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    National Tsing Hua University Institutional Repository > 電機資訊學院 > 資訊工程學系 > 會議論文  >  3-points relationship based parallel algorithm for minimum ultrametric tree construction


    Please use this identifier to cite or link to this item: http://nthur.lib.nthu.edu.tw/dspace/handle/987654321/66366


    Title: 3-points relationship based parallel algorithm for minimum ultrametric tree construction
    Authors: Kun-Ming Yu;Jiayi Zhou;Chun-Yuan Lin;Chuan Yi Tang
    教師: 唐傳義
    Date: 2007
    Publisher: Springer Verlag
    Relation: Lecture Notes in Computer Science,Volume 4671,2007,頁 615-622
    Keywords: 3PR
    DBP
    Ultrametric tree
    algorithm
    Abstract: To construct an evolutionary tree is an important topic in computational biology. An evolutionary tree can symbolize the relationship and histories for a set of species. There are many models had been proposed to resolve these problems. However, most of them are NP-hard problem. Ultrametric tree is one of the most popular models, it is used by a well-accepted tree construction method--unweighted pair group method with arithmetic mean, which is widely used by biologists to observe the relationship among species. However, it is a heuristic algorithm. In this paper, we proposed a 3- points relationship (3PR) based parallel algorithm to solve this problem. 3PR is a relationship between distance matrix and constructed evolutionary trees. The main concept is for any triplet species, two species closer to each other in distance matrix should be closer to each other in evolutionary tree. Then we combined this property and branch-and-bound strategy to reduce the computation time to obtain the optimal solution. Moreover, we put the lower ranked path which is determined by 3PR to delay bound pool (DBP) to accelerate the algorithm execution. DBP is a mechanism which can store the lower ranked path and can be helping algorithm to find a better bounding values speedily. The experimental results show that our proposed algorithm can reduce the computation time compared with algorithm without 3PR. Moreover, it also shows 3PR can reduce the computation time when number of computing nodes increasing.
    URI: http://www.springerlink.com/
    http://nthur.lib.nthu.edu.tw/dspace/handle/987654321/66366
    Appears in Collections:[資訊工程學系] 會議論文

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