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Structurally Robust Control of Complex Networks

Research Project

Project/Area Number 26540125
Research Category

Grant-in-Aid for Challenging Exploratory Research

Allocation TypeMulti-year Fund
Research Field Soft computing
Research InstitutionKyoto University

Principal Investigator

Akutsu Tatsuya  京都大学, 化学研究所, 教授 (90261859)

Project Period (FY) 2014-04-01 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥3,640,000 (Direct Cost: ¥2,800,000、Indirect Cost: ¥840,000)
Fiscal Year 2016: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2015: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2014: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
Keywords複雑ネットワーク / スケールフリーネットワーク / ブーリアンネットワーク / 遺伝子ネットワーク / 最小支配集合 / 構造的可制御性 / ロバストネス
Outline of Final Research Achievements

In this project, we introduced the concept of the robust minimum dominating set for structurally robust control of complex networks by extending the minimum dominating set-based control framework that have been developed by the author and colleagues. We developed an integer programming (ILP)-based method for computing a robust minimum dominating set and theoretically analyzed its size. We extended this concept to the probabilistic minimum dominating set in order to cope with probabilistic edge failures, and developed an ILP-based computation method and theoretically analyzed its size. We also studied controllability and observability of a discrete model (Boolean network, BN) of genetic networks. We analyzed the number of nodes for controlling and observing states of BNs, and applied the obtained techniques to analysis of metabolic networks.

Report

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

    (34 results)

All 2018 2017 2016 2015 2014 Other

All Int'l Joint Research (5 results) Journal Article (16 results) (of which Int'l Joint Research: 4 results,  Peer Reviewed: 16 results,  Open Access: 8 results,  Acknowledgement Compliant: 9 results) Presentation (12 results) (of which Int'l Joint Research: 6 results,  Invited: 7 results) Book (1 results)

  • [Int'l Joint Research] ベングリオン大学(イスラエル)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] 香港大学/西安交通大学(中国)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] 香港大学(中国)

    • Related Report
      2016 Research-status Report
  • [Int'l Joint Research] 国立交通大学(台湾)

    • Related Report
      2016 Research-status Report
  • [Int'l Joint Research] ベングリオン大学(イスラエル)

    • Related Report
      2016 Research-status Report
  • [Journal Article] Discrimination of singleton and periodic attractors in Boolean networks2017

    • Author(s)
      Cheng Xiaoqing、Tamura Takeyuki、Ching Wai-Ki、Akutsu Tatsuya
    • Journal Title

      Automatica

      Volume: 84 Pages: 205-213

    • DOI

      10.1016/j.automatica.2017.07.012

    • NAID

      120006542020

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Critical controllability analysis of directed biological networks using efficient graph reduction2017

    • Author(s)
      M. Ishitsuka1, T. Akutsu, J. C. Nacher
    • Journal Title

      Scientific Reports

      Volume: 7 Issue: 1 Pages: 14361-14361

    • DOI

      10.1038/s41598-017-14334-8

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Critical controllability in proteome-wide protein interaction network integrating transcriptome2016

    • Author(s)
      M. Ishitsuka, T. Akutsu and J.C. Nacher
    • Journal Title

      Scientific Reports

      Volume: 6 Issue: 1 Pages: 1-14

    • DOI

      10.1038/srep23541

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Minimum dominating set-based Methods for Analyzing Biological Networks2016

    • Author(s)
      J.C. Nacher and T. Akutsu
    • Journal Title

      Methods

      Volume: 印刷中 Pages: 57-63

    • DOI

      10.1016/j.ymeth.2015.12.017

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Complex network-based approaches to biomarker discovery2016

    • Author(s)
      Hayashida, M. and Akutsu, T.
    • Journal Title

      Biomarkers in Medicine

      Volume: 10 Issue: 6 Pages: 621-632

    • DOI

      10.2217/bmm-2015-0047

    • Related Report
      2016 Research-status Report
    • Peer Reviewed
  • [Journal Article] Analysis of the effect of degree correlation on the size of minimum dominating sets in complex networks2016

    • Author(s)
      Takemoto K, Akutsu T
    • Journal Title

      PLoS ONE

      Volume: 11 Issue: 6 Pages: e0157868-e0157868

    • DOI

      10.1371/journal.pone.0157868

    • NAID

      120005819482

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Finding and analyzing the minimum set of driver nodes in control of Boolean networks2016

    • Author(s)
      Wenpin Hou, Takeyuki Tamura, Wai-Ki. Ching and Tatsuya Akutsu
    • Journal Title

      Advances in Complex Systems

      Volume: 19 Issue: 03 Pages: 1650006-1650006

    • DOI

      10.1142/s0219525916500065

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Exact identification of the structure of a probabilistic Boolean network from samples2016

    • Author(s)
      X. Cheng, T. Mori, Y. Qiu, W-K. Ching, T. Akutsu
    • Journal Title

      IEEE/ACM Transactions on Computational Biology and Bioinformatics

      Volume: 13 Issue: 6 Pages: 1107-1116

    • DOI

      10.1109/tcbb.2015.2505310

    • NAID

      120006863512

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Finding influential genes using gene expression data and Boolean models of metabolic networks2016

    • Author(s)
      T. Tamura, C-Y. Lin, J-M. Yang, T. Akutsu
    • Journal Title

      Proc. IEEE 16th International Conference on Bioinformatics and Bioengineering

      Volume: - Pages: 57-63

    • DOI

      10.1109/bibe.2016.25

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Computational methods for modification of metabolic networks2015

    • Author(s)
      T. Tamura, W. Liu, T. Akutsu
    • Journal Title

      Computational and Structural Biotechnology Journal

      Volume: 12 Pages: 376-381

    • DOI

      10.1016/j.csbj.2015.05.004

    • NAID

      120005712915

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Matrix Network: A New Data Structure for Efficient Enumeration of Microstates of a Genetic Regulatory Network2015

    • Author(s)
      X. Cong, T. Akutsu
    • Journal Title

      Journal of Information Processing

      Volume: 23 Issue: 6 Pages: 804-813

    • DOI

      10.2197/ipsjjip.23.804

    • NAID

      130005109167

    • ISSN
      1882-6652
    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Determining associations between human diseases and non-coding RNAs with critical roles in network control2015

    • Author(s)
      H. Kagami, T. Akutsu, S. Maegawa, H. Hosokawa, J. C. Nacher
    • Journal Title

      Scientific Reports

      Volume: 5 Issue: 1 Pages: 14577-14577

    • DOI

      10.1038/srep14577

    • NAID

      120005818233

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] A Fixed-Parameter Algorithm for Detecting a Singleton Attractor in an AND/OR Boolean Network with Bounded Treewidth2015

    • Author(s)
      Chia-Jung Chang, Takeyuki Tamura, Kun-Mao Chao and Tatsuya Akutsu
    • Journal Title

      IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences

      Volume: E98.A Issue: 1 Pages: 384-390

    • DOI

      10.1587/transfun.E98.A.384

    • NAID

      130004770922

    • ISSN
      0916-8508, 1745-1337
    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Structurally Robust Control of Complex Networks2015

    • Author(s)
      J.C. Nacher and T. Akutsu
    • Journal Title

      Physical Review E

      Volume: 91 Issue: 1 Pages: 0128261-19

    • DOI

      10.1103/physreve.91.012826

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Computing smallest intervention strategies for multiple metabolic networks in a boolean model.2015

    • Author(s)
      Lu, W., Tamura, T., Song, J. & Akutsu, T.
    • Journal Title

      Journal of computational biology

      Volume: 22 Issue: 2 Pages: 85-110

    • DOI

      10.1089/cmb.2014.0274

    • NAID

      120005657917

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Analysis of critical and redundant nodes in controlling directed and undirected complex networks using dominating sets2014

    • Author(s)
      J.C. Nacher and T. Akutsu
    • Journal Title

      Journal of Complex Networks

      Volume: 2 Issue: 4 Pages: 394-412

    • DOI

      10.1093/comnet/cnu029

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Presentation] On the minimum number of genes required for discriminating steady states under a Boolean model2017

    • Author(s)
      X. Cheng, T. Tamura, W-K. Ching, T. Akutsu
    • Organizer
      情報処理学会第51回バイオ情報学研究会
    • Related Report
      2017 Annual Research Report
  • [Presentation] On exact identification of the structure of a probabilistic Boolean threshold network from samples2017

    • Author(s)
      A. A. Melkman, X. Cheng, W-K. Ching, T. Akutsu
    • Organizer
      情報処理学会第113回MPS・第50回BIO合同研究発表会
    • Related Report
      2017 Annual Research Report
  • [Presentation] 最小支配集合に基づく有向生体ネットワーク解析のための高速アルゴリズム2017

    • Author(s)
      石塚雅之, 阿久津達也, ナチェルホセ
    • Organizer
      情報処理学会第113回MPS・第50回BIO合同研究発表会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Extensions and Applications of the Minimum Dominating Set-Based Approach to Controllability of Complex Networks2016

    • Author(s)
      T. Akutsu
    • Organizer
      Controlling Complex Networks (Satellite Symposium of International School and Conference on Network Science)
    • Place of Presentation
      韓国・ソウル ・K-Hotel
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Minimum Dominating Set-Based Approaches for Controlling and Analyzing Biological Networks2016

    • Author(s)
      T. Akutsu
    • Organizer
      Controlling Complex Network Systems in Biology (Workshop)
    • Place of Presentation
      理研和光キャンパス
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Minimum Dominating Set-based Approaches for Analyzing and Controlling Biological Networks2016

    • Author(s)
      T. Akutsu
    • Organizer
      第26回日本数理生物学会大会
    • Place of Presentation
      九州大学伊都キャンパス
    • Related Report
      2016 Research-status Report
    • Invited
  • [Presentation] Finding Influential Genes Using Gene Expression Data and Boolean Models of Metabolic Networks2016

    • Author(s)
      T. Tamura, C-Y. Lin, J-M. Yang, T. Akutsu
    • Organizer
      IEEE 16th International Conference on Bioinformatics and Bioengineering
    • Place of Presentation
      台湾・台中・Splendor Hotel
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Presentation] Minimum Dominating Set-based Approaches for Analyzing and Controlling Biological Networks2016

    • Author(s)
      T. Akutsu
    • Organizer
      2016 Biotech and Pharmaceutical Service Platform - Biological Network Analysis Conference
    • Place of Presentation
      台湾・国立交通大学
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Minimum Dominating Set-based Approach to Analysis and Control of Biological Networks2015

    • Author(s)
      T. Akutsu
    • Organizer
      The Protein Network Workshop
    • Place of Presentation
      Institute for Mathematical Sciences, NUS, Singapore
    • Year and Date
      2015-06-08
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Minimum Dominating Set-based Approaches for Analyzing and Controlling Biological Networks2015

    • Author(s)
      T. Akutsu
    • Organizer
      9th Asian Biophysics Association Symposium
    • Place of Presentation
      Shangyu International Hotel, China
    • Year and Date
      2015-05-09
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] non-coding RNA-タンパク質相互作用ネットワークとその制御性の特徴分析2014

    • Author(s)
      香々見春菜, 阿久津達也, ホセ・ナチェル
    • Organizer
      情報処理学会バイオ情報学研究会
    • Place of Presentation
      産業技術総合研究所 臨海副都心センター別館
    • Year and Date
      2014-12-18
    • Related Report
      2014 Research-status Report
  • [Presentation] ブーリアントネットワークにおけるアトラクターの検出、観測、制御2014

    • Author(s)
      阿久津達也
    • Organizer
      日本バイオインフォマティクス学会 生命システム理論研究会
    • Place of Presentation
      京都大学 iPS細胞研究所
    • Year and Date
      2014-11-18
    • Related Report
      2014 Research-status Report
    • Invited
  • [Book] Algorithms for Analysis, Inference, and Control of Boolean Networks2018

    • Author(s)
      Tatsuya Akutsu
    • Total Pages
      228
    • Publisher
      World Scientific
    • ISBN
      9789813233423
    • Related Report
      2017 Annual Research Report

URL: 

Published: 2014-04-04   Modified: 2022-02-22  

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