaussian. In Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 207, pp. 35:1-35:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

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@InProceedings{li_et_al:LIPIcs.APPROX/RANDOM.2021.35,
  author =	{Li, Yi and Woodruff, David P.},
  title =	{{The Product of Gaussian Matrices Is Close to Gaussian}},
  booktitle =	{Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2021)},
  pages =	{35:1--35:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-207-5},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{207},
  editor =	{Wootters, Mary and Sanit\`{a}, Laura},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.APPROX/RANDOM.2021.35},
  URN =		{urn:nbn:de:0030-drops-147281},
  doi =		{10.4230/LIPIcs.APPROX/RANDOM.2021.35},
  annote =	{Keywords: random matrix theory, total variation distance, matrix product}
}
Document
DOI: 10.4230/OASIcs.iPMVM.2020.1
Development and Validation of Energy Simulation for Additive Manufacturing

Authors: Li Yi and Jan C. Aurich

Published in: OASIcs, Volume 89, 2nd International Conference of the DFG International Research Training Group 2057 – Physical Modeling for Virtual Manufacturing (iPMVM 2020)

Abstract
Additive manufacturing (AM) is a promising manufacturing technology towards cleaner production systems. Nevertheless, recent studies state that environmental benefits of AM are case-specific and need to be evaluated and confirmed in the design phase. To enable the energy performance evaluation in the design phase, developing convenient tools for energy prediction of AM has been an important research task. Aiming at this problem, this paper presents the research for energy modeling, simulation implementation, and experimental validation of an energy simulation tool of two AM processes: Selective laser melting (SLM) and Fused deposition modeling (FDM). The developed simulation tool can be conveniently used for energy consumption quantification and evaluation during the product and process design for AM.
Cite as

Li Yi and Jan C. Aurich. Development and Validation of Energy Simulation for Additive Manufacturing. In 2nd International Conference of the DFG International Research Training Group 2057 – Physical Modeling for Virtual Manufacturing (iPMVM 2020). Open Access Series in Informatics (OASIcs), Volume 89, pp. 1:1-1:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

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@InProceedings{yi_et_al:OASIcs.iPMVM.2020.1,
  author =	{Yi, Li and Aurich, Jan C.},
  title =	{{Development and Validation of Energy Simulation for Additive Manufacturing}},
  booktitle =	{2nd International Conference of the DFG International Research Training Group 2057 – Physical Modeling for Virtual Manufacturing (iPMVM 2020)},
  pages =	{1:1--1:17},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-183-2},
  ISSN =	{2190-6807},
  year =	{2021},
  volume =	{89},
  editor =	{Garth, Christoph and Aurich, Jan C. and Linke, Barbara and M\"{u}ller, Ralf and Ravani, Bahram and Weber, Gunther H. and Kirsch, Benjamin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.iPMVM.2020.1},
  URN =		{urn:nbn:de:0030-drops-137500},
  doi =		{10.4230/OASIcs.iPMVM.2020.1},
  annote =	{Keywords: Additive manufacturing, fused deposition modeling, selective laser melting, energy simulation, eco-design for AM}
}
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