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Proposal of interactive large scale Bayesian network estimation method and its application to biological data

Research Project

Project/Area Number 15K00402
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Life / Health / Medical informatics
Research InstitutionKansai University (2017-2018)
Osaka University (2015-2016)

Principal Investigator

takenaka yoichi  関西大学, 総合情報学部, 教授 (00324830)

Project Period (FY) 2015-04-01 – 2019-03-31
Project Status Completed (Fiscal Year 2018)
Budget Amount *help
¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000)
Fiscal Year 2017: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2016: ¥2,340,000 (Direct Cost: ¥1,800,000、Indirect Cost: ¥540,000)
Fiscal Year 2015: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Keywords生物情報学 / ベイジアンネットワーク / 遺伝子制御ネットワーク / 一塩基多型 / 大規模データ / 因果関係 / 変数選択 / インタラクティブ性 / 大規模 / 小観測点 / Devide & Reconstruction
Outline of Final Research Achievements

In data analysis, causality that indicates cause and effect between events is more important than correlation that simply indicates that changes between events are similar. Bayesian networks have greatly contributed to small-scale data analysis as a model expressing the causality and a method of estimating the causality. The Bayesian network is a probabilistic model representing causality with conditional probability, and is a non-cyclic directed graph representing causality with directed edges between vertices corresponding to events.

In this study, we proposed a method to expand the number of events that Bayesian networks can estimate and to compare data observed from different sources for the same event. And the effectiveness was clarified through verification using real data in the field of biology.

Academic Significance and Societal Importance of the Research Achievements

ベイジアンネットワークによる因果関係解析は、生物学、医学、薬学に止まらず医師の診断、イメージ認識、言語認識でも用いられる汎用的な手法である。各分野において今後もデータ産生量が増大し続ける事は確実であろう。そのため、因果関係を推定可能の事象数を拡大可能な手法、および観測データ比較を可能とする手法の需要は今後も拡大し続けるであろう。そのため、本研究の成果は生物学に止まらず、他分野データの解析においても新しい知見を獲得するための手段として活躍する事が期待される。

Report

(5 results)
  • 2018 Annual Research Report   Final Research Report ( PDF )
  • 2017 Research-status Report
  • 2016 Research-status Report
  • 2015 Research-status Report
  • Research Products

    (28 results)

All 2019 2018 2017 2016 2015

All Journal Article (6 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 6 results,  Open Access: 5 results,  Acknowledgement Compliant: 1 results) Presentation (22 results) (of which Int'l Joint Research: 17 results,  Invited: 2 results)

  • [Journal Article] Automated transition analysis of activated gene regulation during diauxic nutrient shift in Escherichia coli and adipocyte differentiation in mouse cells2018

    • Author(s)
      Takenaka Yoichi、Mikami Kazuma、Seno Shigeto、Matsuda Hideo
    • Journal Title

      BMC Bioinformatics

      Volume: 19 Issue: S4

    • DOI

      10.1186/s12859-018-2072-y

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Chromatin 3D reconstruction from chromosomal contacts using a genetic algorithm2018

    • Author(s)
      Viacheslav Kapilevich, Shigeto Seno, Hideo Matsuda, Yoichi Takenaka
    • Journal Title

      IEEE/ACM Transactions on Computational Biology and Bioinformatics

      Volume: - Issue: 5 Pages: 1-1

    • DOI

      10.1109/tcbb.2018.2814995

    • Related Report
      2018 Annual Research Report 2017 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Collaborative environmental DNA sampling from petal surfaces of flowering cherry Cerasus?×?yedoensis ‘Somei-yoshino’ across the Japanese archipelago2018

    • Author(s)
      Tazro Ohta, Takeshi Kawashima, Natsuko O. Shinozaki, Akito Dobashi, ◯Satoshi Hiraoka, Tatsuhiko Hoshino, Keiichi Kanno, Takafumi Kataoka, Shuichi Kawashima, Motomu Matsui, Wataru Nemoto, Suguru Nishijima, Natsuki Suganuma, Haruo Suzuki
    • Journal Title

      Journal of Plant Research

      Volume: - Issue: 4 Pages: 1-9

    • DOI

      10.1007/s10265-018-1017-x

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Genotype-Based Epigenetic Differences in Monozygotic Twins Discordant for Positive Antithyroglobulin Autoantibodies2018

    • Author(s)
      Watanabe Mikio、Takenaka Yoichi、Honda Chika、Osaka Twin Research Group、Iwatani Yoshinori
    • Journal Title

      Thyroid

      Volume: 28 Issue: 1 Pages: 110-123

    • DOI

      10.1089/thy.2017.0273

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Automated transition analysis of activated gene regulation during diauxic nutrient shift in Escherichia coli and adipocyte differentiation in mouse cells2018

    • Author(s)
      Yoichi Takenaka, Kazuma Mikami, Shigeto Seno, Hideo Matsuda
    • Journal Title

      BMC bioinformatics

      Volume: 19

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Detecting shifts in gene regulatory networks during time-course experiments at single-time-point temporal resolution2016

    • Author(s)
      Yoichi Takenaka, Shigeto Seno, Hideo Matsuda
    • Journal Title

      J. Bioinformatics and Computational Biology

      Volume: 13 Issue: 05 Pages: 1543002-1543020

    • DOI

      10.1142/s0219720015430027

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Presentation] Transition of regulatory force toward the gene expressions during osteoblast cell differentiation2019

    • Author(s)
      Yoichi Takenaka
    • Organizer
      Pacific Symposium on Biocomputing (PSB)
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Nonconvex Discrete Optimization Approach for High Dimensional Regression2018

    • Author(s)
      Nakagawa Y., Hanada Y., Takenaka, Y., Edirishinghe C.
    • Organizer
      INFORMS annual meeting 2018
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Genotype-based epigenetic factors in identical twins discordant for positive TgAb2018

    • Author(s)
      Watanabe, M., Takenaka, Y., Honda, C., Osaka Twin Research Group, Iwatani, Y.
    • Organizer
      AACC Annual Meeting & Clinical Lab Expo 2018
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Functional analysis of metagenome using composition- based method2018

    • Author(s)
      Meya Cho, Shigeto Seno, Hideo Matsuda and Yoichi Takenaka
    • Organizer
      The 16th Asia Pacific Bioinformatics Conference
    • Related Report
      2018 Annual Research Report 2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] Missing value imputation for gene expression data with Deep Learning2018

    • Author(s)
      Kazumasa Saito, Shigeto Seno, Hideo Matsuda and Yoichi Takenaka
    • Organizer
      The 16th Asia Pacific Bioinformatics Conference
    • Related Report
      2018 Annual Research Report 2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] Automated transition analysis of activated gene regulation during diauxic nutrient shift in Escherichia coli and adipocyte differentiation in mouse cells2018

    • Author(s)
      Yoichi Takenaka, Kazuma Mikami, Shigeto Seno, Hideo Matsuda
    • Organizer
      The 16th Asia Pacific Bioinformatics Conference (APBC2018)
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] Clustering of cells for single cell analysis using Latent Dirichlet Allocation2017

    • Author(s)
      Mitsuhiro Eto, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
    • Organizer
      ISMB/ECCB 2017
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] An accurate estimation method for expression profiles of novel transcripts from RNA-Seq data2016

    • Author(s)
      Fuki Iwasaki, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
    • Organizer
      International Conference on Intelligent Systems for Molecular Biology (ISMB2016)
    • Place of Presentation
      Orlando, Florida, USA
    • Year and Date
      2016-07-10
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Presentation] A method for reducing false positives of target genes of microRNAs by combining two prediction tools2016

    • Author(s)
      Hideo Matsuda, Junko Tsuda, Shigeto Seno, Yoichi Takenaka
    • Organizer
      International Conference on Intelligent Systems for Molecular Biology (ISMB2016)
    • Place of Presentation
      Orlando, Florida, USA
    • Year and Date
      2016-07-10
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Presentation] Bayesian Network Inference from gene expression profiles with a small number of samples2016

    • Author(s)
      Kazumasa Saito, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
    • Organizer
      The 20th Annual International Conference on Research in Computational Molecular Biology, RECOMB2016
    • Place of Presentation
      Loews, Santa Monica, CA, USA
    • Year and Date
      2016-04-18
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Presentation] Dynamic Analysis of Gene Regulations using Leaving-One-Out Expression Profile2016

    • Author(s)
      Yoichi Takenaka, Shigeto Seno, Hideo Matsuda
    • Organizer
      The 20th Annual International Conference on Research in Computational Molecular Biology, RECOMB2016
    • Place of Presentation
      Loews, Santa Monica, CA, USA
    • Year and Date
      2016-04-18
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Presentation] Dynamic Analysis of Gene Regulations using Leaving-One-Out Expression Profile,2016

    • Author(s)
      Yoichi Takenaka, Shgeto Seno, Hideo Matsuda
    • Organizer
      The 20th Annual International Conference on Research in Computational Molecular Biology,
    • Place of Presentation
      LA Santa Monica
    • Year and Date
      2016-04-18
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research
  • [Presentation] Bayesian Network Inference from gene expression profiles with a small number of samples2016

    • Author(s)
      Kazumasa Saito, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
    • Organizer
      The 20th Annual International Conference on Research in Computational Molecular Biology,
    • Place of Presentation
      LA Santa Monica
    • Year and Date
      2016-04-18
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research
  • [Presentation] 乳癌データベースを用いた遺伝子発現プロファイルの数値変換の検討2016

    • Author(s)
      草田義昭, 瀬尾茂人, 竹中要一, 野口眞三郎, 松田秀雄
    • Organizer
      第45回バイオ情報学研究発表会 2016-BIO-45-7
    • Place of Presentation
      JAIST
    • Year and Date
      2016-03-18
    • Related Report
      2015 Research-status Report
  • [Presentation] 小サンプル数データに対するベイジアンネットワークのスコアベース構造学習改善手法2016

    • Author(s)
      齋藤和正, 瀬尾茂人, 竹中要一, 松田秀雄
    • Organizer
      第45回バイオ情報学研究発表会 2016-BIO-45-1
    • Place of Presentation
      JAIST
    • Year and Date
      2016-03-18
    • Related Report
      2015 Research-status Report
  • [Presentation] Detect the time point when organisms toggle gene regulatory networks from their expression profiles2016

    • Author(s)
      Yoichi Takenaka
    • Organizer
      Study Sessions on Bioinformatics and Related Topics, IFrec Osaka University
    • Place of Presentation
      IFrec Osaka
    • Year and Date
      2016-02-04
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Comparative analysis of transformation methods for gene expression profiles in breast cancer datasets2016

    • Author(s)
      Yoshiaki Sota, Shigeto Seno, Yoichi Takenaka, Shinzaburo Noguchi, Hideo Matsuda
    • Organizer
      IEEE 16th International Conference on Bioinformatics and Bioengineering (BIBE 2016)
    • Place of Presentation
      Splendor Hotel, Taichung, Taiwan
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Presentation] Identification of the state-change-time-point of gene regulations from time-course experiments2015

    • Author(s)
      Yoichi Takenaka
    • Organizer
      The second workshop on Advanced Methodologies for Bayesian Networks
    • Place of Presentation
      Yokohama
    • Year and Date
      2015-11-16
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Detecting the shifts of gene regulatory networks during time-course experiments with a single time point temporal resolution2015

    • Author(s)
      Yoichi Takenaka, Shigeto Seno, Hideo Matsuda
    • Organizer
      GIW/InCoB2015
    • Place of Presentation
      Odaiba, Tokyo
    • Year and Date
      2015-09-09
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research
  • [Presentation] 風が吹くといつ桶屋は儲かるの? 遺伝子発現制御の時間変化解析2015

    • Author(s)
      竹中要一
    • Organizer
      第4回NGS現場の会
    • Place of Presentation
      つくば
    • Year and Date
      2015-07-01
    • Related Report
      2015 Research-status Report
  • [Presentation] 共通k-mer種別数に基づくメタゲノム分類手法2015

    • Author(s)
      吉田拓真, 瀬尾茂人, 竹中要一, 松田秀雄
    • Organizer
      第4回NGS現場の会
    • Place of Presentation
      つくば
    • Year and Date
      2015-07-01
    • Related Report
      2015 Research-status Report
  • [Presentation] ダイナミックベイジアンネットワークを用いた遺伝子制御ネットワーク推定の部分問題化による近似解法2015

    • Author(s)
      上木怜, 瀬尾茂人, 竹中要一, 松田秀雄
    • Organizer
      情報処理学会研究報告, 第42回バイオ情報学研究会
    • Place of Presentation
      OIST
    • Year and Date
      2015-06-23
    • Related Report
      2015 Research-status Report

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Published: 2015-04-16   Modified: 2020-03-30  

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