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Research on information fusion methods for multiple genomic data sources with heterogeneity based on hierarchical statistical modeling

Research Project

Project/Area Number 17200020
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section一般
Research Field Statistical science
Research InstitutionThe Institute of Statistical Mathematics

Principal Investigator

HIGUCHI Tomoyuki  The Institute of Statistical Mathematics, モデリング研究系, 教授 (70202273)

Co-Investigator(Kenkyū-buntansha) KAWASAKI Yoshinori  統計数理研究所, モデリング研究系, 准教授 (70249910)
YOSHIDA Ryo  統計数理研究所, モデリング研究・, 助教 (70401263)
TAMADA Yoshinori  統計数理研究所, 統計科学技術センター, 助教
上野 玄太  統計数理研究所, モデリング研究系, 助教 (40370093)
染谷 博司  統計数理研究所, モデリング研究系, 助教 (00333518)
井元 清哉  東京大学, 医科学研究所・ヒトゲノム研究系, 准教授 (10345027)
Co-Investigator(Renkei-kenkyūsha) UENO Genta  統計数理研究所, モデリング研究, 助教 (40370093)
SOMEYA Hiroshi  統計数理研究所, モデリング研究系, 助教 (00333518)
IMOTO Seiya  東京大学, 医科学研究所・ヒトゲノム解析センター, 准教授 (10345027)
Research Collaborator TERMIER Alexandre  情報・システム研究機構, 新領域融合研究センター, 融合プロジェクト特任研究員 (60435823)
ISHIGAKI Tsukasa  総合研究大学院大学複合科学研究科, 博士課程 (20469597)
Project Period (FY) 2005 – 2008
Project Status Completed (Fiscal Year 2008)
Budget Amount *help
¥46,800,000 (Direct Cost: ¥36,000,000、Indirect Cost: ¥10,800,000)
Fiscal Year 2008: ¥12,610,000 (Direct Cost: ¥9,700,000、Indirect Cost: ¥2,910,000)
Fiscal Year 2007: ¥12,610,000 (Direct Cost: ¥9,700,000、Indirect Cost: ¥2,910,000)
Fiscal Year 2006: ¥12,610,000 (Direct Cost: ¥9,700,000、Indirect Cost: ¥2,910,000)
Fiscal Year 2005: ¥8,970,000 (Direct Cost: ¥6,900,000、Indirect Cost: ¥2,070,000)
Keywords階層ベイズ / 状態空間モデル / グラフィカルモデル / ベイジアンネットワーク / マイクロアレイデータ / 遺伝子ネットワーク / カルバックライブラーカーネル / スペクトル判別 / ゲノム / マイクロアレイ / モデル化 / ソフトコンピューティング / プロテオーム
Research Abstract

一般に生物学的知識は,データベースの形に具現化されることが多い.データベースに登録された情報にも信頼度の属性を与え,つまりそれを確率変数として取り扱うことで,データベースの登録上の過誤やその情報の不確実さをモデル化し,今までのモデルをさらに階層化したベイズモデルを構成した.これにより,マイクロアレイデータからの情報抽出,既存の生物学的知識の有効活用,データベースの信頼性の検証などを統一的に可能にする枠組みを構築した.

Report

(5 results)
  • 2008 Annual Research Report   Final Research Report ( PDF )
  • 2007 Annual Research Report
  • 2006 Annual Research Report
  • 2005 Annual Research Report
  • Research Products

    (57 results)

All 2008 2007 2006 2005 2000 Other

All Journal Article (35 results) (of which Peer Reviewed: 21 results) Presentation (6 results) Book (8 results) Remarks (8 results)

  • [Journal Article] Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models2008

    • Author(s)
      O. Hirose, R. Yoshida, S. Imoto, R. Yamaguchi, T. Higuchi, D. S. Charnock-Jones, C. Print, S. Miyano
    • Journal Title

      Bioinformatics Vol. 24, No.7

      Pages: 932-942

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Bayesian learning of biological pathways on genomic data assimilation2008

    • Author(s)
      R. Yoshida, M. Nagasaki, R. Yamaguchi, S. Imoto, S. Miyano, T. Higuchi
    • Journal Title

      Bioinformatics Vol.24, No.22

      Pages: 2592-2601

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Predicting differences in gene regulatory systems by state space models2008

    • Author(s)
      R. Yamaguchi, S. Imoto, M. Yamauchi, M. Nagasaki, R. Yoshida, T. Shimamura, Y. Hatanaka, K. Ueno, T. Higuchi, N. Gotoh, S. Miyano
    • Journal Title

      Genome Informatics 21:

      Pages: 101-113

    • NAID

      130003997534

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models2008

    • Author(s)
      O. Hirose
    • Journal Title

      Bioinformatics Vol. 24, No. 7

      Pages: 932-942

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Bayesian learning of biological pathways on genomic data assimilation2008

    • Author(s)
      R. Yoshida
    • Journal Title

      Bioinformatics Vol. 24, No. 22

      Pages: 2592-2601

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Predicting differences in gene regulatory systems by state space models2008

    • Author(s)
      R. Yamaguchi
    • Journal Title

      Genome Informatics 21

      Pages: 101-113

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Kullback-Leiblerカーネルによる正規化周波数スペクトル判別とその圧力調整器劣化診断への応用2007

    • Author(s)
      石垣司, 樋口知之, 渡辺嘉二郎
    • Journal Title

      電子情報通信学会論文誌D Vol. J90-D, No.10

      Pages: 2787-2797

    • NAID

      110007380586

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Mixed factors analysis: Unsupervized statistical discrimination with kernel feature extraction2007

    • Author(s)
      R. Yoshida, T. Higuchi(他2名)
    • Journal Title

      Proceedings of The International Workshop on Data-Mining and Statistical Science (DMSS2007) No.25

      Pages: 71-88

    • NAID

      130008079498

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Kullback-Leiblerカーネルの正規化スペクトル判別における特性2007

    • Author(s)
      石垣 司, 樋口知之
    • Journal Title

      第4回人工知能学会データマイニングと統計数理研究会(JSAI SIG-DMSM)予稿集

    • NAID

      130008079488

    • Related Report
      2007 Annual Research Report
  • [Journal Article] ArrayCluster: an analytic tool for clustering, data visualization and module finder on gene expression profiles2006

    • Author(s)
      R. Yoshida, T. Higuchi, S. Imoto, S. Miyano
    • Journal Title

      Bioinformatics 22

      Pages: 1538-1539

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Genomic Data Assimilation for Estimating Hybrid Functional Petri Net from Time-course Gene Expression Data2006

    • Author(s)
      M. Nagasaki, R. Yamaguchi, R. Yoshida, S. Imoto, A. Doi, Y. Tamada, H. Matsuno, S. Miyano, T. Higuchi
    • Journal Title

      Genome Informatics(IBSB2006) 17, (1)

      Pages: 46-61

    • NAID

      130003812105

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Spectrum classification for early fault diagnosis of LP gas pressure regulator based on Kullback-Leibler Kernel2006

    • Author(s)
      T. Ishigaki, T. Higuchi, K. Watanabe
    • Journal Title

      Proceedings of the 2006 IEEE Signal Processing Society Workshop(MLSP2006)

      Pages: 453-458

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Kullback-Leibler カーネルを用いたSVMによる高ガス圧力調整器の早期故障診断2006

    • Author(s)
      石垣司, 樋口知之, 渡辺嘉二郎
    • Journal Title

      Proceedings of The International Workshop on Data-Mining and Statistical Science

      Pages: 220-225

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Modeling and Estimation of Dynamic EGFR Pathway by Data Assimilation Approach Using Time Series Proteomic Data2006

    • Author(s)
      S. Tasaki, M. Nagaski, M. Oyama, H. Hata, K. Ueno, R. Yoshida, T. Higuchi, S. Sugano, S. Miyano
    • Journal Title

      Proceedings of Genome Informatics 2006 17(2)

      Pages: 226-238

    • NAID

      130003997452

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] State-space Approach with the Maximum Likelihood Principle to Identify the System-Generating Time Course Gene Expression Date of Yeast2006

    • Author(s)
      R. Yamaguchi, T. Higuchi
    • Journal Title

      International Journal of Data Mining and Bioinformatics Vol.1, No.1

      Pages: 77-87

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Error tolerant model for incorporating biological knowledge with expression data in estimating gene networks Statistical Methodology2006

    • Author(s)
      S.Imoto, T.Higuchi, T.Goto, S. Miyano
    • Journal Title

      Statistical Methodology 3

      Pages: 1-16

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] State-space Approach with the Maximum Likelihood Principle to Identify the System-Generating Time Course Gene Expression Date of Yeast2006

    • Author(s)
      R.Yamaguchi, T.Higuchi
    • Journal Title

      International Journal of Data Mining and Bioinformatics Vol.1, No.1

      Pages: 77-87

    • Related Report
      2006 Annual Research Report
  • [Journal Article] ArrayCluster : An Analytic Tool for Clustering, Data Visualization2006

    • Author(s)
      R.Yoshida, T.Higuchi 他2名
    • Journal Title

      Module Finder on Gene Expression Profiles 22

      Pages: 1538-1539

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Genomic Data Assimilation for Estimating Hybrid Functional Petri Net from Time-course Gene Expression Data2006

    • Author(s)
      M.Nagasaki, T.Higuchi 他7名
    • Journal Title

      Proceedings of The Sixth International Workshop on Bioinformatics and Systems Biology (IBSB2006) 17(1)

      Pages: 46-61

    • NAID

      130003812105

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Spectrum classification for early fault diagnosis of LP gas pressure regulator based on Kullback-Leibler Kernel2006

    • Author(s)
      T.Ishigaki, T.Higuchi 他1名
    • Journal Title

      Proceedings of 2006 IEEE International Workshop on Machine Learning for Signal Processing

      Pages: 453-458

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Kullback-Leiblerカーネルを用いたSVMによる高圧ガス圧力調整器の早期故障診断2006

    • Author(s)
      石垣 司, 樋口 知之 他1名
    • Journal Title

      Proceedings of The International Workshop on Data-Mining and Statistical Science

      Pages: 220-225

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Modeling and Estimation of Dynamic EGFR Pathway by Data Assimilation Approach Using Time Series Proteomic Data2006

    • Author(s)
      S.Tasaki, T.Higuchi 他7名
    • Journal Title

      Proceedings of Genome Informatics 2006 17(2)

      Pages: 226-238

    • NAID

      130003997452

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Error tolerant model for incorporating biological knowledge with expression data in estimating gene networks Statistical Methodology2006

    • Author(s)
      S.Imoto, T.Higuchi, T.Goto, S.Miyano
    • Journal Title

      Statistical Methodology 3

      Pages: 1-16

    • Related Report
      2005 Annual Research Report
  • [Journal Article] State-space Approach with the Maximum Likelihood Principle to Identify the System-Generating Time Course Gene Expression Date of Yeast2006

    • Author(s)
      R.Yamaguchi, T.Higuchi
    • Journal Title

      International Journal of Data Mining and Bioinformatics (in print)

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Residual Bootstrapping and Median Filtering for Robust Estimation of Gene Networks from Microarray Data2005

    • Author(s)
      S. Imoto, T. Higuchi, S. Kim, E. Jeong, S. Miyano
    • Journal Title

      Proceedings of Computational Methods in Systems Biology 3082

      Pages: 149-160

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Estimating gene networks with cDNA microarray Data Using State-space models2005

    • Author(s)
      R. Yamaguchi, S. Yamashita, T. Higuchi
    • Journal Title

      Proceedings of 2005 International Workshop on Data Mining and Bioinformatics 3482

      Pages: 381-388

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] A Penalized Likelihood Estimation on Transcriptional Module-based Clusterintg2005

    • Author(s)
      R.Yoshida, S. Imoto, T. Higuchi
    • Journal Title

      Proceedings of 2005 International Workshop on Data Mining and Bioinformatics 3482

      Pages: 389-401

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Estimating Time-Dependent Gene Networks from Time Series Microarray Data by Dynamic Linear Models with Markov Switching2005

    • Author(s)
      R.Yoshida, S. Imoto, T. Higuchi
    • Journal Title

      Proceedings of Computational Systems Bioinformatics Conference(CSB2005)

      Pages: 289-298

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Residual Bootstrapping and Median Filtering for Robust Estimation of Gene Networks from Microarray Data2005

    • Author(s)
      S.Imoto, T.Higuchi, S.Kim, E.Jeong, S.Miyano
    • Journal Title

      Proceedings of Computational Methods in Systems Biology 3082

      Pages: 149-160

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Estimating gene networks with cDNA microarray Data Using State-space models2005

    • Author(s)
      R.Yamaguchi, S.Yamashita, T.Higuchi
    • Journal Title

      Proceedings of 2005 International Workshop on Data Mining and Bioinformatics 3482

      Pages: 381-388

    • Related Report
      2005 Annual Research Report
  • [Journal Article] A Penalized Likelihood Estimation on Transcriptional Module-based Clustering2005

    • Author(s)
      R.Yoshida, S.Imoto, T.Higuchi
    • Journal Title

      Proceedings of 2005 International Workshop on Data Mining and Bioinformatics 3482

      Pages: 389-401

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Estimating Time-Dependent Gene Networks from Time Series Microarray Data by Dynamic Linear Models with Markov Switching2005

    • Author(s)
      R.Yoshida, S.Imoto, T.Higuchi
    • Journal Title

      Proceedings of Computational Systems Bioinformatics Conference (CSB2005)

      Pages: 289-298

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Kullback-Leibler カーネルによる正規化周波数スペクトル判別とその圧力調整器劣化診断への応用2000

    • Author(s)
      石垣司, 樋口知之, 渡辺嘉二郎
    • Journal Title

      電子情報通信学会論文誌D Vol. J90-D No. 10

      Pages: 2787-2797

    • NAID

      110007380586

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Mixed factors analysis: Unsupervized statistical discrimination with kernel feature extraction2000

    • Author(s)
      R. Yoshida, T. Higuchi, S. Imoto, S. Miyano
    • Journal Title

      Proceedings of The International Workshop on Data-Mining and Statistical Science (DMSS2007) No.25

      Pages: 71-88

    • NAID

      130008079498

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Kullback-Leibler カーネルの正規化スペクトル判別における特性

    • Author(s)
      石垣司,樋口知之
    • Journal Title

      第4 回人工知能学会データマイニングと統計数理研究会(JSAI SIG-DMSM)予稿集

      Pages: 2007-2007

    • NAID

      130008079488

    • Related Report
      2008 Final Research Report
  • [Presentation] Predicting differences in gene regulatory systems by state space models2008

    • Author(s)
      R. Yamaguchi, S. Imoto, M. Yamauchi,M. Nagasaki, R. Yoshida, T. Shimamura, Y. Hatanaka, K. Ueno, T. Higuchi,N. Gotoh, S. Miyano
    • Organizer
      The 19th International Conference on Genome Informatics (GIW2008)
    • Place of Presentation
      Gold Coast ,Australia
    • Year and Date
      2008-12-02
    • Related Report
      2008 Final Research Report
  • [Presentation] Predicting differences in gene regulatory systerms by state space models2008

    • Author(s)
      R. Yamaguchi
    • Organizer
      The 19th International Conference on Genome Informatics (GIW2008)
    • Place of Presentation
      Gold Coast, Australia
    • Year and Date
      2008-12-02
    • Related Report
      2008 Annual Research Report
  • [Presentation] Clustering with time course gene expression profiles and the mixture of state spase models2007

    • Author(s)
      O. Hirose*, R. Yoshida, R. Yamaguchi,S. Imoto, T. Higuchi, S. Miyano
    • Organizer
      The Seventh Annual International Worksyop on Bioinformatics and Systems Biology (IBSB2007)
    • Place of Presentation
      東京大学医科学研究所
    • Year and Date
      2007-08-02
    • Related Report
      2008 Final Research Report
  • [Presentation] Clustering with time course gene expression profiles and the mixture of state space models2007

    • Author(s)
      O. Hirose, T. Higuchi(他3名)
    • Organizer
      The Seventh Annual International Workshop on Bioinformatics and Systems Biology
    • Place of Presentation
      東京大学 医科学研究所
    • Year and Date
      2007-08-02
    • Related Report
      2007 Annual Research Report
  • [Presentation] Genomic Data Assimilation for Estimating Hybrid Functional Petri Net from Time-course Gene Expression Data2006

    • Author(s)
      M. Nagasaki, R. Yamaguchi*, R. Yoshida, S. Imoto, A. Doi, Y. Tamada, H. Matsuno, S. Miyano, T. Higuchi
    • Organizer
      The Sixth International Workshop on Bioinformatics and Systems Biology (IBSB2006)
    • Place of Presentation
      Boston,MA USA
    • Year and Date
      2006-07-24
    • Related Report
      2008 Final Research Report
  • [Presentation] Estimating Time-Dependent Gene Networks from Time Series Microarray Data by Dynamic Linear Models with Markov Switching2005

    • Author(s)
      R. Yoshida, S. Imoto, T. Higuchi*
    • Organizer
      Computational Systems Bioinformatics Conference(CSB2005)
    • Place of Presentation
      Stanford, CA USA
    • Year and Date
      2005-08-09
    • Related Report
      2008 Final Research Report
  • [Book] パターン認識と機械学習 下 - ベイズ理論による統計的予測[翻訳&監訳]2008

    • Author(s)
      樋口知之
    • Total Pages
      433
    • Publisher
      シュプリンガー・ジャパン
    • Related Report
      2008 Final Research Report
  • [Book] パターン認識と機械学習 下-ベイズ理論による統計的予測[翻訳&監訳]2008

    • Author(s)
      樋口知之
    • Total Pages
      433
    • Publisher
      シュプリンガー・ジャパン
    • Related Report
      2008 Annual Research Report
  • [Book] ベイジアンモデリングによる実世界イノベーション 統計数理は隠された未来をあらわにする2007

    • Author(s)
      樋口知之
    • Total Pages
      136
    • Publisher
      東京電機大学出版局
    • Related Report
      2008 Final Research Report
  • [Book] ベイジアンモデリングによる実世界イノベーション 統計数理は隠された未来をあらわにする2007

    • Author(s)
      樋口 知之
    • Total Pages
      136
    • Publisher
      東京電機大学出版局
    • Related Report
      2007 Annual Research Report
  • [Book] バイオインフォマティクス事典 (S. Miyano 他 編集)2006

    • Author(s)
      分担執筆 T. Higuchi
    • Total Pages
      807
    • Publisher
      共立出版
    • Related Report
      2008 Final Research Report
  • [Book] バイオインフォマティクス事典2006

    • Author(s)
      分担執筆(S.Miyano 他 編集)
    • Total Pages
      807
    • Publisher
      共立出版
    • Related Report
      2006 Annual Research Report
  • [Book] モデルヴァリデーション(第3章:地球科学におけるモデルヴァリデーション)2005

    • Author(s)
      樋口知之(他 北川源四郎・岸野洋久・山下智志・川崎能典)
    • Total Pages
      210
    • Publisher
      共立出版
    • Related Report
      2008 Final Research Report
  • [Book] モデルヴァリデーション(第3章:地球科学におけるモデルヴァリデーション)2005

    • Author(s)
      樋口知之(他 北川源四郎, 岸野洋久, 山下智志, 川崎能典)
    • Total Pages
      210
    • Publisher
      共立出版
    • Related Report
      2005 Annual Research Report
  • [Remarks]

    • URL

      http://www.ism.ac.jp/~higuchi/

    • Related Report
      2008 Final Research Report
  • [Remarks]

    • URL

      http://daweb.ism.ac.jp/

    • Related Report
      2008 Final Research Report
  • [Remarks]

    • URL

      http://metagp.ism.ac.jp/

    • Related Report
      2008 Final Research Report
  • [Remarks]

    • URL

      http://daweb.ism.ac.jp/~yoshidar/software/ssm/

    • Related Report
      2008 Final Research Report
  • [Remarks] ソフト開発 Mta Gene Profiler Web インターフェース

    • Related Report
      2008 Final Research Report
  • [Remarks] http://daweb.ism.ac.jp/

    • URL

      http://www.ism.ac.jp/~higuchi/

    • Related Report
      2008 Annual Research Report
  • [Remarks]

    • URL

      http://www.ism.ac.jp/~higuchi/

    • Related Report
      2007 Annual Research Report
  • [Remarks]

    • URL

      http://daweb.ism.ac.jp/

    • Related Report
      2007 Annual Research Report

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Published: 2005-04-01   Modified: 2016-04-21  

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