Fast Similarity Search on Big Data based on SMAD and its applications

• Project/Area Number: 25280002
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Partial Multi-year Fund
• Section: 一般
• Research Field: Theory of informatics
• Research Institution: The University of Tokyo
• Principal Investigator: Shibuya Tetsuo 東京大学, 医科学研究所, 准教授 (60396893)
• Project Period (FY): 2013-04-01 – 2017-03-31
• Project Status: Completed (Fiscal Year 2016)
• Budget Amount: ¥10,400,000 (Direct Cost: ¥8,000,000、Indirect Cost: ¥2,400,000); Fiscal Year 2016: ¥3,120,000 (Direct Cost: ¥2,400,000、Indirect Cost: ¥720,000); Fiscal Year 2015: ¥3,250,000 (Direct Cost: ¥2,500,000、Indirect Cost: ¥750,000); Fiscal Year 2014: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000); Fiscal Year 2013: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
• Keywords: アルゴリズム / ビッグデータ / 検索 / タンパク質立体構造 / 次世代シークエンサー / バイオインフォマティクス / データ検索 / 機械学習

Outline of Final Research Achievements

We aimed to develop very fast indexing and searching algorithms for big-data databases, especially the protein 3-D structure databases, and also aimed to develop application algorithms utilizing them. We succeeded in developing dramatically faster protein function prediction algorithms without any loss of accuracy. We also succeeded in developing faster algorithms for protein 3-D structure searching for wider applications. We also developed several analysis algorithms for next-generation sequencer data.

Research Products

• [Int'l Joint Research] National University of Singapore(シンガポール)
• [Journal Article] Fast Classification of Protein Structures by an Alignment-free Kernel (2016)
  • Author(s): Taku Onodera, Tetsuo Shibuya
  • Journal Title: LNCS Volume: 9954 Pages: 68-79
  • DOI: 10.1007/978-3-319-46049-9_7
  • ISBN: 9783319460482, 9783319460499
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] An O(m log m)-time algorithm for detecting superbubbles (2015)
  • Author(s): Wing-Kin Sung, Kunihiko Sadakane, Tetsuo Shibuya, Abha Belorkar, Iana Pyrogova
  • Journal Title: IEEE/ACM Transactions on Computational Biology and Bioinformatics Volume: 12-4 Issue: 4 Pages: 770-777
  • DOI: 10.1109/tcbb.2014.2385696
  • Peer Reviewed / Open Access
• [Journal Article] Malphite: A Convolutional Neural Network and Ensemble Learning Based Protein Secondary Structure Predictor (2015)
  • Author(s): Yang Li, Tetsuo Shibuya
  • Journal Title: Proc. IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Volume: 1 Pages: 1260-1266
  • DOI: 10.1109/bibm.2015.7359861
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Efficient Approximate 3-Dimensional Point Set Matching Using Root-Mean-Square Deviation Score (2015)
  • Author(s): Yoichi Sasaki, Tetsuo Shibuya, Kimihito Ito, and Hiroki Arimura
  • Journal Title: LNCS Volume: 9371 Pages: 191-203
  • DOI: 10.1007/978-3-319-25087-8_18
  • NAID: 130007699483
  • ISBN: 9783319250861, 9783319250878
  • Peer Reviewed
• [Journal Article] Locating Controlling Regions of Neural Networks Using Constrained Evolutionary Computation (2015)
  • Author(s): Mohammad A. Eita, Tetsuo Shibuya, and Amin A. Shoukry
  • Journal Title: Proc. 2015 IEEE Congress on Evolutionary Computation (CEC2015) Volume: 1 Pages: 1581-1588
  • Peer Reviewed
• [Journal Article] Locating Controlling Regions of Neural Networks Using Constrained Evolutionary Computation (2015)
  • Author(s): Mohammad A. Eita, Tetsuo Shibuya, and Amin A. Shoukry
  • Journal Title: Proc. 2015 IEEE Congress on Evolutionary Computation Volume: 印刷中
  • Peer Reviewed
• [Journal Article] Improving miRNA Classification Using an Exhaustive Set of Features (2014)
  • Author(s): Sherin Moustafa El Gokhy, Tetsuo Shibuya and Amin Shoukry
  • Journal Title: Advances in Intelligent Systems and Computing Volume: 294 Pages: 31-39
  • Peer Reviewed
• [Journal Article] VEM: a Structural Variant Estimation Method using Multi-Mapped Reads on Breakpoints (2014)
  • Author(s): Tomohiko Ohtsuki, Naoki Nariai, Kaname Kojima, Takahiro Mimori, Yukuto Sato, Yosuke Kawai, Yumi Yamaguchi-Kabata, Tetsuo Shibuya and Masao Nagasaki
  • Journal Title: Lecture Notes in Bioinformatics Volume: 8542 Pages: 208-219
  • Peer Reviewed
• [Journal Article] 統計モデルを活用したビッグデータ検索超高速化 (2014)
  • Author(s): 渋谷哲朗
  • Journal Title: 電子情報通信学会誌 Volume: 97 Pages: 384-387
• [Journal Article] SVEM: a Structural Variant Estimation Method using Multi-Mapped Reads on Breakpoints (2014)
  • Author(s): Tomohiko Ohtsuki, Naoki Nariai, Kaname Kojima, Takahiro Mimori, Yukuto Sato, Yosuke Kawai, Yumi Yamaguchi-Kabata, Tetsuo Shibuya and Masao Nagasaki
  • Journal Title: 1st International Conference on Algorithms for Computational Biology Volume: 印刷中
  • Peer Reviewed
• [Journal Article] Improving miRNA Classification Using an Exhaustive Set of Features (2014)
  • Author(s): Sherin Moustafa El Gokhy, Tetsuo Shibuya and Amin Shoukry
  • Journal Title: The 8th International Conference on Practical Applications of Computational Biology & Bioinformatics Volume: 印刷中
  • Peer Reviewed
• [Journal Article] The Gapped Spectrum Kernel for Support Vector Machines (2013)
  • Author(s): Taku Onodera, Tetsuo Shibuya
  • Journal Title: Proc. Machine Learning and Data Mining, LNCS Volume: 7988 Pages: 1-15
  • DOI: 10.1007/978-3-642-39712-7_1
  • ISBN: 9783642397110, 9783642397127
  • Peer Reviewed
• [Presentation] Algorithmic Challenges for Bio Big Data (2017)
  • Author(s): Tetsuo Shibuya
  • Organizer: UTokyo-IITM Workshop
  • Place of Presentation: Chennai, India
  • Year and Date: 2017-03-13
  • Int'l Joint Research / Invited
• [Presentation] Fast Classification of Protein Structures by an Alignment-free Kernel (2016)
  • Author(s): Taku Onodera, Tetsuo Shibuya
  • Organizer: The 23rd International Symposium on String Processing and Information Retrieval
  • Place of Presentation: Beppu, Japan
  • Year and Date: 2016-10-18
  • Int'l Joint Research
• [Presentation] Malphite: A Convolutional Neural Network and Ensemble Learning Based Protein Secondary Structure Predictor (2015)
  • Author(s): Yang Li, Tetsuo Shibuya
  • Organizer: 情報処理学会 バイオ情報学研究会
  • Place of Presentation: 京都大学iPS細胞研究所(京都府京都市)
  • Year and Date: 2015-12-07
• [Presentation] Algorithm Design Paradigm Shift Needed for Bio Big Data (2015)
  • Author(s): Tetsuo Shibuya
  • Organizer: Genomic Medicine 2015
  • Place of Presentation: Ho Chi Minh, Vietnam
  • Year and Date: 2015-07-21
  • Int'l Joint Research / Invited
• [Presentation] Efficient Approximate 3-Dimensional Point Set Matching and Its Application to Molecular Pattern Matching (2015)
  • Author(s): Yoichi Sasaki, Tetsuo Shibuya, Kimito Ito, Hiroki Arimura
  • Organizer: 情報処理学会 バイオ情報学研究会
  • Place of Presentation: 沖縄科学技術大学院大学(沖縄県国頭郡)
  • Year and Date: 2015-06-15
• [Presentation] Algorithmic Challenges to Bio Big Data, (2015)
  • Author(s): Tetsuo Shibuya
  • Organizer: The 11th International Workshop on Advanced Genomics
  • Place of Presentation: 一橋講堂(東京都千代田区)
  • Year and Date: 2015-05-22
  • Int'l Joint Research / Invited
• [Presentation] Designing Faster Algorithms For Big Data (2014)
  • Author(s): Tetsuo Shibuya
  • Organizer: UK-Japan Workshop on Big Data
  • Place of Presentation: 英国大使館、東京
  • Invited
• [Presentation] Fast Indexing Methods for Protein 3-D Structure Searching (2013)
  • Author(s): Tetsuo Shibuya
  • Organizer: NII Shonan Seminar 29
  • Place of Presentation: Shonan Village Center, Kanagawa
  • Invited
• [Book] アルゴリズム (2016)
  • Author(s): 渋谷哲朗
  • Total Pages: 157
  • Publisher: 丸善出版