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Informatic approach to hypothesis discovery: Finding implicit gene-disease associations

Research Project

Project/Area Number 19700147
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeSingle-year Grants
Research Field Intelligent informatics
Research InstitutionKobe University

Principal Investigator

SEKI Kazuhiro  Kobe University, 自然科学系先端融合研究環重点研究部, 助教 (30444566)

Project Period (FY) 2007 – 2008
Project Status Completed (Fiscal Year 2008)
Budget Amount *help
¥3,510,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥210,000)
Fiscal Year 2008: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2007: ¥2,600,000 (Direct Cost: ¥2,600,000)
Keywordsテキストマイニング / 仮説生成 / 仮説発見 / オントロジー / 遺伝的関連 / 全文データ / 情報検索 / 推論ネットワーク
Research Abstract

本研究では,疾病と遺伝子の関係を遺伝子機能と表現型を介してモデル化し,文献解析による原因遺伝子の予測を試みた.
その結果,従来一般的であった抄録だけを使った場合と比較し,全文データを用いた場合は5%程度の予測性能の向上が見られた.また,オントロジーに記述された概念間の関係を利用して確率パラメタを伝播したとき,システム性能の向上が見られた.
代表的な先行研究と比較した場合も,提案手法の予測性能が最大で20%程度高いことが分かった.

Report

(3 results)
  • 2008 Annual Research Report   Final Research Report ( PDF )
  • 2007 Annual Research Report
  • Research Products

    (30 results)

All 2009 2008 2007 Other

All Journal Article (11 results) (of which Peer Reviewed: 11 results) Presentation (14 results) Book (5 results)

  • [Journal Article] Discovering Implicit Associations among Critical Biological Entities2009

    • Author(s)
      Kazuhiro Seki and Javed Mostafa
    • Journal Title

      International Journal of Data Mining and Bioinformatics Vol. 3, No. 2

      Pages: 105-123

    • NAID

      120001681716

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] 英語音韻を考慮した情報検索のための多様なカタカナ異表記生成2009

    • Author(s)
      服部弘幸, 関和広, 上原邦昭
    • Journal Title

      情報処理学会論文誌 : 数理モデル化と応用 2

      Pages: 145-155

    • NAID

      110007989920

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Adaptive Subjective Triggers for Opinionated Document Retrieval2009

    • Author(s)
      Kazuhiro Seki, Kuniaki Uehara
    • Journal Title

      Proceedings of the Second ACM International Conference on Web Search and Data Mining

      Pages: 25-33

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Gene Ontology Annotation as Text Categorization: An Empirical Study2008

    • Author(s)
      Kazuhiro Seki and Javed Mostafa
    • Journal Title

      Information Processing & Management Vol. 44, No. 5

      Pages: 1754-1770

    • NAID

      120001506668

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] モスタファジャビド. 多様な遺伝子名認識と文書分類を用いたGene Ontologyアノテーション2008

    • Author(s)
      関和広
    • Journal Title

      電子情報通信学会論文誌 Vol. J91-D, No. 04

      Pages: 1033-1041

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Gene Ontology Annotation as Text Categorization : An Empirical Study2008

    • Author(s)
      Kazuhiro Seki, Javed Mostafa
    • Journal Title

      Information Processing & Management 44

      Pages: 1754-1770

    • NAID

      120001506668

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Generating Diverse Katakana Variants Based on Phonemic Mapping2008

    • Author(s)
      Kazuhiro Seki, Hiroyuki Hattori, and Kuniaki Uehara
    • Journal Title

      Proceedings of the 28th annual international ACM SIGIR conference on research and development in information retrieval

      Pages: 793-794

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 多様な遺伝子名認識と文書分類を用いたGene Ontologyアノテーション2008

    • Author(s)
      関和広, モスタファジャビド
    • Journal Title

      電子情報通信学会論文誌 J91-D

      Pages: 1033-1041

    • NAID

      110007381049

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Literature-Based Discovery by an Enhanced Information Retrieval Model2007

    • Author(s)
      Kazuhiro Seki and Javed Mostafa
    • Journal Title

      In Proceedings of the 10th International Conference on Discovery Science (DS 2007)

      Pages: 185-196

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Literature-Based Discovery by an Enhanced Information Retrieval Model2007

    • Author(s)
      Kazuhiro Seki, Javed Mostafa
    • Journal Title

      Proceedings of the Tenth lnternational Cflnference on Discovery Science

      Pages: 185-196

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 主観的トリガー言語モデルによる意見情報検索

    • Author(s)
      関和広, 上原邦昭
    • Journal Title

      情報処理学会論文誌 : 数理モデル化と応用 (採録決定)

    • NAID

      110007126884

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Presentation] 生物医学文献からの知識抽出とイベント間のつながりを考慮した発見性を伴う仮説の提示2009

    • Author(s)
      宮西大樹, 関和広, 上原邦昭
    • Organizer
      第1回データ工学と情報マネジメントに関するフォーラム/第7回日本データベース学会年次大会
    • Place of Presentation
      静岡
    • Year and Date
      2009-03-08
    • Related Report
      2008 Annual Research Report
  • [Presentation] リンク構造とコンテンツを相補的に用いた極少訓練事例からのスプログ発見2009

    • Author(s)
      佐藤翔平, 関和広, 上原邦昭
    • Organizer
      第1回データ工学と情報マネジメントに関するフォーラム/第7回日本データベース学会年次大会
    • Place of Presentation
      静岡
    • Year and Date
      2009-03-08
    • Related Report
      2008 Annual Research Report
  • [Presentation] 生物医学文献からの知識抽出とイベント間のつながりを考慮した発見性を伴う仮説の提示.第1回データ工学と情報マネジメントに関するフォーラム2009

    • Author(s)
      宮西大樹,関和広,上原邦昭
    • Organizer
      第7回日本データベース学会年次大会
    • Place of Presentation
      静岡
    • Related Report
      2008 Final Research Report
  • [Presentation] 相同分子種を考慮した遺伝子機能アノテーションへの多階層分類の適用2008

    • Author(s)
      木野嘉祐,関和広,上原邦昭
    • Organizer
      情報処理学会研究報告、2008-MPS-72
    • Place of Presentation
      大阪
    • Year and Date
      2008-12-17
    • Related Report
      2008 Final Research Report
  • [Presentation] 相同分子種を考慮した遺伝子機能アノテーションへの多階層分類の適用2008

    • Author(s)
      木野嘉祐, 関和広, 上原邦昭
    • Organizer
      情報処理学会研究報告2008-MPS-72
    • Place of Presentation
      大阪
    • Year and Date
      2008-12-17
    • Related Report
      2008 Annual Research Report
  • [Presentation] 主観的トリガー言語モデルによる意見情報検索2008

    • Author(s)
      関和広, 上原邦昭
    • Organizer
      情報処理学会研究報告2008-MPS-72
    • Place of Presentation
      大阪
    • Year and Date
      2008-12-17
    • Related Report
      2008 Annual Research Report
  • [Presentation] Biomedical Association Discovery via Complementary TDM2008

    • Author(s)
      Kazuhiro Seki and Kuniaki Uehara
    • Organizer
      Semantic Knowledge Discovery, Organization and Use
    • Place of Presentation
      ニューヨーク
    • Year and Date
      2008-11-14
    • Related Report
      2008 Annual Research Report
  • [Presentation] 相同分子種を利用した動的多階層分類による遺伝子機能アノテーション2008

    • Author(s)
      木野嘉祐, 関和広, 上原邦昭
    • Organizer
      iDBフォーラム2008
    • Place of Presentation
      福島
    • Year and Date
      2008-09-21
    • Related Report
      2008 Annual Research Report
  • [Presentation] ブログを対象とした統計的意見情報検索2008

    • Author(s)
      佐藤翔平
    • Organizer
      言語処理学会第14回年次大会
    • Place of Presentation
      東京大学
    • Year and Date
      2008-03-18
    • Related Report
      2007 Annual Research Report
  • [Presentation] 相同分子種を利用した動的多階層分類による遺伝子機能アノテーション2008

    • Author(s)
      木野嘉祐,関和広,上原邦昭
    • Organizer
      iDBフォーラム2008、205-210
    • Place of Presentation
      福島
    • Related Report
      2008 Final Research Report
  • [Presentation] 情報検索モデルを用いた潜在的遺伝病原因遺伝子の予測2007

    • Author(s)
      関和広
    • Organizer
      DBWeb2007
    • Place of Presentation
      東京大学
    • Year and Date
      2007-11-27
    • Related Report
      2007 Annual Research Report
  • [Presentation] TREC 2007 Blog Track Experiments at Kobe University2007

    • Author(s)
      Kazuhiro Seki
    • Organizer
      The 16th text retrieval conference (TREC 2007)
    • Place of Presentation
      米国標準技術局
    • Year and Date
      2007-11-07
    • Related Report
      2007 Annual Research Report
  • [Presentation] 英音索変換を用いたカタカナ異表記の自動生成2007

    • Author(s)
      服部弘幸
    • Organizer
      情報処理学会自然言語処理研究会
    • Place of Presentation
      東京大学
    • Year and Date
      2007-09-28
    • Related Report
      2007 Annual Research Report
  • [Presentation] 原言語音韻を考慮した多様な異表記生成モデル2007

    • Author(s)
      服部弘幸
    • Organizer
      情報処理学会数理モデル化と問題解決研究会
    • Place of Presentation
      ホテル椿館
    • Year and Date
      2007-03-05
    • Related Report
      2007 Annual Research Report
  • [Book] IGI Global

    • Author(s)
      Kazuhiro Seki, Javed Mostafa, Kuniaki Uehara
    • Publisher
      Finding Explicit and Implicit Knowledge: Biomedical Text Data Mining. In Leon S.L. Wang and Tzung-Pei Hong (Eds.), Intelligent Soft Computation and Evolving Data Mining: Integrating Advanced Technology.
    • Related Report
      2008 Final Research Report
  • [Book] In Jake Chen, Stefano Lonardi, and Randi Cohen (Eds.), Biological Data Mining. Chapman & Hall/CRC Press

    • Author(s)
      Javed Mostafa, Kazuhiro Seki, and Weimao Ke
    • Publisher
      Beyond Information Retrieval: Literature Mining for Biomedical Knowledge Discovery
    • Related Report
      2008 Final Research Report
  • [Book] Statistical Anaphora Resolution for Japanese Zero Pronouns. In Timothy Baldwin, Francis Bond, Kentaro Inui, Shun Ishizaki, Hiroshi Nakagawa, and Akira Shimazu (Eds.), Readings in Japanese Natural Language Processing

    • Author(s)
      Kazuhiro Seki, Atsushi Fujii, and Tetsuya Ishikawa
    • Publisher
      CSLI Publications(採録決定)
    • Related Report
      2008 Annual Research Report
  • [Book] Beyond Information Retrieval : Literature Mining for Biomedical Knowledge Discovery. In Jake Chen, Stefano Lonardi, and Randi Cohen (Eds.), Biological Data Mining

    • Author(s)
      Javed Mostafa, Kazuhiro Seki, and Weimao Ke
    • Publisher
      Chapman & Hall/CRC Press(採録決定)
    • Related Report
      2008 Annual Research Report
  • [Book] Finding Explicit and Implicit Knowledge : Biomedical Text Data Mining. In Leon S. L. Wang and Tzung-Pei Hong (Eds.), Intelligent Soft Computation and Evolving Data Mining : Integrating Advanced Technology

    • Author(s)
      Kazuhiro Seki, Javed Mostafa, Kuniaki Uehara
    • Publisher
      IGI Global(採録決定)
    • Related Report
      2008 Annual Research Report

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Published: 2007-04-01   Modified: 2016-04-21  

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