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Validation Measures for Clustering Algorithms Incorporating Biological Information 结合生物信息的聚类算法的验证方法
First International Multi-Symposiums on Computer and Computational Sciences (IMSCCS'06) Pub Date : 2006-06-20 DOI: 10.1109/IMSCCS.2006.139
S. Datta, S. Datta
{"title":"Validation Measures for Clustering Algorithms Incorporating Biological Information","authors":"S. Datta, S. Datta","doi":"10.1109/IMSCCS.2006.139","DOIUrl":"https://doi.org/10.1109/IMSCCS.2006.139","url":null,"abstract":"A cluster analysis is the most commonly performed procedure (often regarded as a first step) on a set of gene expression profiles. A closely related problem is that of selecting a clustering algorithm that is optimal in some way from a rather impressive list of clustering algorithms that currently exist. In this paper, we propose two validation measures each with two parts: one measuring the statistical consistency (stability) of the clusters produced and the other representing their biological functional consistency, so that a good clustering algorithm should have a small value for these measures. We illustrate our methods using two sets of expression profiles obtained from a breast cancer data set. Six well known clustering algorithms UPGMA, k-means, Diana, Fanny, model-based and SOM were evaluated. Whereas the exact ordering depends on the particular data set (expression profiles) used and the validation measure employed, overall UPGMA appears to be the optimal for this cancer data set that we considered","PeriodicalId":202629,"journal":{"name":"First International Multi-Symposiums on Computer and Computational Sciences (IMSCCS'06)","volume":"20 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116128473","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 5
Computer Analysis Method for Clinical CT Image 临床CT图像的计算机分析方法
First International Multi-Symposiums on Computer and Computational Sciences (IMSCCS'06) Pub Date : 2006-06-20 DOI: 10.1109/IMSCCS.2006.49
Weiguo Bian, Shao-jie Tang, Huazi Xu
{"title":"Computer Analysis Method for Clinical CT Image","authors":"Weiguo Bian, Shao-jie Tang, Huazi Xu","doi":"10.1109/IMSCCS.2006.49","DOIUrl":"https://doi.org/10.1109/IMSCCS.2006.49","url":null,"abstract":"This paper describes a new computer analysis method for the judgment of vertebral canal stenosis of lumbar spin by X-ray CT images, where a large number of technologies on computer image analysis and digital image processing are utilized such as image segmentation, morphology, coordinates transform, Hough transform, histogram equalization of image gray level, etc. For the boundaries extraction of every defined region in lumbar spin, we propose a new and concise algorithm with radial or polar sampling on the binary CT images. Although adopting computer program to automatically process some routine manual works is still very primary at present research, we believe that it is an excellent orientation for the clinical aided diagnosis. An example of processing realistic CT images is used to validate the feasibility of the whole procedure","PeriodicalId":202629,"journal":{"name":"First International Multi-Symposiums on Computer and Computational Sciences (IMSCCS'06)","volume":"349 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131161312","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Parallelization of Similarity Search in Large Time Series Databases 大型时间序列数据库中相似度搜索的并行化
First International Multi-Symposiums on Computer and Computational Sciences (IMSCCS'06) Pub Date : 2006-06-20 DOI: 10.1109/IMSCCS.2006.100
Jonathan Qiao, Yang Ye, Chaoyang Zhang
{"title":"Parallelization of Similarity Search in Large Time Series Databases","authors":"Jonathan Qiao, Yang Ye, Chaoyang Zhang","doi":"10.1109/IMSCCS.2006.100","DOIUrl":"https://doi.org/10.1109/IMSCCS.2006.100","url":null,"abstract":"In this paper, an efficient parallel algorithm to search large time series databases is proposed. There are existing parallel algorithms for performing such tasks, which generally utilize multidimensional tree structures and thus are subjected to the performance of multidimensional trees. On the other hand, there have been a number of serial algorithms proposed in the past decade. Most of them use certain transformation techniques to reduce the dimensionality and then build an index to facilitate the search process. This again results in performance degradation. This work develops a parallel algorithm to process range query and k-nearest neighbor query in parallel time series databases, assuming a shared nothing multi-processor architecture. Both analytical and experimental results show that the new approach has near linear scaleup and linear speedup with little more effort than non-index based sequential scan and thus another alternative to index based approach","PeriodicalId":202629,"journal":{"name":"First International Multi-Symposiums on Computer and Computational Sciences (IMSCCS'06)","volume":"65 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131741355","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
A Hybrid Approach for Overlay Multicast 一种覆盖组播的混合方法
First International Multi-Symposiums on Computer and Computational Sciences (IMSCCS'06) Pub Date : 2006-06-20 DOI: 10.1109/IMSCCS.2006.10
Qi Zhao, Yun He, Jianzhong Zhang
{"title":"A Hybrid Approach for Overlay Multicast","authors":"Qi Zhao, Yun He, Jianzhong Zhang","doi":"10.1109/IMSCCS.2006.10","DOIUrl":"https://doi.org/10.1109/IMSCCS.2006.10","url":null,"abstract":"Existing overlay multicast (also called application layer multicast) protocols can be categorized into tree-first and mesh-first approaches by the type of overlay they build. These two approaches complement each other in terms of performance and scalability. In this paper, we propose and evaluate hybrid overlay multicast protocol (HOMP), which is specifically designed for low-delay, many-to-many applications with large receiver sets. HOMP constructs and maintains a hybrid overlay composed of a core mesh and many attached trees for data transmission, thus it shows some properties of both mesh-first and tree-first approaches. Our simulation results reveal that HOMP is a promising application layer overlay construction technique","PeriodicalId":202629,"journal":{"name":"First International Multi-Symposiums on Computer and Computational Sciences (IMSCCS'06)","volume":"15 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127681425","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 4
OD: A General Resource Scheduling Algorithm for Computational Grid* 一种通用的计算网格资源调度算法*
First International Multi-Symposiums on Computer and Computational Sciences (IMSCCS'06) Pub Date : 2006-06-20 DOI: 10.1109/IMSCCS.2006.93
Tao Wang, Xingshe Zhou, Qiu-rang Liu, Zhiyi Yang, Zhao-feng Yang
{"title":"OD: A General Resource Scheduling Algorithm for Computational Grid*","authors":"Tao Wang, Xingshe Zhou, Qiu-rang Liu, Zhiyi Yang, Zhao-feng Yang","doi":"10.1109/IMSCCS.2006.93","DOIUrl":"https://doi.org/10.1109/IMSCCS.2006.93","url":null,"abstract":"Task scheduling is a critical design issue of distributed computing. The emerging grid computing infrastructure consists of heterogeneous resource in widely distributed autonomous domains, which makes task scheduling even more challenging. In this paper, a general resource scheduling algorithm for computational grid, OD (on-demand) is present. According to the computational grid job's personal resource requirements, the different importance of these requirements and the system load of the computational grid nodes, OD chooses an appropriate node for computational grid job from the candidates finally. The experiments show the performance improvement for applications and achieve better load balance by this algorithm","PeriodicalId":202629,"journal":{"name":"First International Multi-Symposiums on Computer and Computational Sciences (IMSCCS'06)","volume":"54 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121602111","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
PVM: A Memory Management under Vertical Architecture PVM:垂直架构下的内存管理
First International Multi-Symposiums on Computer and Computational Sciences (IMSCCS'06) Pub Date : 2006-06-20 DOI: 10.1109/IMSCCS.2006.108
Xinghui Zhu, Guang Lu, Fei Yu, Shuqiang Yang, Miaoliang Zhu
{"title":"PVM: A Memory Management under Vertical Architecture","authors":"Xinghui Zhu, Guang Lu, Fei Yu, Shuqiang Yang, Miaoliang Zhu","doi":"10.1109/IMSCCS.2006.108","DOIUrl":"https://doi.org/10.1109/IMSCCS.2006.108","url":null,"abstract":"In today's operating system, memory management policies based on the data-copying and hidden mechanisms blocks the system performance which is far from expectation. This paper introduces an innovative memory management system powered by vertical architecture PVM. The paper first describes the model and architecture of PVM, followed by an analysis of lazy management of virtual address space and the management of two-layer-cached physical memory","PeriodicalId":202629,"journal":{"name":"First International Multi-Symposiums on Computer and Computational Sciences (IMSCCS'06)","volume":"37 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121073995","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A Cyclic Force Decomposition Algorithm for Parallelising Three-Body Interactions in Molecular Dynamics Simulations 分子动力学模拟中并行化三体相互作用的循环力分解算法
First International Multi-Symposiums on Computer and Computational Sciences (IMSCCS'06) Pub Date : 2006-06-20 DOI: 10.1109/IMSCCS.2006.3
Jianhui Li, Zhongwu Zhou, R. Sadus
{"title":"A Cyclic Force Decomposition Algorithm for Parallelising Three-Body Interactions in Molecular Dynamics Simulations","authors":"Jianhui Li, Zhongwu Zhou, R. Sadus","doi":"10.1109/IMSCCS.2006.3","DOIUrl":"https://doi.org/10.1109/IMSCCS.2006.3","url":null,"abstract":"A cyclic force decomposition algorithm is examined for parallelising three body interactions. The algorithm is based on the decomposition of a 3D force matrix into slices of 2D force matrixes in cyclic task assignments. The proposed decomposition algorithm is implemented using MPI and tested in computational experiments of MD simulations. The performance of the decomposition method is studied in terms of load balance, achieved speedup and parallel efficiency. Theoretical analysis of effective triplets is proposed and conducted by which load balance status can be predicted and compared with benchmark measurements. Reasonably good overall performance is achieved with the proposed algorithm. Both theoretical analysis and computation experiments demonstrate that the load balance is a key factor that impacts the parallel efficiency of the system examined in this study","PeriodicalId":202629,"journal":{"name":"First International Multi-Symposiums on Computer and Computational Sciences (IMSCCS'06)","volume":"254 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124001849","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 8
An Fast Transparent Failover Scheme for Service Availability 一个快速透明的服务可用性故障切换方案
First International Multi-Symposiums on Computer and Computational Sciences (IMSCCS'06) Pub Date : 2006-06-20 DOI: 10.1109/IMSCCS.2006.33
Jigang Wang, Guochang Gu, Shibo Xie, Lifeng Xu
{"title":"An Fast Transparent Failover Scheme for Service Availability","authors":"Jigang Wang, Guochang Gu, Shibo Xie, Lifeng Xu","doi":"10.1109/IMSCCS.2006.33","DOIUrl":"https://doi.org/10.1109/IMSCCS.2006.33","url":null,"abstract":"Fault tolerance schemes can be used to increase the availability and reliability of network service systems. One aspect of such schemes is failover - the reconfiguration of available resources and restoration of state required to continue providing the service despite the loss of some of the resources and corruption of parts of the state. Most of the techniques used for increasing the availability of network services do not provide fault tolerance for requests being processed at the time of server failure. Other schemes require deterministic servers or changes to the client. These limitations are unacceptable for many current and future network services. This paper proposes an efficient transparent failover scheme for service availability (SAFailover) to provide fault-tolerant network service that does not have the limitations mentioned above. The scheme is based on a hot standby backup server that maintains logs of requests and replies. The implementation includes modifications to the Linux kernel and to the Apache Web server, using their respective module mechanisms. The paper describe the implementation and present an evaluation of the impact of the backup scheme in terms of throughput, latency, and CPU processing cycles overhead. Experiment results indicate this scheme have short failover times and low overhead during fault-free operation","PeriodicalId":202629,"journal":{"name":"First International Multi-Symposiums on Computer and Computational Sciences (IMSCCS'06)","volume":"23 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129981698","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Decease I/O Mean Response Time Using Software Pipelining 使用软件流水线减少I/O平均响应时间
First International Multi-Symposiums on Computer and Computational Sciences (IMSCCS'06) Pub Date : 2006-06-20 DOI: 10.1109/IMSCCS.2006.52
Ke Zhou, Zhongying Niu
{"title":"Decease I/O Mean Response Time Using Software Pipelining","authors":"Ke Zhou, Zhongying Niu","doi":"10.1109/IMSCCS.2006.52","DOIUrl":"https://doi.org/10.1109/IMSCCS.2006.52","url":null,"abstract":"Compared with the storage device in traditional direct attached systems, the I/O access pattern in a storage area network is different. In this paper we use fibre channel RAIDs and study how to decease I/O mean response time by software pipelining, so to enable the overlapping of different phases of the operation such as fibre channel transfer and disk access. Calculations and tests show that software pipelining can decrease I/O mean response time effectively. Further, we discuss the speedup of mean response time that is mainly influenced by two parameters: concurrent I/O request number and request data size","PeriodicalId":202629,"journal":{"name":"First International Multi-Symposiums on Computer and Computational Sciences (IMSCCS'06)","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129653597","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Simulation of Transmembrane Potential Propagation in Three-Dimensional Bidomain Cardiac Tissue 三维双域心脏组织跨膜电位传播的模拟
First International Multi-Symposiums on Computer and Computational Sciences (IMSCCS'06) Pub Date : 2006-06-20 DOI: 10.1109/IMSCCS.2006.125
Yin Zhou, P. Jung, Chaoyan Zhu
{"title":"Simulation of Transmembrane Potential Propagation in Three-Dimensional Bidomain Cardiac Tissue","authors":"Yin Zhou, P. Jung, Chaoyan Zhu","doi":"10.1109/IMSCCS.2006.125","DOIUrl":"https://doi.org/10.1109/IMSCCS.2006.125","url":null,"abstract":"The transmembrane potential propagation in a slab of three-dimensional cardiac tissue stimulated by an unipolar extracellular shock on epicardium is simulated for a full cycle of action potential duration. A semi-implicit method is implemented for the first time on a single cpu workstation to numerically calculate the transmembrane potential field in a three-dimensional bidomain incorporating rotational anisotropy and active ionic currents. A fast preconditioned Krylov subspace iterative method is found to efficiently solve the huge number of linear equations at each time step. It is suggested that this methodology can be used to simulate transmembrane potential in cardiac tissue for seconds after an electric defibrillation shock, which requires long time three-dimensional bidomain simulation","PeriodicalId":202629,"journal":{"name":"First International Multi-Symposiums on Computer and Computational Sciences (IMSCCS'06)","volume":"17 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130565835","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
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