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Constructing state-space models that fit hierarchical networks to multitude of event sequences

Research Project

Project/Area Number 26280007
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypePartial Multi-year Fund
Section一般
Research Field Statistical science
Research InstitutionKyoto University

Principal Investigator

Shinomoto Shigeru  京都大学, 理学研究科, 准教授 (60187383)

Project Period (FY) 2014-04-01 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥12,610,000 (Direct Cost: ¥9,700,000、Indirect Cost: ¥2,910,000)
Fiscal Year 2018: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000)
Fiscal Year 2017: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000)
Fiscal Year 2016: ¥2,730,000 (Direct Cost: ¥2,100,000、Indirect Cost: ¥630,000)
Fiscal Year 2015: ¥2,730,000 (Direct Cost: ¥2,100,000、Indirect Cost: ¥630,000)
Fiscal Year 2014: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
Keywords神経スパイク / 状態空間法 / 大規模データ / 統計的因果性の解析 / 統計学 / 階層ネットワーク / 微視的不安定性 / ビッグデータ解析 / ネットワーク / 時系列解析 / 神経データ
Outline of Final Research Achievements

In this project, we have tackled the problem of reconstructing neuronal circuitry from a large number of parallel spike trains recorded from cortical neurons in vivo. The original idea of inferring neuronal synaptic connections from parallel spike trains was proposed by Perkel, Gerstein, and Moore in more than 50 years ago. The existing methods can give plausible inferences about connections but also have produced a lot of false inferences due to large fluctuations in neuronal activity. We constructed a new analytical method by applying a Generalized Linear Model to a cross-correlation between spike trains for a pair of neurons. The new method has the potential to capture the difference in neuronal computation in different brain regions. It took us 6 years to complete the study before we published the result in Nature Communications in 2019. We have also obtained a lot of other studies during this period.

Academic Significance and Societal Importance of the Research Achievements

近年は計測技術の急速な進展によって膨大な神経スパイク信号が得られるようになっているので,同時計測された信号列から神経回路に関する知見が得られるようになると期待される.また解析手法は一般的なものなので神経信号のみならず,社会データにも適用することによって社会の構造に対する知見が得られるようになると考えられる.

Report

(7 results)
  • 2019 Annual Research Report   Final Research Report ( PDF )
  • 2018 Annual Research Report
  • 2017 Annual Research Report
  • 2016 Annual Research Report
  • 2015 Annual Research Report
  • 2014 Annual Research Report
  • Research Products

    (34 results)

All 2020 2019 2018 2017 2016 2015 2014 Other

All Int'l Joint Research (7 results) Journal Article (10 results) (of which Int'l Joint Research: 6 results,  Peer Reviewed: 10 results,  Open Access: 5 results,  Acknowledgement Compliant: 5 results) Presentation (16 results) (of which Int'l Joint Research: 12 results,  Invited: 8 results) Remarks (1 results)

  • [Int'l Joint Research] NIH(米国)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] Juelich Research Center(ドイツ)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] University of Namur(Belgium)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] CMU(米国)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] Institute of Neuroscience and Medicine(Germany)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] National Institute of Mental Health(米国)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] Czech Academy of Sciences(チェコ)

    • Related Report
      2016 Annual Research Report
  • [Journal Article] Reconstructing neuronal circuitry from parallel spike trains2019

    • Author(s)
      Kobayashi Ryota、Kurita Shuhei、Kurth Anno、Kitano Katsunori、Mizuseki Kenji、Diesmann Markus、Richmond Barry J.、Shinomoto Shigeru
    • Journal Title

      Nature Communications

      Volume: 10 Issue: 1 Pages: 4468-4468

    • DOI

      10.1038/s41467-019-12225-2

    • NAID

      120006728081

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Identifying exogenous and endogenous activity in social media2018

    • Author(s)
      Fujita Kazuki、Medvedev Alexey、Koyama Shinsuke、Lambiotte Renaud、Shinomoto Shigeru
    • Journal Title

      Physical Review E

      Volume: 98 Issue: 5 Pages: 052304-052304

    • DOI

      10.1103/physreve.98.052304

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Computational Neuroscience: class FormattedString { value: Mathematical and Statistical Perspectives }2018

    • Author(s)
      Kass Robert E.、Amari Shun-Ichi、Arai Kensuke、Brown Emery N.、Diekman Casey O.、Diesmann Markus、Doiron Brent、Eden Uri T.、Fairhall Adrienne L.、Fiddyment Grant M.、Fukai Tomoki、Gr?n Sonja、Harrison Matthew T.、Helias Moritz、Nakahara Hiroyuki、Teramae Jun-nosuke、et.al
    • Journal Title

      Annual Review of Statistics and Its Application

      Volume: 5 Issue: 1 Pages: 183

    • DOI

      10.1146/annurev-statistics-041715-033733

    • URL

      https://localhost/en/publications/859555c0-fbc7-4dd9-8325-0c77c9587ae3

    • Related Report
      2018 Annual Research Report 2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Correlations and forecast of death tolls in the Syrian conflict.2017

    • Author(s)
      K. Fujita, S. Shinomoto, and L.E.C. Rocha
    • Journal Title

      Scientific Reports

      Volume: 7 Issue: 1 Pages: 15737-15737

    • DOI

      10.1038/s41598-017-15945-x

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Emergence of event cascades in inhomogeneous networks2016

    • Author(s)
      Tomokatsu Onaga, Shigeru Shinomoto
    • Journal Title

      Scientific Reports

      Volume: 6 Issue: 1 Pages: 33321-33321

    • DOI

      10.1038/srep33321

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Similarity in neuronal firing regimes across mammalian species2016

    • Author(s)
      Yasuhiro Mochizuki, ..., Ichiro Fujita, et al.
    • Journal Title

      Journal of Neuroscience

      Volume: 36 Issue: 21 Pages: 5736-5747

    • DOI

      10.1523/jneurosci.0230-16.2016

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Efficient information transfer by Poisson neurons2016

    • Author(s)
      Lubomir Kostal and Shigeru Shinomoto
    • Journal Title

      Mathematical Biosciences and Engineering

      Volume: 13 Issue: 3 Pages: 509-520

    • DOI

      10.3934/mbe.2016004

    • Related Report
      2016 Annual Research Report 2015 Annual Research Report
    • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Microscopic instability in recurrent neural networks.2015

    • Author(s)
      Y. Yamanaka, S. Amari, and S. Shinomoto
    • Journal Title

      Physical Review E

      Volume: 91 Issue: 3 Pages: 032921-032921

    • DOI

      10.1103/physreve.91.032921

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Analog and digital codes in the brain.2014

    • Author(s)
      Y. Mochizuki and S. Shinomoto
    • Journal Title

      Physical Review E

      Volume: 89 Issue: 2 Pages: 022705-022705

    • DOI

      10.1103/physreve.89.022705

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Bursting transition in a linear self-exciting point process.2014

    • Author(s)
      T. Onaga and S. Shinomoto
    • Journal Title

      Physical Review E

      Volume: 89 Issue: 4 Pages: 042817-042817

    • DOI

      10.1103/physreve.89.042817

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Presentation] Reconstructing neuronal circuitry from spiking signals.2020

    • Author(s)
      Shigeru Shinomoto
    • Organizer
      AIMR Advanced Target Projects
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Estimating Neuronal Connectivity from Spike Trains2020

    • Author(s)
      Ryota Kobayashi
    • Organizer
      NetSci-X 2020
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] A method for estimating synaptic connections from parallel spike trains2019

    • Author(s)
      Ryota Kobayashi
    • Organizer
      ICMNS 2019
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Inferring the source of fluctuations in neuronal activity2018

    • Author(s)
      Shigeru Shinomoto and Kazuki Fujita
    • Organizer
      Neural Coding workshop
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Estimation of synaptic connections from parallel spike trains2018

    • Author(s)
      Ryota Kobayashi, Shuhei Kurita, Katsunori Kitano, Kenji Mizuseki, Barry J. Richmond, Shigeru Shinomoto
    • Organizer
      Neural Coding workshop
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Criticality of dynamical epidemic burst spreading through inhomogeneous networks2017

    • Author(s)
      Shigeru Shinomoto and Tomokatsu Onaga
    • Organizer
      4th INCF Japan Node International Workshop
    • Place of Presentation
      RIKEN BSI
    • Year and Date
      2017-05-18
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Emergence of cascades in the linear and nonlinear Hawkes processes2017

    • Author(s)
      Shigeru Shinomoto
    • Organizer
      BIRS workshop “Brain Dynamics and Statistics: Simulation versus Data”
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Inferring the origin of nonstationary fluctuation in event occurrences.2017

    • Author(s)
      Kazuki Fujita, Shinsuke Koyama, and Shigeru Shinomoto
    • Organizer
      Eighth International Workshop Statistical Analysis of Neuronal Data (SAND8)
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Inferring the source of fluctuation in neuronal activity.2017

    • Author(s)
      Shigeru Shinomoto
    • Organizer
      ICERM on Integrating Dynamics and Statistics in Neuroscience
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Review of single spike train analyses2016

    • Author(s)
      Shigeru Shinomoto
    • Organizer
      Modeling Neural Activity 2 (MONA2)
    • Place of Presentation
      Waikoloa, Hawaii, US
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Relating neuronal firing to epidemics and tweets2015

    • Author(s)
      Shigeru Shinomoto
    • Organizer
      Mathematical Modeling and Statistical Analysis in Neuroscience
    • Place of Presentation
      Nice
    • Year and Date
      2015-09-08
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Criticality of dynamical epidemic burst spreading through a network of individuals2015

    • Author(s)
      Tomokatsu Onaga and Shigeru Shinomoto
    • Organizer
      NetSci 2015
    • Place of Presentation
      Zaragoza, Spain
    • Year and Date
      2015-06-01
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Criticality of dynamical epidemic burst spreading through a network of individuals2015

    • Author(s)
      Tomokatsu Onaga and Shigeru Shinomoto
    • Organizer
      Seventh International workshop Statistical Analysis of Neuronal Data (SAND7)
    • Place of Presentation
      Pittsburgh, USA
    • Year and Date
      2015-05-26
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Bursting activity spreading through asymmetric interactions.2014

    • Author(s)
      Tomokatsu Onaga, Shigeru Shinomoto
    • Organizer
      Complex Networks 2014
    • Place of Presentation
      Marrakech, Morocco
    • Year and Date
      2014-11-24
    • Related Report
      2014 Annual Research Report
  • [Presentation] Intrinsic fluctuation in networks of spiking neurons.2014

    • Author(s)
      Tomokatsu Onaga, Shigeru Shinomoto
    • Organizer
      Neural Coding 2014
    • Place of Presentation
      Versailles, France
    • Year and Date
      2014-10-09
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Endogenous fluctuation in neuronal firing rate.2014

    • Author(s)
      Shigeru Shinomoto
    • Organizer
      Mathematical Modeling and Statistical Analysis in Neuroscience
    • Place of Presentation
      Copenhagen, Denmark
    • Year and Date
      2014-06-02 – 2014-06-04
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Remarks] Toolbox for constructing the best histograms

    • URL

      http://www.ton.scphys.kyoto-u.ac.jp/~shino/histograms/

    • Related Report
      2017 Annual Research Report

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Published: 2014-04-04   Modified: 2023-03-23  

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