Algorithms for solving the sum-of-ratios problem using polynomialrelaxations and its application to sequence alignment

• Project/Area Number: 19510135
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Social systems engineering/Safety system
• Research Institution: Muroran Institute of Technology
• Principal Investigator: SHI Jianming Muroran Institute of Technology, 工学部, 准教授 (70287465)
• Project Period (FY): 2007 – 2008
• Project Status: Completed (Fiscal Year 2008)
• Budget Amount: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2008: ¥520,000 (Direct Cost: ¥400,000、Indirect Cost: ¥120,000); Fiscal Year 2007: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000)
• Keywords: 最適化 / 分数和情報学計画 / 生体情報学 / Mathematical Programming / ACO / ACS / Sequence Multiple Alignment / Ant Algorithm / Sum of ratios problem / Fractional Programming / Motif finding / NP-hard problem / 数理計画 / 分数和計画 / モチーフ / バイオインフォマティクス

Research Abstract

生体生命における情報の中に共通配列(モチーフ)を探し出すことを研究の目的である. モチーフを評価するため, 情報量に基き, ある種の分数和を最大化することが必要である. 本研究はこのような既存の分数和を最大にする計算方法(アルゴリズム)を研究し, 2005に発表されたモチーフ抽出アルゴリズムを大幅改良した. 数値実験の結果では,計算速度を2900倍に速くすることに成功した.

Research Products

• [Journal Article] A Modified Algorithm for Sequence Alignment Using Ant Colony System (2009)
  • Author(s): Ai Mikami, Jianming Shi
  • Journal Title: IPSJ Transactions on Bioinformatics Vol 2 Pages: 63-73
  • Peer Reviewed
• [Journal Article] A modified algorithm for sequence alignment using Ant Colony System (2009)
  • Author(s): Ai Mikami/Jianming Shi
  • Journal Title: IPSJ Transaction on Bioinformatics 2 Pages: 1-11
  • Peer Reviewed
• [Journal Article] ACOを用いたモチーフ抽出アルゴリズムに関する研究 (2007)
  • Author(s): 三上あい/施建明
  • Journal Title: IPSJ SIG Technical Report 2007-BIO-11 Pages: 203-210
  • NAID: 110006595427
• [Journal Article] ACOを用いたモチーフ抽出アルゴリズムに関数する研究 (2007)
  • Author(s): 三上あい、施建明
  • Journal Title: 情報処理学会研究報告 MPS-67 Pages: 203-210
• [Presentation] Solving Sum of Linear Ratios Problem using Linear Relaxation (2009)
  • Author(s): Jianming Shi
  • Organizer: International Conference on the Dynamics of Information Systems
  • Place of Presentation: Hilton University of Florida, Gainesville, FL
  • Year and Date: 2009-01-30
• [Presentation] Solving Sum of Linear Ratios Problem using Linear Relaxation (2008)
  • Author(s): J. Shi
  • Place of Presentation: Hilton University of Florida, Gainesville, FL
• [Presentation] A new algorithm for solving sum-of-linear-ratio problem (2007)
  • Author(s): Jianming Shi
  • Organizer: ICOTA7
  • Place of Presentation: International Convention Center, Kobe, Japan
  • Year and Date: 2007-12-13
• [Presentation] Algorithms for Sum-of-ratios (2007)
  • Author(s): Jianming Shi
  • Organizer: Informs 2007
  • Place of Presentation: Washington State Convention & Trade Center, Seattle, WA
  • Year and Date: 2007-11-07
• [Presentation] Optmization of Sum-Of-Ratios Problem and its Applications (2007)
  • Author(s): Jianming Shi
  • Organizer: INFORMS
  • Place of Presentation: Seattle, Washington, USA
  • Year and Date: 2007-11-07
• [Presentation] INFORS 2007 (2007)
  • Author(s): J. Shi
  • Organizer: Washington State Convention & Trade Center
  • Place of Presentation: Washington State Convention & Trade Center, Seattle, WA
  • Year and Date: 2007-04-07
• [Presentation] A new algorithm for solving the sum-of-linear-ratio problem (2007)
  • Author(s): J.Shi
  • Organizer: ICOTA7
  • Place of Presentation: International Convention Center, Kobe
• [Remarks]
  • URL: http://www.mmm.muroran-it.ac.jp/~shi/