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Effcient and secure search via graph annymization techniques for large individual genome database

Research Project

Project/Area Number 20K21827
Research Category

Grant-in-Aid for Challenging Research (Exploratory)

Allocation TypeMulti-year Fund
Review Section Medium-sized Section 62:Applied informatics and related fields
Research InstitutionThe University of Tokyo

Principal Investigator

Shibuya Tetsuo  東京大学, 医科学研究所, 教授 (60396893)

Project Period (FY) 2020-07-30 – 2023-03-31
Project Status Completed (Fiscal Year 2022)
Budget Amount *help
¥6,240,000 (Direct Cost: ¥4,800,000、Indirect Cost: ¥1,440,000)
Fiscal Year 2022: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
Fiscal Year 2021: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
Fiscal Year 2020: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
Keywordsアルゴリズム理論 / プライバシー保護 / 差分プライバシー / データ保護 / 個人ゲノム / プライバシー / 検索技術 / グラフ理論
Outline of Research at the Start

本研究では、今後の個人ゲノム時代の超大規模ゲノムデータベースを活用して医科学をさらに発展させるため、大規模個人ゲノムデータベースに対し、究極の個人情報ともいわれるゲノムデータの倫理的特性にあった安全かつ効率的な検索・解析手法を実現することを目指す。この実現には、データを棄損しない効率的な匿名化技術の開発が必要である。そのための必要なデータを保持しつつ匿名化が達成できるグラフ匿名化手法の確立をめざすとともに、将来の個人ゲノム研究の基盤として開拓することを狙い、匿名化されたデータに対する検索・解析技術基盤の開拓を狙う。

Outline of Final Research Achievements

We developed differential privacy-based new technologies to publish various statistics of genome wide association study (GWAS), such as Chi-square statistic, Cochran-Armitage trend test, TDT test, and the k-top associated genes. We also developed a method of combining differential privacy and k-anonymization, related graph theory, a graph-based genome compression algorithm, graph feature extraction methods for various databases, data protection methods.

Academic Significance and Societal Importance of the Research Achievements

これらの研究によって公開が可能となったゲノムワイド関連解析における多くの統計値は、大規模個人ゲノム解析におけるもっとも基盤的な重要データであり、これらをプライバシーの保護を図りつつ公開できるようになったことは非常にインパクトのある成果である。特に統計上位遺伝子の公開に関する研究は、プライバシー保護分野のトップ国際会議においてIEEE Outstanding Paper Awardを受賞するなど、国際的にも高い評価を得た。

Report

(4 results)
  • 2022 Annual Research Report   Final Research Report ( PDF )
  • 2021 Research-status Report
  • 2020 Research-status Report
  • Research Products

    (33 results)

All 2023 2022 2021 2020 Other

All Int'l Joint Research (1 results) Journal Article (21 results) (of which Int'l Joint Research: 4 results,  Peer Reviewed: 21 results,  Open Access: 12 results) Presentation (11 results) (of which Int'l Joint Research: 6 results,  Invited: 6 results)

  • [Int'l Joint Research] Bogazici University(トルコ)

    • Related Report
      2021 Research-status Report
  • [Journal Article] Genetic algorithm-based feature selection with manifold learning for cancer classification using microarray data2023

    • Author(s)
      Wang Zixuan、Zhou Yi、Takagi Tatsuya、Song Jiangning、Tian Yu-Shi、Shibuya Tetsuo
    • Journal Title

      BMC Bioinformatics

      Volume: 24 Issue: 1

    • DOI

      10.1186/s12859-023-05267-3

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Privacy-Preserving Statistical Analysis of Genomic Data Using Compressive Mechanism with Haar Wavelet Transform2023

    • Author(s)
      Yamamoto Akito、Shibuya Tetsuo
    • Journal Title

      Journal of Computational Biology

      Volume: 30 Issue: 2 Pages: 176-188

    • DOI

      10.1089/cmb.2022.0246

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] (ε, k)-Randomized Anonymization: ε-Differentially Private Data Sharing with k-Anonymity2023

    • Author(s)
      Yamamoto Akito、Kimura Eizen、Shibuya Tetsuo
    • Journal Title

      Proceedings of the 16th International Joint Conference on Biomedical Engineering Systems and Technologies

      Volume: 1 Pages: 287-297

    • DOI

      10.5220/0011665600003414

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Hardness of Bounding Influence via Graph Modification2023

    • Author(s)
      Barish Robert D.、Shibuya Tetsuo
    • Journal Title

      LNCS

      Volume: 13878 Pages: 129-143

    • DOI

      10.1007/978-3-031-23101-8_9

    • ISBN
      9783031231001, 9783031231018
    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Developing Language Resources and NLP Tools for the North Korean Language2022

    • Author(s)
      Arda Akdemir, Yeojoo Jeon and Tetsuo Shibuya
    • Journal Title

      Proc. 13th Conference on Language Resources and Evaluation

      Volume: 1 Pages: 5595-5600

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Optimally Confining Lattice Polymers, Proc. Canadian Conference on Computational Geometry2022

    • Author(s)
      Robert Barish, Tetsuo Shibuya
    • Journal Title

      Proc. CCCG

      Volume: 1 Pages: 24-31

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Proper Colorability of Segment Intersection Graphs2022

    • Author(s)
      Barish Robert D.、Shibuya Tetsuo
    • Journal Title

      Proc. COCOON

      Volume: 1 Pages: 573-584

    • DOI

      10.1007/978-3-031-22105-7_51

    • ISBN
      9783031221040, 9783031221057
    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Efficient and Highly Accurate Differentially Private Statistical Genomic Analysis using Discrete Fourier Transform2022

    • Author(s)
      Yamamoto Akito、Shibuya Tetsuo
    • Journal Title

      Proc. The 21st IEEE International Conference on Trust, Security and Privacy in Computing and Communications

      Volume: 1 Pages: 525-532

    • DOI

      10.1109/trustcom56396.2022.00078

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] String Editing Under Pattern Constraints2022

    • Author(s)
      Barish Robert D.、Shibuya Tetsuo
    • Journal Title

      New Trends in Computer Technologies and Applications. ICS 2022. Communications in Computer and Information Science,

      Volume: 1723 Pages: 13-24

    • DOI

      10.1007/978-981-19-9582-8_2

    • ISBN
      9789811995811, 9789811995828
    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Efficient Differentially Private Methods for a Transmission Disequilibrium Test in Genome Wide Association Studies2022

    • Author(s)
      Akito Yamamoto, Tetsuo Shibuya
    • Journal Title

      Pacific Symposium on Biocomputing

      Volume: 27 Pages: 85-96

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Privacy-Preserving Statistical Analysis of Genomic Data using Compressive Mechanism with Haar Wavelet Transform2022

    • Author(s)
      Akito Yamamoto, Tetsuo Shibuya
    • Journal Title

      RECOMB Privacy and Security Workshop

      Volume: 1

    • Related Report
      2021 Research-status Report
    • Peer Reviewed
  • [Journal Article] Developing Language Resources and NLP Tools for the North Korean Language2022

    • Author(s)
      Arda Akdemir, Yeojoo Jeon and Tetsuo Shibuya
    • Journal Title

      Conference on Language Resources and Evaluation

      Volume: 13

    • Related Report
      2021 Research-status Report
    • Peer Reviewed
  • [Journal Article] More practical differentially private publication of key statistics in GWAS2021

    • Author(s)
      Yamamoto Akito、Shibuya Tetsuo
    • Journal Title

      Bioinformatics Advances

      Volume: 1 Issue: 1 Pages: 1-10

    • DOI

      10.1093/bioadv/vbab004

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Compression of Multiple k-mer Sets by Iterative SPSS Decomposition2021

    • Author(s)
      Kazushi Kitaya and Tetsuo Shibuya
    • Journal Title

      Proc. WABI 2021, Leibniz International Proceedings in Informatics (LIPIcs)

      Volume: 201(12) Pages: 1-12

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Solving teleportation mazes with limited visibility2021

    • Author(s)
      Robert Barish and Tetsuo Shibuya
    • Journal Title

      The 23rd Thailand-Japan Conference on Discrete and Computational Geometry, Graphs, and Games

      Volume: 1 Pages: 110-111

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Differentially Private Linkage Analysis with TDT ? the case of two affected children per family2021

    • Author(s)
      Yamamoto Akito、Shibuya Tetsuo
    • Journal Title

      Proceedings of BIBM

      Volume: IEEE Pages: 765-770

    • DOI

      10.1109/bibm52615.2021.9669365

    • Related Report
      2021 Research-status Report
    • Peer Reviewed
  • [Journal Article] UDON: Unsupervised Data SelectiON for Biomedical Entity Recognition2021

    • Author(s)
      Akdemir Arda、Shibuya Tetsuo
    • Journal Title

      Proceedings of 4th International Conference on Computing and Big Data (ICCBD)

      Volume: ACM Pages: 1-7

    • DOI

      10.1145/3507524.3507525

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] A Comprehensive Analysis of Subword Contextual Embeddings for Languages with Rich Morphology2021

    • Author(s)
      Akdemir Arda、Shibuya Tetsuo、Gungur Tunga
    • Journal Title

      Advances in Intelligent Systems and Computing

      Volume: 1395 Pages: 31-72

    • DOI

      10.1007/978-981-16-3357-7_2

    • ISBN
      9789811633560, 9789811633577
    • Related Report
      2021 Research-status Report
    • Peer Reviewed
  • [Journal Article] Transfer Learning for Biomedical Question Answering2020

    • Author(s)
      Arda Akdemir, Tetsuo Shibuya
    • Journal Title

      Proc. CLEF 2020, CEUR Workshop Proceedings

      Volume: 2696 Pages: 1-15

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Wear Leveling Revisited2020

    • Author(s)
      Taku Onodera, Tetsuo Shibuya
    • Journal Title

      Leibniz International Proceedings in Informatics (LIPIcs)

      Volume: 181(65) Pages: 1-17

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Subword Contextual Embeddings for Languages with Rich Morphology2020

    • Author(s)
      Arda Akdemir, Tetsuo Shibuya, Tunga Gungor
    • Journal Title

      Proc. ICMLA 2020

      Volume: 1 Pages: 994-1001

    • DOI

      10.1109/icmla51294.2020.00161

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] Efficient and Highly Accurate Differentially Private Statistical Genomic Analysis using Discrete Fourier Transform2023

    • Author(s)
      Akito Yamamoto, Tetsuo Shibuya
    • Organizer
      IPSJ CSEC-100
    • Related Report
      2022 Annual Research Report
  • [Presentation] 個人医療時代のバイオインフォマティクス2023

    • Author(s)
      渋谷哲朗
    • Organizer
      学習院桜友回寄付講座(生命情報社会学)シンポジウム
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] Differentially Private Methods in Bioinformatics2023

    • Author(s)
      Tetsuo Shibuya
    • Organizer
      Combinatorial Problems of Strings and Graphs and Their Applications in Bioinformatics
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Privacy-Preserving Statistical Analysis of Genomic Data using Compressive Mechanism with Haar Wavelet Transform2022

    • Author(s)
      Akito Yamamoto, Tetsuo Shibuya
    • Organizer
      RECOMB Privacy and Security Workshop
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Counting on a rainbow connection2022

    • Author(s)
      Robert Barish, Tetsuo Shibuya
    • Organizer
      Italian Conference on Theoretical Computer Science
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 大規模医療データが変えるこれからの医科学研究2022

    • Author(s)
      渋谷哲朗
    • Organizer
      シンポジウム『超高齢社会を考えるⅥ』
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] Privacy preserving technologies toward safe medical science2022

    • Author(s)
      Tetsuo Shibuya
    • Organizer
      The 47th Annual Meeting of the Japanese Society for Investigative Dermatology (JSID)
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Efficient Differentially Private Methods for a Transmission Disequilibrium Test2021

    • Author(s)
      Akito Yamamoto, Tetsuo Shibuya
    • Organizer
      第67回バイオ情報学研究会
    • Related Report
      2021 Research-status Report
  • [Presentation] UDON: Unsupervised Data SelectiON for Biomedical Entity Recognition2021

    • Author(s)
      Arda Akdemir, Tetsuo Shibuya
    • Organizer
      The 27th East Asia Joint Symposium
    • Related Report
      2021 Research-status Report
    • Int'l Joint Research
  • [Presentation] Algorithmic Challenges for Biomedical Big Data2021

    • Author(s)
      Tetsuo Shibuya
    • Organizer
      The 11th International Conference on Bioscience, Biochemistry and Bioinformatics
    • Related Report
      2020 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] スパコンシステム「SHIROKANE」とゲノム医療2020

    • Author(s)
      渋谷哲朗
    • Organizer
      第9回生命医薬情報連合大会
    • Related Report
      2020 Research-status Report
    • Invited

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Published: 2020-08-03   Modified: 2024-01-30  

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