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Mathematical analysis of locomotion, learning, and memory using stochastic models

Planned Research

Project AreaSystems molecular ethology to understand the operating principle of the nervous system
Project/Area Number 20115009
Research Category

Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

Allocation TypeSingle-year Grants
Review Section Biological Sciences
Research InstitutionThe University of Tokyo

Principal Investigator

MASUDA Naoki  東京大学, 大学院・情報理工学系研究科, 准教授 (40415295)

Co-Investigator(Kenkyū-buntansha) OHKUBO Jun  京都大学, 情報学研究科, 講師 (70451888)
Co-Investigator(Renkei-kenkyūsha) NOZAKI Daichi  東京大学, 教育学研究科, 教授 (70360683)
Project Period (FY) 2008 – 2012
Project Status Completed (Fiscal Year 2012)
Budget Amount *help
¥33,930,000 (Direct Cost: ¥26,100,000、Indirect Cost: ¥7,830,000)
Fiscal Year 2012: ¥6,630,000 (Direct Cost: ¥5,100,000、Indirect Cost: ¥1,530,000)
Fiscal Year 2011: ¥6,630,000 (Direct Cost: ¥5,100,000、Indirect Cost: ¥1,530,000)
Fiscal Year 2010: ¥6,630,000 (Direct Cost: ¥5,100,000、Indirect Cost: ¥1,530,000)
Fiscal Year 2009: ¥6,630,000 (Direct Cost: ¥5,100,000、Indirect Cost: ¥1,530,000)
Fiscal Year 2008: ¥7,410,000 (Direct Cost: ¥5,700,000、Indirect Cost: ¥1,710,000)
Keywordsネットワーク / 統計物理学 / 確率過程 / ランダム・ウォーク / 走性 / 学習 / 脳・神経 / 数理工学 / ゲノム / 行動学 / 遺伝子
Research Abstract

First, we analyzed a data set obtained from locomotion of Caenorhabditis elegans and revealed its long-tailed nature. Second, we proposed a measure of importance of nodes in directed networks, corresponding to neurons, for example, in biological networks, using the so-called Laplacian matrix of the network. Third, we used a coupled oscillator model to quantify the precision of oscillatory rhythms in synchronous cell networks. Fourth, we applied the maximum entropy model to data of brain networks to estimate the network structure to find that the proposed method inferred the anatomical network with a higher accuracy than previous methods did. Fifth, we analyzed general temporal networks in which events were dynamical objects on links in networks.

Report

(7 results)
  • 2012 Annual Research Report   Final Research Report ( PDF )
  • 2011 Annual Research Report
  • 2010 Annual Research Report   Self-evaluation Report ( PDF )
  • 2009 Annual Research Report
  • 2008 Annual Research Report
  • Research Products

    (67 results)

All 2013 2012 2011 2010 2009 2008 Other

All Journal Article (45 results) (of which Peer Reviewed: 45 results) Presentation (17 results) Book (2 results) Remarks (3 results)

  • [Journal Article] Systematic analysis of neural projections in the Drosophila brain as a composition of clonally associated units2013

    • Author(s)
      Ito, M., Masuda, N., Shinomiya, K., Endo, K., and Ito, K
    • Journal Title

      Current Biology

      Volume: 23 Pages: 644-655

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] A pairwise maximum entropy model accurately describes resting-state human brain networks2013

    • Author(s)
      Watanabe, T., Hirose, S., Wada, H., Imai, Y., Machida, T., Shirouzu, I., Konishi, S., Miyashita, Y., and Masuda, N
    • Journal Title

      Nature Communications

      Volume: 4 Pages: 1370-1370

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] A pairwise maximum entropy model accurately describes resting-state human brain networks.2013

    • Author(s)
      渡部喬光
    • Journal Title

      Nature Communications

      Volume: 4 Issue: 1 Pages: 1370-1370

    • DOI

      10.1038/ncomms2388

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Systematic Analysis of Neural Projections Reveals Clonal Composition of the Drosophila Brain2013

    • Author(s)
      Masayoshi Ito, Naoki Masuda, Kazunori Shinomiya, Keita Endo, Ito Kei
    • Journal Title

      Current Biology

      Volume: 23 Issue: 8 Pages: 644-655

    • DOI

      10.1016/j.cub.2013.03.015

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Indirect reciprocity with trinary reputations2013

    • Author(s)
      Shoma Tanabe, Hideyuki Suzuki, Naoki Masuda (第一著者:Shoma Tanabe)
    • Journal Title

      Journal of Theoretical Biology

      Volume: 317 Pages: 338-347

    • DOI

      10.1016/j.jtbi.2012.10.031

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Groupwise information sharing promotes ingroup favoritism in indirect reciprocity2012

    • Author(s)
      Nakamura, M., and Masuda, N
    • Journal Title

      BMC Evolutionary Biology

      Volume: 12 Pages: 213-213

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] One-parameter extension of the Doi-Peliti formalism and its relation with orthogonal polynomials2012

    • Author(s)
      Ohkubo, J
    • Journal Title

      Physical Review E

      Volume: 86 Pages: 42102-42102

    • NAID

      120004945140

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Counting statistics for genetic switches based on effective-interaction approximation2012

    • Author(s)
      Ohkubo J
    • Journal Title

      Journal of Chemical Physics

      Volume: 137 Pages: 125102-125102

    • NAID

      120004873983

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Structure of cell networks critically determines oscillation regularity2012

    • Author(s)
      Kori, H., Kawamura, Y., and Masuda, N
    • Journal Title

      Journal of Theoretical Biology

      Volume: 297 Pages: 61-72

    • Related Report
      2012 Final Research Report 2011 Annual Research Report 2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Dopamine modulates the rest period length without perturbation of its power law distribution in Drosophila melanogaster2012

    • Author(s)
      Ueno, T., Masuda, N., Kume, S., and Kume, K
    • Journal Title

      PLoS ONE

      Volume: 7

    • NAID

      120004997256

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Importance of individual events in temporal networks2012

    • Author(s)
      Takaguchi, T., Sato, N., Yano, K., and Masuda, N
    • Journal Title

      New Journal of Physics

      Volume: 14 Pages: 93003-93003

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] One-parameter extension of the Doi-Peliti formalism and its relation with orthogonal polynomials2012

    • Author(s)
      J. Ohkubo
    • Journal Title

      Physical Review E

      Volume: 86 Pages: 042102-042102

    • NAID

      120004945140

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Counting statistics for genetic switches based on effective-interaction approximation2012

    • Author(s)
      J. Ohkubo
    • Journal Title

      Journal of Chemical Physics

      Volume: 137 Issue: 12 Pages: 125102-125102

    • DOI

      10.1063/1.4754537

    • NAID

      120004873983

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Groupwise information sharing promotes ingroup favoritism in indirect reciprocity2012

    • Author(s)
      M. Nakamura, N. Masuda
    • Journal Title

      BMC Evolutionary Biology

      Volume: 12 Issue: 1 Pages: 213-213

    • DOI

      10.1186/1471-2148-12-213

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Dopamine modulates the rest period length without perturbation of itspower law distribution in Drosophila melanogaster2012

    • Author(s)
      T. Ueno, N. Masuda, S. Kume, K. Kume
    • Journal Title

      PLoS ONE

      Volume: 7 Issue: 2 Pages: e32007-e32007

    • DOI

      10.1371/journal.pone.0032007

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Approximation scheme based on effective interactions for stochastic gene regulation2011

    • Author(s)
      Ohkubo, J
    • Journal Title

      Physical Review E

      Volume: 83 Pages: 41915-41915

    • NAID

      120003338851

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Nonparametric model reconstruction for stochastic differential equation from discretely observed time-series data2011

    • Author(s)
      Ohkubo, J
    • Journal Title

      Physical Review E

      Volume: 84 Pages: 77802-77802

    • NAID

      120003779166

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Clustering in large networks does not promote upstream reciprocity2011

    • Author(s)
      Masuda, N
    • Journal Title

      PLoS ONE

      Volume: 6

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Nonparametric model reconstruction for stochastic differential equation from discretely observed time-series data2011

    • Author(s)
      J. Ohkubo
    • Journal Title

      Physical Review E

      Volume: 84 Issue: 6 Pages: 66702-66702

    • DOI

      10.1103/physreve.84.066702

    • NAID

      120003779166

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Approximation scheme based on effective interactions for stochastic gene regulation2011

    • Author(s)
      J. Ohkubo
    • Journal Title

      Physical Review E

      Volume: 83 Issue: 4

    • DOI

      10.1103/physreve.83.041915

    • NAID

      120003338851

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Nonparametric model reconstruction for stochastic differential equation from discretely observed time-seriea data2011

    • Author(s)
      Jun Ohkubo
    • Journal Title

      Physical Review E

      Volume: 84

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Approximation scheme based on effective interactions for stochastic gene regulation2011

    • Author(s)
      Jun Ohkubo
    • Journal Title

      Physical Review E

      Volume: 83

    • NAID

      120003338851

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Direct numerical method for counting statistics in stochastic processes2010

    • Author(s)
      Ohkubo, J., and Eggel, T
    • Journal Title

      Journal of Statistical Mechanics

      Volume: P06013

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Long-tail behavior in locomotion of Caenorhabditis elegans2010

    • Author(s)
      Ohkubo, J., Yoshida, K., Iino, Y., and Masuda, N
    • Journal Title

      Journal of Theoretical Biology

      Volume: 267 Pages: 213-222

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Dynamics-based centrality for general directed networks2010

    • Author(s)
      Masuda, N., and Kori, H
    • Journal Title

      Physical Review E

      Volume: 82 Pages: 56107-56107

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Enhancing the spectral gap of networks by node removal2010

    • Author(s)
      Watanabe, T., and Masuda, N
    • Journal Title

      Physical Review E

      Volume: 82 Pages: 46102-46102

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Upstream reciprocity in heterogeneous networks2010

    • Author(s)
      Iwagami, A., and Masuda, N
    • Journal Title

      Journal of Theoretical Biology

      Volume: 265 Pages: 297-305

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Collective fluctuations in networks of noisy components2010

    • Author(s)
      Masuda, N., Kawamura, Y., and Kori, H
    • Journal Title

      New Journal of Physics

      Volume: 12 Pages: 93007-93007

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Long-tail behavior in locomotion of Caenorhabditis elegans.2010

    • Author(s)
      J.Ohkubo, K.Yoshida, Y.Iino, N.Masuda.
    • Journal Title

      Journal of Theoretical Biology 267

      Pages: 213-222

    • Related Report
      2010 Self-evaluation Report
    • Peer Reviewed
  • [Journal Article] Direct numerical method for counting statistics in stochastic processes.2010

    • Author(s)
      J.Ohkubo, T.Eggel.
    • Journal Title

      Journal of Statistical Mechanics. P06013

    • Related Report
      2010 Self-evaluation Report
    • Peer Reviewed
  • [Journal Article] Collective fluctuations in networks of noisy components.2010

    • Author(s)
      N.Masuda, Y.Kawamura, H.Kori.
    • Journal Title

      New Journal of Physics 12

      Pages: 93007-93007

    • Related Report
      2010 Self-evaluation Report
    • Peer Reviewed
  • [Journal Article] Posterior probability and fluctuation theorem in stochastic processes2009

    • Author(s)
      Ohkubo, J
    • Journal Title

      Journal of the Physical Society of Japan

      Volume: 78 Pages: 123001-123001

    • NAID

      130005437256

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Analysis of relative influence of nodes in directed networks2009

    • Author(s)
      Masuda, N., Kawamura, Y., and Kori, H
    • Journal Title

      Physical Review E

      Volume: 80 Pages: 46114-46114

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Impact of hierarchical modular structure on ranking of individual nodes in directed networks2009

    • Author(s)
      Masuda, N., Kawamura, Y., and Kori, H
    • Journal Title

      New Journal of Physics

      Volume: 11 Pages: 113002-113002

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Impact of hierarchical modular structure on ranking of individual nodes in directed networks.2009

    • Author(s)
      N.Masuda, Y.Kawamura, H.Kori.
    • Journal Title

      New Journal of Physics 11

      Pages: 113002-113002

    • Related Report
      2010 Self-evaluation Report
    • Peer Reviewed
  • [Journal Article] Impact of hierarchical modular structure on ranking of individual nodes in directed networks2009

    • Author(s)
      Naoki Masuda, Yoji Kawamura, Hiroshi Kori
    • Journal Title

      New Journal of Physics

      Volume: 11

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Analysis of relative influence of nodes in directed networks2009

    • Author(s)
      Naoki Masuda, Yoji Kawamura, Hiroshi Kori
    • Journal Title

      Physical Review E

      Volume: 80

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Posterior probability and fluctuation theorem in stochastic processes2009

    • Author(s)
      Jun Ohkubo
    • Journal Title

      Journal of the Physical Society of Japan

      Volume: 78

    • NAID

      130005437256

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Evolutionary dynamics and fixation probabilities in directed networks2009

    • Author(s)
      N.Masuda, H.Ohtsuki
    • Journal Title

      New Journal of Physics 11

      Pages: 33012-33012

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Priority queues with bursty arrivals of incoming tasks2009

    • Author(s)
      N.Masuda, J.S.Kim, B.Kahng
    • Journal Title

      Physical Review E 79

      Pages: 36106-36106

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Directionality of contact networks suppresses selection pressure in evolutionary dynamics2009

    • Author(s)
      N.Masuda
    • Journal Title

      Journal of Theoretical Biology 258

      Pages: 323-334

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Posterior probability and fluctuation theorem in stochastic processes2009

    • Author(s)
      J.Ohkubo
    • Journal Title

      Journal of the Physical Society of Japan 78

      Pages: 123001-123001

    • NAID

      130005437256

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The stochastic pump current and the non-adiabatic geometrical phase.2008

    • Author(s)
      J.Ohkubo.
    • Journal Title

      Journal of Statistical Mechanics P02011

    • Related Report
      2010 Self-evaluation Report
    • Peer Reviewed
  • [Journal Article] The stochastic pump current and the non-adiabatic geometrical phase2008

    • Author(s)
      J.Ohkubo
    • Journal Title

      Journal of Statistical Mechanics

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The stochastic pump current and the non-adiabatic geometrical phase

    • Author(s)
      Ohkubo, J
    • Journal Title

      Journal of Statistical Mechanics

      Volume: P02011

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Presentation] Simplicity of human brain networks: resting-state functional brain networks can be accurately described by a pairwise maximum entropy model2013

    • Author(s)
      T. Watanabe, S. Hirose, H. Wada, Y. Imai, T. Machida, I. Shirouzu, S. Konishi, Y. Miyashita, N. Masuda
    • Organizer
      第36回日本神経科学大会
    • Place of Presentation
      国立京都国際会館、京都
    • Year and Date
      2013-06-20
    • Related Report
      2012 Annual Research Report
  • [Presentation] Second-order maximum entropy models applied to macroscopic resting-sate networks in human brains2013

    • Author(s)
      T. Watanabe, S. Hirose, H. Wada, Y. Imai, T. Machida, I. Shirouzu, S. Konishi, Y. Miyashita, N. Masuda
    • Organizer
      NetSci2013
    • Place of Presentation
      Copenhagen, Denmark
    • Year and Date
      2013-06-03
    • Related Report
      2012 Annual Research Report
  • [Presentation] Network structure dependence of collective enhancement of temporal precision in coupled noisy oscillators2013

    • Author(s)
      Kori, H., Kawamura, Y., and Masuda, N
    • Organizer
      The First Annual Winter q-bio Meeting
    • Place of Presentation
      Waikiki, Hawaii
    • Related Report
      2012 Final Research Report
  • [Presentation] Dependence of oscillation regularity on structure of networks2012

    • Author(s)
      Naoki Masuda
    • Organizer
      Anomalous Statistics, Generalized Entropies and Information Geometry invited
    • Place of Presentation
      奈良・奈良女子大学
    • Year and Date
      2012-03-08
    • Related Report
      2011 Annual Research Report
  • [Presentation] Quantifying importance of interaction events in temporal networks2012

    • Author(s)
      Masuda, N
    • Organizer
      Toward Mathematical Foundations of Complex Network Theory
    • Place of Presentation
      Kyoto, Japan
    • Related Report
      2012 Final Research Report
  • [Presentation] Dependence of oscillation regularity on network structure in coupled noisy oscillators2012

    • Author(s)
      Kori, H., Kawamura, Y., and Masuda, N
    • Organizer
      European Conference on Complexf Systems (ECCS'12)
    • Place of Presentation
      Brussel, Belgium
    • Related Report
      2012 Final Research Report
  • [Presentation] A centrality measure for interaction events in temporal networks2012

    • Author(s)
      Takaguchi, T., Sato, N., Yano, K., and Masuda. N
    • Organizer
      European Conference on Complex Systems (ECCS'12)
    • Place of Presentation
      Brussel, Belgium
    • Related Report
      2012 Final Research Report
  • [Presentation] Detecting important interaction events in temporal networks2012

    • Author(s)
      Takaguchi, T., Sato, N., Yano, K., and Masuda, N
    • Organizer
      NetSci 2012
    • Place of Presentation
      Evanston, Illinois, USA
    • Related Report
      2012 Final Research Report
  • [Presentation] Dependence of oscillation regularity on structure of networks. Anomalous Statistics2012

    • Author(s)
      Masuda, N
    • Organizer
      Generalized Entropies and Information Geometry
    • Place of Presentation
      Nara, Japan
    • Related Report
      2012 Final Research Report
  • [Presentation] Network structure dependence of oscillation regularity in coupled noisy oscillators2011

    • Author(s)
      Kori, H., Kawamura, Y., and Masuda, N
    • Organizer
      Engineering of Chemical Complexity
    • Place of Presentation
      Berlin, Germany
    • Related Report
      2012 Final Research Report
  • [Presentation] Design principle of precise neural clocks2011

    • Author(s)
      Kori, H., Kawamura, Y., and Masuda, N
    • Organizer
      The 3rd International Conference on Cognitive Neurodynamics (ICCN2011)
    • Place of Presentation
      Hilton Niseko Village, Hokkaido, Japan
    • Related Report
      2012 Final Research Report
  • [Presentation] Sequential node removal to increase the spectral gap of networks2011

    • Author(s)
      Watanabe, T. and Masuda, N
    • Organizer
      NetSci 2011
    • Place of Presentation
      Budapest, Hungary
    • Related Report
      2012 Final Research Report
  • [Presentation] Collective phase diffusion in networks of noisy oscillators2011

    • Author(s)
      Masuda, N., Kawamura, Y., and Kori, H
    • Organizer
      SIAM Conference on Applications of Dynamical Systems. Workshop: Linking Neuronal Network Architecture and Collective Dynamics
    • Place of Presentation
      Snowbird, Utah, USA
    • Related Report
      2012 Final Research Report
  • [Presentation] A dynamic model of sensory integration of conflicting stimuli in AIA interneurons of C.elegans2011

    • Author(s)
      中林潤, 増田直紀
    • Organizer
      第34回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜
    • Related Report
      2010 Annual Research Report
  • [Presentation] 有向ネットワークの中心性とペースメーカー系の同期現象について2010

    • Author(s)
      増田直紀, 河村洋史, 郡宏
    • Organizer
      日本物理学会第65回年次大会
    • Place of Presentation
      岡山大学
    • Year and Date
      2010-03-20
    • Related Report
      2009 Annual Research Report
  • [Presentation] Theory of collective enhancement of temporal precision in oscillator networks2010

    • Author(s)
      Kori, H., Kawamura, Y., and Masuda, N
    • Organizer
      Biosignal 2010
    • Place of Presentation
      Berlin, Germany
    • Related Report
      2012 Final Research Report
  • [Presentation] Theory of collective enhancement of temporal precision in oscillator networks.2010

    • Author(s)
      H.Kori, Y.Kawamura, N.Masuda.
    • Organizer
      Biosignal 2010
    • Place of Presentation
      Berlin, Germany
    • Related Report
      2010 Self-evaluation Report
  • [Book] 複雑ネットワーク 基礎から応用まで2010

    • Author(s)
      増田直紀,今野紀雄
    • Publisher
      近代科学社
    • Related Report
      2012 Final Research Report
  • [Book] 複雑ネットワーク-基礎から応用まで2010

    • Author(s)
      増田直紀, 今野紀雄
    • Publisher
      近代科学社
    • Related Report
      2010 Self-evaluation Report
  • [Remarks] いくつかの研究成果の日本語による解説を以下のホームページで行っている

    • URL

      http://www.stat.t.u-tokyo.ac.jp/~masuda/

    • Related Report
      2012 Final Research Report
  • [Remarks] 増田直紀のウェブサイト

    • URL

      http://www.stat.t.u-tokyo.ac.jp/~masuda/

    • Related Report
      2012 Annual Research Report
  • [Remarks]

    • URL

      http://www.stat.t.u-tokyo.ac.jp/~masuda/

    • Related Report
      2011 Annual Research Report

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Published: 2008-04-01   Modified: 2018-03-28  

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