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STUDY ON EFFICIENT SEARCH ALGORITHMS

Research Project

Project/Area Number 06680326
Research Category

Grant-in-Aid for General Scientific Research (C)

Allocation TypeSingle-year Grants
Research Field 計算機科学
Research InstitutionKYUSHU UNIVERSITY

Principal Investigator

MIYANO Satoru  KYUSHU UNIVERSITY,FACULTY OF SCIENCE PROFESSOR, 理学部, 教授 (50128104)

Co-Investigator(Kenkyū-buntansha) SHIMOZONO Shinichi  KYUSHU INSTITUTE OF TECHNOLOGY,ASSISTANT DEPARTMENT OF ARTIFICIAL INTELLIGENCE, 情報工学部, 助手 (70243988)
SHINOHARA Ayumi  KYUSHU UNIVERSITY,FACULTY OF SCIENCE ASSOCIATE PROFESSOR, 理学部, 助教授 (00226151)
SHOUDAI Takayoshi  KYUSHU UNIVERSITY,FACULTY OF SCIENCE ASSOCIATE PROFESSOR, 理学部, 助教授 (50226304)
Project Period (FY) 1994 – 1995
Project Status Completed (Fiscal Year 1995)
Budget Amount *help
¥2,200,000 (Direct Cost: ¥2,200,000)
Fiscal Year 1995: ¥700,000 (Direct Cost: ¥700,000)
Fiscal Year 1994: ¥1,500,000 (Direct Cost: ¥1,500,000)
KeywordsSearvh algorithm / Bioinformatics / Genome Informatics / Knowledge acquisition / Machine learning / Machine discovery / Parallel algorithm / アルゴリズム / ゲノム情報 / 近似アルゴリズム / 計算量理論
Research Abstract

Technologies for discoverring knowledge from nucleic acid and amino acid sequences are most expected in Genome Informatics/Molecular Bioinformatics. Various search techniques have traditionally playd a very important role in knowledge discovery from sequence. Our goal of this research are to establish the fundamental search strategies and to analyze its computational complexity. The following are the selection of the result for our study on efficient seach algorithms :
We define a new framework for rewriting graphs, called a formal graph system (FGS) , which is a logic program having hypergraphs instead of terms in first-order logic. We show that the refutation tree problem for three subclasses of FGSs are computed efficiently in parallel.
A partial walk in an undirected edge-colored graph G is a path in G.If a partial walk in G contains all edges of G,it is called a walk in G.The graph inference from walk is, given a string x, to find the smallest graph which can realize x as a walk in G.We prove that the graph inference from a walk for tree of bounded degree 3 is NP-complete.
The knowledge on sequences is often expressed as a motif which is a pattern common to a family of sequences. We presents a greedy strategy for finding such motifs wich ambiguity just from positive and negative examples by exploiting the probabilistic argument.
We have developed a parallel machine discovery system BONSAI Garden by employing these results. This system has succeeded in discovering resonable knowledge on a hodgepodge of amino acid sequences.

Report

(3 results)
  • 1995 Annual Research Report   Final Research Report Summary
  • 1994 Annual Research Report
  • Research Products

    (25 results)

All Other

All Publications (25 results)

  • [Publications] Shinichi Shimozono: "Complexity of finding alphabet indexing" IEICE Transactions on Information and Systems. E78-D. 13-18 (1995)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Tomoyuki Uchida: "Parallel algorithms for refutation tree problem on formal graph systems" IEICE Transactions on Information and Systems. E78-D. 99-112 (1995)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Takayoshi Shoudai: "Using maximal independent sets to solve problems in parallel" Theoretical Computer Science. 148. 57-65 (1995)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Osamu Maruyama: "Graph inference from a walk for trees of bounded degree3 is NP-Complete" Proceedings of the 20th Symposium on Mathematical Foundations of Computer Science(Lecture Notes in Computer Science). 969. 257-266 (1995)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Shinichi Shimozono: "An approximation algorithm for alphabet indexing problem" Algorithms and Computation, 6th International Symposium,ISAAC'95 (Lecture Notes in Computer Science). 1004. 2-11 (1995)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Erika Tateishi: "A greedy strategy for finding motifs from yes-no examples" Pacific Symposium on BIOCOMPUTING 96. 599-613 (1996)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] E.Tateishi: "A greedy strategy for finding motifs from yes-no examples" Pacific Symposium on BIOCOMPUTING 96, Hunter, L.and Klein, T.E.(eds.). 599-613 (1996)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] S.Shimozono: "An approximation algorithm for alphabet indexing problem" Algorithms and Computation, 6th International Symposium, ISAAC'95 (Lecture Notes in Computer Science 1004), Staples, J., Eades, P., Katoh, N., and Moffat, A.(eds.). 2-11 (1995)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] O.Maruyama: "Graph inference from a walk for trees of bounded degree 3 is NP-Complete" Proceedings of the 20th symposium on Mathematical Foundations of Computer Science (Lecture Notes in Computer Science 969), Wiedermann, J.and Hajed, P.(eds.). 257-266 (1995)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] T.Shoudai: "Using maximal independent sets to solve problems in parallel" Theoretical Computer Science. 148. 57-65 (1995)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] T.Uchida: "Parallel algorithms for refutation tree problem on formal graph systems" IEICE Transactions on Information and Systems. E78-D,2. 99-112 (1995)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] S.Shimozono: "Complexity of finding alphabet indexing" IEICE Transactions on Information and Systems. E78-D,1. 13-18 (1995)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] T.Uchida: "Polynomial time algorithm solving the refutation tree problem for formal graph systems" Bulletin of Informatics and Cybernetics. 26,1-2. 55-74 (1994)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Shinichi Shimozono: "Complexity of finding alphabet indexing" IEICE Transactions on Information and Systems. E78-D. 13-18 (1995)

    • Related Report
      1995 Annual Research Report
  • [Publications] Tomoyuki Uchida: "Parallel algorithms for refutation tree problem on formal graph systems" IEICE Transactions on Information and Systems. E78-D. 99-112 (1995)

    • Related Report
      1995 Annual Research Report
  • [Publications] Takayoshi Shoudai: "Using maximal independent sets to solve problems in parallel" Theoretical Computer Science. 148. 57-65 (1995)

    • Related Report
      1995 Annual Research Report
  • [Publications] Osamu Maruyama: "Graph inference from a walk for trees of bounded degree 3 is NP-Complete" Proceedings of the 20th Symposium on Mathematical Foundations of Computer Science (Lecture Notes in Computer Science). 969. 257-266 (1995)

    • Related Report
      1995 Annual Research Report
  • [Publications] Shinichi Shimozono: "An approximation algorithm for alphabet indexing problem" Algorithms and Computation, 6th International Symposium, ISAAC '95 (Lecture Notes in Computer Science). 1004. 2-11 (1995)

    • Related Report
      1995 Annual Research Report
  • [Publications] Erika Tateishi: "A greedy strategy for finding motifs from yes-no examples" Pacific Symposium on BIOCOMPUTING 96. 599-613 (1996)

    • Related Report
      1995 Annual Research Report
  • [Publications] 宮野悟,篠原歩,有川節夫: "ゲノム情報における機械学習の計算量" 人工知能学会誌. 9. 350-357 (1994)

    • Related Report
      1994 Annual Research Report
  • [Publications] M.Karpinski,W.Rytter and A.Shinohara: "Pattern-Matching for Strings with Short Descriptions" INSTITUT FUR INFORMATIK DER UNIVERSITAT BONN. 85124-CS. 1-10 (1994)

    • Related Report
      1994 Annual Research Report
  • [Publications] 宮野悟他: "BONSAI Garden:学習アルゴリズムによるアミノ酸配列からの並列知識獲得システム" 情処研報. 94. 41-47 (1994)

    • Related Report
      1994 Annual Research Report
  • [Publications] S.Shimozono他: "Knowledge acquisition from amino acid sequences by machine learning system BONSAI" 情報処理学会論文誌. 35. 2009-2018 (1994)

    • Related Report
      1994 Annual Research Report
  • [Publications] T.Uchida,T.Shoudai and S.Miyano: "Polynomial time algorithm solving the refutation tree problem for formal graph systems" Bulletin of Informatics and Cybernetics. 26. 55-74 (1994)

    • Related Report
      1994 Annual Research Report
  • [Publications] S.Shimozono and S.Miyano: "Complexity of Finding Alphabet Indexing" IEICE Trans.Inf.and Syst.E78-D. 13-18 (1995)

    • Related Report
      1994 Annual Research Report

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Published: 1994-04-01   Modified: 2016-04-21  

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