• Search Research Projects
  • Search Researchers
  • How to Use
  1. Back to previous page

Development of Data-driven Mathematical Analysis for Single Cells and Singularity Cells

Planned

Project AreaSingularity biology
Project/Area Number 18H05413
Research Category

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

Allocation TypeSingle-year Grants
Review Section Complex systems
Research InstitutionHokkaido University

Principal Investigator

小松崎 民樹  北海道大学, 電子科学研究所, 教授 (30270549)

Co-Investigator(Kenkyū-buntansha) 中村 篤祥  北海道大学, 情報科学研究院, 教授 (50344487)
小野 峻佑  東京工業大学, 情報理工学院, 准教授 (60752269)
Project Period (FY) 2018-06-29 – 2023-03-31
Project Status Granted (Fiscal Year 2022)
Budget Amount *help
¥98,280,000 (Direct Cost: ¥75,600,000、Indirect Cost: ¥22,680,000)
Fiscal Year 2022: ¥18,720,000 (Direct Cost: ¥14,400,000、Indirect Cost: ¥4,320,000)
Fiscal Year 2021: ¥18,720,000 (Direct Cost: ¥14,400,000、Indirect Cost: ¥4,320,000)
Fiscal Year 2020: ¥18,200,000 (Direct Cost: ¥14,000,000、Indirect Cost: ¥4,200,000)
Fiscal Year 2019: ¥18,200,000 (Direct Cost: ¥14,000,000、Indirect Cost: ¥4,200,000)
Fiscal Year 2018: ¥24,440,000 (Direct Cost: ¥18,800,000、Indirect Cost: ¥5,640,000)
Keywords情報計測 / 因果推論 / バンディット手法 / 1細胞ラマン分光イメージング / スパース学習 / 1細胞ラマン分光 / バンディットアルゴリズム / 1細胞ラマン分光 / 異常検知
Outline of Annual Research Achievements

単細胞生物でコロニーを形成するアメーバDictyostelium discoideum(Dicty)を例に、その離合集散のダイナミクスに隠れている因果関係(リーダーおよびフォロワー細胞の役割分化)を見積もる方法論を開発した。あらかじめリーダー、フォロワー細胞を事前に設定した改良Vicsekモデルに基づく細胞動態シミュレーションの軌跡データ集合から、移動エントロピー、固有情報量、共有情報量、シナジー情報量を用いた因果解析により背後の相互作用距離およびリーダー・フォロワー細胞を同定するデータ解析手法を新規に開発した。さらに、阪大産研永井教授と徳島大学堀川一樹教授らによるcAMPプローブを用いたDicty細胞の離合集散の画像ファイルから抜き出された10コ程度のCAMPパルス列から、速度ベクトル場を粗視化することで、cAMPの濃度場や細胞の個々の運動を個々に並列して追跡できることを見出した。その理論的検証を展開し、cAMPのパルスパターンからシンギュラリティ現象を定量、探索する。
細胞毎の発火状態時系列から伝搬時差推定をアライメントベースで行い伝搬グラフを構築する手法を開発した。また、シンギュラリティ現象が起こる前にリーダーやフォロワーの推定が可能であるかを評価する特徴量の迅速抽出をめざし、バンディット手法を用いたモンテカルロ木探索による識別規則の迅速探索法を開発した。
スパース性を始めとする様々な事前知識を取り入れることで,定常成分・シンギュラリティ成分・ノイズや外乱を同時に分離しながら推定するための数理モデルを定式化した。実際のデータを用いてシンギュラリティ現象の抽出が可能化どうか検証する予定である。

Current Status of Research Progress
Current Status of Research Progress

1: Research has progressed more than it was originally planned.

Reason

論文(Mach. Learn.2020、J. Phys. Chem. B., 2019, FEBS Lett. 2019(表紙カバー、Editor’s Choiceに選出)、情報系学会プロシーディング(SDM2019 ICIP2019,ICASSP2019)などコンスタントな研究成果を出すことができている。理論的整備が完了したため、今後、領域内連携を加速する。

Strategy for Future Research Activity

リーダー・フォロワーの因果律の検証ならびに相互作用領域の新規推定手法を継続開発し、より多体系の相互作用様式を理解するため、移動エントロピーの物理的成因を解明すべく情報理論的分解を検討する。A03-2班から入手した細胞性粘菌のマルチスケールイメージング画像ムービーに適用するとともに、実データに対するリーダー・フォロワー検定とその動態を解析する。開発した伝搬グラフを構築する手法を拡張し、位置などの他の情報や発火の度合いなどより詳細な情報を扱えるようにし、予測精度の向上を図る。定常成分・シンギュラリティ成分・ノイズや外乱を同時に分離しながら推定するための数理モデルの定式化を継続し、それを最適化するためのアルゴリズムを開発する.また,理論解析を行い,収束条件・レート等を導出する.加えて,シミュレーションによって理論解析結果との整合性を評価する。

Report

(2 results)
  • 2019 Annual Research Report
  • 2018 Annual Research Report

Research Products

(49 results)

All 2020 2019 2018

All Journal Article (7 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 7 results,  Open Access: 2 results) Presentation (40 results) (of which Int'l Joint Research: 16 results,  Invited: 7 results) Book (2 results)

  • [Journal Article] A bad arm existence checking problem: How to utilize asymmetric problem structure?2020

    • Author(s)
      Tabata Koji、Nakamura Atsuyoshi、Honda Junya、Komatsuzaki Tamiki
    • Journal Title

      Journal of Machine Learning Research

      Volume: 109 Pages: 327-372

    • DOI

      10.1007/s10994-019-05854-7

    • NAID

      120006955200

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Raman spectroscopic histology using machine learning for nonalcoholic fatty liver disease2019

    • Author(s)
      Khalifa Mohammad Helal, James Nicholas Taylor, Harsono Cahyadi, Akira Okajima, Koji Tabata, Yoshito Itoh, Hideo Tanaka, Katsumasa Fujita, Yoshinori Harada, Tamiki Komatsuzaki
    • Journal Title

      FEBS Letters

      Volume: 593 Pages: 2535-2544

    • DOI

      10.1002/1873-3468.13520

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] High-Resolution Raman Microscopic Detection of Follicular Thyroid Cancer Cells with Unsupervised Machine Learning2019

    • Author(s)
      J. Nicholas Taylor, Kentaro Mochizuki, Kosuke Hashimoto, Yasuaki Kumamoto, Yoshinori Harada, Katsumasa Fujita, Tamiki Komatsuzaki
    • Journal Title

      The Journal of Physical Chemistry B

      Volume: 123 Pages: 4358-4372

    • DOI

      10.1021/acs.jpcb.9b01159

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Feature selection as Monte-Carlo Search in Growing Single Rooted Directed Acyclic Graph by Best Leaf Identification2019

    • Author(s)
      Pelissier A, Nakamura A, Tabata K
    • Journal Title

      Proceedings of the 2019 SIAM International Conference on Data Mining

      Volume: - Pages: 450-458

    • DOI

      10.1137/1.9781611975673.51

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Deciphering Molecular Complexity in Dynamics and Kinetics - From the Single Molecule to the Single Cell Level2019

    • Author(s)
      Komatsuzaki T, Press S, Senet P
    • Journal Title

      J. Phys. Chem. B

      Volume: 123 Pages: 2535-2544

    • DOI

      10.1021/acs.jpcb.9b05382

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Mixed Noise Removal for Hyperspectral Images Using Hybrid Spatio-Spectral Total Variation2019

    • Author(s)
      Takeyama Saori、Ono Shunsuke、Kumazawa Itsuo
    • Journal Title

      Proceedings of ICIP'19

      Volume: - Pages: 3128-3132

    • DOI

      10.1109/icip.2019.8803239

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Efficient Constrained Signal Reconstruction by Randomized Epigraphical Projection2019

    • Author(s)
      Ono Shunsuke
    • Journal Title

      Proceedings of ICASSP'19

      Volume: - Pages: 4993-4997

    • DOI

      10.1109/icassp.2019.8682191

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Presentation] シンギュラリティ生物学における情報計測2020

    • Author(s)
      小松﨑 民樹
    • Organizer
      シンギュラリティ生物学×細胞ダイバース合同ワークショップ
    • Related Report
      2019 Annual Research Report
  • [Presentation] An Information-theoretic approach to identify the interaction radius of a group of collectively moving animals2019

    • Author(s)
      Udoy. S Basak, Sulimon Sattari, Tamiki Komatsuzaki
    • Organizer
      The 20th RIES-HOKUDAI International Symposium
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] A sandbox model system for analyzing leadership in collective motion2019

    • Author(s)
      Sulimon Sattari, Udoy Basak, Sky Nicholson, Jason Green, Mikito Toda, Tamiki Komatsuzaki
    • Organizer
      The 20th RIES-HOKUDAI International Symposium
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Bad Arm Existence Checking Algorithm with Bandit Feeedback2019

    • Author(s)
      Koji Tabata, Atsuyoshi Nakamura, Tamiki Komatsuzaki
    • Organizer
      The 20th RIES-HOKUDAI International Symposium
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Raman Microscopic Histology using Ensemble Learning for Non-alcoholic Fatty Liver Disease2019

    • Author(s)
      Khalifa Mohammad Helal, Harsono Cahyadi, J. Nicholas Taylor, Akira Okajima, Yasuaki Kumamoto, Hideo Tanaka, Yoshinori Harada, Tamiki Komatsuzaki
    • Organizer
      The 20th RIES-HOKUDAI International Symposium
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] High Resolution Raman Microscopic Detection of Follicular Thyroid Cancer Cells with Unsupervised Machine Learning2019

    • Author(s)
      J. Nicholas Taylor, Kentaro Mochizuki, Kosuke Hashimoto, Yasuaki Kumamoto, Yoshinori Harada, Katsumasa Fujita, Tamiki Komatsuzaki
    • Organizer
      The 20th RIES-HOKUDAI International Symposium
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] On-the-fly Raman image microscopy by reinforcement machine learning2019

    • Author(s)
      Tamiki Komatsuzaki
    • Organizer
      Biomedical Raman Imaging 2019
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Raman Hyperspectral Image Analysis Using Ensemble Learning for Non-alcoholic Fatty Liver Disease2019

    • Author(s)
      Khalifa Mohammad Helal, Harsono Cahyadi, J. Nicholas Taylor, Akira Okajima, Yasuaki Kumamoto, Hideo Tanaka, Yoshinori Harada, Tamiki Komatsuzaki
    • Organizer
      Biomedical Raman Imaging 2019
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Causal inference in Leader-follower relationship2019

    • Author(s)
      Tamiki Komatsuzaki
    • Organizer
      ICSB 2019: Singularity Biology: small elements change the function of the whole systems
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] A leadership-based phase transition in a flocking model with activated and un-activated agents2019

    • Author(s)
      Sulimon Sattari, Tamiki Komatusaki, Mikito Toda, Sky Nicholson, Jason Green, Udoy Basak
    • Organizer
      第57回日本生物物理学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] An Information-theoretic approach toward identifying the leader(s) and aggregation place in Dictyostelium Discoideum colony2019

    • Author(s)
      Basak Udoy Sankar, Sattari Sulimon, Horikawa Kazuki, Komatsuzaki Tamiki
    • Organizer
      第57回日本生物物理学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Raman pathology and its phenotypic landscape for Non-alcoholic fatty liver diseases2019

    • Author(s)
      Tamiki Komatsuzaki
    • Organizer
      The Complexity of Dynamics and Kinetics from Single Molecules to Cells
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] アデニレートキナーゼの一分子観察データから再構成するエネルギー地形の階層性2019

    • Author(s)
      James Nicholas Taylor, Menahem Pirchi, Gilad Haran, 小松崎 民樹
    • Organizer
      第22回理論化学討論会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Deciphering hierarchical features in reaction network and energy landscape2019

    • Author(s)
      Tamiki Komatsuzaki
    • Organizer
      Network analysis to elucidate natural system dynamics, diversity and performance
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] バンディット問題の方策を用いたモンテカルロ木探索による最適属性集合 探索2019

    • Author(s)
      中村篤祥, ペリシエ オレリアン, 田畑 公次, 小松崎 民樹
    • Organizer
      第19回日本蛋白質科学会年会第71回日本細胞生物学会大会合同年次大会
    • Related Report
      2019 Annual Research Report
  • [Presentation] モンテカルロ木特徴探索に基づく非線形グラフ分類回帰2019

    • Author(s)
      白川稜, 中村篤祥, 工藤峰一
    • Organizer
      第22回情報論的学習理論ワークショップ
    • Related Report
      2019 Annual Research Report
  • [Presentation] Learning a Nonlinear Model of Subgraph Features Using Monte Carlo Tree Search2019

    • Author(s)
      Ryo Shirakawa, Atsuyoshi Nakamura, Mineichi Kudo
    • Organizer
      ACML 2019 Workshop on Statistics & Machine Learning Researchers in Japan
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 空間-波長正則化を用いた圧縮pansharpening2019

    • Author(s)
      武山 彩織, 小野 峻佑
    • Organizer
      第34回信号処理シンポジウム
    • Related Report
      2019 Annual Research Report
  • [Presentation] Identification of Leader(s) in a Dictyostelium Discoideum colony: An Information-theoretic Approach2019

    • Author(s)
      Udoy Sankar Basak, Sulimon Sattari, Sosuke Ito, Kazuki Horikawa, Tamiki Komatsuzaki
    • Organizer
      生物物理・回折構造生物学 合同研究会
    • Related Report
      2018 Annual Research Report
  • [Presentation] A sandbox model system for understanding leadership in collective motion2019

    • Author(s)
      Sulimon Sattari, Udoy Basak, Schuyler Nicholson, Jason Green, Mikito Toda, Tamiki Komatsuzaki
    • Organizer
      生物物理・回折構造生物学 合同研究会
    • Related Report
      2018 Annual Research Report
  • [Presentation] ハイパースペクトルイメージングのための圧縮pansharpeningの検討2019

    • Author(s)
      Saori Takeyama, Shunsuke Ono, Itsuo Kumazawa
    • Organizer
      電子情報通信学会信号処理研究会
    • Related Report
      2018 Annual Research Report
  • [Presentation] ブラックボックス関数の閾値以上の値の存在チェックのアルゴリズム2019

    • Author(s)
      Naoki Ito, Atsuyoshi Nakamura, Mineichi Kudo
    • Organizer
      第11回データ工学と情報マネジメントに関するフォーラム
    • Related Report
      2018 Annual Research Report
  • [Presentation] In combining single cell hyperspectral Raman images for the diagnosis of follicular thyroid carcinoma measured at different data2019

    • Author(s)
      Aurelien Pelissier
    • Organizer
      バイオ情報計測技術研究会
    • Related Report
      2018 Annual Research Report
  • [Presentation] High resolution Raman microscopic detection of follicular thyroid cancer cells with unsupervised machine learning2019

    • Author(s)
      Nicholas Taylor
    • Organizer
      バイオ情報計測技術研究会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Mathematical information measurement science: acceleration of Raman spectroscopy by bridging information science2019

    • Author(s)
      Tamiki Komatsuzaki
    • Organizer
      バイオ情報計測技術研究会
    • Related Report
      2018 Annual Research Report
  • [Presentation] A bad arm existence checking problem: how to utilize asymmetric problem structure?2019

    • Author(s)
      Koji Tabata
    • Organizer
      バイオ情報計測技術研究会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Nonsmooth Convex Optimization and Sparse Regularization in Signal and Information Processing2019

    • Author(s)
      Shunsuke Ono
    • Organizer
      ICMMA’18
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 1分子時系列情報からどのように背後の反応ネットワークを抽出できるのか?2019

    • Author(s)
      Tamiki Komatsuzaki
    • Organizer
      「生命動態の理解と制御のための基盤技術の創出」研究領域第7 回領域会議・第11 回数理デザイン道場
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] How can one bridge information science and measurement science to accelerate the measurements?2019

    • Author(s)
      Tamiki Komatsuzaki
    • Organizer
      The 22nd SANKEN International Symposium The 17th SANKEN Nanotechnology International Symposium “Next Generation Science and Technology for Super Smart Society”
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Hyperspectral Pansharpening Using Noisy Panchromatic Image2018

    • Author(s)
      Saori Takeyama, Shunsuke Ono, Itsuo Kumazawa
    • Organizer
      Asia-Pacific Signal and Information Processing Association Annual Summit and Conference (APSIPA ASC) 2018
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 非対称性を利用した悪腕存在チェックアルゴリズム2018

    • Author(s)
      Koji Tabata, Atsuyoshi Nakamura, Tamiki Komatsuzaki
    • Organizer
      第21回情報論的学習理論ワークショップ
    • Related Report
      2018 Annual Research Report
  • [Presentation] ガウシアンノイズを考慮したハイパースペクトル画像とマルチスペクトル画像の合成法2018

    • Author(s)
      Saori Takeyama, Shunsuke Ono, Itsuo Kumazawa
    • Organizer
      第33回信号処理シンポジウム
    • Related Report
      2018 Annual Research Report
  • [Presentation] A Randomized Epigraphical Projection Approach to Constrained Signal Reconstruction2018

    • Author(s)
      Shunsuke Ono
    • Organizer
      第33回信号処理シンポジウム
    • Related Report
      2018 Annual Research Report
  • [Presentation] DOO アルゴリズムの悪腕存在チェック問題への応用2018

    • Author(s)
      Naoki Ito, Atsuyoshi Nakamura, Mineichi Kudo
    • Organizer
      情報処理北海道シンポジウム2018
    • Related Report
      2018 Annual Research Report
  • [Presentation] A sandbox model system for studying leadership in collective motion2018

    • Author(s)
      Sulimon Sattari, Udoy Basak, Schuyler Nicholson, Jason Green, Mikito Toda, Tamiki Komatsuzaki
    • Organizer
      研究会「理論と実験」2018
    • Related Report
      2018 Annual Research Report
  • [Presentation] Classification of Raman Spectra of Healthy and Cancerous Human Follicular Thyroid Cells2018

    • Author(s)
      Nicholas Taylor, Kentaro Mochizuki, Katsumasa Fujita, Tamiki Komatsuzaki
    • Organizer
      研究会「理論と実験」2018
    • Related Report
      2018 Annual Research Report
  • [Presentation] ラマン計測と情報科学:情報科学は計測を迅速化できるか2018

    • Author(s)
      Tamiki Komatsuzaki
    • Organizer
      第1回計測インフォマティクス研究会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Information theoretic approach to reveal singularity in biology2018

    • Author(s)
      Tamiki Komatsuzaki
    • Organizer
      The 56th Annual Meeting of The Biophysical Society of Japan
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Machine Learning Approaches to Raman Micro-spectroscopic Images2018

    • Author(s)
      Helal Khalifa Mohammad, Cahyadi Harsono, Taylor J. Nicholas, Okajima Akira, Kumamoto Yasuaki, Tanaka Hideo, Harada Yoshinori, Komatsuzaki Tamiki
    • Organizer
      The 56th Annual Meeting of The Biophysical Society of Japan
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] ハイパースペクトル画像の混合ノイズ除去におけるパラメータ設定に関する検討2018

    • Author(s)
      Saori Takeyama, Shunsuke Ono, Itsuo Kumazawa
    • Organizer
      2018年電子情報通信学会ソサイエティ大会
    • Related Report
      2018 Annual Research Report
  • [Book] The Personality of Small Numbers: Do Molecules Have Personality?2018

    • Author(s)
      Tamiki Komatsuzaki
    • Total Pages
      7
    • Publisher
      Springer
    • ISBN
      9789811320828
    • Related Report
      2018 Annual Research Report
  • [Book] Good arm identification via bandit feedback2018

    • Author(s)
      Hideaki Kano, Junya Honda, Kentaro Sakamaki, Kentaro Matsuura, Atsuyoshi Nakamura, Masashi Sugiyama
    • Total Pages
      25
    • Publisher
      Springer
    • Related Report
      2018 Annual Research Report

URL: 

Published: 2018-07-20   Modified: 2022-07-01  

Information User Guide FAQ News Terms of Use Attribution of KAKENHI

Powered by NII kakenhi