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Reinforcement learning on Caenorhabditis elegans

Research Project

Project/Area Number 20K21805
Research Category

Grant-in-Aid for Challenging Research (Exploratory)

Allocation TypeMulti-year Fund
Review Section Medium-sized Section 61:Human informatics and related fields
Research InstitutionThe University of Tokyo

Principal Investigator

Iino Yuichi  東京大学, 大学院理学系研究科(理学部), 教授 (40192471)

Project Period (FY) 2020-07-30 – 2024-03-31
Project Status Completed (Fiscal Year 2023)
Budget Amount *help
¥6,500,000 (Direct Cost: ¥5,000,000、Indirect Cost: ¥1,500,000)
Fiscal Year 2021: ¥3,250,000 (Direct Cost: ¥2,500,000、Indirect Cost: ¥750,000)
Fiscal Year 2020: ¥3,250,000 (Direct Cost: ¥2,500,000、Indirect Cost: ¥750,000)
Keywords線虫 / 強化学習 / 行動モデル / 確率モデル / 4Dイメージング / 全脳イメージング / 化学走性学習 / シナプス可塑性 / 確率的生成モデル / 行動制御 / 光遺伝学 / シナプス伝達 / 学習 / 化学走性 / 線虫C.elegans / Brain-machine interface / C. elegans / オプトジェネティクス / 走性行動 / MDN-RNN
Outline of Research at the Start

本研究計画では、強化学習を用いて生物機能を向上させる方法論を開発する。そのために、体制が単純で試験的な研究に適した線虫C. elegansを用い、強化学習を用いて機械学習を行うことにより、線虫の学習能力を制御することを試みる。コンピュータは強化学習により、線虫を目的の場所に向かわせるための刺激を学習する。さらに、線虫の学習能力を高める刺激を学習する。

Outline of Final Research Achievements

In this study, we generated a neural network model which predicts the behavior of the nematode C. elegans at the next time step based on previous sequence of the behavior and external stimuli, by training the network using observed data of real animals. We next used this model nematode and trained a reinforcement learning model so as to regulate the model animal and succeeded in controlling the behavior of real C. elegans. We also observed the neural activity of the whole brain region of the animal and succeeded in predicting the reversal behavior at the next time step. We also found the synapse that change by learning and found that the phosphorylation of syntaxin, a key molecule for synaptic transmission, is regulated by learning and underlie the behavioral changes.

Academic Significance and Societal Importance of the Research Achievements

脳の情報の読み取りや操作は脳科学の大きな目標のひとつである。本研究では、線虫を用いて行動モデルを作成し、その上で強化学習を行い、これにより行動を自在にコントロールする方法を取得し、実際の線虫をその方法で制御できることを示した。さらに、分子的な行動制御にも成功し、全頭部のイメージングによる脳活動の読み取り、行動予測にも成功した。これら一連の読み取り、制御技術は将来ブレインマシンインターフェースにより神経損傷患者のリハビリ支援などの技術を開発する際の基盤的な学術的知見として有用となることが期待される。

Report

(5 results)
  • 2023 Annual Research Report   Final Research Report ( PDF )
  • 2022 Research-status Report
  • 2021 Research-status Report
  • 2020 Research-status Report
  • Research Products

    (25 results)

All 2024 2023 2022 2021 2020 Other

All Journal Article (11 results) (of which Peer Reviewed: 11 results,  Open Access: 11 results) Presentation (13 results) (of which Int'l Joint Research: 9 results,  Invited: 1 results) Remarks (1 results)

  • [Journal Article] Neuronal sensorimotor integration guiding salt concentration navigation in Caenorhabditis elegans2024

    • Author(s)
      Matsumoto, A., Toyoshima, Y., Zhang, C., Isozaki, A., Goda, K., and Iino, Y.
    • Journal Title

      Proceedings of the National Academy of Sciences

      Volume: 121 Issue: 5

    • DOI

      10.1073/pnas.2310735121

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Ensemble dynamics and information flow deduction from whole-brain imaging data2024

    • Author(s)
      Toyoshima, Y., Sato, H., Nagata, D., Kanamori, M., Jang, M.S., Kuze, K., Oe, S., Teramoto, T., Iwasaki, Y., Yoshida, R., Ishihara, T., Iino, Y.
    • Journal Title

      PLOS Computational Biology

      Volume: 20 Issue: 3 Pages: e1011848-e1011848

    • DOI

      10.1371/journal.pcbi.1011848

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Multiple p38/JNK mitogen-activated protein kinase (MAPK) signaling pathways mediate salt chemotaxis learning in C. elegans2023

    • Author(s)
      Huang, T., Suzuki, K., Kunitomo, H., Tomioka, M., and Iino, Y.
    • Journal Title

      G3: Genes|Genomes|Genetics

      Volume: 13 Issue: 9

    • DOI

      10.1093/g3journal/jkad129

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Antagonistic regulation of salt and sugar chemotaxis plasticity by a single chemosensory neuron in Caenorhabditis elegans2023

    • Author(s)
      Tomioka, M., Umemura, Y., Ueoka, Y., Chin, R., Katae, K., Uchiyama, C., Ike, Y., and Iino, Y.
    • Journal Title

      PLOS Genetics

      Volume: 19 Issue: 9 Pages: e1010637-e1010637

    • DOI

      10.1371/journal.pgen.1010637

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] WormTensor: a clustering method for time-series whole-brain activity data from C. elegans2023

    • Author(s)
      Tsuyuzaki, K., Yamamoto, K., Toyoshima, Y., Sato, H., Kanamori, M., Teramoto, T., Ishihara, T., Iino, Y., and Nikaido, I.
    • Journal Title

      BMC Bioinformatics

      Volume: 24 Issue: 1 Pages: 254-254

    • DOI

      10.1186/s12859-023-05230-2

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Different modes of stimuli delivery elicit changes in glutamate driven, experience-dependent interneuron response in C. elegans2023

    • Author(s)
      Mabardi Llian、Sato Hirofumi、Toyoshima Yu、Iino Yuichi、Kunitomo Hirofumi
    • Journal Title

      Neuroscience Research

      Volume: 186 Pages: 33-42

    • DOI

      10.1016/j.neures.2022.10.004

    • Related Report
      2022 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Molecular encoding and synaptic decoding of context during salt chemotaxis in C. elegans2022

    • Author(s)
      Hiroki Shingo、Yoshitane Hikari、Mitsui Hinako、Sato Hirofumi、Umatani Chie、Kanda Shinji、Fukada Yoshitaka、Iino Yuichi
    • Journal Title

      Nature Communications

      Volume: 13 Issue: 1 Pages: 2928-2928

    • DOI

      10.1038/s41467-022-30279-7

    • Related Report
      2022 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] The redundancy and diversity between two novel PKC isotypes that regulate learning in Caenorhabditis elegans.2022

    • Author(s)
      Hiroki S, Iino, Y.
    • Journal Title

      Proceedings of the National Academy of Sciences of the United States of America

      Volume: 119(3) Issue: 3

    • DOI

      10.1073/pnas.2106974119

    • Related Report
      2022 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] DAF-2c signaling promotes taste avoidance after starvation in Caenorhabditis elegans by controlling distinct phospholipase C isozymes2022

    • Author(s)
      Masahiro Tomioka, Moon Sun Jang, Yuichi Iino
    • Journal Title

      Communications Biology

      Volume: 5 Issue: 1 Pages: 30-30

    • DOI

      10.1038/s42003-021-02956-8

    • Related Report
      2022 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Probabilistic generative modeling and reinforcement learning extract the intrinsic features of animal behavior2022

    • Author(s)
      Keita Mori, Naohiro Yamauchi, Haoyu Wang, Ken Sato, Yu Toyoshima, Yuichi Iino
    • Journal Title

      Neural Networks

      Volume: 145 Pages: 107-120

    • DOI

      10.1016/j.neunet.2021.10.002

    • Related Report
      2022 Research-status Report 2021 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Neuron ID dataset facilitates neuronal annotation for whole-brain activity imaging of C. elegans2020

    • Author(s)
      Yu Toyoshima, Stephen Wu, Manami Kanamori, Hirofumi Sato, Moon Sun Jang, Suzu Oe, Yuko Murakami, Takayuki Teramoto, Chanhyun Park, Yuishi Iwasaki, Takeshi Ishihara, Ryo Yoshida & Yuichi Iino
    • Journal Title

      BMC Biology

      Volume: 18 Issue: 1 Pages: 30-30

    • DOI

      10.1186/s12915-020-0745-2

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Presentation] Analysis of the decreased brain-wide neural correlations in aging C. elegans2023

    • Author(s)
      曾 敬萱
    • Organizer
      線虫研究の未来を創る会2023
    • Related Report
      2023 Annual Research Report
  • [Presentation] The progeny of C.elegans that have been exposed to high salt conditions in its parent generation avoid high salt conditions2023

    • Author(s)
      Manami Dote
    • Organizer
      24th International C. elegans Conference
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Dye-uptake of amphid neurons enhances phototaxis behavior in a LITE-1 dependent manner2023

    • Author(s)
      Hirofumi Kunitomo
    • Organizer
      24th International C. elegans Conference
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Classification of C. elegans behaviors based on centroid movement and posture analyses2023

    • Author(s)
      Yuichi Iino
    • Organizer
      24th International C. elegans Conference
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 線虫C. elegansにおける糖濃度学習の機能解析2023

    • Author(s)
      富永 慶子
    • Organizer
      日本動物学会関東支部第75回大会国
    • Related Report
      2023 Annual Research Report
  • [Presentation] Investigating how worms integrate sensory and motor information in salt klinotaxis2022

    • Author(s)
      Ayaka Matsumoto, Chenqi Zhang, Akihiro Isozaki, Keisuke Goda, Yu Toyoshima, Yuichi Iino
    • Organizer
      CeNeuro2022
    • Related Report
      2022 Research-status Report
    • Int'l Joint Research
  • [Presentation] Molecules and neural network underlying salt preference2022

    • Author(s)
      Shingo Hiroki, Hirofumi Sato, Yu Toyoshima, Llian Mabardi, Hikari Yoshitane, Hinako Mitsui, Manami Kanamori, Chie Umatani, Shinji Kanda, Mashiro Tomoioka, Koichi Hashimoto, Hirofumi Kunitomo, Yoshitaka Fukada, Takeshi Ishihara & Yuichi Iino
    • Organizer
      CeNeuro2022(C. elegans Topic Meeting: Neuronal Development, Synaptic Function and Behavior)
    • Related Report
      2022 Research-status Report
    • Int'l Joint Research
  • [Presentation] Analysis of neural activity underlying turning movement by tracking-imaging of freely moving C. elegans.2022

    • Author(s)
      Ukyo T. Tazawa, Koyo Kuze, Ayaka Matsumoto, Yu Toyoshima, Suzu Oe, Takayuki Teramoto, Takeshi Ishihara, Yuichi Iino
    • Organizer
      NEURO2022
    • Related Report
      2022 Research-status Report
    • Int'l Joint Research
  • [Presentation] 線虫が侵害受容から忌避応答を引き起こす神経回路の解析2022

    • Author(s)
      久世晃暢、田澤右京、豊島有、大江紗、寺本孝行、石原健、飯野雄一
    • Organizer
      NEURO2022
    • Related Report
      2022 Research-status Report
    • Int'l Joint Research
  • [Presentation] Molecules and neural network underlying salt preference2022

    • Author(s)
      Shingo Hiroki, Hirofumi Sato, Yu Toyoshima, Llian Mabardi, Hikari Yoshitane, Hinako Mitsui, Manami Kanamori, Chie Umatani, Shinji Kanda, Mashiro Tomoioka, Koichi Hashimoto, Hirofumi Kunitomo, Yoshitaka Fukada, Takeshi Ishihara & *Yuichi Iino
    • Organizer
      CeNeuro2022 (C. elegans Topic Meeting: Neuronal Development, Synaptic Function and Behavior)
    • Related Report
      2022 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] 線虫の行動制御神経回路機構の強化学習による探索2021

    • Author(s)
      山内直寛、森啓太、飯野雄一、銅谷賢治
    • Organizer
      第44回日本神経科学大会
    • Related Report
      2021 Research-status Report
  • [Presentation] Disentangling behavioral dynamics with MDN-RNN2020

    • Author(s)
      Keita Mori
    • Organizer
      NeurIPS2020
    • Related Report
      2020 Research-status Report
    • Int'l Joint Research
  • [Presentation] 線虫の混合密度再帰型ニューラルネットワークによる行動シミュレーションと強化学習による行動制御2020

    • Author(s)
      山内直寛
    • Organizer
      第43回神経科学大会
    • Related Report
      2020 Research-status Report
  • [Remarks] 飯野研究室

    • URL

      http://molecular-ethology.bs.s.u-tokyo.ac.jp/labHP/J/JTop.html

    • Related Report
      2022 Research-status Report 2021 Research-status Report 2020 Research-status Report

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Published: 2020-08-03   Modified: 2025-01-30  

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