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GPGPU-based data parallel region growing algorithm for cell nuclei detection

GPGPU-based data parallel region growing algorithm for cell ...

引用

International Symposium on Computational Intelligence and Informatics

作者： Sándor Szénási Zoltán Vámossy Miklós Kozlovszky John von Neumann Faculty of Informatics Óbuda University Budapest Hungary Laboratory of Parallel and Distributed Computing MTA SZTAKI Budapest Hungary

Nowadays microscopic analysis of tissue samples is done more and more by using digital imagery and special immunodiagnostic software. These are typically specific applications developed for one distinct field, but some subroutines are commonly repeated, for example several applications contain steps that can detect cell nuclei in a sample image. The aim of our research is developing a new data parallel algorithm that can be implemented even in a GPGPU environment and that is capable of counting hematoxylin eosin (HE) stained cell nuclei and of identifying their exact locations and sizes (using a variation of the region growing method). Our presentation contains the detailed description of the algorithm, the peculiarity of the CUDA implementation, and the evaluation of the created application (regarding its accuracy and the decrease in the execution time).

关键词： Graphics processing unit Kernel Instruction sets Computer architecture Algorithm design and analysis Microprocessors Synchronization

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An Intelligent Broker Approach to Semantics-Based Service Composition

An Intelligent Broker Approach to Semantics-Based Service Co...

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IEEE Annual International Computer Software and Applications Conference (COMPSAC)

作者： Yufeng Zhang Hong Zhu National Laboratory for Parallel and Distributed Processing Department of Computing Science National University of Defense Technology Changsha China Department of Computing and Electronics Oxford Brookes University Oxford UK

This paper proposes an intelligent broker approach to service composition and collaboration. The broker employs a planner to generate service composition plans according to service usage and workflow knowledge, dynamically searches for services according to the plan, then invokes and coordinates the executions of the selected services at runtime. A prototype called I-Broker has been implemented to support the approach, which can be instantiated by populating the knowledge-base with domain specific knowledge to form domain specific brokers. This paper also reports experiments that evaluate the scalability of the approach.

关键词： Knowledge based systems Ontologies Semantics Complexity theory Planning Scalability Prototypes

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An energy-efficient scheduling algorithm for sporadic real-time tasks in multiprocessor systems

An energy-efficient scheduling algorithm for sporadic real-t...

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13th IEEE International Workshop on FTDCS 2011, the 8th International Conference on ATC 2011, the 8th International Conference on UIC 2011 and the 13th IEEE International Conference on HPCC 2011

作者： Zhang, Dong-Song Chen, Fang-Yuan Li, Hong-Hua Jin, Shi-Yao Guo, De-Ke National Laboratory for Parallel and Distributed Processing School of Computer National University of Defense Technology Changsha 410073 China School of Computing Science Simon Fraser University 8888 University Drive Burnaby BC V5A 1S6 Canada National Laboratory for Information System Engineering School of Information Systems and Management National University of Defense Technology Changsha 410073 China

ISBN: (纸本)9780769545387

As the energy consumption of embedded multiprocessor systems becomes increasingly prominent, the real-time energy-efficient scheduling in multiprocessor systems becomes an urgent problem to reduce the system energy consumption while meeting real-time constraints. For a multiprocessor with independent DVFS and DPM at each processor, this paper proposes an energy-efficient real-time scheduling algorithm named LRE-DVFS-EACH, based on LRE-TL which is an optimal real-time scheduling algorithm for sporadic tasks. LRE-DVFS-EACH utilizes the concept of TL plane and the idea of fluid scheduling to dynamically scale the voltage and frequency of processors at the initial time of each TL plane as well as the release time of a sporadic task in each TL plane. Consequently, LRE-DVFS-EACH can obtain a reasonable tradeoff between the real-time constraints and the energy saving. LRE-DVFS-EACH is also adaptive to the change of workload caused by the dynamic release of sporadic tasks, which can obtain more energy savings. The experimental results show that compared with existing algorithms, LRE-DVFS-EACH can not only guarantee the optimal feasibility of sporadic tasks, but also achieve more energy savings in all cases, especially in the case of high workloads. © 2011 IEEE.

关键词： Real time systems

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Biomedical image processing with GPGPU using CUDA

Biomedical image processing with GPGPU using CUDA

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Proceedings of the International Convention MIPRO

作者： A. R. Firstauthor I. B. Secondauthor G. V. Thirdauthor P. B. Fourthauthor M. K. Fifthauthor Óbuda University/John von Neumann Faculty of Informatics Budapest Hungary Semmelweiss University/Znd Department of Internal Medicine Budapest Hungary MTA SZTAKI/Laboratory of Parallel and Distributed Computing Budapest Hungary

The main aim of this work is to show, how the GPGPUs can be used to speed up certain image processing methods. The algorithm explained in this paper is used to detect nuclei on (HE - hematoxilin eosin) stained colon tissue sample images, and includes a Gauss blurring, an RGB-HSV color space conversion, a fixed binarization, an ultimate erode procedure and a local maximum search. Since the images retrieved from the digital slides require significant storage space (up to few hundred megapixels), the usage of GPGPUs to speed up image processing operations is necessary in the interest of achieving reasonable processing time. The CUDA software development kit was used to develop algorithms to GPUs made by NVIDIA. This work focuses on how to achieve coalesced global memory access when working with three-channel RGB images, and how to use the on-die shared memory efficiently. The exact test algorithm also included a linear connected component labeling, which was running on the CPU, and with iterative optimization of the GPU code, we managed to achieve significant speed up in well defined test environment.

关键词： Graphics processing unit Instruction sets Image processing Kernel Optimization Memory management Pixel

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parallel biomedical image processing with GPGPUs in cancer research

Parallel biomedical image processing with GPGPUs in cancer r...

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International Symposium on Logistics and Industrial Informatics, LINDI

作者： Attila Reményi Sándor Szénási István Bándi Zoltán Vámossy Gábor Valcz Pál Bogdanov Szabolcs Sergyán Miklos Kozlovszky John von Neumann Faculty of Informatics Óbuda University Budapest Hungary 2nd Department of Internal Medicine Semmelweiss University Budapest Hungary Laboratory of Parallel and Distributed Computing MTA SZTAKI Budapest Hungary

The main aim of this work is to show, how GPGPUs can facilitate certain type of image processing methods. The software used in this paper is used to detect special tissue part, the nuclei on (HE - hematoxilin eosin) stained colon tissue sample images. Since pathologists are working with large number of high resolution images - thus require significant storage space -, one feasible way to achieve reasonable processing time is the usage of GPGPUs. The CUDA software development kit was used to develop processing algorithms to NVIDIA type GPUs. Our work focuses on how to achieve better performance with coalesced global memory access when working with three-channel RGB tissue images, and how to use the on-die shared memory efficiently.

关键词： Graphics processing unit Instruction sets Image processing Memory management Optimization Kernel Colon

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An Energy-Efficient Scheduling Algorithm for Sporadic Real-Time Tasks in Multiprocessor Systems

An Energy-Efficient Scheduling Algorithm for Sporadic Real-T...

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IEEE International Conference on High Performance computing and Communications (HPCC)

作者： Dong-Song Zhang Fang-Yuan Chen Hong-Hua Li Shi-Yao Jin De-Ke Guo National Laboratory for Parallel and Distributed Processing School of Computer National University of Defense Technology Changsha China School of Computing Science Simon Fraser University Burnaby BC Canada National Laboratory for Information System Engineering School of Information Systems and Management National University of Defense Technology Changsha China

关键词： Real time systems Scheduling algorithm Time frequency analysis Scheduling Heuristic algorithms Power demand

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Automatic synthesis of processor arrays with local memories on FPGAs

Automatic synthesis of processor arrays with local memories ...

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2010 International Conference on Field-Programmable Technology, FPT'10

作者： Wu, Guiming Dou, Yong Wang, Miao National Laboratory for Parallel and Distributed Processing National University of Defense Technology Changsha 410073 China Jiangnan Institute of Computing Technology Wuxi 214083 China

ISBN: (纸本)9781424489817

In this paper, we present an automatic synthesis framework to map loop nests to processor arrays with local memories on FPGAs. An affine transformation approach is firstly proposed to address space-time mapping problem. Then a data-driven architecture model is introduced to enable automatic generation of processor arrays by extracting this data-driven architecture model from transformed loop nests. Some techniques including memory allocation, communication generation and control generation are presented. Synthesizable RTL codes can be easily generated from the architecture model built by these techniques. A preliminary synthesis tool is implemented based on PLUTO, an automatic polyhedral source-to-source transformation and parallelization framework. © 2010 IEEE.

关键词： Field programmable gate arrays (FPGA)

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High performance and memory efficient implementation of matrix multiplication on FPGAs

High performance and memory efficient implementation of matr...

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2010 International Conference on Field-Programmable Technology, FPT'10

ISBN: (纸本)9781424489817

We present a high performance and memory efficient hardware implementation of matrix multiplication for dense matrices of any size on the FPGA devices. By applying a series of transformations and optimizations on the original serial algorithm, we can obtain an I/O and memory optimized block algorithm for matrix multiplication on FPGAs. A linear array of processing elements (PEs) is proposed to implement this block algorithm. We show significant reduction in hardware resources consuming compared to the related work while increasing clock frequency. Moreover, the memory requirement can be reduced to O(S) from O(S 2), where S is the block size. Therefore, more PEs can be integrated into the same FPGA devices. © 2010 IEEE.

关键词： Field programmable gate arrays (FPGA)

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Towards building efficient content-based publish/subscribe systems over structured P2P overlays

Towards building efficient content-based publish/subscribe s...

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International Conference on parallel Processing

作者： Zhang, Shengdong Wang, Ji Shen, Rui Xu, Jie National Laboratory for Parallel and Distributed Processing National University of Defense Technology Changsha 410073 China School of Computing University of Leeds Leeds LS2 9JT United Kingdom

ISBN: (纸本)9780769541563

In this paper, we introduce a generic model to deal with the event matching problem of content-based publish/ subscribe systems over structured P2P overlays. In this model, we claim that there are three methods (eventoriented, subscription-oriented and hybrid) to make all the matched pairs (event, subscription) meet in a system. By theoretically analyzing the inherent problem of both eventoriented and subscription-oriented methods, we propose PEM (Popularity-based Event Matching), a variant of hybrid method. PEM can achieve better trade-off between event processing load and subscription storage load of a system. PEM has been verified through both mathematical and simulation-based evaluation. © 2010 IEEE.

关键词： Message passing

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Routing with uncertainty in wireless mesh networks

Routing with uncertainty in wireless mesh networks

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2010 IEEE 18th International Workshop on Quality of Service, IWQoS 2010

作者： Chen, Fajun Liu, Jiangchuan Li, Zongpeng Wang, Yijie Key Laboratory of Science and Technology for National Defence of Parallel and Distributed Processing School of Computer National University of Defense Technology China School of Computing Science Simon Fraser University Canada Department of Computer Science University of Caglary Canada

ISBN: (纸本)9781424459889

Existing routing protocols for Wireless Mesh Networks (WMNs) are generally optimized with statistical link measures, while not addressing on the intrinsic uncertainty of wireless links. We show evidence that, with the transient link uncertainties at PHY and MAC layers, a pseudo-deterministic routing protocol that relies on average or historic statistics can hardly explore the full potentials of a multi-hop wireless mesh. We study optimal WMN routing using probing-based online anypath forwarding, with explicit consideration of transient link uncertainties. We show the underlying connection between WMN routing and the classic Canadian Traveller Problem (CTP) [1]. Inspired by a stochastic recoverable version of CTP (SRCTP), we develop a practical SRCTP-based online routing algorithm under link uncertainties. We study how dynamic next hop selection can be done with low cost, and derive a systematic selection order for minimizing transmission delay. We conduct simulation studies to verify the effectiveness of the SRCTP algorithms under diverse network configurations. In particular, compared to deterministic routing, reduction of end-to-end delay (51:15∼73:02%) and improvement on packet delivery ratio (99:76%) are observed.

关键词： Routing protocols

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