Development of basic technology for privacy-preserving bioinformatics and its application

• Project/Area Number: 25540131
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Multi-year Fund
• Research Field: Life / Health / Medical informatics
• Research Institution: Waseda University (2014-2015); The University of Tokyo (2013)
• Principal Investigator: Hamada Michiaki 早稲田大学, 理工学術院, 准教授 (00596538)
• Co-Investigator(Kenkyū-buntansha): Shimizu Kana 早稲田大学, 理工学術院, 准教授 (60367050)
• Co-Investigator(Renkei-kenkyūsha): Hanaoka Goichiro 独立行政法人産業技術総合研究所, 研究グループ長 (30415731) ; Tsuda Koji 東京大学, 大学院新領域創成科学研究科, 教授 (90357517) ; Frith Martin 産業技術総合研究所, 人工知能研究センター, 主任研究員 (40462832) ; Asai Kiyoshi 東京大学, 大学院新領域創成科学研究科, 教授 (30356357)
• Project Period (FY): 2013-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2015)
• Budget Amount: ¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000); Fiscal Year 2015: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000); Fiscal Year 2014: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000); Fiscal Year 2013: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
• Keywords: プライバシー保護 / 化合物検索 / アラインメント / 隠れマルコフモデル / PPDM / 配列アラインメント / 準同型暗号 / プライバシー / ゲノム / 化合物 / 暗号 / データベース検索 / 配列検索

Outline of Final Research Achievements

It is highly demanded to deal with the information of personal genome and chemical compound secretly, because they are sensitive information that should not be leaked. On the other hand, from a viewpoint of "open" science, it is important to perform data-mining by combining those sensitive information with other data. In this study, we have developed several methods to perform data-mining, making those information secret. Specifically, we developed (i) privacy-preserving search for chemical database, (ii) privacy-preserving genome sequence search with hidden Markov Model (HMM) and (iii) privacy preserving sequence alignment, all of which will be useful toward open science of biology.

Research Products

• [Journal Article] Privacy-preserving search for chemical compound databases (2015)
  • Author(s): Kana Shimizu, Koji Nuida, Hiromi Arai, Shigeo Mitsunari, Nuttapong Attrapadung, Michiaki Hamada, Koji Tsuda, Takatsugu Hirokawa, Jun Sakuma, Goichiro Hanaoka, Kiyoshi Asai
  • Journal Title: BMC Bioinformatics Volume: 16(Suppl 18):S6 Issue: S18 Pages: 1-14
  • DOI: 10.1186/1471-2105-16-s18-s6
  • NAID: 120007128511
  • Peer Reviewed / Open Access
• [Presentation] 疾患リスクの評価へ向けた加法準同型性暗号によるプライバシー保護ＨＭＭの実装と評価 (2016)
  • Author(s): 三品 気吹, 浜田道昭
  • Organizer: 情報処理学会 第108回MPS・第46回BIO合同研究発表会
  • Place of Presentation: 沖縄
  • Year and Date: 2016-07-04
• [Presentation] Privacy-preserving search for a chemical compound database (2013)
  • Author(s): Kana Shimizu, Hiromi Arai, Koji Nuida, Michiaki Hamada, Koji Tsuda, Jun Sakuma, Takatsugu Hirokawa, Goichiro Hanaoka, Kiyoshi Asai,
  • Organizer: ISMB/ECCB 2013
  • Place of Presentation: ベルリン、ドイツ
• [Presentation] 次世代バイオインフォマティクス技術の研究開発 (2013)
  • Author(s): 浜田道昭
  • Organizer: 医薬会セミナー
  • Place of Presentation: 国立国際医療研究センター、東京都
  • Invited
• [Book] 生命情報処理における機械学習 (2016)
  • Author(s): 瀬々潤、浜田道昭
  • Publisher: 講談社