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Design automation of multi-element gene circuits

Research Project

Project/Area Number 26280094
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypePartial Multi-year Fund
Section一般
Research Field Soft computing
Research InstitutionThe University of Tokyo

Principal Investigator

Iba Hitoshi  東京大学, 大学院情報理工学系研究科, 教授 (40302773)

Project Period (FY) 2014-04-01 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥13,260,000 (Direct Cost: ¥10,200,000、Indirect Cost: ¥3,060,000)
Fiscal Year 2016: ¥4,810,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥1,110,000)
Fiscal Year 2015: ¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000)
Fiscal Year 2014: ¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000)
Keywords遺伝的プログラミング / 進化計算 / 遺伝子ネットワーク / 進化発生アプローチ / 遺伝子アルゴリズム / 力学系 / 動的適応システム / 遺伝的アルゴリズム / Evo-Devアプローチ / 進化発達系 / 発生型アプローチ / 発生型システム / Evo-devアプローチ / 進化型ロボット
Outline of Final Research Achievements

As a result of the recent revival in Evo-Devo (Evolutionary Developmental Biology), dramatic changes are occurring in regard to our understanding of the genetic control networks of organisms. In this direction, there are high expectations for the application of gene regulatory networks (GRNs) to various fields, e.g., robotics, engineering design, architectures, etc., because of their intrinsic robustness and modularity as well as the possibility of evolution and compression of complex expression. We have established the evolutionary framework of GRNs through differential evolution for learning of networks that generate multiple motion, and verifies whether the networks generate motion correctly using simulators and actual robots.

Report

(5 results)
  • 2017 Annual Research Report   Final Research Report ( PDF )
  • 2016 Annual Research Report
  • 2015 Annual Research Report
  • 2014 Annual Research Report
  • Research Products

    (32 results)

All 2018 2017 2016 2015 2014 Other

All Journal Article (6 results) (of which Int'l Joint Research: 4 results,  Peer Reviewed: 6 results,  Open Access: 4 results,  Acknowledgement Compliant: 3 results) Presentation (15 results) (of which Int'l Joint Research: 6 results) Book (8 results) Remarks (3 results)

  • [Journal Article] Pulse Detecting Genetic Circui--A New Design Approach2016

    • Author(s)
      Nasimul Noman , Mara Inniss, Hitoshi Iba, Jeffrey C. Way
    • Journal Title

      PLOS ONE

      Volume: 12 Issue: 12 Pages: 1-13

    • DOI

      10.1371/journal.pone.0167162

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Evolving Robust Gene Regulatory Networks2015

    • Author(s)
      Noman,N., Monjo,T., Moscato,P., Iba,H.
    • Journal Title

      PLoS ONE

      Volume: 10 Issue: 1 Pages: 1-21

    • DOI

      10.1371/journal.pone.0116258

    • Related Report
      2015 Annual Research Report 2014 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] An Effective Method for Evolving Reaction Networks in Synthetic Biochemical Systems2015

    • Author(s)
      Dinh,H., Aubert,N., Noman,N., Fujii,T., Rondelez,Y., Iba,H.
    • Journal Title

      IEEE Transactions on Evolutionary Computation

      Volume: 19 Issue: 3 Pages: 374-386

    • DOI

      10.1109/tevc.2014.2326863

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Improved sampling using loopy belief propagation for probabilistic model building genetic programming2015

    • Author(s)
      Sato,H., Hasegawa,Y., Bollegala,D., Iba,H.
    • Journal Title

      Swarm and Evolutionary Computation

      Volume: 23 Pages: 1-10

    • DOI

      10.1016/j.swevo.2015.02.002

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Oscillatory synthetic biological system construction using interactive evolutionary computations2014

    • Author(s)
      Dinh,H., Noman,N., Iba,H.
    • Journal Title

      Journal of Computer Science

      Volume: 10 Pages: 2640-2652

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Converting Motion between Different Types of Humanoid Robots Using Genetic Algorithms2014

    • Author(s)
      Nishiyama,M., Iba,H
    • Journal Title

      International Journal of Computer Theory and Engineering

      Volume: 7 Pages: 97-102

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Presentation] Coevolution of mapping functions for linear SVM2017

    • Author(s)
      Satish Kumar Jaiswal, Hitoshi Iba
    • Organizer
      2017 IEEE Congress on Evolutionary Computation (CEC2017)
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] パラメトリック遺伝的プログラミング2017

    • Author(s)
      堀場貴裕,伊庭斉志
    • Organizer
      進化計算シンポジウム2017
    • Related Report
      2017 Annual Research Report
  • [Presentation] 遺伝的アルゴリズムを用いた誤判定音声合成2017

    • Author(s)
      楊奕,伊庭斉志
    • Organizer
      進化計算シンポジウム2017
    • Related Report
      2017 Annual Research Report
  • [Presentation] 動的環境最適化におけるAffinity Propagationを用いた粒子群最適化2017

    • Author(s)
      鈴木一弘,伊庭斉志
    • Organizer
      進化計算シンポジウム2017
    • Related Report
      2017 Annual Research Report
  • [Presentation] 進化計算を用いた時間依存型確率的化学反応の推定2017

    • Author(s)
      海内映吾,伊庭斉志
    • Organizer
      進化計算シンポジウム2017
    • Related Report
      2017 Annual Research Report
  • [Presentation] Optimization of artificial operon construction by consultation algorithms utilizing LCS2016

    • Author(s)
      Changhee Han, Kenji Tsuge, Hitoshi Iba
    • Organizer
      IEEE Congress on Evolutionary Computation, CEC 2016
    • Place of Presentation
      Vancouver, BC, Canada
    • Year and Date
      2016-07-24
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Vanishing ideal genetic programming2016

    • Author(s)
      Hiroshi Kera, Hitoshi Iba
    • Organizer
      IEEE Congress on Evolutionary Computation, CEC 2016
    • Place of Presentation
      Vancouver, BC, Canada
    • Year and Date
      2016-07-24
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Feature selection and classification using ensembles of genetic programs and within-class and between-class permutations2015

    • Author(s)
      Ivert,A., Aranha,C., Iba,H.
    • Organizer
      2015 IEEE Congress on Evolutionary Computation (CEC)
    • Place of Presentation
      仙台国際センター(宮城県,仙台市)
    • Year and Date
      2015-05-25
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Evolutionary design of oscillatory genetic networks in silico2015

    • Author(s)
      Naruse,Y., Hamada,H., Hanai,T., Iba,H.
    • Organizer
      2015 IEEE Congress on Evolutionary Computation (CEC)
    • Place of Presentation
      仙台国際センター(宮城県,仙台市)
    • Year and Date
      2015-05-25
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] A double swarm methodology for parameter estimation in oscillating Gene Regulatory Networks2015

    • Author(s)
      Nobile,M.S., Iba,H.
    • Organizer
      2015 IEEE Congress on Evolutionary Computation (CEC)
    • Place of Presentation
      仙台国際センター(宮城県,仙台市)
    • Year and Date
      2015-05-25
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Nonlinear protein degradation for temperature compensation2014

    • Author(s)
      Peng,Y., Hasegawa,Y., Noman,N., Iba,H.
    • Organizer
      GIW / ISCB-Asia 2014
    • Place of Presentation
      国際交流館、東京都
    • Year and Date
      2014-12-15 – 2014-12-17
    • Related Report
      2014 Annual Research Report
  • [Presentation] Designing Robust Network Topology with Surrogate Assisted Genetic Algorithm2014

    • Author(s)
      Noman,N., Iba,H., Pablo,M.
    • Organizer
      The 15th International Conference on Systems Biology (ICSB)
    • Place of Presentation
      メルボルン、オーストラリア
    • Year and Date
      2014-09-14 – 2014-09-18
    • Related Report
      2014 Annual Research Report
  • [Presentation] Nonlinear Protein Degradation for Temperature Compensation2014

    • Author(s)
      Peng,Y., Hasegawa,Y., Noman,N., Iba,H.
    • Organizer
      International conference on computer science and manufacturing technologies (CMST-2014)
    • Place of Presentation
      バリ、インドネシア
    • Year and Date
      2014-08-02 – 2014-08-03
    • Related Report
      2014 Annual Research Report
  • [Presentation] Applying conversion matrix to robots for imitating motion using genetic algorithms2014

    • Author(s)
      Nishiyama,M., Iba,H.
    • Organizer
      IEEE Congress on Evolutionary Computation 2014 (CEC2014)
    • Place of Presentation
      北京,中国
    • Year and Date
      2014-07-06 – 2014-07-11
    • Related Report
      2014 Annual Research Report
  • [Presentation] Converting Motion Between Different Types of Humanoid Robots Using Genetic Algorithms2014

    • Author(s)
      Nishiyama,M., Iba,H.
    • Organizer
      The 6th International Conference on Future Computer and Communication (ICFCC 2014)
    • Place of Presentation
      シドニー、オーストラリア
    • Year and Date
      2014-05-29 – 2014-05-30
    • Related Report
      2014 Annual Research Report
  • [Book] Evolutionary Approach to Machine Learning and Deep Neural Networks: Neuro-Evolution and Gene Regulatory Networks2018

    • Author(s)
      Hitoshi Iba
    • Total Pages
      260
    • Publisher
      Springer
    • Related Report
      2017 Annual Research Report
  • [Book] 人工知能の創発2017

    • Author(s)
      伊庭斉志
    • Total Pages
      240
    • Publisher
      株式会社オーム社
    • ISBN
      4274220648
    • Related Report
      2017 Annual Research Report
  • [Book] 東京大学工学教程 情報工学 知識情報処2016

    • Author(s)
      伊庭斉志, ダヌシカ・ボレガラ
    • Total Pages
      134
    • Publisher
      丸善出版
    • Related Report
      2016 Annual Research Report
  • [Book] Excelで学ぶ進化計算―ExcelによるGAシミュレーション―2016

    • Author(s)
      伊庭斉志
    • Total Pages
      255
    • Publisher
      オーム社
    • Related Report
      2016 Annual Research Report
  • [Book] プログラミングで愉しむ数理パズル―未解決の難問やAIの課題に挑戦―2016

    • Author(s)
      伊庭斉志
    • Total Pages
      215
    • Publisher
      コロナ社
    • Related Report
      2016 Annual Research Report
  • [Book] Evolutionary Computation in Gene Regulatory Network Research2016

    • Author(s)
      Hitoshi Iba, Nasimul Noman
    • Total Pages
      439
    • Publisher
      Wiley
    • Related Report
      2016 Annual Research Report
  • [Book] 進化計算と深層学習―創発する知能―2015

    • Author(s)
      伊庭斉志
    • Total Pages
      182
    • Publisher
      オーム社
    • Related Report
      2015 Annual Research Report
  • [Book] 人工知能の方法2014

    • Author(s)
      伊庭斉志
    • Total Pages
      253
    • Publisher
      コロナ社
    • Related Report
      2014 Annual Research Report
  • [Remarks] 伊庭研究室

    • URL

      http://www.iba.k.u-tokyo.ac.jp/

    • Related Report
      2017 Annual Research Report
  • [Remarks] 伊庭研究室

    • URL

      http://www.iba.t.u-tokyo.ac.jp/

    • Related Report
      2016 Annual Research Report
  • [Remarks] 東京大学・伊庭研究室

    • URL

      http://www.iba.t.u-tokyo.ac.jp/

    • Related Report
      2015 Annual Research Report

URL: 

Published: 2014-04-04   Modified: 2019-03-29  

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