7 Search Results for "Kim, Anthony"

Document
DOI: 10.4230/LIPIcs.SEA.2024.8
Practical Computation of Graph VC-Dimension

Authors: David Coudert, Mónika Csikós, Guillaume Ducoffe, and Laurent Viennot

Published in: LIPIcs, Volume 301, 22nd International Symposium on Experimental Algorithms (SEA 2024)

Abstract
For any set system ℋ = (V,ℛ), ℛ ⊆ 2^V, a subset S ⊆ V is called shattered if every S' ⊆ S results from the intersection of S with some set in ℛ. The VC-dimension of ℋ is the size of a largest shattered set in V. In this paper, we focus on the problem of computing the VC-dimension of graphs. In particular, given a graph G = (V,E), the VC-dimension of G is defined as the VC-dimension of (V, N), where N contains each subset of V that can be obtained as the closed neighborhood of some vertex v ∈ V in G. Our main contribution is an algorithm for computing the VC-dimension of any graph, whose effectiveness is shown through experiments on various types of practical graphs, including graphs with millions of vertices. A key aspect of its efficiency resides in the fact that practical graphs have small VC-dimension, up to 8 in our experiments. As a side-product, we present several new bounds relating the graph VC-dimension to other classical graph theoretical notions. We also establish the W[1]-hardness of the graph VC-dimension problem by extending a previous result for arbitrary set systems.
Cite as

David Coudert, Mónika Csikós, Guillaume Ducoffe, and Laurent Viennot. Practical Computation of Graph VC-Dimension. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 8:1-8:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{coudert_et_al:LIPIcs.SEA.2024.8,
  author =	{Coudert, David and Csik\'{o}s, M\'{o}nika and Ducoffe, Guillaume and Viennot, Laurent},
  title =	{{Practical Computation of Graph VC-Dimension}},
  booktitle =	{22nd International Symposium on Experimental Algorithms (SEA 2024)},
  pages =	{8:1--8:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-325-6},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{301},
  editor =	{Liberti, Leo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2024.8},
  URN =		{urn:nbn:de:0030-drops-203731},
  doi =		{10.4230/LIPIcs.SEA.2024.8},
  annote =	{Keywords: VC-dimension, graph, algorithm}
}
Document
DOI: 10.4230/LIPIcs.SEA.2024.17
Barcode Selection and Layout Optimization in Spatial Transcriptomics

Authors: Frederik L. Jatzkowski, Antonia Schmidt, Robert Mank, Steffen Schüler, and Matthias Müller-Hannemann

Published in: LIPIcs, Volume 301, 22nd International Symposium on Experimental Algorithms (SEA 2024)

Abstract
An important special case of the quadratic assignment problem arises in the synthesis of DNA microarrays for high-resolution spatial transcriptomics. The task is to select a suitable subset from a set of barcodes, i. e. short DNA strings that serve as unique identifiers, and to assign the selected barcodes to positions on a two-dimensional array in such a way that a position-dependent cost function is minimized. A typical microarray with dimensions of 768×1024 requires 786,432 many barcodes to be placed, leading to very challenging large-scale combinatorial optimization problems. The general quadratic assignment problem is well-known for its hardness, both in theory and in practice. It turns out that this also holds for the special case of the barcode layout problem. We show that the problem is even hard to approximate: It is MaxSNP-hard. An ILP formulation theoretically allows the computation of optimal results, but it is only applicable for tiny instances. Therefore, we have developed layout constructing and improving heuristics with the aim of computing near-optimal solutions for instances of realistic size. These include a sorting-based algorithm, a greedy algorithm, 2-OPT-based local search and a genetic algorithm. To assess the quality of the results, we compare the generated solutions with the expected cost of a random layout and with lower bounds. A combination of the greedy algorithm and 2-OPT local search produces the most promising results in terms of both quality and runtime. Solutions to large-scale instances with arrays of dimension 768×1024 show a 37% reduction in cost over a random solution and can be computed in about 3 minutes. Since the universe of suitable barcodes is much larger than the number of barcodes needed, this can be exploited. Experiments with different surpluses of barcodes show that a significant improvement in layout quality can be achieved at the cost of a reasonable increase in runtime. Another interesting finding is that the restriction of the barcode design space by biochemical constraints is actually beneficial for the overall layout cost.
Cite as

Frederik L. Jatzkowski, Antonia Schmidt, Robert Mank, Steffen Schüler, and Matthias Müller-Hannemann. Barcode Selection and Layout Optimization in Spatial Transcriptomics. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 17:1-17:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{jatzkowski_et_al:LIPIcs.SEA.2024.17,
  author =	{Jatzkowski, Frederik L. and Schmidt, Antonia and Mank, Robert and Sch\"{u}ler, Steffen and M\"{u}ller-Hannemann, Matthias},
  title =	{{Barcode Selection and Layout Optimization in Spatial Transcriptomics}},
  booktitle =	{22nd International Symposium on Experimental Algorithms (SEA 2024)},
  pages =	{17:1--17:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-325-6},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{301},
  editor =	{Liberti, Leo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2024.17},
  URN =		{urn:nbn:de:0030-drops-203821},
  doi =		{10.4230/LIPIcs.SEA.2024.17},
  annote =	{Keywords: Spatial Transcriptomics, Array Layout, Optimization, Computational Complexity, GPU Computing, Integer Linear Programming, Metaheuristics}
}
Document
DOI: 10.4230/LIPIcs.SEA.2024.23
Engineering A* Search for the Flip Distance of Plane Triangulations

Authors: Philip Mayer and Petra Mutzel

Published in: LIPIcs, Volume 301, 22nd International Symposium on Experimental Algorithms (SEA 2024)

Abstract
The flip distance for two triangulations of a point set is defined as the smallest number of edge flips needed to transform one triangulation into another, where an edge flip is the act of replacing an edge of a triangulation by a different edge such that the result remains a triangulation. We adapt and engineer a sophisticated A* search algorithm acting on the so-called flip graph. In particular, we prove that previously proposed lower bounds for the flip distance form consistent heuristics for A* and show that they can be computed efficiently using dynamic algorithms. As an alternative approach, we present an integer linear program (ILP) for the flip distance problem. We experimentally evaluate our approaches on a new real-world benchmark data set based on an application in geodesy, namely sea surface reconstruction. Our evaluation reveals that A* search consistently outperforms our ILP formulation as well as a naive baseline, which is bidirectional breadth-first search. In particular, the runtime of our approach improves upon the baseline by more than two orders of magnitude. Furthermore, our A* search successfully solves most of the considered sea surface instances with up to 41 points. This is a substantial improvement compared to the baseline, which struggles with subsets of the real-world data of size 25. Lastly, to allow the consideration of global sea level data, we developed a decomposition-based heuristic for the flip distance. In our experiments it yields optimal flip distance values for most of the considered sea level data and it can be applied to large data sets due to its fast runtime.
Cite as

Philip Mayer and Petra Mutzel. Engineering A* Search for the Flip Distance of Plane Triangulations. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 23:1-23:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{mayer_et_al:LIPIcs.SEA.2024.23,
  author =	{Mayer, Philip and Mutzel, Petra},
  title =	{{Engineering A* Search for the Flip Distance of Plane Triangulations}},
  booktitle =	{22nd International Symposium on Experimental Algorithms (SEA 2024)},
  pages =	{23:1--23:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-325-6},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{301},
  editor =	{Liberti, Leo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2024.23},
  URN =		{urn:nbn:de:0030-drops-203887},
  doi =		{10.4230/LIPIcs.SEA.2024.23},
  annote =	{Keywords: Computational Geometry, Triangulations, Flip Distance, A-star Search, Integer Linear Programming}
}
Document
DOI: 10.4230/LIPIcs.ECRTS.2024.1
JuMP2start: Time-Aware Stop-Start Technology for a Software-Defined Vehicle System

Authors: Anam Farrukh and Richard West

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

Abstract
Software-defined vehicle (SDV) systems replace traditional ECU architectures with software tasks running on centralized multicore processors in automotive-grade PCs. However, PC boot delays to cold-start an integrated vehicle management system (VMS) are problematic for time-critical functions, which must process sensor and actuator data within specific time bounds. To tackle this challenge, we present JuMP2start: a time-aware multicore stop-start approach for SDVs. JuMP2start leverages PC-class suspend-to-RAM techniques to capture a system snapshot when the vehicle is stopped. Upon restart, critical services are resumed-from-RAM within order of milliseconds compared to normal cold-start times. This work showcases how JuMP2start manages global suspension and resumption mechanisms for a state-of-the-art dual-domain vehicle management system comprising real-time OS (RTOS) and Linux SMP guests. JuMP2start models automotive tasks as continuable or restartable to ensure timing- and safety-critical function pipelines are reactively resumed with low latency, while discarding stale task state. Experiments with the VMS show that critical CAN traffic processing resumes within 500 milliseconds of waking the RTOS guest, and reaches steady-state throughput in under 7ms.
Cite as

Anam Farrukh and Richard West. JuMP2start: Time-Aware Stop-Start Technology for a Software-Defined Vehicle System. In 36th Euromicro Conference on Real-Time Systems (ECRTS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 298, pp. 1:1-1:27, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{farrukh_et_al:LIPIcs.ECRTS.2024.1,
  author =	{Farrukh, Anam and West, Richard},
  title =	{{JuMP2start: Time-Aware Stop-Start Technology for a Software-Defined Vehicle System}},
  booktitle =	{36th Euromicro Conference on Real-Time Systems (ECRTS 2024)},
  pages =	{1:1--1:27},
  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.2024.1},
  URN =		{urn:nbn:de:0030-drops-203046},
  doi =		{10.4230/LIPIcs.ECRTS.2024.1},
  annote =	{Keywords: Time-aware stop-start, Real-time power management, Suspend-to-RAM, Partitioning hypervisor, Vehicle management system, Vehicle-OS, Software-defined vehicles (SDV)}
}
Document
DOI: 10.4230/LIPIcs.ECRTS.2024.7
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
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
DOI: 10.4230/LIPIcs.APPROX-RANDOM.2016.12
Online Energy Storage Management: an Algorithmic Approach

Authors: Anthony Kim, Vahid Liaghat, Junjie Qin, and Amin Saberi

Published in: LIPIcs, Volume 60, Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2016)

Abstract
Motivated by the importance of energy storage networks in smart grids, we provide an algorithmic study of the online energy storage management problem in a network setting, the first to the best of our knowledge. Given online power supplies, either entirely renewable supplies or those in combination with traditional supplies, we want to route power from the supplies to demands using storage units subject to a decay factor. Our goal is to maximize the total utility of satisfied demands less the total production cost of routed power. We model renewable supplies with the zero production cost function and traditional supplies with convex production cost functions. For two natural storage unit settings, private and public, we design poly-logarithmic competitive algorithms in the network flow model using the dual fitting and online primal dual methods for convex problems. Furthermore, we show strong hardness results for more general settings of the problem. Our techniques may be of independent interest in other routing and storage management problems.
Cite as

Anthony Kim, Vahid Liaghat, Junjie Qin, and Amin Saberi. Online Energy Storage Management: an Algorithmic Approach. In Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 60, pp. 12:1-12:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)

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@InProceedings{kim_et_al:LIPIcs.APPROX-RANDOM.2016.12,
  author =	{Kim, Anthony and Liaghat, Vahid and Qin, Junjie and Saberi, Amin},
  title =	{{Online Energy Storage Management: an Algorithmic Approach}},
  booktitle =	{Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2016)},
  pages =	{12:1--12:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-018-7},
  ISSN =	{1868-8969},
  year =	{2016},
  volume =	{60},
  editor =	{Jansen, Klaus and Mathieu, Claire and Rolim, Jos\'{e} D. P. and Umans, Chris},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.APPROX-RANDOM.2016.12},
  URN =		{urn:nbn:de:0030-drops-66355},
  doi =		{10.4230/LIPIcs.APPROX-RANDOM.2016.12},
  annote =	{Keywords: Online Algorithms, Competitive Analysis, Routing, Storage, Approximation Algorithms, Power Control}
}
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