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Mixture modeling of regularization terms with optimization sampling strategies and its application to biological large scale data

Research Project

Project/Area Number 26330330
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Life / Health / Medical informatics
Research InstitutionKyushu University

Principal Investigator

Maruyama Osamu  九州大学, マス・フォア・インダストリ研究所, 准教授 (20282519)

Project Period (FY) 2014-04-01 – 2017-03-31
Project Status Completed (Fiscal Year 2016)
Budget Amount *help
¥4,810,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥1,110,000)
Fiscal Year 2016: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2015: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
Fiscal Year 2014: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Keywords正則化 / マルコフ連鎖モンテカルロ法 / タンパク質複合体 / ガウス分布 / ベイズ推定 / タンパク質間相互作用 / 教師付き学習 / べき法則 / 混合正則化 / モデリング / バイオインフォマティクス / 相互排他 / ガウス分布のベイズ推定 / サンプリング / マルコフ連鎖モンテカルロ / 遺伝子発現ネットワーク / ガウシアン・グラフィカル・モデル
Outline of Final Research Achievements

Based on regularization modeling and Markov chain Monte Carlo algorithms, we have developed methods for the protein complex prediction problem and the Bayes estimation of Gaussian distributions. Especially, for the protein complex prediction problem, we have empirically shown the effectiveness of a regularization term based on the information of mutually exclusive protein-protein interactions. In addition, we have developed a supervised learning algorithm for protein complexes with 2 or 3 components. Furthermore, we have designed a regularization term for controlling overlaps between predicted complexes, and showed that the new method with that regularization term outperforms others.

Report

(4 results)
  • 2016 Annual Research Report   Final Research Report ( PDF )
  • 2015 Research-status Report
  • 2014 Research-status Report
  • Research Products

    (13 results)

All 2017 2016 2015 2014 Other

All Int'l Joint Research (1 results) Journal Article (6 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 5 results,  Acknowledgement Compliant: 3 results,  Open Access: 2 results) Presentation (5 results) (of which Int'l Joint Research: 3 results) Remarks (1 results)

  • [Int'l Joint Research] National University of Singapore(Singapore)

    • Related Report
      2015 Research-status Report
  • [Journal Article] Two Challenging Difficulties of Protein Complex Prediction2017

    • Author(s)
      Osamu Maruyama
    • Journal Title

      Agriculture as a metaphor for creativity in all human endeavors -Proceedings of Forum "Math-for-Industry" 2016

      Volume: -

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] RocSampler: Regularizing overlapping protein complexes in protein-protein interaction networks2016

    • Author(s)
      Osamu Maruyama and Yuki Kuwahara
    • Journal Title

      Proc. of 2016 IEEE 6th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)

      Volume: - Pages: 1-1

    • DOI

      10.1109/iccabs.2016.7802774

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Regularizing predicted complexes by mutually exclusive protein-protein interactions2015

    • Author(s)
      Osamu Maruyama and Limsoon Wong
    • Journal Title

      2015 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM)

      Volume: なし Pages: 1068-1075

    • DOI

      10.1145/2808797.2808817

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] ReSAPP: predicting overlapping protein complexes by merging multiple-sampled partitions of proteins2014

    • Author(s)
      So Kokibi, Osamu Maruyama
    • Journal Title

      Journal of Bioinformatics and Computational Biology

      Volume: 12 Issue: 06 Pages: 1442004-1442004

    • DOI

      10.1142/s0219720014420049

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Discovery of small protein complexes from PPI networks with size-specific supervised weighting2014

    • Author(s)
      Chern Han Yong, Osamu Maruyama, Limsoon Wong,
    • Journal Title

      BMC systems biology

      Volume: 8 Issue: Suppl 5 Pages: S3-S3

    • DOI

      10.1186/1752-0509-8-s5-s3

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Markov Chain Monte Carlo Algorithms2014

    • Author(s)
      Osamu Maruyama
    • Journal Title

      A Mathematical Approach to Research Problems of Science and Technology

      Volume: 5 Pages: 349-363

    • DOI

      10.1007/978-4-431-55060-0_26

    • ISBN
      9784431550594, 9784431550600
    • Related Report
      2014 Research-status Report
  • [Presentation] Two Challenging Difficulties of Protein Complex Prediction2016

    • Author(s)
      Osamu Maruyama
    • Organizer
      Forum "Math-for-Industry" 2016
    • Place of Presentation
      Queensland University of Technology, Brisbane, Australia
    • Year and Date
      2016-11-21
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] RocSampler: Regularizing overlapping protein complexes in protein-protein interaction networks2016

    • Author(s)
      Osamu Maruyama
    • Organizer
      2016 IEEE 6th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)
    • Place of Presentation
      Georgia Institute of Technology, Atlanta, GA, USA
    • Year and Date
      2016-10-13
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Regularizing predicted complexes by mutually exclusive protein-protein interactions2015

    • Author(s)
      Osamu Maruyama
    • Organizer
      International Symposium on Network Enabled Health Informatics, Biomedicine and Bioinformatics
    • Place of Presentation
      Paris, France
    • Year and Date
      2015-08-25
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research
  • [Presentation] ReSAPP: predicting overlapping protein complexes by merging multiple-sampled partitions of proteins2014

    • Author(s)
      So Kobiki
    • Organizer
      The 25th Anniversary GIW International Conference on Genome Informatics & the 4th International Society for Computational Biology Asia Conference
    • Place of Presentation
      Tokyo, Japan
    • Year and Date
      2014-12-15 – 2014-12-17
    • Related Report
      2014 Research-status Report
  • [Presentation] A scale-free structure prior for Bayesian inference of Gaussian graphical models2014

    • Author(s)
      Osamu Maruyama
    • Organizer
      IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2014
    • Place of Presentation
      Belfast, UK
    • Year and Date
      2014-11-02 – 2014-11-05
    • Related Report
      2014 Research-status Report
  • [Remarks] MARUYAMA Osamu Home page

    • URL

      http://imi.kyushu-u.ac.jp/~om/

    • Related Report
      2014 Research-status Report

URL: 

Published: 2014-04-04   Modified: 2018-03-22  

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