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IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology (CIBCB)

作者： Fa Zhang Lin Xu Jingchun Chen Zhiyong Liu Bo Yuan Key Laboratory of Computer System and architecture the Institute of Computing Technology Chinese Academy and Sciences China Graduate School Chinese Academy and Sciences China Department of Biomedical Informatics Ohio State Uinversity USA National Natural Science Foundation China

Recently, large-scale protein-protein interactions were recovered using the similar two-hybrid system for the model systems. This information allows us to investigate the protein interaction network from a systematic point of view. However, experimentally determined interactions are susceptible to errors. A previous assessment estimated that only ~10% of the interactions can be supported by more than one independent experiment, and about half of the interactions may be false positives. These false positives might unnecessarily link unrelated proteins, resulting in huge apparent interaction clusters, which complicate elucidation for the biological importance of these interactions. Address this problem, we present an approach to integrate, assess and characterize all available protein-protein interactions in model organisms yeast and fly. We first integrate all available protein-protein interaction databases of yeast and fly, and merge all the datasets. We then use machine learning techniques to score the reliability for each interaction, and to rigorously validate the scoring scheme of yeast protein-protein interactions from different aspects. Our results show that this scoring scheme provides a good basis for selecting reliable protein-protein interaction dataset

关键词： Proteins Fungi Databases Electronics packaging Machine learning Genetics Laboratories Biomedical computing computer architecture Biomedical informatics

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Multiple Coupling Effects Oriented Path Delay Test Generation

Multiple Coupling Effects Oriented Path Delay Test Generatio...

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26th IEEE VLSI Test Symposium (VTS 2008)

作者： Minjin Zhang Huawei Li Xiaowei Li Graduate School of Chinese Academy of Sciences Beijing China Key Laboratory of Computer System and Architecture Chinese Academy of Sciences Beijing China Academy of Sciences Key Laboratory of Computer System and Architecture Institute of Computing Technology Chinese Academy and Sciences Beijing China

We propose a two-phase test generation method to generate patterns targeting maximal path delay caused by multiple crosstalk effects. A timing analysis method based on transition map is proposed to manage the timing information of aggressor lines and victim lines in the first phase, followed by an ordinary ATPG engine with a few alterations in the second phase. This two-phase method avoids complex timing processing in ATPG algorithm. Using transition map instead of timing window in timing analysis, our method can more efficiently calculate the accumulative crosstalk-induced delay and find the sub-paths which cause maximal coupling effects. We can trade off accuracy and efficiency by controlling the size of timescale used in transition map, which makes this approach highly scalable.

关键词： Delay effects Testing Timing Test pattern generators Crosstalk Automatic test pattern generation Information analysis Information management Engines Cause effect analysis

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A Highly Efficient Inter-domain Communication Channel

A Highly Efficient Inter-domain Communication Channel

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International Conference on computer and Information Technology (CIT)

作者： Hongyong Zang Kuiyan Gu Yaqiong Li Yuzhong Sun Dan Meng Chinese Academy of Sciences Beijing China Institute of Computing Technology Key Laboratory of Computer System and Architecture Institute of Computing Technology Chinese Academy and Sciences Beijing China Dongxin Geology Research Institute of Shengli Oilfield Dongying Shandong China

With virtual machine technology, distributed services deployed in multiple cooperative virtual machines, such as multi-tier Web services, may reside on one physical machine. This situation requires an efficient inter-domain communication channel, and meanwhile transparency and security should be guaranteed, for diverse existing distributed applications are serving on plenty of machines. In this paper, we have implemented a highly efficient inter-domain communication channel, called SChannel, with full transparency to both user applications and network protocol stack, and security between guest domains on Xen platform. Between two co-resident domains, SChannel establishes a two-way shared memory channel with elastic size, which is set up using static shared memory mechanism, instead of high-cost dynamic shared memory. Furthermore, SChannel avoids one additional copy from the shared data channel on the receiver domain side. In our evaluation using a number of standard benchmarks, SChannel increases the throughput 5 times than standard inter-domain mechanism offered by the hypervisor. Compared with other typical transparent inter-domain communication mechanism, SChannel achieves approximately 44.5% improvement of throughput, and reduces more than 3500 CPU cycles per packet.

关键词： Communication channels Virtual machine monitors Virtual machining Protocols Throughput Hardware Data security Costs Distributed computing Physics computing

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Find Your Online Social Friends from Mobile Internet Traffic

Find Your Online Social Friends from Mobile Internet Traffic

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IEEE International Conference on Network Infrastructure and Digital Content (IC-NIDC)

作者： Yi Zhang Yuanyuan Qiao Yanting Zhang Nanfei Shu Yizhe Song Jie Yang Beijing Key Laboratory of Network System Architecture and Convergence Beijing University of Posts and Telecommunications Beijing China Technology Research Institute Aisino Corporation Beijing China School of Electronic Engineering and Computer Science Queen Mary University of London London England

Increasingly more mobile Internet traffic is produced which contains ample personal information related to user mobility and website browsing behavior. Prior research has attempted to recommend friends based on Global Position system (GPS) in location based social networks (LBSN). However, the study of friend recommendation in general social network according to position from the base station is relatively understudied. This paper introduces a novel feature set extracted from mobile Internet traffic according to base station location and Uniform Resource Locator (URL). We train classification models using these features to predict friendship between pairs of Weibo users. Results show that both base station location and URL when acted alone can already effectively reflect friendships even in general social network. We further show that by fusing the two features together, the model obtains even better performance. Finally, we demonstrate that the location and URL features can improve prediction performance than only using the common friends.

关键词： Uniform resource locators Feature extraction Social network services Base stations Internet Global Positioning system Predictive models

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A survey on edge computing systems and tools

arXiv

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arXiv 2019年

作者： Liu, Fang Tang, Guoming Li, Youhuizi Cai, Zhiping Zhang, Xingzhou Zhou, Tongqing School of Data and Computer Science Sun Yat-sen University GuangzhouGuangdong China Key Laboratory of Science and Technology on Information System Engineering National University of Defense Technology ChangshaHunan China School of Compute Science and Technology Hangzhou Dianzi University China College of Computer National University of Defense Technology ChangshaHunan China State Key Laboratory of Computer Architecture Institute of Computing Technology Chinese Academy of Sciences China

—Driven by the visions of Internet of Things and 5G communications, the edge computing systems integrate computing, storage and network resources at the edge of the network to provide computing infrastructure, enabling developers to quickly develop and deploy edge applications. Nowadays the edge computing systems have received widespread attention in both industry and academia. To explore new research opportunities and assist users in selecting suitable edge computing systems for specific applications, this survey paper provides a comprehensive overview of the existing edge computing systems and introduces representative projects. A comparison of open source tools is presented according to their applicability. Finally, we highlight energy efficiency and deep learning optimization of edge computing systems. Open issues for analyzing and designing an edge computing system are also studied in this survey. Copyright © 2019, The Authors. All rights reserved.

关键词： Energy efficiency

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Enhanced LCCG: A novel test clock generation scheme for faster-than-at-speed delay testing

Enhanced LCCG: A novel test clock generation scheme for fast...

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Asia and South Pacific Design Automation Conference

作者： Songwei Pei Ye Geng Huawei Li Jun Liu Song Jin Beijing University of Chemical Technology Beijing 100029 China Key Laboratory of Computer System and Architecture Institute of Computing Technology Chinese Academy of Sciences Beijing CN School of Computer and Information University of Technology Hefei China School of Electrical and Electronic Engineering North China Electric Power University Baoding China

ISBN: (纸本)9781479977932

On-chip faster-than-at-speed delay testing provides a promising way for small delay defect detection. However, the frequency of on-chip generated test clock would be impacted by process variations. Hence, it requires determining the actual frequency of generated test clock to ensure the effectiveness of faster-than-at-speed delay testing. In this paper, we present a novel test clock generation scheme, namely Enhanced LCCG, for faster-than-at-speed delay testing. In the proposed scheme, faster-than-at-speed test clock is firstly generated by configuring the corresponding control information specified in the test pattern into Enhanced LCCG. Then, by constructing oscillation paths and counting the corresponding oscillation iteration numbers, the actual frequency of test clock can be measured and calculated with high resolution. Experimental results are presented to validate the proposed method.

关键词： Delays Clocks Oscillators Testing Frequency measurement Logic gates

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A parallel optimization model for massive data stream application

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Ruan Jian Xue Bao/Journal of Software 2009年第SUPPL. 1期20卷 23-33页

作者： Sun, Xiao-Juan Sun, Ning-Hui Lei, Bin Key Laboratory of Technology in Geo-Spatial Information Processing and Application System Institute of Electronics The Chinese Academy of Sciences Beijing 100190 China Key Laboratory of Computer System and Architecture Institute of Computing Technology The Chinese Academy of Sciences Beijing 100190 China

While computing is entering a new phase in which CPU improvements are driven by the addition of multiple cores on a single chip, rather than higher frequencies. Parallel processing on these systems is in a primitive stage, and requires the explicit use and knowledge of underlying thread architecture. Based on the features of massive data stream application, this paper proposes three-level pipelining programming model of multithreading system, which realizes the new synchronization mechanism with no contention of shared structures and is capable to provide differential service for data streams. Then the paper applies the new model to remote sensing information processing system and backbone network intrusion detection system, and evaluates the improved system on several multicore platforms. In performance analysis, the optimized effects of backbone network intrusion detection system are evaluated in several aspects of throughput scalability on both SPARC T1 and x86 platforms, the impacts of different multithreading mapping methods on throughput, and the comparison of response time and service quality before and after optimization. The experimental results show that the system throughput has good scalability on both platforms, the values of response time are greatly improved and the prioritized streams achieve better response time with the differential service mechanism. © by Institute of Software, the Chinese Academy of Sciences. All rights reserved.

关键词： Metadata

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Optimizing MPI Alltoall Communication of Large Messages in Multicore Clusters

Optimizing MPI Alltoall Communication of Large Messages in M...

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IEEE International Conference on Parallel and Distributed Computing, Applications and Technologies (PDCAT)

作者： Qiang Li Zhigang Huo Ninghui Sun Graduate University of Chinese Academy of Sciences Beijing China Key Laboratory of Computer System and Architecture Chinese Academy of Sciences Beijing China Institute of Computing Technology Chinese Academy of Sciences Beijing China Institute of Computing Technology Chinese Academy of Sciences Beijing CN

MPI All to all communication is widely used in many high performance computing (HPC) applications. In All to all communication, each process sends a distinct message to all other participating processes. In multicore clusters, processes within a node simultaneously contend for the same network resource of the node in All to all communication. However, many small synchronization messages are required in All to all communication of large messages. With the contention, their latency is orders of magnitude larger than that without contention. As a result, the synchronization overhead is significantly increased and accounts for a large proportion to the whole latency of All to all communication. In this paper, we analyse the considerable overhead of synchronization messages. Base on the analysis, an optimization is presented to reduce the number of synchronization messages from 3N to 2¡ÌN. Evaluations on a 240-core cluster show that the performance is improved by almost constant ratio, which is mainly determined by message size and independent of system scale. The performance of All to all communication is improved by 25% for 32K and 64K bytes messages. For FFT application, performance is improved by 20%.

关键词： Synchronization Protocols Multicore processing Receivers Bandwidth Program processors Benchmark testing

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Integrating DBMSs as a Read-Only Execution Layer into Hadoop

Integrating DBMSs as a Read-Only Execution Layer into Hadoop

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IEEE International Conference on Parallel and Distributed Computing, Applications and Technologies (PDCAT)

作者： Mingyuan An Yang Wang Weiping Wang Ninghui Sun Chinese Academy of Sciences Beijing China Institute of Computing Technology Chinese Academy and Sciences Beijing China University of the Chinese Academy of Sciences Beijing Beijing CN Key Laboratory of Computer System and Architecture Institute of Computing Technology Chinese Academy and Sciences Beijing China

To obtain the efficiency of DBMS, HadoopDB combines Hadoop and DBMS, and claims the superiority over Hadoop in terms of performance. However, the approach of HadoopDB is simply putting Map Reduce onto unmodified single-machined DBMSs which has several obvious weaknesses. In essence, HadoopDB is a parallel DBMS with fault tolerance, which incurs unnecessary overhead due to the DBMS legacy. Instead of augmenting DBMS with Hadoop techniques, we propose a new system architecture integrating modified DBMS engines as a read-only execution layer into Hadoop, where DBMS plays a role of providing efficient read-only operators rather than managing the data. Besides the obtained efficiency from DBMS engine, there are other advantages. The modified DBMS engine is able to directly process data from the HDFS (Hadoop Distributed File system) files at the block level, which means that the data replication can be handled by HDFS naturally, and the block-level parallelism is easily achieved. The global index access mechanism is added according to the Map Reduce paradigm. The data loading speed is also guaranteed by directly writing the data into HDFS with simplified logic. Experiments show that our system outperforms both original Hadoop and HadoopDB styled system.

关键词： Engines Fault tolerance Fault tolerant systems Indexes Loading Parallel processing

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Trajectory Design for Energy Harvesting UAV Networks: A Foraging Approach

Trajectory Design for Energy Harvesting UAV Networks: A Fora...

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IEEE Conference on Wireless Communications and Networking

作者： Xuanlin Liu Mingzhe Chen Sihua Wang Walid Saad Changchuan Yin Beijing Key Laboratory of Network System Architecture and Convergence Beijing Laboratory of Advanced Information Network Beijing University of Posts and Telecommunications Beijing China Department of Electrical Engineering Princeton University Princeton NJ USA Wireless@VT Bradley Department of Electrical and Computer Engineering Virginia Tech Blacksburg VA USA

ISBN: (数字)9781728131061

ISBN: (纸本)9781728131078

In this paper, the problem of trajectory design for energy harvesting unmanned aerial vehicles (UAVs) is studied. In the considered model, the UAV acts as a moving base station to serve the ground users, while collecting energy from the charging stations located at the center of a user group. Meanwhile, to serve ground users and harvest energy, the UAV must be examined and repaired regularly. In consequence, it is necessary to optimize the trajectory design of the UAV while jointly considering the maintenance costs, the number of users that are served by the UAV, and the energy consumption and harvesting. To capture the relationship among these factors, we first model the completion of service and the harvested energy as reward, and the energy consumption during the deployment as cost. Then, the deployment profitability is defined as the reward to the cost of the UAV trajectory. Based on this definition, the trajectory design problem is formulated as an optimization problem whose goal is to maximize the deployment profitability of the UAV. To solve this problem, a foraging algorithm is proposed to find the optimal trajectory so as to maximize the deployment profitability. The proposed algorithm can find the optimal trajectory for the UAV with a polynomial time complexity. Fundamental analysis shows that the proposed algorithm can achieve the maximal deployment profitability. Simulation results show that the proposed algorithm can effectively reduce the operation time and achieve up to 25.6% gain in terms of the deployment profitability compared to Q-learning algorithm.

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