Analysis of Repetition Structure in Huge Sequences

• Project/Area Number: 25280079
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Partial Multi-year Fund
• Section: 一般
• Research Field: Intelligent informatics
• Research Institution: Hokkaido University
• Principal Investigator: Nakamura Atsuyoshi 北海道大学, 情報科学研究科, 准教授 (50344487)
• Co-Investigator(Kenkyū-buntansha): KUDO Mineichi 北海道大学, 大学院情報科学研究科, 教授 (60205101) ; TAKIGAWA Ichigaku 北海道大学, 大学院情報科学研究科, 准教授 (10374597)
• Co-Investigator(Renkei-kenkyūsha): MAMITSUKA Hiroshi 京都大学, 化学研究所, 教授 (00346107) ; KIDA Takuya 北海道大学, 大学院情報科学研究科, 准教授 (70343316) ; OKUBO Yoshiaki 北海道大学, 大学院情報科学研究科, 助教 (40271639)
• Project Period (FY): 2013-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2015)
• Budget Amount: ¥8,320,000 (Direct Cost: ¥6,400,000、Indirect Cost: ¥1,920,000); Fiscal Year 2015: ¥2,340,000 (Direct Cost: ¥1,800,000、Indirect Cost: ¥540,000); Fiscal Year 2014: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000); Fiscal Year 2013: ¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000)
• Keywords: 知識発見とデータマイニング / シーケンスマイニング / ゲノム情報処理 / 頻出パターンマイニング

Outline of Final Research Achievements

We developed an algorithm for enumerating frequent approximate string patterns, and proposed a method of extracting occurrence regions of the enumerated patterns as a method of extracting interspersed repetitive elements in a huge sequence like a DNA sequence. Patterns of proposed methods have occurrences of clear boundaries, so there is little chance to count essentially the same region more than once. Furthermore, our enumeration algorithm runs very fast and with small memory. According to our empirical results using human chromosome 21, a half of the known Alu regions, which are famous interspersed repetitive elements, is extracted as occurrence regions of 100 representative patterns that were selected from enumerated frequent approximate patterns.

Research Products

• [Journal Article] Mining approximate patterns with frequent locally optimal occurrences (2016)
  • Author(s): Nakamura A, Takigawa I, Tosaka H, Kudo M, Mamitsuka H
  • Journal Title: Discrete Applied Mathematics Volume: 200 Pages: 123-152
  • DOI: 10.1016/j.dam.2015.07.002
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Noise Free Multi-armed Bandit Game (2016)
  • Author(s): Atsuyoshi Nakamura, David P. Helmbold, Manfred K. Warmuth
  • Journal Title: Lecture Notes in Computer Science Volume: 9618 Pages: 412-423
  • DOI: 10.1007/978-3-319-30000-9_32
  • NAID: 130008061481
  • ISBN: 9783319299990, 9783319300009
  • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] An improved upper bound on the expected regret of UCB-type policies for a matching-selection bandit problem (2015)
  • Author(s): Ryo Watanabe, Atsuyoshi Nakamura, Mineichi Kudo
  • Journal Title: Operations Research Letters Volume: 43(6) Issue: 6 Pages: 558-563
  • DOI: 10.1016/j.orl.2015.08.008
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] An Algorithm for Influence Maximization in a Two-Terminal Series Parallel Graph and its Application to a Real Network (2015)
  • Author(s): Koji Tabata, Atsuyoshi Nakamura, Mineichi Kudo
  • Journal Title: Lecture Notes in Computer Science Volume: 9356 Pages: 275-283
  • DOI: 10.1007/978-3-319-24282-8_23
  • ISBN: 9783319242811, 9783319242828
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Diversity Measures and Margin Criteria in Multi-class Majority Vote Ensemble (2015)
  • Author(s): Ayako Mikami, Mineichi Kudo, Atsuyoshi Nakamura
  • Journal Title: Lecture Notes in Computer Science Volume: 9132 Pages: 27-37
  • DOI: 10.1007/978-3-319-20248-8_3
  • ISBN: 9783319202471, 9783319202488
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] MED26 regulates the transcription of snRNA genes through the recruitment of little elongation complex (2015)
  • Author(s): Takahashi, H., Takigawa, I., Watanabe, M., Anwar, D., Shibata, M., Tomomori-Sato, C., Sato, S., Ranjan, A., Seidel, C.W., Tsukiyama, T., Mizushima, W., Hayashi, M., Ohkawa, Y., Conaway, J.W., Conaway, R.C. and Hatakeyama, S
  • Journal Title: Nature Commun. Volume: 5 Issue: 1 Pages: 5941-5941
  • DOI: 10.1038/ncomms6941
  • NAID: 120005621881
  • Peer Reviewed / Open Access
• [Journal Article] A UCB-Like Strategy of Collaborative Filtering (2014)
  • Author(s): Atsuyoshi Nakamura
  • Journal Title: JMLR: Workshop and Conference Proceedings Volume: 39 Pages: 315-329
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Average-case linear-time similar substring searching by the q-gram distance. (2014)
  • Author(s): H. Hanada, M. Kudo and A. Nakamura
  • Journal Title: Theoretical Computer Science Volume: 530 Pages: 23-41
  • DOI: 10.1016/j.tcs.2014.02.022
  • NAID: 120005593436
  • Peer Reviewed
• [Journal Article] UCB型協調フィルタリングに関する考察 (2014)
  • Author(s): 中村篤祥
  • Journal Title: 人工知能基本問題研究会 Volume: 93 Pages: 45-48
• [Journal Article] 二端子直並列グラフにおける影響最大化頂点集合発見アルゴリズム (2014)
  • Author(s): 田畑 公次, 中村 篤祥, 工藤 峰一
  • Journal Title: 人工知能基本問題研究会 Volume: 92 Pages: 35-40
• [Journal Article] 順列バンディット問題における新しいUCB型アルゴリズム (2013)
  • Author(s): 渡辺 僚, 中村 篤祥, 工藤 峰一
  • Journal Title: 電子情報通信学会技術研究報告 Volume: COMP113(198) Pages: 9-16
• [Presentation] ランダム仮説下での出現回数分布を利用した散在反復配列の発見 (2016)
  • Author(s): 中村武憲，中村篤祥，工藤峰一
  • Organizer: 第8回データ工学と情報マネジメントに関するフォーラム
  • Place of Presentation: ヒルトン福岡シーホーク
  • Year and Date: 2016-02-29
• [Presentation] 予算制約つき多腕バンディット問題に対するKL-UCBの拡張戦略 (2015)
  • Author(s): 渡辺僚, 中村篤祥, 工藤峰一
  • Organizer: 第18回情報論的学習理論ワークショップ(IBIS2015)
  • Place of Presentation: つくば国際会議場
  • Year and Date: 2015-11-25
• [Presentation] HedgeとExp3アルゴリズム間の橋渡し (2015)
  • Author(s): 中村篤祥
  • Organizer: 第21回情報論的学習理論と機械学習 (IBISML) 研究会
  • Place of Presentation: 沖縄科学技術大学院大学
  • Year and Date: 2015-06-23
• [Presentation] 処理時間の長短を考慮した確率的多腕バンディット問題へのUCB戦略の拡張 (2015)
  • Author(s): 渡辺 僚，中村 篤祥，工藤 峰一
  • Organizer: 人工知能基本問題研究会（第 96 回）
  • Place of Presentation: 名古屋工業大学
  • Year and Date: 2015-01-13 – 2015-01-14
• [Presentation] A New UCB-Like Algorithm for Permutation Bandit Problem (2013)
  • Author(s): Ryo Watanabe, Atsuyoshi Nakamura, Mineichi Kudo
  • Organizer: NIPS 2013 workshop on Bayesian optimization
  • Place of Presentation: Harveys Lake Tahoe(USA)
• [Presentation] インターネットにおけるオンライン学習 (2013)
  • Author(s): 中村篤祥
  • Organizer: 第１２回情報科学技術フォーラム
  • Place of Presentation: 鳥取大学(鳥取市)
  • Invited