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RNA secondary structure prediction based on density-based clustering

ICIC Express Letters 2015年第7期9卷 1965-1970页

作者： Wang, Changwu Wang, Xiuqin Wang, Baowen Liu, Wenyuan Wei, Zhenzhen Li, Yongqiang School of Information Science and Engineering Yanshan University No. 438 Hebei Ave Qinhuangdao China The Key Laboratory for Computer Virtual Technology and System Integration of Hebei Province Yanshan University No. 438 Hebei Ave Qinhuangdao China Department of Information The First Hospital of Qinhuangdao No. 258 Hebei Ave Qinhuangdao China

The ribonucleic acid (RNA) secondary structure prediction has designed to characterize the ensemble of structures, instead of only computing the minimum free energy structure. Clustering methods are brought to aid in the characterization of the structure ensemble. These methods group the structures into a small number of clusters. A representative structure for each cluster is computed to characterize the central tendency for the structures in each cluster and used to predict the true secondary structure. This paper introduces a density based clustering with extensible radius dubbed ER-DBSCAN for handling varying density clustering. The basic idea of ER-DBSCAN is to use different values of radius for different densities. It starts from the highest density object towards the lowest density object, and the radius of the cluster is automatically adjusted during cluster expansion according to the density distribution and density variation. Our results indicate that ER-DBSCAN can detect and handle clusters of varying density, and cluster RNA secondary structures effectively. © 2015, ISSN 1881-803X.

关键词： RNA

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The study of a hierarchical hadoop architecture in multiple data centers environment

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Open Cybernetics and systemics Journal 2015年第1期9卷 131-137页

作者： Shengtao, Sun Aizhi, Wu Xiaoyang, Liu School of Information Science and Engineering Yanshan University QinhuangdaoHebei066004 China College of Vehicles and Energy Yanshan University QinhuangdaoHebei066004 China Data Industry Research Institute Limited Company QinhuangdaoHebei066004 China Key Laboratory for Computer Virtual Technology and System Integration of Hebei Province QinhuangdaoHebei066004 China

Hadoop is a reasonable tool for cloud computing in big data era and MapReduce paradigm may be a highly successful programming model for large-scale data-intensive computing application, but the conventional MapReduce model and Hadoop framework limit themselves to implement jobs within single cluster. Traditional single-cluster Hadoop may not suitable for situations when data and compute resources are widely distributed this paper focuses on the application of Hadoop across multiple data centers and clusters. A hierarchical distributed computing architecture of Hadoop is designed and the virtual Hadoop file system is proposed to provide global data view across multiple data centers. The job submitted by user can be decomposed automatically into several sub-jobs which are then allocated and executed on corresponding clusters by location-aware manner. The prototype based on this architecture shows encouraging results. © Shengtao et al.

关键词： MapReduce

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Dynamic spectrum allocation scheme with real-time traffic and its performance optimization

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ICIC Express Letters, Part B: Applications 2015年第8期6卷 2243-2250页

作者： Shi, Guoying Jin, Shunfu Li, Yongqiang School of Information Science and Engineering Yanshan University No. 438 Hebei Avenue Qinhuangdao China Key Laboratory for Computer Virtual Technology and System Integration of Hebei Province Yanshan University No. 438 Hebei Avenue Qinhuangdao China The First Hospital of Qinhuangdao No. 258 Wenhua Road Qinhuangdao China

Aiming at relieving the shortage problem of wireless frequency resource, sec- ondary users in cognitive radio networks occupy the spectrum hole opportunistically. In cognitive radio networks, primary users have preemptive priority for the licensed spectrum, and the data transmission of a secondary user is possible to be interrupted by a primary user at any time. For the applications with real-time traffic, the interrupted data is supposed to be discarded by the system. A continuous time queueing model with potential transmission interruption is established accordingly. By using the Laplace transform, the performance measures, such as the average latency, the normalized throughput and the spectrum switching ratio, are presented. The individually and socially optimal strategies are investigated with a non-cooperative game theory, and then a pricing policy for the secondary users is proposed. Experimental results show that the dynamic spectrum allocation scheme with real-time traffic can be optimized socially. © 2015, ICIC International.

关键词： Laplace transforms

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A load balancing algorithm for multi-root ONS

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Journal of Computational Information systems 2014年第7期10卷 2735-2742页

作者： Hao, Fengzhai Liu, Yongshan Chen, Wei College of Information Science and Engineering Yanshan University Qinhuangdao 066004 China The Key Laboratory for Computer Virtual Technology and System Integration of Hebei Province Yanshan University Qinhuangdao 066004 China Data Industry Research Lab. Qinhuangdao 066004 China

In order to solve the overload problem of root ONS in the EPC network, a load balancing algorithm based on multi-root ONS is proposed. Based on the proposed load balancing ONS (LB ONS) architecture, the ONS Root is defined to have two states, idle or busy. According to CPU utilization and memory utilization of the ONS Root and in combination with threshold controlling to periodically update the ONS Root states, which makes the requests coming from client applications be transferred to an ONS Root which is idle. Experiment results show that the algorithm can reduce query hops and query delays effectively and offer lookup service efficiently. © 2014 Binary Information Press.

关键词： Internet of things

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Edge collapse mesh simplification algorithm based on detail features preserving

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Journal of Computational Information systems 2014年第7期10卷 2883-2890页

作者： Jia, Qi Liu, Yongshan Gu, Xiaoying College of Information Science and Engineering Yanshan University Qinhuangdao 066004 China The Key Laboratory for Computer Virtual Technology and System Integration of Hebei Province Yanshan University Qinhuangdao 066004 China Data Industry Research Lab. Qinhuangdao 066004 China

The existing model simplification algorithm in simplified speed and quality can't reach a better compromise, so we present an improved quadric error metrics edge collapse mesh simplification algorithm. This algorithm makes the local region unevenness of vertex, the local region average area of vertex and edge length as constraint factors add to the edge collapse cost, by changing the order of the edge collapse to retain the important detail features of the original model. New vertex position is calculated on the different types of edge, keeping the boundary characteristics of the mesh model. Experimental results show that the improved algorithm not only runs faster, but also maintains a higher degree on the model feature region. © 2014 Binary Information Press.

关键词： Mesh generation

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Redundant filter-based efficient Minkwoski sum computation of polyhedra

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ICIC Express Letters 2014年第10期8卷 2939-2944页

作者： Zhang, Jianfei Guo, Xijuan Key Laboratory for Computer Virtual Technology and System Integration of Hebei Province College of Information Science and Engineering Yanshan University No. 438 West Section of Hebei Avenue Haigang District Qinhuangdao 066004 China College of Computer and Control Engineering Qiqihar University No. 42 Wenhua Street Qiqihar 161006 China

On the basis of the introduction to basic theory of Minkowski sum, we analyze the procedure of constructing the boundary of Minkowski sum and present a new method that can compute Minkowski sum of the polyhedra based on redundant information filtering. The method can filter the edges and facets that can be processed in the next computational stage, and reduce the number of the edges and facets that must be computed to improve the computing performance. The experiments show that the presented method has better performance including computing efficiency, accuracy and degeneration problems and fits for application domains that require high efficient and accurate computation. © 2014 ICIC International.

关键词： Information filtering

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Critical node measuring method improved based on pagerank and betweenness

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ICIC Express Letters, Part B: Applications 2016年第11期7卷 2381-2387页

作者： Wang, Lei Dong, Jun Ren, Jiadong College of Information Science and Engineering Yanshan University No. 438 Hebei Ave. Qinhuangdao066004 China The Key Laboratory for Computer Virtual Technology and System Integration of Hebei Province No. 438 Hebei Ave. Qinhuangdao066004 China E&A College Hebei Normal University of Science and Technology No. 360 Hebei Ave. Qinhuangdao066004 China

In software execution network, PageRank and betweenness methods are used to determine the importance of nodes. The experiment results show that the differences between nodes are not strong and cannot reflect the software nodes’ importance degree. In order to solve this problem, this paper adds the entropy weight method to the calculation of node weights, and puts the weights of nodes into the computing of two measuring methods above. Finally, we get the ranking result of nodes’ importance which means we can find out the critical nodes from top ones. Experimental results indicate that the method is efficient for critical node measuring. © 2016 ICIC International.

关键词： Surveying

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Mining weighted frequent traversal pattern from software executing graph

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ICIC Express Letters 2015年第11期9卷 2893-2900页

作者： He, Haitao Yin, Tengteng Pei, Caiyan Wu, Hongfei Ren, Jiadong College of Information Science and Engineering No. 438 West Hebei Ave. Qinhuangdao China The Key Laboratory for Computer Virtual Technology and System Integration of Hebei Province Yanshan University No. 438 West Hebei Ave. Qinhuangdao China School of Mathematics and Information Science and Technology Hebei Normal University of Science and Technology No. 360 West Hebei Street Qinhuangdao China

Mining important patterns in complex software executing network plays an important role in analyzing software security. The general sequential pattern mining algorithms may lead to poor performance due to the lack of consideration on the continuous property of software path traversals and the different importance of functions. To address the issue, a novel approach called weighted frequent traversal pattern miner (WFTPMiner) to mine weighted frequent traversal pattern from software executing graph is presented in this paper. In WFTPMiner, weighted software executing graph (WSEG) is modeled firstly. Secondly, software path traversals are extracted from WSEG by depthfirst- search (DFS) strategy. Thirdly, according to continuity characteristics of software path traversals, a potential frequent suffix sequence tree (PFSS-Tree) is defined to store the potential weighted frequent traversal patterns. A pruning strategy is adopted by PFSSTree. The pruning strategy can prune infrequent patterns effectively. The experimental results show that WFTPMiner has better efficiency compared with some previous algorithms. © 2015 ICIC International.

关键词： Forestry

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BAT: Mining Binary-API Topic for Multi-service Application Development

BAT: Mining Binary-API Topic for Multi-service Application D...

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International Conference on computer Supported Cooperative Work in Design

作者： Pengfei He Linlin Liu Dianlong You Limin Shen Zhen Chen School of Information Science and Engineering Yanshan University Qinhuangdao China National Science Libraries Chinese Academy of Sciences Beijing China The Key Laboratory for Computer Virtual Technology and System Integration of Hebei Province Qinhuangdao China

With the growing popularity of API-driven multiservice application (mashup) development, the burgeoning web APIs have left developers drowning in the sea of web API selections. Matching developers with the most appropriate APIs is the key to improving user satisfaction and promoting more popular web applications. As a result, more and more researchers pay attention to web API recommender systems based on collaborative filtering. However, employing collaborative filtering to recommend APIs is challenging due to the severe sparsity of mashup and API interactions. To address this problem, we propose a probabilistic generative model, called the Binary-API Topic model (BAT), to parameterize mashups and APIs. Technically, BAT is equipped with a mechanism to extract binary-APIs and predict unknown pairwise interactions. To improve generality and capture more relevance from a limited number of interactions, we learn binary-API topics by directly modeling the generation of API co-occurrence patterns across the repository (all mashup collections from ***). The main advantage of BAT is that it preserves API co-occurrence patterns in model learning and exploits the rich global relevance. Finally, through extensive experiments, we demonstrate that BAT can achieve the highest performance on the sparse real-world data set.

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Performance analysis of synchronization buffering mechanism in peer-to-peer live streaming systems

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ICIC Express Letters, Part B: Applications 2012年第6期3卷 1665-1672页

作者： Jin, Shunfu Liu, Na Ma, Zhanyou College of Information Science and Engineering Yanshan University No. 438 Hebei Avenue Qinhuangdao 066004 China Key Laboratory for Computer Virtual Technology and System Integration of Hebei Province Yanshan University No. 438 Hebei Avenue Qinhuangdao 066004 China College of Science Yanshan University No. 438 Hebei Avenue Qinhuangdao 066004 China

In the peer-to-peer (P2P) live streaming systems, a single stream is decomposed into multiple sub-streams. For the participating nodes, data blocks of different sub-streams are stored in different sub-buffers for synchronization, then forwarded and assembled to the original video stream in chronological order. In this paper, regarding the sub-buffers as multiple queues with homogeneous Poisson arrival processes, the data block forwarding procedure as a polling service, the forwarding suspension in an empty sub-buffer as a service delay state, a symmetric polling model is constructed. By using the method of embedded Markov chain, the mean queueing length and the probability for one queue to be empty when it is visited are derived in steady-state. Moreover, the performance measures in terms of average synchronization buffering length and video continuity level are obtained accordingly. Finally, numerical results are given to demonstrate that an appropriate number of sub-streams and a reasonable time limit for forwarding suspension can enhance the system performance.© 2012 ISSN 2185-2766.

关键词： Synchronization

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