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A network clustering algorithm for detection of protein families

A network clustering algorithm for detection of protein fami...

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Annual International Conference of the IEEE engineering in Medicine and Biology Society (EMBC)

作者： Jiang Xie Minchao Wang Dongbo Dai Huiran Zhang Wu Zhang School of Computer Engineering and Science Shanghai University Shanghai China Department of Mathematics University of California Irvine Irvine CA USA School of Computer Engineering and Science High Performance Computing Center Shanghai University Shanghai China

Detection of protein families in large scale database is a difficult but important biological problem. Computational clustering methods can effectively address the problem. Although there exist many clustering algorithms, most of them are just based on the threshold. Their computational performances are affected by the weight distribution greatly, and they are only valid for some special networks. A new network clustering algorithm, Markov Finding and Clustering (MFC), is proposed to cluster the proteins into their functionally specific families accurately in this paper. The MFC algorithm makes an improvement in the random walk process and reduces the affection of the noise on the clustering result. It has a good performance on these networks which are not well addressed by existing algorithms sensitive to the noise. Finally, experiments on the protein sequence datasets demonstrate that the algorithm is effective in the detection of protein families and has a better performance than the current algorithms.

关键词： Clustering algorithms Proteins Educational institutions Noise Accuracy Bioinformatics Legged locomotion

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Automatic Refactoring of Legacy Fortran Code to the Array Slicing Notation

Automatic Refactoring of Legacy Fortran Code to the Array Sl...

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International Conference on Parallel and Distributed Systems (ICPADS)

作者： Chandrasehar Rajaseharan Wen Jun Tan Wai Teng Tang Stephen John Turner Shyh-Hao Kuo Rick Siow Mong Goh Weng-Fai Wong School of Computer Engineering Nanyang Technological University Singapore Agency for Science Technology and Research Institute of High Performance Computing Singapore Agency for Science Technology and Research Singapore SG Department of Computer Science National University of Singapore Singapore

There are many legacy Fortran programs still in use today, especially scientific codes which were written decades ago. Many of these codes use explicit DO-loops in programs that tend to clutter the code and make it harder to understand and maintain. Modern features of the Fortran language, such as the array slicing notation and introduction of commonly used intrinsic functions, go a long way in helping programmers write code that is easier to read and maintain. We introduce a refactoring tool that can help to transform code to make use of the array slicing notation and related intrinsic functions.

关键词： Arrays Educational institutions Jacobian matrices Optimization Java Clutter Transforms

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Photonic crystals in proton-exchanged LiNbO3 waveguides for photonic applications

Photonic crystals in proton-exchanged LiNbO3 waveguides for ...

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2012 Photonics Global Conference, PGC 2012

作者： Jun, Deng Jia Wei Kumar, Vanga Sudheer Png, Ching Eng Bettiol, Andrew A. Danner, Aaron J. Department of Electrical and Computer Engineering National University of Singapore Singapore 117576 Singapore Institute of High Performance Computing Agency for Science Technology and Research 1 Fusionopolis Way #16-16 Connexis Singapore 138632 Singapore Henan Key Laboratory of Laser and Opto-electric Information Technology Zhengzhou University Henan 450052 China Department of Physics National University of Singapore Singapore 117542 Singapore

ISBN: (纸本)9781467325165

Photonic crystals realized in LiNbO3 have a great potential to reduce the size and increase the functionality of integrated optical devices. In order to accomplish these aims, fabrication know-how must be mastered yet it remains relatively uncharted. In this work we report the fabrication and optical characterization of photonic crystal structures in annealed proton exchanged (APE) LiNbO3 waveguides. In our work, channel waveguides were fabricated by photolithography patterning followed by immersing LiNbO 3 wafers in molten benzoic acid at 235°C for 5 h. The thickness and the composition profiles of the APE waveguides were measured using the secondary ion mass spectroscopy (SIMS) method. The experimental characterization of the photonic crystal waveguides was performed and a photonic stop band with good sharpness can be observed from the transmission spectra. © 2012 IEEE.

关键词： Niobium compounds

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A Combined Dual-stage Framework for Robust Scheduling of Scientific Applications in Heterogeneous Environments with Uncertain Availability

A Combined Dual-stage Framework for Robust Scheduling of Sci...

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IEEE International Symposium on Parallel and Distributed Processing Workshops and Phd Forum (IPDPSW)

作者： Florina M. Ciorba Timothy Hansen Srishti Srivastava Ioana Banicescu Anthony A. Maciejewski Howard Jay Siegel Center for Information Services and High Performance Computing Technische Universität Dresden Dresden Germany Department of Electrical and Computer Engineering Colorado State University Fort Collins CO USA Department of Computer Science and Engineering Mississippi State University Mississippi MS USA Department of Electrical and Computer Engineering Department of Computer Science Colorado State University Fort Collins CO USA

Scheduling parallel applications on existing or emerging computing platforms is challenging, and, among other attributes, must be efficient and robust. A dual-stage framework is proposed in this paper to evaluate the robustness of efficient resource allocation and dynamic load balancing of scientific applications in heterogeneous computing environments with uncertain availability. The first stage employs robust resource allocation heuristics, while the second stage incorporates robust dynamic loop scheduling techniques. The combined dual-stage framework constitutes a comprehensive framework that enables and provides guarantees for the robust execution of scientific applications in computing systems where uncertainty is caused by various unpredictable perturbations. The paper reports on studies for determining the best techniques to be used for each stage that: (a) maximize the probability that the system make span satisfies a deadline, and (b) minimize the system make span for every given availability level in the system. The usefulness and benefits of the proposed framework are demonstrated via a small scale example.

关键词： Availability Robustness Resource management Uncertainty Runtime Dynamic scheduling Program processors

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A Static Binary Instrumentation Threading Model for Fast Memory Trace Collection

A Static Binary Instrumentation Threading Model for Fast Mem...

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high performance computing, Networking, Storage and Analysis (SCC), SC Companion:

作者： Michael A. Laurenzano Joshua Peraza Laura Carrington Ananta Tiwari William A. Ward Roy Campbell Performance Modeling and Characterization Laboratory San Diego Supercomputer Center University of California San Diego USA Department of Computer Science and Engineering University of California San Diego USA High Performance Computing Modernization Program United States Department of Defense USA

In order to achieve a high level of performance, data intensive applications such as the real-time processing of surveillance feeds from unmanned aerial vehicles will require the strategic application of multi/many-core processors and coprocessors using a hybrid of inter-process message passing (e.g. MPI and SHMEM) and intra-process threading (e.g. pthreads and OpenMP). To facilitate program design decisions, memory traces gathered through binary instrumentation can be used to understand the low-level interactions between a data intensive code and the memory subsystem of a multi-core processor or many-core co-processor. Toward this end, this paper introduces the addition of threading support for PMaCs Efficient Binary Instrumentation Toolkit for Linux/x86 (PEBIL) and compares PEBILs threading model to the threading models of two other popular Linux/x86 binary instrumentation platforms - Pin and Dyninst - on both theoretical and empirical grounds. The empirical comparisons are based on experiments which collect memory address traces for the OpenMP-threaded implementations of the NASA Advanced Supercomputing Parallel Benchmarks (NPBs). This work shows that the overhead of collecting full memory address traces for multithreaded programs is higher in PEBIL (7.7x) than in Pin (4.7x), both of which are significantly lower than Dyninst (897x). This work also shows that PEBIL, uniquely, is able to take advantage of interval-based sampling of a memory address trace by rapidly disabling and re-enabling instrumentation at the transitions into and out of sampling periods in order to achieve significant decreases in the overhead of memory address trace collection. For collecting the memory address streams of each of the NPBs at a 10% sampling rate, PEBIL incurs an average slowdown of 2.9x compared to 4.4x with Pin and 897x with Dyninst.

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On the Development of Global Plasma-Ionosphere FDTD Algorithms for Electromagnetic Calculations in the Earth- Ionosphere System

On the Development of Global Plasma-Ionosphere FDTD Algorith...

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International Conference on Electromagnetics in Advanced Applications

作者： Yaxin Yu Jamesina J. Simpson Erping Li Institute of High Performance Computing Agency for Science Technology and Research (A*STAR) 1 Fusionopolis Way #16-16 Connexis North Tower Singapore 138632 Electrical and Computer Engineering Department University of New Mexico Albuquerque NM 87106 USA

ISBN: (纸本)9781467303330

This paper reports the development of global FDTD models incorporated with a quasi-real anisotropic ionosphere consisting of magnetized cold plasmas. Compared to the existing global models utilizing simple conductivity ionospheric profiles, the algorithms reported in this paper can sufficiently extend the global-scale electromagnetic simulations to much higher altitudes as the physics introduced by the spatially-varied ionospheric plasmas and the geomagnetic field can be fully included in calculations.

关键词： paper reports global FDTD extend the global-scale

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Photonic crystals in proton-exchanged LiNbO3 waveguides for photonic applications

Photonic crystals in proton-exchanged LiNbO3 waveguides for ...

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IEEE PhotonicsGlobal@Singapore, IPGC

作者： Deng Jun Jia Wei Vanga Sudheer Kumar Ching Eng Png Andrew A. Bettiol Aaron J. Danner Institute of High Performance Computing Agency for Science Technology and Research (ASTAR) Singapore Department of Electrical and Computer Engineering National University of Singapore Singapore Henan Key Laboratory of Laser and O pto-electric Information Technology Zhengzhou University Henan China Department of Physics National University of Singapore Singapore

Photonic crystals realized in LiNbO 3 have a great potential to reduce the size and increase the functionality of integrated optical devices. In order to accomplish these aims, fabrication know-how must be mastered yet it remains relatively uncharted. In this work we report the fabrication and optical characterization of photonic crystal structures in annealed proton exchanged (APE) LiNbO 3 waveguides. In our work, channel waveguides were fabricated by photolithography patterning followed by immersing LiNbO 3 wafers in molten benzoic acid at 235°C for 5 h. The thickness and the composition profiles of the APE waveguides were measured using the secondary ion mass spectroscopy (SIMS) method. The experimental characterization of the photonic crystal waveguides was performed and a photonic stop band with good sharpness can be observed from the transmission spectra.

关键词： Photonics Optical fibers Optical device fabrication Optical imaging Optical polarization

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Using spatial correlations in distributed video coding

Using spatial correlations in distributed video coding

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International Symposium on Artificial Intelligence and Signal Processing

作者： Fathy, Mahmood Haqqani, Mohammad High Performance Computing Lab. Computer Engineering Department Iran University of Science and Technology Tehran Iran

ISBN: (纸本)9781424498345

Distributed video coding (DVC) is a new paradigm of coding that makes very interest to itself in the past decade. It's usually based on temporal correlations between successive frames which are called key frames. But this approach failed for high object motion in a scene and need very complex decoder to cover it. In this paper we propose a novel technique to use spatial correlation instead of temporal correlation in a frame by dividing a single frame to two sub frames which one of them is used as a key frame for generate side information at the decoder. Simulation results show a significant improvement on rate distortion parameter in DVC schema. © 2011 IEEE.

关键词： Decoding

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Developing an Automated Mechanism for Cluster computing in computerized Classroom

Developing an Automated Mechanism for Cluster Computing in C...

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International Conference on Computational science (ICCS) on the Ascent of Computational Excellence

作者： Wang, Shuen-Tai Li, Chin-Hung Chang, Hsi-Ya Chen, Ying-Chuan Hsu, Ching-Hsien National Center for High-Performance Computing Taiwan Department of Computer Science and Information Engineering Chung Hua University Taiwan

Scientific computing has become one of the key players in the advance of modern science and technologies. In the meantime, due to the success of developments in processor fabrication, the computing power of Personal computer (PC) is not to be ignored as well. Lots of high throughput type of applications can be satisfied by using the current desktop PCs, especially for those in computerized classrooms, and leave the supercomputers for the demands from large scale high performance parallel computations. The goal of this work is to develop an automated mechanism for cluster computing to utilize the computing power such as resides in computerized classroom. The PCs in computerized classroom are usually setup for education and training purpose during the daytime, and shut down at night. After well deployment, these PCs can be transformed into a pre-configured cluster computing resource immediately without touching the existing education/training environment installed on these PCs. Thus, the training activities will not be affected by this additional activity to harvest idle computing cycles. To echo today's energy saving issues, a dynamic power management is also developed to minimize energy cost. This development not only greatly reduces the management efforts and time to build a cluster, but also implies the reduction of the power consumption by such a mechanism.

关键词： Personal computer cluster computing computerized classroom dynamic power management

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Implementation of a green power management algorithm for virtual machines on cloud computing

Implementation of a green power management algorithm for vir...

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Lecture Notes in computer science

作者： Yang, Chao-Tung Wang, Kuan-Chieh Cheng, Hsiang-Yao Kuo, Cheng-Ta Hsu, Ching-Hsien High-Performance Computing Laboratory Department of Computer Science Tunghai University Taichung 40704 Taiwan Department of Computer Science and Information Engineering Chung Hua University Hsinchu 300 Taiwan

ISBN: (纸本)9783642236402

With the development of electronic of government and business, the implementation of these services are increasing the demand for servers, each year a considerable number of the procurement server and out of the server are too old to provide better service. However, due to the speed of the server out of nowhere near the rate of increase, the continued expansion of the server, on behalf of our need to prepare more space, power, air conditioning, network, human and other infrastructure. Derived from these costs, long years, the often less than the purchase price of the server. And the provision of these services is actually quite energy-intensive, especially when the server is running at low utilization, the making idle resources, waste, which is caused by the energy efficiency of data centers the main reason for the low. Even in a very low load, such as 10% CPU utilization, the total power consumption is more than 50% in the peak. Similarly, if the disk, network, or any such resource is the bottleneck, it will increase the waste of other resources. The "Green" became a hot key word recently. And we aimed the topic and proposed power management approach with virtualization technology. © 2011 Springer-Verlag.

关键词： Virtualization

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