11 Search Results for "Wang, Qi"


Document
Optimizing Per-Core Priorities to Minimize End-To-End Latencies

Authors: Francesco Paladino, Alessandro Biondi, Enrico Bini, and Paolo Pazzaglia

Published in: LIPIcs, Volume 298, 36th Euromicro Conference on Real-Time Systems (ECRTS 2024)


Abstract
Logical Execution Time (LET) allows decoupling the schedule of real-time periodic tasks from their communication, with the advantage of isolating the communication pattern from the variability of the schedule. However, when such tasks are organized in chains, the usage of LET at the task level does not necessarily transfer the same LET properties to the chain level. In this paper, we extend a LET-like model from tasks to chains spanning over multiple cores. We leverage the designed constant latency chains to optimize per-core priority assignment. Finally, we also provide a set of heuristic algorithms, that are compared in a large-scale experimental evaluation.

Cite as

Francesco Paladino, Alessandro Biondi, Enrico Bini, and Paolo Pazzaglia. Optimizing Per-Core Priorities to Minimize End-To-End Latencies. In 36th Euromicro Conference on Real-Time Systems (ECRTS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 298, pp. 6:1-6:25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)


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@InProceedings{paladino_et_al:LIPIcs.ECRTS.2024.6,
  author =	{Paladino, Francesco and Biondi, Alessandro and Bini, Enrico and Pazzaglia, Paolo},
  title =	{{Optimizing Per-Core Priorities to Minimize End-To-End Latencies}},
  booktitle =	{36th Euromicro Conference on Real-Time Systems (ECRTS 2024)},
  pages =	{6:1--6:25},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-324-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{298},
  editor =	{Pellizzoni, Rodolfo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECRTS.2024.6},
  URN =		{urn:nbn:de:0030-drops-203094},
  doi =		{10.4230/LIPIcs.ECRTS.2024.6},
  annote =	{Keywords: Cause-Effect Chains, Logical Execution Time, End-to-End Latency, Design Optimization, Task Priorities, Data Age, Reaction Time}
}
Document
The Omnivisor: A Real-Time Static Partitioning Hypervisor Extension for Heterogeneous Core Virtualization over MPSoCs

Authors: Daniele Ottaviano, Francesco Ciraolo, Renato Mancuso, and Marcello Cinque

Published in: LIPIcs, Volume 298, 36th Euromicro Conference on Real-Time Systems (ECRTS 2024)


Abstract
Following the needs of industrial applications, virtualization has emerged as one of the most effective approaches for the consolidation of mixed-criticality systems while meeting tight constraints in terms of space, weight, power, and cost (SWaP-C). In embedded platforms with homogeneous processors, a wealth of works have proposed designs and techniques to enforce spatio-temporal isolation by leveraging well-understood virtualization support. Unfortunately, achieving the same goal on heterogeneous MultiProcessor Systems-on-Chip (MPSoCs) has been largely overlooked. Modern hypervisors are designed to operate exclusively on main cores, with little or no consideration given to other co-processors within the system, such as small microcontroller-level CPUs or soft-cores deployed on programmable logic (FPGA). Typically, hypervisors consider co-processors as I/O devices allocated to virtual machines that run on primary cores, yielding full control and responsibility over them. Nevertheless, inadequate management of these resources can lead to spatio-temporal isolation issues within the system. In this paper, we propose the Omnivisor model as a paradigm for the holistic management of heterogeneous platforms. The model generalizes the features of real-time static partitioning hypervisors to enable the execution of virtual machines on processors with different Instruction Set Architectures (ISAs) within the same MPSoC. Moreover, the Omnivisor ensures temporal and spatial isolation between virtual machines by integrating and leveraging a variety of hardware and software protection mechanisms. The presented approach not only expands the scope of virtualization in MPSoCs but also enhances the overall system reliability and real-time performance for mixed-criticality applications. A full open-source reference implementation of the Omnivisor based on the Jailhouse hypervisor is provided, targeting ARM real-time processing units and RISC-V soft-cores on FPGA. Experimental results on real hardware show the benefits of the solution, including enabling the seamless launch of virtual machines on different ISAs and extending spatial/temporal isolation to heterogenous cores with enhanced regulation policies.

Cite as

Daniele Ottaviano, Francesco Ciraolo, Renato Mancuso, and Marcello Cinque. The Omnivisor: A Real-Time Static Partitioning Hypervisor Extension for Heterogeneous Core Virtualization over MPSoCs. In 36th Euromicro Conference on Real-Time Systems (ECRTS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 298, pp. 7:1-7:27, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)


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@InProceedings{ottaviano_et_al:LIPIcs.ECRTS.2024.7,
  author =	{Ottaviano, Daniele and Ciraolo, Francesco and Mancuso, Renato and Cinque, Marcello},
  title =	{{The Omnivisor: A Real-Time Static Partitioning Hypervisor Extension for Heterogeneous Core Virtualization over MPSoCs}},
  booktitle =	{36th Euromicro Conference on Real-Time Systems (ECRTS 2024)},
  pages =	{7:1--7:27},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-324-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{298},
  editor =	{Pellizzoni, Rodolfo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECRTS.2024.7},
  URN =		{urn:nbn:de:0030-drops-203107},
  doi =		{10.4230/LIPIcs.ECRTS.2024.7},
  annote =	{Keywords: Mixed-Criticality, Embedded Virtualization, Real-Time Systems, MPSoCs}
}
Document
Response Time Analysis for Fixed-Priority Preemptive Uniform Multiprocessor Systems

Authors: Binqi Sun, Tomasz Kloda, and Marco Caccamo

Published in: LIPIcs, Volume 298, 36th Euromicro Conference on Real-Time Systems (ECRTS 2024)


Abstract
We present a response time analysis for global fixed-priority preemptive scheduling of constrained-deadline tasks upon a uniform multiprocessor where each processor can be characterized by a different speed. A fixed-priority scheduler assigns the jobs with the highest priorities to the fastest processors. Since determining whether all tasks can meet their deadlines is generally intractable even with identical processors, we propose two sufficient schedulability tests that calculate upper bounds on the task’s worst-case response time within polynomial and pseudo-polynomial time. The proposed tests leverage the linear programming model to upper bound the interference of the higher-priority tasks. Furthermore, we identify specific conditions and platforms upon which the problem can be solved more efficiently within linear time. These formulations are used to iteratively evaluate and refine possible solutions until a safe upper bound on the task’s worst-case response time is found. Additionally, we demonstrate that, with specific minor modifications, the proposed tests are compatible with Audsley’s optimal priority assignment. Experimental evaluations performed on synthetic task sets show that the proposed approach outperforms the state-of-the-art methods.

Cite as

Binqi Sun, Tomasz Kloda, and Marco Caccamo. Response Time Analysis for Fixed-Priority Preemptive Uniform Multiprocessor Systems. In 36th Euromicro Conference on Real-Time Systems (ECRTS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 298, pp. 17:1-17:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)


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@InProceedings{sun_et_al:LIPIcs.ECRTS.2024.17,
  author =	{Sun, Binqi and Kloda, Tomasz and Caccamo, Marco},
  title =	{{Response Time Analysis for Fixed-Priority Preemptive Uniform Multiprocessor Systems}},
  booktitle =	{36th Euromicro Conference on Real-Time Systems (ECRTS 2024)},
  pages =	{17:1--17:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-324-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{298},
  editor =	{Pellizzoni, Rodolfo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECRTS.2024.17},
  URN =		{urn:nbn:de:0030-drops-203201},
  doi =		{10.4230/LIPIcs.ECRTS.2024.17},
  annote =	{Keywords: Real-time scheduling, Uniform multiprocessor, Response time analysis}
}
Document
Track A: Algorithms, Complexity and Games
Fast Approximate Counting of Cycles

Authors: Keren Censor-Hillel, Tomer Even, and Virginia Vassilevska Williams

Published in: LIPIcs, Volume 297, 51st International Colloquium on Automata, Languages, and Programming (ICALP 2024)


Abstract
We consider the problem of approximate counting of triangles and longer fixed length cycles in directed graphs. For triangles, Tětek [ICALP'22] gave an algorithm that returns a (1±ε)-approximation in Õ(n^ω/t^{ω-2}) time, where t is the unknown number of triangles in the given n node graph and ω < 2.372 is the matrix multiplication exponent. We obtain an improved algorithm whose running time is, within polylogarithmic factors the same as that for multiplying an n× n/t matrix by an n/t × n matrix. We then extend our framework to obtain the first nontrivial (1± ε)-approximation algorithms for the number of h-cycles in a graph, for any constant h ≥ 3. Our running time is Õ(MM(n,n/t^{1/(h-2)},n)), the time to multiply n × n/(t^{1/(h-2)}) by n/(t^{1/(h-2)) × n matrices. Finally, we show that under popular fine-grained hypotheses, this running time is optimal.

Cite as

Keren Censor-Hillel, Tomer Even, and Virginia Vassilevska Williams. Fast Approximate Counting of Cycles. In 51st International Colloquium on Automata, Languages, and Programming (ICALP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 297, pp. 37:1-37:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)


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@InProceedings{censorhillel_et_al:LIPIcs.ICALP.2024.37,
  author =	{Censor-Hillel, Keren and Even, Tomer and Vassilevska Williams, Virginia},
  title =	{{Fast Approximate Counting of Cycles}},
  booktitle =	{51st International Colloquium on Automata, Languages, and Programming (ICALP 2024)},
  pages =	{37:1--37:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-322-5},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{297},
  editor =	{Bringmann, Karl and Grohe, Martin and Puppis, Gabriele and Svensson, Ola},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2024.37},
  URN =		{urn:nbn:de:0030-drops-201809},
  doi =		{10.4230/LIPIcs.ICALP.2024.37},
  annote =	{Keywords: Approximate triangle counting, Approximate cycle counting Fast matrix multiplication, Fast rectangular matrix multiplication}
}
Document
Track A: Algorithms, Complexity and Games
Improved Lower Bounds for Approximating Parameterized Nearest Codeword and Related Problems Under ETH

Authors: Shuangle Li, Bingkai Lin, and Yuwei Liu

Published in: LIPIcs, Volume 297, 51st International Colloquium on Automata, Languages, and Programming (ICALP 2024)


Abstract
In this paper we present a new gap-creating randomized self-reduction for the parameterized Maximum Likelihood Decoding problem over 𝔽_p (k-MLD_p). The reduction takes a k-MLD_p instance with k⋅ n d-dimensional vectors as input, runs in O(d2^{O(k)}n^{1.01}) time for some computable function f, outputs a (3/2-ε)-Gap-k'-MLD_p instance for any ε > 0, where k' = O(k²log k). Using this reduction, we show that assuming the randomized Exponential Time Hypothesis (ETH), no algorithms can approximate k-MLD_p (and therefore its dual problem k-NCP_p) within factor (3/2-ε) in f(k)⋅ n^{o(√{k/log k})} time for any ε > 0. We then use reduction by Bhattacharyya, Ghoshal, Karthik and Manurangsi (ICALP 2018) to amplify the (3/2-ε)-gap to any constant. As a result, we show that assuming ETH, no algorithms can approximate k-NCP_p and k-MDP_p within γ-factor in f(k)⋅ n^{o(k^{ε_γ})} time for some constant ε_γ > 0. Combining with the gap-preserving reduction by Bennett, Cheraghchi, Guruswami and Ribeiro (STOC 2023), we also obtain similar lower bounds for k-MDP_p, k-CVP_p and k-SVP_p. These results improve upon the previous f(k)⋅ n^{Ω(poly log k)} lower bounds for these problems under ETH using reductions by Bhattacharyya et al. (J.ACM 2021) and Bennett et al. (STOC 2023).

Cite as

Shuangle Li, Bingkai Lin, and Yuwei Liu. Improved Lower Bounds for Approximating Parameterized Nearest Codeword and Related Problems Under ETH. In 51st International Colloquium on Automata, Languages, and Programming (ICALP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 297, pp. 107:1-107:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)


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@InProceedings{li_et_al:LIPIcs.ICALP.2024.107,
  author =	{Li, Shuangle and Lin, Bingkai and Liu, Yuwei},
  title =	{{Improved Lower Bounds for Approximating Parameterized Nearest Codeword and Related Problems Under ETH}},
  booktitle =	{51st International Colloquium on Automata, Languages, and Programming (ICALP 2024)},
  pages =	{107:1--107:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-322-5},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{297},
  editor =	{Bringmann, Karl and Grohe, Martin and Puppis, Gabriele and Svensson, Ola},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2024.107},
  URN =		{urn:nbn:de:0030-drops-202500},
  doi =		{10.4230/LIPIcs.ICALP.2024.107},
  annote =	{Keywords: Nearest Codeword Problem, Hardness of Approximations, Fine-grained Complexity, Parameterized Complexity, Minimum Distance Problem, Shortest Vector Problem}
}
Document
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
Position
Grounding Stream Reasoning Research

Authors: Pieter Bonte, Jean-Paul Calbimonte, Daniel de Leng, Daniele Dell'Aglio, Emanuele Della Valle, Thomas Eiter, Federico Giannini, Fredrik Heintz, Konstantin Schekotihin, Danh Le-Phuoc, Alessandra Mileo, Patrik Schneider, Riccardo Tommasini, Jacopo Urbani, and Giacomo Ziffer

Published in: TGDK, Volume 2, Issue 1 (2024): Special Issue on Trends in Graph Data and Knowledge - Part 2. Transactions on Graph Data and Knowledge, Volume 2, Issue 1


Abstract
In the last decade, there has been a growing interest in applying AI technologies to implement complex data analytics over data streams. To this end, researchers in various fields have been organising a yearly event called the "Stream Reasoning Workshop" to share perspectives, challenges, and experiences around this topic. In this paper, the previous organisers of the workshops and other community members provide a summary of the main research results that have been discussed during the first six editions of the event. These results can be categorised into four main research areas: The first is concerned with the technological challenges related to handling large data streams. The second area aims at adapting and extending existing semantic technologies to data streams. The third and fourth areas focus on how to implement reasoning techniques, either considering deductive or inductive techniques, to extract new and valuable knowledge from the data in the stream. This summary is written not only to provide a crystallisation of the field, but also to point out distinctive traits of the stream reasoning community. Moreover, it also provides a foundation for future research by enumerating a list of use cases and open challenges, to stimulate others to join this exciting research area.

Cite as

Pieter Bonte, Jean-Paul Calbimonte, Daniel de Leng, Daniele Dell'Aglio, Emanuele Della Valle, Thomas Eiter, Federico Giannini, Fredrik Heintz, Konstantin Schekotihin, Danh Le-Phuoc, Alessandra Mileo, Patrik Schneider, Riccardo Tommasini, Jacopo Urbani, and Giacomo Ziffer. Grounding Stream Reasoning Research. In Special Issue on Trends in Graph Data and Knowledge - Part 2. Transactions on Graph Data and Knowledge (TGDK), Volume 2, Issue 1, pp. 2:1-2:47, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)


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@Article{bonte_et_al:TGDK.2.1.2,
  author =	{Bonte, Pieter and Calbimonte, Jean-Paul and de Leng, Daniel and Dell'Aglio, Daniele and Della Valle, Emanuele and Eiter, Thomas and Giannini, Federico and Heintz, Fredrik and Schekotihin, Konstantin and Le-Phuoc, Danh and Mileo, Alessandra and Schneider, Patrik and Tommasini, Riccardo and Urbani, Jacopo and Ziffer, Giacomo},
  title =	{{Grounding Stream Reasoning Research}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{2:1--2:47},
  ISSN =	{2942-7517},
  year =	{2024},
  volume =	{2},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.2.1.2},
  URN =		{urn:nbn:de:0030-drops-198597},
  doi =		{10.4230/TGDK.2.1.2},
  annote =	{Keywords: Stream Reasoning, Stream Processing, RDF streams, Streaming Linked Data, Continuous query processing, Temporal Logics, High-performance computing, Databases}
}
Document
Position
Standardizing Knowledge Engineering Practices with a Reference Architecture

Authors: Bradley P. Allen and Filip Ilievski

Published in: TGDK, Volume 2, Issue 1 (2024): Special Issue on Trends in Graph Data and Knowledge - Part 2. Transactions on Graph Data and Knowledge, Volume 2, Issue 1


Abstract
Knowledge engineering is the process of creating and maintaining knowledge-producing systems. Throughout the history of computer science and AI, knowledge engineering workflows have been widely used given the importance of high-quality knowledge for reliable intelligent agents. Meanwhile, the scope of knowledge engineering, as apparent from its target tasks and use cases, has been shifting, together with its paradigms such as expert systems, semantic web, and language modeling. The intended use cases and supported user requirements between these paradigms have not been analyzed globally, as new paradigms often satisfy prior pain points while possibly introducing new ones. The recent abstraction of systemic patterns into a boxology provides an opening for aligning the requirements and use cases of knowledge engineering with the systems, components, and software that can satisfy them best, however, this direction has not been explored to date. This paper proposes a vision of harmonizing the best practices in the field of knowledge engineering by leveraging the software engineering methodology of creating reference architectures. We describe how a reference architecture can be iteratively designed and implemented to associate user needs with recurring systemic patterns, building on top of existing knowledge engineering workflows and boxologies. We provide a six-step roadmap that can enable the development of such an architecture, consisting of scope definition, selection of information sources, architectural analysis, synthesis of an architecture based on the information source analysis, evaluation through instantiation, and, ultimately, instantiation into a concrete software architecture. We provide an initial design and outcome of the definition of architectural scope, selection of information sources, and analysis. As the remaining steps of design, evaluation, and instantiation of the architecture are largely use-case specific, we provide a detailed description of their procedures and point to relevant examples. We expect that following through on this vision will lead to well-grounded reference architectures for knowledge engineering, will advance the ongoing initiatives of organizing the neurosymbolic knowledge engineering space, and will build new links to the software architectures and data science communities.

Cite as

Bradley P. Allen and Filip Ilievski. Standardizing Knowledge Engineering Practices with a Reference Architecture. In Special Issue on Trends in Graph Data and Knowledge - Part 2. Transactions on Graph Data and Knowledge (TGDK), Volume 2, Issue 1, pp. 5:1-5:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)


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@Article{allen_et_al:TGDK.2.1.5,
  author =	{Allen, Bradley P. and Ilievski, Filip},
  title =	{{Standardizing Knowledge Engineering Practices with a Reference Architecture}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{5:1--5:23},
  ISSN =	{2942-7517},
  year =	{2024},
  volume =	{2},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.2.1.5},
  URN =		{urn:nbn:de:0030-drops-198623},
  doi =		{10.4230/TGDK.2.1.5},
  annote =	{Keywords: knowledge engineering, knowledge graphs, quality attributes, software architectures, sociotechnical systems}
}
Document
Track A: Algorithms, Complexity and Games
Parallel Self-Testing of EPR Pairs Under Computational Assumptions

Authors: Honghao Fu, Daochen Wang, and Qi Zhao

Published in: LIPIcs, Volume 261, 50th International Colloquium on Automata, Languages, and Programming (ICALP 2023)


Abstract
Self-testing is a fundamental feature of quantum mechanics that allows a classical verifier to force untrusted quantum devices to prepare certain states and perform certain measurements on them. The standard approach assumes at least two spatially separated devices. Recently, Metger and Vidick [Metger and Vidick, 2021] showed that a single EPR pair of a single quantum device can be self-tested under computational assumptions. In this work, we generalize their results to give the first parallel self-test of N EPR pairs and measurements on them in the single-device setting under the same computational assumptions. We show that our protocol can be passed with probability negligibly close to 1 by an honest quantum device using poly(N) resources. Moreover, we show that any quantum device that fails our protocol with probability at most ε must be poly(N,ε)-close to being honest in the appropriate sense. In particular, our protocol can test any distribution over tensor products of computational or Hadamard basis measurements, making it suitable for applications such as device-independent quantum key distribution [Metger et al., 2021] under computational assumptions. Moreover, a simplified version of our protocol is the first that can efficiently certify an arbitrary number of qubits of a single cloud quantum computer using only classical communication.

Cite as

Honghao Fu, Daochen Wang, and Qi Zhao. Parallel Self-Testing of EPR Pairs Under Computational Assumptions. In 50th International Colloquium on Automata, Languages, and Programming (ICALP 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 261, pp. 64:1-64:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)


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@InProceedings{fu_et_al:LIPIcs.ICALP.2023.64,
  author =	{Fu, Honghao and Wang, Daochen and Zhao, Qi},
  title =	{{Parallel Self-Testing of EPR Pairs Under Computational Assumptions}},
  booktitle =	{50th International Colloquium on Automata, Languages, and Programming (ICALP 2023)},
  pages =	{64:1--64:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-278-5},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{261},
  editor =	{Etessami, Kousha and Feige, Uriel and Puppis, Gabriele},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2023.64},
  URN =		{urn:nbn:de:0030-drops-181160},
  doi =		{10.4230/LIPIcs.ICALP.2023.64},
  annote =	{Keywords: Quantum complexity theory, self-testing, LWE}
}
Document
Faster Pan-Genome Construction for Efficient Differentiation of Naturally Occurring and Engineered Plasmids with Plaster

Authors: Qi Wang, R. A. Leo Elworth, Tian Rui Liu, and Todd J. Treangen

Published in: LIPIcs, Volume 143, 19th International Workshop on Algorithms in Bioinformatics (WABI 2019)


Abstract
As sequence databases grow, characterizing diversity across extremely large collections of genomes requires the development of efficient methods that avoid costly all-vs-all comparisons [Marschall et al., 2018]. In addition to exponential increases in the amount of natural genomes being sequenced, improved techniques for the creation of human engineered sequences is ushering in a new wave of synthetic genome sequence databases that grow alongside naturally occurring genome databases. In this paper, we analyze the full diversity of available sequenced natural and synthetic plasmid genome sequences. This diversity can be represented by a data structure that captures all presently available nucleotide sequences, known as a pan-genome. In our case, we construct a single linear pan-genome nucleotide sequence that captures this diversity. To process such a large number of sequences, we introduce the plaster algorithmic pipeline. Using plaster we are able to construct the full synthetic plasmid pan-genome from 51,047 synthetic plasmid sequences as well as a natural pan-genome from 6,642 natural plasmid sequences. We demonstrate the efficacy of plaster by comparing its speed against another pan-genome construction method as well as demonstrating that nearly all plasmids align well to their corresponding pan-genome. Finally, we explore the use of pan-genome sequence alignment to distinguish between naturally occurring and synthetic plasmids. We believe this approach will lead to new techniques for rapid characterization of engineered plasmids. Applications for this work include detection of genome editing, tracking an unknown plasmid back to its lab of origin, and identifying naturally occurring sequences that may be of use to the synthetic biology community. The source code for fully reconstructing the natural and synthetic plasmid pan-genomes as well for plaster are publicly available and can be downloaded at https://gitlab.com/qiwangrice/plaster.git.

Cite as

Qi Wang, R. A. Leo Elworth, Tian Rui Liu, and Todd J. Treangen. Faster Pan-Genome Construction for Efficient Differentiation of Naturally Occurring and Engineered Plasmids with Plaster. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 19:1-19:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@InProceedings{wang_et_al:LIPIcs.WABI.2019.19,
  author =	{Wang, Qi and Elworth, R. A. Leo and Liu, Tian Rui and Treangen, Todd J.},
  title =	{{Faster Pan-Genome Construction for Efficient Differentiation of Naturally Occurring and Engineered Plasmids with Plaster}},
  booktitle =	{19th International Workshop on Algorithms in Bioinformatics (WABI 2019)},
  pages =	{19:1--19:12},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-123-8},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{143},
  editor =	{Huber, Katharina T. and Gusfield, Dan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2019.19},
  URN =		{urn:nbn:de:0030-drops-110492},
  doi =		{10.4230/LIPIcs.WABI.2019.19},
  annote =	{Keywords: comparative genomics, sequence alignment, pan-genome, engineered plasmids}
}
Document
Invited Talk
Some Geometric and Computational Challenges Arising in Structural Molecular Biology (Invited Talk)

Authors: Bruce R. Donald

Published in: LIPIcs, Volume 129, 35th International Symposium on Computational Geometry (SoCG 2019)


Abstract
Computational protein design is a transformative field with exciting prospects for advancing both basic science and translational medical research. New algorithms blend discrete and continuous geometry to address the challenges of creating designer proteins. I will discuss recent progress in this area and some interesting open problems. I will motivate this talk by discussing how, by using continuous geometric representations within a discrete optimization framework, broadly-neutralizing anti-HIV-1 antibodies were computationally designed that are now being tested in humans - the designed antibodies are currently in eight clinical trials, one of which is Phase 2a (NCT03721510). These continuous representations model the flexibility and dynamics of biological macromolecules, which are an important structural determinant of function. However, reconstruction of biomolecular dynamics from experimental observables requires the determination of a conformational probability distribution. These distributions are not fully constrained by the limited geometric information from experiments, making the problem ill-posed in the sense of Hadamard. The ill-posed nature of the problem comes from the fact that it has no unique solution. Multiple or even an infinite number of solutions may exist. To avoid the ill-posed nature, the problem must be regularized by making (hopefully reasonable) assumptions. I will present new ways to both represent and visualize correlated inter-domain protein motions. We use Bingham distributions, based on a quaternion fit to circular moments of a physics-based quadratic form. To find the optimal solution for the distribution, we designed an efficient, provable branch-and-bound algorithm that exploits the structure of analytical solutions to the trigonometric moment problem. Hence, continuous conformational PDFs can be determined directly from NMR measurements. The representation works especially well for multi-domain systems with broad conformational distributions. For more information please see Y. Qi et al. Jour. Mol. Biol. 2018; 430(18 Pt B):3412-3426. doi: 10.1016/j.jmb.2018.06.022. Ultimately, this method has parallels to other branches of geometric computing that balance discrete and continuous representations, including physical geometric algorithms, robotics, computational geometry, and robust optimization. I will advocate for using continuous distributions for protein modeling, and describe future work and open problems.

Cite as

Bruce R. Donald. Some Geometric and Computational Challenges Arising in Structural Molecular Biology (Invited Talk). In 35th International Symposium on Computational Geometry (SoCG 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 129, pp. 2:1-2:2, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@InProceedings{donald:LIPIcs.SoCG.2019.2,
  author =	{Donald, Bruce R.},
  title =	{{Some Geometric and Computational Challenges Arising in Structural Molecular Biology}},
  booktitle =	{35th International Symposium on Computational Geometry (SoCG 2019)},
  pages =	{2:1--2:2},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-104-7},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{129},
  editor =	{Barequet, Gill and Wang, Yusu},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SoCG.2019.2},
  URN =		{urn:nbn:de:0030-drops-104065},
  doi =		{10.4230/LIPIcs.SoCG.2019.2},
  annote =	{Keywords: Geometric computing, combutational biology, Continuous Interdomain Orientation Distributions of Protein Conformations}
}
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