Development of high accurate method for parameter estimation by the combination of numerical optimization and symbolic computation

• Project/Area Number: 23700358
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Bioinformatics/Life informatics
• Research Institution: Kyoto University
• Principal Investigator: NAKATSUI Masahiko 京都大学, 大学院・薬学研究科, 特定研究員 (10509532)
• Project Period (FY): 2011 – 2012
• Project Status: Completed (Fiscal Year 2012)
• Budget Amount: ¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000); Fiscal Year 2012: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000); Fiscal Year 2011: ¥2,340,000 (Direct Cost: ¥1,800,000、Indirect Cost: ¥540,000)
• Keywords: 生体生命システム情報学 / 数値最適化 / パラメータ推定 / 動的システム / 記号計算 / 反応パラメータ推定

Research Abstract

We proposed highly accurate parameter estimation method based on time-series data, by introducing constraints equations among estimated parameters derived rationally by symbolic computing technique to numerical optimization method. The performance of our proposed method of parameter accuracy is demonstrated by some representative model in biology, especially negative feed-back model which yields oscillations. The highly accurate parameter estimation method for dynamical systems we proposed will be the basis of systemically identification, analysis, control, and design of biological phenomena.

Research Products

• [Journal Article] A General Procedure for Accurate parameter Estimation in Dynamic Systems Using New Estimation Errors (2012)
  • Author(s): Masahiko Nakatsui, Alexandre Sedglavic, Francois Lemaire, Francois Boulier, Asli Urguplu, and Katsuhisa Horimoto
  • Journal Title: Algebraic and Numeric Biology, Lecture Notes in Computer Science Volume: Volume 6479 Pages: 149-166
  • Peer Reviewed
• [Journal Article] Efficient numerical optimization algorithm based on new real-coded genetic algorithm, AREX + JGG, and application to the inverse problem in systems biology (2012)
  • Author(s): Asako Komori, Yukihiro Maki, Masahiko Nakatsui, Isao Ono, and Masahiro Okamoto
  • Journal Title: Applied Mathematics Volume: 3 Pages: 1463-1470
  • Peer Reviewed
• [Journal Article] Efficient numerical optimization algorithm based on new real-coded genetic algorithm, AREX + JGG and application to the inverse problem in systems biology (2012)
  • Author(s): Asako Komori, Yukihiro Maki, Masahiko Nakatsui, Isao Ono, and Masahiro Okamoto
  • Journal Title: Applied Mathematis Volume: 3 Issue: 10 Pages: 1463-1470
  • DOI: 10.4236/am.2012.330205
  • Peer Reviewed
• [Journal Article] A General Procedure for Accurate Parameter Estimation in Dynamic Systems Using New Estimation Errors (2012)
  • Author(s): Nakatsui, M., Sedoglavic, A., Lemaire, F., Boulier, F., Urguplu, A., and Horimoto, K.
  • Journal Title: Algebraic and Numeric Biology, Lecture Notes in Computer Science Volume: Volume 6479/2012 Pages: 149-166
  • DOI: 10.1007/978-3-642-28067-2_9
  • ISBN: 9783642280665, 9783642280672
  • Peer Reviewed
• [Journal Article] Brute force meets Bruno force in parameter optimization: introduction of novel constraints for parameter accuracy improvement by symbolic computation (2011)
  • Author(s): Masahiko Nakatsui, Katsuhisa Horimoto, Francois Lemaire, Asli Urguplu, Alexandre Sedglavic, Francois Boulier
  • Journal Title: IET Systems Biology Volume: Volume 5 Issue 5 Pages: 281-292
  • Peer Reviewed
• [Journal Article] Brute force meets Bruno force in parameter optimisation: introduction of novel constraints for parameter accuracy improvement by symbolic computation (2011)
  • Author(s): Nakatsui, M., Horimoto, K., Lemaire, F., Urguplu, A., Sedoglavic, A., Boulier, F.
  • Journal Title: IET Systems Biology Volume: Volume:5 Issue:5 Issue: 5 Pages: 281-292
  • DOI: 10.1049/iet-syb.2010.0051
  • Peer Reviewed
• [Presentation] Chemogenomic approach to comprehensive predictions of ligand-target interactions: A comparative study (2012)
  • Author(s): J. B. Brown, Satoshi Niijima, Akira Shiraishi, Masahiko Nakatsui, and Yasuyuki Okuno
  • Organizer: 2012 Workshop on Pharmaco-Informatics for Drug Discovery, in Conjunction with 2012 IEEE International Conference on Bioinformatics and Biomedicine
  • Place of Presentation: Philadelphia, PA, USA
• [Remarks] S-system ネットワーク推定プラットホーム
  • URL: http://bp.scitec.kobe-u.ac.jp:10031/sweb