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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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Performance evaluation of an enhanced Ethernet energy saving mechanism in IEEE 802.3az

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Journal of Information and Computational Science 2014年第5期11卷 1605-1613页

作者： Zhi, Shengyang Jin, Shunfu Meng, Chao College of Information Science and Engineering Yanshan University Qinhuangdao 066004 China Key Laboratory for Computer Virtual Technology and System Integration of Hebei Province Qinhuangdao 066004 China

In order to reduce the energy consumption and improve the response performance, by introducing the strategies of sleep-delay, pre-awake and split timing to IEEE 802.3az, an enhanced Ethernet energy saving mechanism is proposed. Considering the digital nature of modern communications, a discrete-time queueing model with multiple-vacation and N-strategy is built. With the method of an embedded Markov chain, we evaluate the energy saving efficiency of the system and the response performance of the data frames mathematically. Numerical experiments and simulation results show that, in the enhanced Ethernet energy saving mechanism, the average packet latency is reduced, while the energy saving ratio is satisfactory. © 2014 by Binary Information Press.

关键词： Energy conservation

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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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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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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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Inference rules based on XML functional dependency and XML multi-valued dependency

Inference rules based on XML functional dependency and XML m...

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2014 International Conference on Future Information Engineering and Manufacturing Science(FIEMS 2014)

作者： Zhongping Zhang Shanshan Shi The School of Information Science and Engineering Yanshan University The Key Laboratory for Computer Virtual Technology and System Integration of Hebei Province

ISBN: (纸本)9781138026445

There not only exists the relation of the functional dependency and multi-valued dependency in XML data constraint,but also exists the relation of data dependency obtained only from a certain existing relationship instance that is *** reducing data redundancy,in this paper,the concepts of XML functional dependency and XML multi-valued dependency based on the path expression in the Document Type Definition are *** then the inference rules on the condition of the coexistence of functional dependency and multi-valued dependency in XML are ***,the validity and completeness of the inference rules are *** above-mentioned fundamentally solves the problems of implication of functional dependency and multi-valued dependency in XML data,laying a theoretical foundation for XML database design.

关键词： Extensible Markup Language inference rules functional dependency multi-valued dependency

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Directional relation reasoning based on boundary sensitive model in three-dimensional space

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Journal of Computational Information systems 2015年第17期11卷 6345-6354页

作者： Kong, Dehan Liu, Yongshan Ma, Junlei Wang, Yuzheng Han, Ameng Department of Information Science and Engineering Yanshan University Qinhuangdao China The Key Laboratory for Computer Virtual Technology and System Integration of Hebei Province Yanshan University Qinhuangdao China Data Industry Research Lab Qinhuangdao China Telecommunications Engineering with Management Beijing University of Posts and Telecommunications Beijing China Information Technology Office of Yanshan University Qinhuangdao China

In three-dimension space, with the minimum bounding rectangular (MBR) of any type of object's projections in xoy and xoz planes, there are four possible types of projection: minimum bounding rectangular, horizontal line, vertical line and point, then a boundary sensitive directional relationship matrix model (BSDRM) is proposed, the model can unified representation direction relations between objects of the four different types of projection, further, the three dimensional direction relation is inferred by combining the two direction matrixes in plane xoy and plane xoz. Based on this model, single direction relation reasoning table and multi direction relation reasoning method are proposed. Finally, direction relation reasoning arithmetic is given and proved to be true. © 2015, by Binary Information Press

关键词： Boundary Sensitive Combinative Reasoning Table Directional Relationship Matrix Model Relationship Reasoning Three-dimension Directional

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A filtering algorithm for scattered point cloud based on curvature features classification

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Journal of Information and Computational Science 2015年第2期12卷 525-532页

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

In order to remove the noise of three-dimensional scattered point cloud, and to smooth point cloud model effectively, an algorithm which uses different filtering strategies on different feature regions of a point cloud model is proposed. The algorithm firstly estimates the normal vectors of a point cloud model by using covariance analysis method, then estimates Gaussian curvatures of the point cloud model by using parabolic fitting method, and uses the average Gaussian curvature in the k-neighborhood as the threshold, to divide the point cloud model into flat neighborhood type regions and mutant neighborhood type regions, and, we use improved median filtering algorithm and bilateral filtering algorithm on different feature regions, so as to achieve the purpose of smoothing scattered point cloud. Experimental results show that it has a very good smoothing effect and maintains the detail features of the point cloud model, which has proved the algorithm is simple and effective. Copyright © 2015 Binary Information Press.

关键词： Three dimensional computer graphics

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K-means sequence clustering algorithm based on Two-stage center sequences selection

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Journal of Computational Information systems 2014年第6期10卷 2351-2358页

作者： Wu, Di Ren, Jiadong College of Information Science and Engineering Yanshan University Qinhuangdao 066004 China Department of Information and Electronic Engineering Hebei University of Engineering Handan 056038 China Key Lab of Computer Virtual Manufacturing and System Integration of Hebei Province Yanshan University Qinhuangdao 066004 China

K-means sequence clustering is a hot topic in data mining. However, the clustering quality of K-means is affected heavily by outliers and noises. In this paper, a new sequence similarity measurement, sequence density and Q neighborhoods of sequence are deffned and then a novel K-means sequence clustering algorithm TCSSK-means (Two-stage center sequences selection-based K-means) is proposed. In the first stage, the sequence with the minimum density neighborhood is viewed as initial clustering center, and the distances between each initial clustering center are as far as possible, the KICCSS (K initial clustering center sequences set) is obtained. In the second stage, by selecting the mean sequence of the larger similarity sequences set, which meets certain conditions with clustering centers in the T-1-th round, K clustering centers of sequence databases in the T-th round are updated. Repeat the renewal process of sequence clustering centers until the sequence clustering criterion function converges. K final sequence clusters are gained finally. The experimental results and analysis show that the performance of TCSSK-means is better in clustering quality and running time. Copyright © 2014 Binary Information Press.

关键词： Data mining

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The constructions of ternary sequence pairs with two-level autocorrelation

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Journal of Information and Computational Science 2014年第13期11卷 4605-4612页

作者： Jia, Yanguo Duan, Xiaobei Shi, Yan Shen, Xiumin Key Laboratory for Computer Virtual Technology and System Integration of Hebei Province School of Information Science and Engineering Yanshan University Qinhuangdao China

In this letter, a periodic autocorrelation signal is presented, which is the ternary sequence pair with two-level autocorrelation. The methods of constructing ternary sequence pairs based on binary sequence pairs and cyclotomy are presented by us. Then we have a discussion about perfect binary sequence pairs, pseudorandom binary sequence pairs, difference set pairs and ternary sequence pairs. These signals enrich the theory of sequence pair discrete correlation signals. Copyright © 2014 Binary Information Press.

关键词： Autocorrelation

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