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A Distributed-Processing System for Accelerating Biological Research Using Data-Staging 利用数据分期加速生物研究的分布式处理系统
Pub Date : 2008-03-15 DOI: 10.2197/IPSJDC.4.250
Y. Kido, S. Seno, S. Date, Y. Takenaka, H. Matsuda
The number of biological databases has been increasing rapidly as a result of progress in biotechnology. As the amount and heterogeneity of biological data increase, it becomes more difficult to manage the data in a few centralized databases. Moreover, the number of sites storing these databases is getting larger, and the geographic distribution of these databases has become wider. In addition, biological research tends to require a large amount of computational resources, i.e., a large number of computing nodes. As such, the computational demand has been increasing with the rapid progress of biological research. Thus, the development of methods that enable computing nodes to use such widely-distributed database sites effectively is desired. In this paper, we propose a method for providing data from the database sites to computing nodes. Since it is difficult to decide which program runs on a node and which data are requested as their inputs in advance, we have introduced the notion of “data-staging” in the proposed method. Data-staging dynamically searches for the input data from the database sites and transfers the input data to the node where the program runs. We have developed a prototype system with data-staging using grid middleware. The effectiveness of the prototype system is demonstrated by measurement of the execution time of similarity search of several-hundred gene sequences against 527 prokaryotic genome data.
由于生物技术的进步,生物数据库的数量迅速增加。随着生物数据的数量和异构性的增加,在几个集中的数据库中管理数据变得越来越困难。此外,储存这些数据库的地点越来越多,这些数据库的地理分布也越来越广。此外,生物研究往往需要大量的计算资源,即大量的计算节点。因此,随着生物研究的快速发展,对计算的需求也在不断增加。因此,需要开发使计算节点能够有效地使用这种广泛分布的数据库站点的方法。在本文中,我们提出了一种从数据库站点向计算节点提供数据的方法。由于很难事先决定在节点上运行哪个程序以及请求哪些数据作为其输入,因此我们在建议的方法中引入了“数据分段”的概念。数据暂存动态地从数据库站点搜索输入数据,并将输入数据传输到程序运行的节点。我们利用网格中间件开发了一个具有数据分段功能的原型系统。通过对527个原核生物基因组数据进行数百个基因序列相似性搜索的执行时间测量,验证了原型系统的有效性。
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引用次数: 0
A Generalized Hidden Markov Model Approach to Transmembrane Region Prediction with Poisson Distribution as State Duration Probabilities 以泊松分布为状态持续概率的跨膜区域预测的广义隐马尔可夫模型方法
Pub Date : 2008-03-15 DOI: 10.2197/IPSJDC.4.193
T. Kaburagi, Takashi Matsumoto
We present a novel algorithm to predict transmembrane regions from a primary amino acid sequence. Previous studies have shown that the Hidden Markov Model (HMM) is one of the powerful tools known to predict transmembrane regions; however, one of the conceptual drawbacks of the standard HMM is the fact that the state duration, i.e., the duration for which the hidden dynamics remains in a particular state follows the geometric distribution. Real data, however, does not always indicate such a geometric distribution. The proposed algorithm utilizes a Generalized Hidden Markov Model (GHMM), an extension of the HMM, to cope with this problem. In the GHMM, the state duration probability can be any discrete distribution, including a geometric distribution. The proposed algorithm employs a state duration probability based on a Poisson distribution. We consider the two-dimensional vector trajectory consisting of hydropathy index and charge associated with amino acids, instead of the 20 letter symbol sequences. Also a Monte Carlo method (Forward/Backward Sampling method) is adopted for the transmembrane region prediction step. Prediction accuracies using publicly available data sets show that the proposed algorithm yields reasonably good results when compared against some existing algorithms.
我们提出了一种新的算法来预测跨膜区域从初级氨基酸序列。先前的研究表明,隐马尔可夫模型(HMM)是已知的预测跨膜区域的强大工具之一;然而,标准HMM在概念上的缺点之一是状态持续时间,即隐藏动力学保持在特定状态的持续时间遵循几何分布。然而,实际数据并不总是显示出这样的几何分布。该算法利用广义隐马尔可夫模型(GHMM)来解决这一问题,该模型是隐马尔可夫模型的扩展。在GHMM中,状态持续概率可以是任意离散分布,包括几何分布。该算法采用基于泊松分布的状态持续概率。我们考虑由亲水指数和与氨基酸相关的电荷组成的二维矢量轨迹,而不是20个字母符号序列。跨膜区域预测步骤采用蒙特卡罗方法(前向/后向采样方法)。使用公开可用数据集的预测精度表明,与一些现有算法相比,所提出的算法产生了相当好的结果。
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引用次数: 2
Maintaining Multiple Populations with Different Diversities for Evolutionary Optimization Based on Probability Models 基于概率模型的多种群多样性维持进化优化
Pub Date : 2008-03-15 DOI: 10.2197/IPSJDC.4.268
Takayuki Higo, K. Takadama
This paper proposes a novel method, Hierarchical Importance Sampling (HIS) that can be used instead of population convergence in evolutionary optimization based on probability models (EOPM)such as estimation of distribution algorithms and cross entropy methods. In HIS, multiple populations are maintained simultaneously such that they have different diversities, and the probability model of one population is built through importance sampling by mixing with the other populations. This mechanism can allow populations to escape from local optima. Experimental comparisons reveal that HIS outperforms general EOPM.
本文提出了一种新的基于概率模型(EOPM)的进化优化算法,如分布估计算法和交叉熵方法,可以用来代替种群收敛。在HIS中,同时维持多个种群,使其具有不同的多样性,并通过与其他种群混合进行重要抽样,建立一个种群的概率模型。这种机制可以使种群脱离局部最优状态。实验比较表明,HIS优于一般EOPM。
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引用次数: 3
Exploring Factors Effecting the Continuance of Purchasing Behavior in Internet Shopping: Extrinsic Benefits and Intrinsic Benefits 网络购物中影响购买行为持续的因素:外在利益与内在利益
Pub Date : 2008-02-15 DOI: 10.2197/IPSJDC.4.91
K. Atchariyachanvanich, H. Okada, N. Sonehara
Previous research examined how extrinsic and intrinsic factors influence customers to shop online. Conversely, the impact of these factors on customer retention in Internet shopping has not been examined. This study is one of the few attempts to investigate the perceived benefit factors effecting customers’ continuance of purchasing items through the Internet. According to an online questionnaire filled out by 1,111 online customers to conduct a multiple regression analysis, extrinsic benefits measured in terms of time and money savings, social adjustment, and self-enhancement as well as intrinsic benefits measured in terms of pleasure and novelty as well as fashion involvement have strong effects on the continuance of purchasing. Our findings indicate that customer retention must be promoted in Internet shopping by guaranteeing not only extrinsic benefits but also intrinsic benefits. This study discusses the relevant techniques providing those benefits to customers and guidelines for future research.
之前的研究考察了外在因素和内在因素是如何影响顾客网购的。相反,这些因素对网络购物中客户保留的影响尚未得到检验。本研究是为数不多的尝试调查影响顾客持续透过网路购买物品的感知利益因素之一。通过对1111名在线消费者的在线问卷调查进行多元回归分析发现,以节省时间和金钱、社会适应、自我提升为衡量标准的外在利益,以及以愉悦、新奇、时尚参与为衡量标准的内在利益,对购买的持续性有很强的影响。我们的研究结果表明,在网络购物中,顾客留存率的提升不仅要保证外在利益,还要保证内在利益。本研究讨论了为客户提供这些好处的相关技术和未来研究的指导方针。
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引用次数: 20
Merging String Sequences by Longest Common Prefixes 按最长公共前缀合并字符串序列
Pub Date : 2008-02-15 DOI: 10.2197/IPSJDC.4.69
Waihong Ng, K. Kakehi
We present LCP Merge, a novel merging algorithm for merging two ordered sequences of strings. LCP Merge substitutes string comparisons with integer comparisons whenever possible to reduce the number of character-wise comparisons as well as the number of key accesses by utilizing the longest common prefixes (LCP) between the strings. As one of the applications of LCP Merge, we built a string merge sort based on recursive merge sort by replacing the merging algorithm with LCP Merge and we call it LCP Merge sort. In case of sorting strings, the computational complexity of recursive merge sort tends to be greater than O(n lg n) because string comparisons are generally not constant time and depend on the properties of the strings. However, LCP Merge sort improves recursive merge sort to the extent that its computational complexity remains O(n lg n) on average. We performed a number of experiments to compare LCP Merge sort with other string sorting algorithms to evaluate its practical performance and the experimental results showed that LCP Merge sort is efficient even in the real-world.
提出了一种新的LCP合并算法,用于合并两个有序字符串序列。LCP Merge利用字符串之间的最长公共前缀(LCP),尽可能用整数比较代替字符串比较,以减少字符比较的次数以及键访问的次数。作为LCP归并的应用之一,我们在递归归并的基础上,用LCP归并代替归并算法,构建了一个字符串归并排序,我们称之为LCP归并排序。在对字符串进行排序的情况下,递归归并排序的计算复杂度往往大于O(nlgn),因为字符串比较通常不是常数时间,并且取决于字符串的属性。然而,LCP归并排序改进了递归归并排序,其计算复杂度平均保持为O(n lgn)。我们进行了大量的实验,将LCP合并排序与其他字符串排序算法进行比较,以评估其实际性能,实验结果表明LCP合并排序即使在现实世界中也是有效的。
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引用次数: 14
d-ACTM/VT: A Distributed Virtual AC Tree Detection Method d-ACTM/VT:分布式虚拟交流树检测方法
Pub Date : 2008-02-15 DOI: 10.2197/IPSJDC.4.79
N. Kawaguchi, H. Shigeno, Ken-ichi Okada
In this paper, we propose d-ACTM/VT, a network-based worm detection method that effectively detects hit-list worms using distributed virtual AC tree detection. To detect a kind of hit-list worms named Silent worms in a distributed manner, d-ACTM was proposed. d-ACTM detects the existence of worms by detecting tree structures composed of infection connections as edges. Some undetected infection connections, however, can divide the tree structures into small trees and degrade the detection performance. To address this problem, d-ACTM/VT aggregates the divided trees as a tree named Virtual AC tree in a distributed manner and utilizes the tree size for detection. Simulation result shows d-ACTM/VT reduces the number of infected hosts before detection by 20% compared to d-ACTM.
在本文中,我们提出了一种基于网络的蠕虫检测方法d-ACTM/VT,该方法使用分布式虚拟交流树检测来有效地检测命中列表蠕虫。为了对静默蠕虫进行分布式检测,提出了d-ACTM算法。d-ACTM通过检测由感染连接组成的树形结构作为边缘来检测蠕虫的存在。然而,一些未被检测到的感染连接可能会将树结构分成小树,从而降低检测性能。为了解决这一问题,d-ACTM/VT将划分的树以分布式的方式聚合成一棵树,命名为Virtual AC tree,并利用树的大小进行检测。仿真结果表明,与d-ACTM相比,d-ACTM/VT在检测前将感染主机的数量减少了20%。
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引用次数: 2
Web Resource Categorization by Detecting Potential Relations 通过检测潜在关系对Web资源进行分类
Pub Date : 2008-02-15 DOI: 10.2197/IPSJDC.4.103
Minghua Pei, Kotaro Nakayama, T. Hara, S. Nishio
Since Semantic Web is increasing in size and variety of resources, it is difficult for users to find the information that they really need. Therefore, it is necessary to provide an efficient and precise method without explicit specification for the Web resources. In this paper, we proposed the novel approach of integrating four processes for Web resource categorization. The processes can extract both the explicit relations extracted from the ontologies in a traditional way and the potential relations inferred from existing ontologies by focusing on some new challenges such as extracting important class names, using WordNet relations and detecting the methods of describing the Web resources. We evaluated the effectiveness by applying the categorization method to a Semantic Web search system, and confirmed that our proposed method achieves a notable improvement in categorizing the valuable Web resources based on incomplete ontologies.
由于语义网的规模和资源种类不断增加,用户很难找到他们真正需要的信息。因此,有必要为Web资源提供一种无需明确规范的高效、精确的方法。本文提出了一种集成四个过程的Web资源分类新方法。通过对重要类名的提取、WordNet关系的使用和Web资源描述方法的检测等新挑战,该流程既可以提取传统方法中提取的本体的显式关系,也可以从现有本体中推断出潜在的关系。通过将该方法应用于语义Web搜索系统,验证了该方法在基于不完整本体的有价值Web资源分类方面的显著改进。
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引用次数: 0
Design and Implementation of an Inter-Device Authentication Framework Guaranteeing Explicit Ownership 保证明确所有权的设备间认证框架的设计与实现
Pub Date : 2008-02-06 DOI: 10.2197/IPSJDC.4.114
Manabu Hirano, T. Okuda, S. Yamaguchi
Future networks everywhere will be connected to innumerable Internet-ready home appliances. A device accepting connections over a network must be able to verify the identity of a connecting device in order to prevent device spoofing and other malicious actions. In this paper, we propose a security mechanism for an inter-device communication. We state the importance of a distingushing and binding mechanism between a device's identity and its ownership information to realize practical inter-device authentication. In many conventional authentication systems, the relationship between the device's identity and the ownership information is not considered. Therefore, we propose a novel inter-device authentication framework guaranteeing this relationship. Our prototype implementation employs a smart card to maintain the device's identity, the ownership information and the access control rules securely. Our framework efficiently achieves secure inter-device authentication based on the device's identity, and authorization based on the ownership information related to the device. We also show how to apply our smart card system for inter-device authentication to the existing standard security protocols.
未来任何地方的网络都将连接到无数可以上网的家用电器上。通过网络接受连接的设备必须能够验证连接设备的身份,以防止设备欺骗和其他恶意行为。本文提出了一种设备间通信的安全机制。我们指出了在设备的身份和所有权信息之间建立区分和绑定机制对于实现实际的设备间认证的重要性。在许多传统的身份验证系统中,没有考虑设备的身份和所有权信息之间的关系。因此,我们提出了一种新的设备间认证框架来保证这种关系。我们的原型实现采用智能卡来安全维护设备的身份、所有权信息和访问控制规则。我们的框架有效地实现了基于设备身份的设备间安全认证,以及基于与设备相关的所有权信息的授权。我们还展示了如何将我们的智能卡系统用于设备间身份验证,以应用于现有的标准安全协议。
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引用次数: 3
Automatic Construction of Program Transformation Templates 程序转换模板的自动构建
Pub Date : 2008-01-15 DOI: 10.2197/IPSJDC.4.44
Yuki Chiba, Takahito Aoto, Y. Toyama
Program transformation by templates (Huet and Lang, 1978)is a technique to improve the efficiency of programs. In this technique, programs are transformed according to a given program transformation template. To enhance the variety of program transformation, it is important to introduce new transformation templates. Up to our knowledge, however, few works discuss about the construction of transformation templates. Chiba, et al. (2006) proposed a framework of program transformation by template based on term rewriting and automated verification of its correctness. Based on this framework, we propose a method that automatically constructs transformation templates from similar program transformations. The key idea of our method is a second-order generalization, which is an extension of Plotkin's first-order generalization (1969). We give a second-order generalization algorithm and prove the soundness of the algorithm. We then report about an implementation of the generalization procedure and an experiment on the construction of transformation templates.
模版程序转换(Huet and Lang, 1978)是一种提高程序效率的技术。在这种技术中,程序根据给定的程序转换模板进行转换。为了增强程序转换的多样性,引入新的转换模板是很重要的。然而,据我们所知,很少有著作讨论转换模板的构造。Chiba等(2006)提出了一种基于术语重写和正确性自动验证的模板程序转换框架。基于这个框架,我们提出了一种从类似的程序转换中自动构造转换模板的方法。我们的方法的关键思想是二阶泛化,这是Plotkin的一阶泛化(1969)的扩展。给出了一种二阶泛化算法,并证明了该算法的有效性。然后,我们报告了一个泛化过程的实现和一个转换模板构造的实验。
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引用次数: 4
Evaluation of the Integration Effect of Content Location and Request Routing in Content Distribution Networks 内容分发网络中内容定位与请求路由集成效果评价
Pub Date : 2008-01-15 DOI: 10.2197/IPSJDC.4.1
H. Miura, M. Yamamoto
Recently the content distribution networks (CDNs) have been highlighted as the new network paradigm which can improve latency for Web access. In CDNs, the content location strategy and request routing techniques are important technical issues. Both of them should be used in an integrated manner in general, but CDN performance applying both these technologies has not been evaluated in detail. In this paper, we investigate the effect of integration of these techniques. For request routing, we focus on a request routing technique applied active network technology, Active Anycast, which improves both network delay and server processing delay. For content distribution technology, we propose a new strategy, Popularity-Probability, whose aim corresponds with that of Active Anycast. Performance evaluation results show that integration of Active Anycast and Popularity-Probability can hold stable delay characteristics.
近年来,内容分发网络(cdn)作为一种能够改善Web访问延迟的新型网络范式而备受关注。在cdn中,内容定位策略和请求路由技术是重要的技术问题。一般来说,这两种技术都应该以集成的方式使用,但应用这两种技术的CDN性能尚未得到详细的评估。在本文中,我们研究了这些技术的集成效果。对于请求路由,我们重点研究了一种应用主动网络技术的请求路由技术——主动任播,它既改善了网络延迟,又改善了服务器处理延迟。对于内容分发技术,我们提出了一种新的策略——流行-概率策略,其目标与主动任播的目标相一致。性能评估结果表明,主动任播与流行概率相结合可以保持稳定的时延特性。
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引用次数: 0
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Ipsj Digital Courier
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