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Tensor decomposition based unsupervised feature extraction applied to bioinformatics

Research Project

Project/Area Number 17K00417
Research Category

Grant-in-Aid for Scientific Research (C)

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

Principal Investigator

Taguchi Y-h.  中央大学, 理工学部, 教授 (30206932)

Project Period (FY) 2017-04-01 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000)
Fiscal Year 2019: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2018: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2017: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Keywordsテンソル分解 / 教師無し学習 / 変数選択 / 遺伝子発現プロファイル / マルチオミックス / インシリコ創薬 / バイオマーカー / AI創薬 / エピジェネティクス / テンソル分解を用いた教師無し学習による変数選択 / AI創薬 / 社会性昆虫 / 乳がん / マルチビューデータ / 心的外傷後ストレス障害 / 心臓病 / 生体生命情報学
Outline of Final Research Achievements

In these three years, I have published the paper that proposed "Tensor decomposition based unsupervised feature extraction" and wrote a 300+ pages length monograph on the same topic from the world-known publisher, Springer. I can also successfully performed various international collaborations including those with Prof. Ka-Lok at Asia University, Taiwan, Prof. Wang at Institute of Statistics, National Chiao Tung University, Taiwan, and Prof. Turki Turki at King Abdulaziz University, Saudi Arabia.

Academic Significance and Societal Importance of the Research Achievements

テンソル分解を用いた教師無し学習による変数選択法はインシリコ創薬、バイオマーカー探索、疾患原因遺伝子の探索などに広く使えることが3年間の研究で判明した。また、この方法について成書を英文で書いたことにより、この方法が世界的に広まって学術の進歩に多く貢献することが期待される。

Report

(4 results)
  • 2019 Annual Research Report   Final Research Report ( PDF )
  • 2018 Research-status Report
  • 2017 Research-status Report
  • Research Products

    (40 results)

All 2020 2019 2018 2017 Other

All Int'l Joint Research (2 results) Journal Article (18 results) (of which Int'l Joint Research: 6 results,  Peer Reviewed: 10 results,  Open Access: 6 results) Presentation (18 results) (of which Int'l Joint Research: 7 results,  Invited: 1 results) Book (2 results)

  • [Int'l Joint Research] IIT Madras(インド)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] King Abdulaziz University(サウジアラビア)

    • Related Report
      2019 Annual Research Report
  • [Journal Article] Neurological Disorder Drug Discovery from Gene Expression with Tensor Decomposition2020

    • Author(s)
      Taguchi Y-h.、Turki Turki
    • Journal Title

      Current Pharmaceutical Design

      Volume: 25 Issue: 43 Pages: 4589-4599

    • DOI

      10.2174/1381612825666191210160906

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Identifying suitable tools for variant detection and differential gene expression using RNA-seq data2020

    • Author(s)
      Dharshini S. Akila Parvathy、Taguchi Y.-H.、Gromiha M. Michael
    • Journal Title

      Genomics

      Volume: 112 Issue: 3 Pages: 2166-2172

    • DOI

      10.1016/j.ygeno.2019.12.011

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Development of a novel anti-hepatitis B virus agent via Sp12020

    • Author(s)
      Hayakawa Michiyo、Umeyama Hideaki、Iwadate Mitsuo、Taguchi Y.-H.、Yano Yoshihiko、Honda Takashi、Itami-Matsumoto Saori、Kozuka Ritsuzo、Enomoto Masaru、Tamori Akihiro、Kawada Norifumi、Murakami Yoshiki
    • Journal Title

      Scientific Reports

      Volume: 10 Issue: 1 Pages: 47-47

    • DOI

      10.1038/s41598-019-56842-9

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Discovery of a Robust Gene Regulatory Network with a Complex Transcription Factor Network on Organ Cancer Cell-line RNA Sequence Data2019

    • Author(s)
      Kalbuaji Bharata、Taguchi Y-H.、Konagaya Akihiko
    • Journal Title

      Chem-Bio Informatics Journal

      Volume: 19 Issue: 0 Pages: 32-55

    • DOI

      10.1273/cbij.19.32

    • NAID

      130007723654

    • ISSN
      1347-0442, 1347-6297
    • Year and Date
      2019-09-30
    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Exploring the selective vulnerability in Alzheimer disease using tissue specific variant analysis2019

    • Author(s)
      Akila Parvathy Dharshini S.、Taguchi Y-h.、Michael Gromiha M.
    • Journal Title

      Genomics

      Volume: 111 Issue: 4 Pages: 936-949

    • DOI

      10.1016/j.ygeno.2018.05.024

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Machine learning algorithms for predicting drugs?tissues relationships2019

    • Author(s)
      Turki Turki、Taguchi Y-h.
    • Journal Title

      Expert Systems with Applications

      Volume: 127 Pages: 167-186

    • DOI

      10.1016/j.eswa.2019.02.013

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Multiomics Data Analysis Using Tensor Decomposition Based Unsupervised Feature Extraction2019

    • Author(s)
      Taguchi Y-h.
    • Journal Title

      Intelligent Computing Theories and Application

      Volume: 1 Pages: 565-574

    • DOI

      10.1007/978-3-030-26763-6_54

    • ISBN
      9783030267629, 9783030267636
    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Tensor Decomposition-Based Unsupervised Feature Extraction Applied to Single-Cell Gene Expression Analysis2019

    • Author(s)
      Taguchi Y-h.、Turki Turki
    • Journal Title

      Frontiers in Genetics

      Volume: 10 Pages: 864-864

    • DOI

      10.3389/fgene.2019.00864

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Tensor Decomposition Based Unsupervised Feature Extraction Applied to Bioinformatics2019

    • Author(s)
      Taguchi Y-h.
    • Journal Title

      Application of Omics, AI and Blockchain in Bioinformatics Research

      Volume: 1 Pages: 159-187

    • DOI

      10.1142/9789811203589_0010

    • ISBN
      9789811203572, 9789811203589
    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Investigating the energy crisis in Alzheimer disease using transcriptome study2019

    • Author(s)
      Dharshini S. Akila Parvathy、Taguchi Y.-h.、Gromiha M. Michael
    • Journal Title

      Scientific Reports

      Volume: 9 Issue: 1 Pages: 18509-18509

    • DOI

      10.1038/s41598-019-54782-y

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Drug candidate identification based on gene expression of treated cells using tensor decomposition-based unsupervised feature extraction for large-scale data2019

    • Author(s)
      Taguchi Y-h.
    • Journal Title

      BMC Bioinformatics

      Volume: 19 Issue: S13 Pages: 338-338

    • DOI

      10.1186/s12859-018-2395-8

    • Related Report
      2018 Research-status Report
  • [Journal Article] Tensor decomposition-based and principal-component-analysis-based unsupervised feature extraction applied to the gene expression and methylation profiles in the brains of social insects with multiple castes2018

    • Author(s)
      Taguchi Y.-H.
    • Journal Title

      BMC Bioinformatics

      Volume: 19 Issue: S4 Pages: 99-99

    • DOI

      10.1186/s12859-018-2068-7

    • Related Report
      2018 Research-status Report
  • [Journal Article] Tensor Decomposition?Based Unsupervised Feature Extraction for Integrated Analysis of TCGA Data on MicroRNA Expression and Promoter Methylation of Genes in Ovarian Cancer2018

    • Author(s)
      Taguchi Y-h.、Ng Ka-Lok
    • Journal Title

      IEEE BIBE2018

      Volume: 1 Pages: 1-1

    • DOI

      10.1109/bibe.2018.00045

    • Related Report
      2018 Research-status Report
  • [Journal Article] Tensor decomposition-based unsupervised feature extraction applied to matrix products for multi-view data processing2017

    • Author(s)
      Taguchi Y-h.
    • Journal Title

      PLOS ONE

      Volume: 12 Issue: 8 Pages: e0183933-e0183933

    • DOI

      10.1371/journal.pone.0183933

    • Related Report
      2017 Research-status Report
  • [Journal Article] Genetic Association between Amyotrophic Lateral Sclerosis and Cancer2017

    • Author(s)
      Taguchi Y-h.、Wang Hsiuying
    • Journal Title

      Genes

      Volume: 8 Issue: 10 Pages: 243-243

    • DOI

      10.3390/genes8100243

    • Related Report
      2017 Research-status Report
  • [Journal Article] One-class Differential Expression Analysis using Tensor Decomposition-based Unsupervised Feature Extraction Applied to Integrated Analysis of Multiple Omics Data from 26 Lung Adenocarcinoma Cell Lines2017

    • Author(s)
      Taguchi Y-h.
    • Journal Title

      BIBE2017

      Volume: 1 Pages: 1-12

    • DOI

      10.1109/bibe.2017.00-66

    • Related Report
      2017 Research-status Report
  • [Journal Article] Identification of candidate drugs using tensor-decomposition-based unsupervised feature extraction in integrated analysis of gene expression between diseases and DrugMatrix datasets2017

    • Author(s)
      Taguchi Y.-h.
    • Journal Title

      Scientific Reports

      Volume: 7 Issue: 1 Pages: 13733-13733

    • DOI

      10.1038/s41598-017-13003-0

    • Related Report
      2017 Research-status Report
  • [Journal Article] Tensor decomposition-based unsupervised feature extraction identifies candidate genes that induce post-traumatic stress disorder-mediated heart diseases2017

    • Author(s)
      Taguchi Y.-H.
    • Journal Title

      BMC Medical Genomics

      Volume: 10 Issue: S4 Pages: 67-67

    • DOI

      10.1186/s12920-017-0302-1

    • Related Report
      2017 Research-status Report
  • [Presentation] Sp1を標的としたHBVウィルスの新規阻害剤の探索2020

    • Author(s)
      早川 路代 , 梅山 秀明 , 岩舘 満雄 , 田口 善弘 , 村上 善基
    • Organizer
      情報処理学会第61回BIO研究発表会
    • Related Report
      2019 Annual Research Report
  • [Presentation] テンソル分解を用いた教師無し学習による変数選択法の一細胞RNA-seq解析への応用2020

    • Author(s)
      田口 善弘
    • Organizer
      電子情報通信学会情報論的学習理論と機械学習 (IBISML) 研究会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Multiomics Data Analysis Using Tensor Decomposition Based Unsupervised Feature Extraction2019

    • Author(s)
      Taguchi Y-h.
    • Organizer
      International Conference on Intelligent Computing
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] バイオインフォマティクスと倫理・社会2019

    • Author(s)
      田口 善弘
    • Organizer
      電子情報通信学会技術と社会・倫理研究会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] テンソル分解を用いた教師なし学習による変数選択法のTCGAデータベースにおける卵巣がんデータのmicroRNA発現プロファイルとメチル化プロファイルへの適用2019

    • Author(s)
      田口 善弘 , 呉 家樂
    • Organizer
      情報処理学会第60回BIO研究発表会
    • Related Report
      2019 Annual Research Report
  • [Presentation] テンソル分解に基づく教師なし学習による変数選択はMicroRNAトランスフェクションにより仲介されるmRNAの配列非特異的オフターゲット調節の普遍的性質を同定することができる2019

    • Author(s)
      田口 善弘
    • Organizer
      情報処理学会第59回BIO研究発表会
    • Related Report
      2019 Annual Research Report
  • [Presentation] テンソル分解と主成分分解を用いた教師なし学習による社会性昆虫のカーストの脳の遺伝子発現プロファイルとDNAメチル化の解析2019

    • Author(s)
      田口 善弘
    • Organizer
      情報処理学会第58回BIO研究発表会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Drug candidate identification based on gene expression of treated cells using tensor decomposition-based unsupervised feature extraction for large-scale data2018

    • Author(s)
      Y-h. Taguchi
    • Organizer
      InCob2018
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] Tensor Decomposition Based Unsupervised Feature Extraction for Integrated Analysis of TCGA Data on MicroRNA Expression and Promoter Methylation of Genes in Ovarian Cancer2018

    • Author(s)
      YH Taguchi, Ka-Lok Ng
    • Organizer
      IEEE BIBE 2018
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] テンソル分解に基づく1クラスの示差的発現解析による26の肺腺癌細胞株からの複数のオミックスデータの統合解析への適用2018

    • Author(s)
      田口善弘
    • Organizer
      情報処理学会第53回BIO研究発表会
    • Related Report
      2017 Research-status Report
  • [Presentation] マイクロRNAのパスウェイ解析システムの開発2018

    • Author(s)
      樋口 千洋, 田口善弘
    • Organizer
      情報処理学会第53回BIO研究発表会
    • Related Report
      2017 Research-status Report
  • [Presentation] Tensor decomposition/principal component analysis based unsupervised feature extraction applied to brain gene expression and methylation profiles of social insects with multiple castes2018

    • Author(s)
      Y-h. Taguchi
    • Organizer
      The Sixteenth Asia Pacific Bioinformatics Conference
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] 主成分分析を用いた教師なし学習による変数選択のデング出血熱患者血液遺伝子発現プロファイル解析への応用2017

    • Author(s)
      田口善弘
    • Organizer
      情報処理学会第113回MPS・第50回BIO合同研究発表会
    • Related Report
      2017 Research-status Report
  • [Presentation] テンソル分解を用いた教師なし学習による心的外傷後ストレス障害由来の心臓病原因遺伝子の同定2017

    • Author(s)
      田口善弘
    • Organizer
      情報処理学会第51回BIO研究発表会
    • Related Report
      2017 Research-status Report
  • [Presentation] 主成分分析を用いた教師なし学習による筋萎縮性側索硬化症とがんの遺伝的関連性の解明2017

    • Author(s)
      田口善弘、王 秀瑛
    • Organizer
      情報処理学会第52回バイオ情報学研究会
    • Related Report
      2017 Research-status Report
  • [Presentation] Tensor decomposition-based unsupervised feature extraction identifies candidate genes that induce post-traumatic stress disorder-mediated heart diseases2017

    • Author(s)
      Y-h. Taguchi
    • Organizer
      The 16th International Conference on Bioinformatics
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] Tensor Decomposition based Unsupervised Feature Extraction Identified universal nature of Sequence-non-specific Off-target Regulation of mRNA Mediated by microRNA Transfection2017

    • Author(s)
      Y-h. Taguchi
    • Organizer
      The 28th International Conference on Genome Informatics
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] One-class Differential Expression Analysis using Tensor Decomposition-based Unsupervised Feature Extraction Applied to Integrated Analysis of Multiple Omics Data from 26 Lung Adenocarcinoma Cell Lines2017

    • Author(s)
      Y-h. Taguchi
    • Organizer
      2017 IEEE 17th International Conference on Bioinformatics and Bioengineering
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Book] Unsupervised Feature Extraction Applied to Bioinformatics: A PCA Based and TD Based Approach2019

    • Author(s)
      Y-h. Taguchi
    • Total Pages
      321
    • Publisher
      Springer International
    • ISBN
      9783030224554
    • Related Report
      2019 Annual Research Report
  • [Book] Regulatory microRNA2019

    • Author(s)
      Y-h. Taguchi, Hsiuying Wang
    • Total Pages
      348
    • Publisher
      MDPI
    • ISBN
      9783038977698
    • Related Report
      2019 Annual Research Report

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Published: 2017-04-28   Modified: 2021-02-19  

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