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On the Use of Binary Trees for DNA Hydroxymethylation Analysis 17th

On the Use of Binary Trees for DNA Hydroxymethylation Analys...

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17th international conference on algorithms and architectures for parallel processing (ica3pp)

作者： Gonzalez, Cesar Perez, Mariano Orduna, Juan M. Chaves, Javier Garcia, Ana-Barbara Univ Valencia Dept Informat Avda Univ S-N Valencia 46100 Spain CIBERDEM Carlos III Hlth Inst INCLIVA Hlth Res Inst Avda Menendez Pelayo 4 Accesorio Valencia 46010 Spain

ISBN: (纸本)9783319654829;9783319654812

DNA methylation (mC) and hydroxymethylation (hmC) can have a significant effect on normal human development, health and disease status. Hydroxymethylation studies require specific treatment of DNA, as well as software tools for their analysis. In this paper, we propose a parallel software tool for analyzing the DNA hydroxymethylation data obtained by TAB-seq. the software is based on the use of binary trees for searching the different occurrences of methylation and hydroxymethylation in DNA samples. the binary trees allow to efficiently store and access the information about the methylation of each methylated/hydroxymethylated cytosines in the samples. Evaluation results shows that the performance of the application is only limited by the computer input/output bandwidth, even for the case of very long samples.

关键词： High performance computing DNA hydroxymethylation parallel pipeline

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Massively parallel Sequence Alignment with BLAST through Work Distribution Implemented Using PCJ Library 17th

Massively Parallel Sequence Alignment with BLAST Through Wor...

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17th international conference on algorithms and architectures for parallel processing (ica3pp)

作者： Nowicki, Marek Bzhalava, Davit Bala, Piotr Nicolaus Copernicus Univ Fac Math & Comp Sci Chopina 12-18 PL-87100 Torun Poland Karolinska Inst Dept Lab Med F46 S-14186 Stockholm Sweden Univ Warsaw Interdisciplinary Ctr Math & Computat Modelling Pawinskiego 5a PL-02106 Warsaw Poland

ISBN: (纸本)9783319654829;9783319654812

this article presents massively parallel execution of the BLAST algorithm on supercomputers and HPC clusters using thousands of processors. Our work is based on the optimal splitting up the set of queries running with the non-modified NCBI-BLAST package for sequence alignment. the work distribution and search management have been implemented in Java using a PCJ (parallel Computing in Java) library. the PCJ-BLAST package is responsible for reading sequence for comparison, splitting it up and start multiple NCBI-BLAST executables. We also investigated a problem of parallel I/O and thanks to PCJ library we deliver high throughput execution of BLAST. the presented results show that using Java and PCJ library we achieved very good performance and efficiency. In result, we have significantly reduced time required for sequence analysis. We have also proved that PCJ library can be used as an efficient tool for fast development of the scalable applications.

关键词： Sequence alignment NGS Next Generation Sequencing parallel programming Java BLAST NCBI-BLAST PCJ

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parallel Multi-objective Optimization for High-Order Epistasis Detection 17th

Parallel Multi-objective Optimization for High-Order Epistas...

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17th international conference on algorithms and architectures for parallel processing (ica3pp)

作者： Gallego-Sanchez, Daniel Granado-Criado, Jose M. Santander-Jimenez, Sergio Rubio-Largo, Alvaro Vega-Rodriguez, Miguel A. Univ Extremadura Caceres Spain Univ Lisbon Lisbon Portugal Univ NOVA Lisboa Lisbon Portugal

ISBN: (纸本)9783319654829;9783319654812

Many studies have shown that there is a direct relationship between Single Nucleotide Polymorphisms (SNPs) and the appearance of complex diseases, such as Alzheimer's or Parkinson's. However, recent advances in the Study of the Complete Genome Association indicate that the relationship between SNPs and these diseases goes beyond a simple one-to-one relationship, that is, the appearance of multiple SNPs (epistasis) influences the appearance of these diseases. In this sense, this work proposes the application of the NSGA-II multi-objective algorithm for the detection of epistasis of multiple loci in a database with 31,341 SNPs. Moreover, a parallel study has been performed to reduce the execution time of this problem. Our implementation not only achieves a reasonable good parallel performance and scalability, but also its biological significance overcomes other approaches published in the literature.

关键词： parallelism NSGA-II Epistasis SNP

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Pipelining Computation and Optimization Strategies for Scaling GROMACS on the Sunway Many-Core Processor 17th

Pipelining Computation and Optimization Strategies for Scali...

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17th international conference on algorithms and architectures for parallel processing (ica3pp)

作者： Yu, Yang An, Hong Chen, Junshi Liang, Weihao Xu, Qingqing Chen, Yong Univ Sci & Technol China Hefei Anhui Peoples R China Texas Tech Univ Dept Comp Sci Lubbock TX 79409 USA

ISBN: (纸本)9783319654829;9783319654812

the increasing gap between plentiful computing elements and limited memory bandwidth makes it increasingly difficult and sometimes even infeasible for HPC community to port more applications onto many-core processor architectures. the Sunway many-core processor SW26010 used to build the Sunway TaihuLight System contains a total of 260 heterogeneous cores. All these cores can be divided into 4 core groups (CGs). Each CG includes a Management processing Element (MPE) core and 64 Computing processing Elements (CPEs) cores. In this paper, we refactor an important molecular dynamics (MD) application GROMACS on the Sunway Taihulight system. By rewriting the compute-intensive kernel of GROMACS, we exploit a suitable parallelism for CPE cluster and implement pipelining computation between MPE and CPE cluster. Optimization strategies including the efficient use of scratchpad, the software-emulated cache and a hybrid parallel algorithm are adopted to solve the challenging memory bandwidth limitation. When comparing the refactored version using MPE and 64 CPEs with the original ported version using only MPE, we achieve a 16x speedup for the compute-intensive kernel. For simulating a molecule with 3 million atoms, we currently have managed to scale to 798,720 cores. Moreover, we analyze the adaptability of our mapping and optimization strategies for solving the memory bandwidth limitation when refactoring a real-world application on the Sunway heterogeneous many-core processor system.

关键词： Sunway TaihuLight system GROMACS parallel model Performance optimization Bandwidth competition Adaptability

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the Impact of international Inter-City Investment on Enterprises Performance: Pluralistic Interpretation of Geographical Death 17th

The Impact of International Inter-City Investment on Enterpr...

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17th international conference on algorithms and architectures for parallel processing (ica3pp)

作者： Zhan, Yanghao Chen, Yan Zhai, Ruirui Beijing Univ Posts & Telecommun Beijing Peoples R China

ISBN: (纸本)9783319654829;9783319654812

this paper aims to test the impact of inter-city investment on enterprises performance. By using a panel dataset of Chinese firms which have invested in 43 countries and regions over the of 2003-2009 and gravity model, we find that institutional distance is favorable to Chinas outward direct investment, which implies that the Chinese multinationals dont seem willing to enter those countries that have similar institutions with their home country, in this sense, Chinese enterprises outward direct investment can be interpreted as being driven by the motivation of institutional escape. Technology distance displays an Inversed-U shape which suggests some technical distance is the premise for ODI and may reflect the fact of simultaneous existence of both the technology utilization ODI and the technology-seeking ODI of China. Geographical distance has no significant impact on Chinas outward direct investment which supports the proposition of death of distance. these findings point to the importance of going beyond firm boundary to consider various distances between home and host countries in making investment decisions, which not only overcome the defects of the existing studies, but also propose new theoretical explanations for the phenomenon that Chinese enterprises are still capable of ODI even when the ownership advantages are missing. According to the results of this paper, Chinese enterprises should choose to invest in the countries with large institutional distance, small economic and medium technical distance from the home country, and, at the same time, they should not bother geographical distance too much.

关键词： ODI Enterprises performance Geographical distance

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An Algorithm to Embed a Family of Node-Disjoint 3D Meshes into Locally Twisted Cubes 1

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14th international conference on algorithms and architectures for parallel processing (ica3pp)

作者： You, Lantao Han, Yuejuan Soochow Univ Suzhou Ind Pk Inst Serv Outsourcing Suzhou 215000 Peoples R China Soochow Univ Ctr Informat Dev & Management Suzhou 215000 Peoples R China

ISBN: (数字)9783319111940

ISBN: (纸本)9783319111940;9783319111933

In this paper, embeddings of a family of 3D meshes in locally twisted cubes are studied. Let LTQ(n)(V, E) denotes the n-dimensional locally twisted cube. We find two major results in this paper:(1) For any integer n >= 4, two node-disjoint 3D meshes of size 2 x 2 x 2(n-3) can be embedded into LTQ(n) with dilation 1 and expansion 2. (2) For any integer n = 6, four node-disjoint 4x2x2(n-5) meshes can be embedded into LTQ(n) with dilation 1 and expansion 4. Further, an embedding algorithm can be constructed based on our embedding method. the obtained results are optimal in the sense that the dilations of the embeddings are 1.

关键词： Interconnection networks locally twisted cube 3D mesh embedding parallel computing

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A Binary Code Sequence Based Tracking Algorithm in Wireless Sensor Networks 19th

A Binary Code Sequence Based Tracking Algorithm in Wireless ...

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19th international conference on algorithms and architectures for parallel processing (ica3pp)

作者： Zhang, Yang Ren, Qianqian Pan, Yu Li, Jinbao Heilongjiang Univ Key Lab Database & Parallel Comp Heilongjiang Pro Harbin Peoples R China Heilongjiang Univ Key Lab Elect Engn Coll Heilongjiang Prov Harbin Peoples R China Heilongjiang Univ Sch Comp Sci & Technol Harbin Peoples R China

ISBN: (纸本)9783030389611;9783030389604

this paper proposes a binary code sequence based tracking algorithm in wireless sensor network. the proposed algorithm can release the influence of sensed data on localization results via building the map between target's occurrence region and a binary code sequence. To solve the ambiguity problem existing in occurrence region determination, the paper further gives a Voronoi diagram based location refinement algorithm. the simulation results show the tracking results under difference trajectories.

关键词： Target localization RSSI Voronoi

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algorithms and architectures for parallel processing 1

引用

丛书名： Lecture Notes in Computer Science

1000年

作者： Shadi Ibrahim Kim-Kwang Raymond Choo Zheng Yan Witold Pedrycz

ISBN: (数字)9783319654829

ISBN: (纸本)9783319654812

this book constitutes the proceedings of the 17th international conference on algorithms and architectures for parallel processing, ica3pp 2017, held in Helsinki, Finland, in August 2017.;the 25 full papers presented were carefully reviewed and selected from 117 submissions. they cover topics such as parallel and distributed architectures; software systems and programming models; distributed and network-based computing; big data and its applications; parallel and distributed algorithms; applications of parallel and distributed computing; service dependability and security in distributed and parallel systems; service dependability and security in distributed and parallel systems; performance modeling and evaluation.;this volume also includes 41 papers of four workshops, namely: the 4th international Workshop on Data, Text, Web, and Social Network Mining (DTWSM 2017), the 5th international Workshop on parallelism in Bioinformatics (PBio 2017);, the First international Workshop on Distributed Autonomous Computing in Smart City (DACSC 2017), and the Second international Workshop on Ultrascale Computing for Early Researchers (UCER 2017).

关键词： Algorithm Analysis and Problem Complexity Software Engineering Computer Communication Networks Information Systems Applications (incl. Internet)

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TAMM: A New Topology-Aware Mapping Method for parallel Applications on the Tianhe-2A Supercomputer 18th

TAMM: A New Topology-Aware Mapping Method for Parallel Appli...

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18th international conference on algorithms and architectures for parallel processing (ica3pp)

作者： Chen, Xinhai Liu, Jie Li, Shengguo Xie, Peizhen Chi, Lihua Wang, Qinglin Natl Univ Def Technol Sci & Technol Parallel & Distributed Proc Lab Changsha 410073 Peoples R China Hunan Inst Traff Engn Inst Adv Sci & Technol Hengyang 421001 Peoples R China

ISBN: (纸本)9783030050511;9783030050504

With the increasing size of high performance computing systems, the expensive communication overhead between processors has become a key factor leading to the performance bottleneck. However, default process-to-processor mapping strategies do not take into account the topology of the interconnection network, and thus the distance spanned by communication messages may be particularly far. In order to enhance the communication locality, we propose a new topology-aware mapping method called TAMM. By generating an accurate description of the communication pattern and network topology, TAMM employs a two-step optimization strategy to obtain an efficient mapping solution for various parallel applications. this strategy first extracts an appropriate subset of all idle computing resources on the underlying system and then constructs an optimized one-to-one mapping with a refined iterative algorithm. Experimental results demonstrate that TAMM can effectively improve the communication performance on the Tianhe-2A supercomputer.

关键词： High performance computing systems Topology-aware mapping Communication pattern Network topology

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ParaMoC: A parallel Model Checker for Pushdown Systems 19th

ParaMoC: A Parallel Model Checker for Pushdown Systems

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19th international conference on algorithms and architectures for parallel processing (ica3pp)

作者： Wei, Hansheng Ye, Xin Shi, Jianqi Huang, Yanhong East China Normal Univ Natl Trusted Embedded Software Engn Technol Res C Shanghai Peoples R China Res Ctr Hardware Software Codesign Technol & Applicat Eng Shanghai Peoples R China Shanghai Key Lab Trustworthy Comp Shanghai Peoples R China LIPN Paris France Paris Univ 7 Paris France

ISBN: (纸本)9783030389611;9783030389604

Model checking on Pushdown Systems (PDSs) has been extensively used to deal with numerous practical problems. However, the existing model checkers for pushdown systems are executed on the central processing unit (CPU), the performance is hampered by the computing power of the CPU. Compared with the CPU, the graphics processing unit (GPU) has more processing cores, which are suitable and efficient for parallel computing. therefore, it is very attractive to accelerate model checking of PDSs on the GPU. In this paper, we present a new parallel model checker, named ParaMoC, to speed up the performance of model checking problems for pushdown systems (PDSs). Moreover, we focus on how to use Graphics processing Units (GPUs) to accelerate the reachability verification and the LTL model checking of PDSs. the ParaMoC running on a state-of-the-art GPU can be 100 times faster than the traditional PDS model checker.

关键词： Graphics processing unit

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