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Estimating data structure embedded in semi-structured data

Research Project

Project/Area Number 24300054
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypePartial Multi-year Fund
Section一般
Research Field Intelligent informatics
Research InstitutionKyoto University

Principal Investigator

Mamitsuka Hiroshi  京都大学, 化学研究所, 教授 (00346107)

Co-Investigator(Renkei-kenkyūsha) Takigawa Ichigaku  北海道大学, 情報科学研究科, 准教授 (10374597)
Hancock Timothy  京都大学, 化学研究所, 助教 (80600709)
Shiga Motoki  岐阜大学, 工学部, 助教 (20437263)
Tsuda Koji  東京大学, 新領域創成科学研究科, 教授 (90357517)
Kayano Mitsunori  帯広畜産大学, グローバルアグロメディシン研究センター, 講師 (20590095)
Nguyen Canh Hao  京都大学, 化学研究所, 助教 (90626889)
Project Period (FY) 2012-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥17,940,000 (Direct Cost: ¥13,800,000、Indirect Cost: ¥4,140,000)
Fiscal Year 2014: ¥6,110,000 (Direct Cost: ¥4,700,000、Indirect Cost: ¥1,410,000)
Fiscal Year 2013: ¥6,500,000 (Direct Cost: ¥5,000,000、Indirect Cost: ¥1,500,000)
Fiscal Year 2012: ¥5,330,000 (Direct Cost: ¥4,100,000、Indirect Cost: ¥1,230,000)
Keywords知識発見とデータマイニング / グラフマイニング / 機械学習 / 生体生命情報学 / 人工知能 / ゲノム / プロテオーム
Outline of Final Research Achievements

The objective of this research is to build machine learning solutions for a variety of problems of semi-structured data, particularly graphs and networks. Particular problem focus was "label propagation" and "link prediction". We have not only built machine learning techniques but also applied our technique to real data, particularly those in life sciences.

Report

(5 results)
  • 2015 Annual Research Report   Final Research Report ( PDF )
  • 2014 Annual Research Report
  • 2013 Annual Research Report
  • 2012 Annual Research Report
  • Research Products

    (38 results)

All 2016 2015 2014 2013 2012 Other

All Int'l Joint Research (2 results) Journal Article (22 results) (of which Peer Reviewed: 22 results,  Acknowledgement Compliant: 10 results) Presentation (12 results) (of which Invited: 6 results) Book (1 results) Remarks (1 results)

  • [Int'l Joint Research] Lille 1 University(France)

    • Related Report
      2015 Annual Research Report
  • [Int'l Joint Research] Fudan University(中国)

    • Related Report
      2015 Annual Research Report
  • [Journal Article] Mining approximate patterns with frequent locally optimal occurrences2016

    • 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

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Current Status and Prospects of Computational Resources for Natural Product Dereplication: A Review.2016

    • Author(s)
      Mohamed, A., Nguyen, C. H. and Mamitsuka, H.
    • Journal Title

      Briefings in Bioinformatics

      Volume: 17 Issue: 2 Pages: 309-321

    • DOI

      10.1093/bib/bbv042

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Non-negative Matrix Factorization with Auxiliary Information on Overlapping Groups2015

    • Author(s)
      Motoki Shiga, Hiroshi Mamitsuka
    • Journal Title

      IEEE Transactions on Knowledge and Data Engineering

      Volume: 27 Issue: 6 Pages: 1615-1628

    • DOI

      10.1109/tkde.2014.2373361

    • NAID

      120005663300

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] MeSHLabeler: Improving the Accuracy of Large-scale MeSH indexing by Integrating Diverse Evidence.2015

    • Author(s)
      Liu, K., Peng, S., Wu, J., Zhai, C., Mamitsuka H. and Zhu S.
    • Journal Title

      Bioinformatics

      Volume: 31 Issue: 12 Pages: i339-i347

    • DOI

      10.1093/bioinformatics/btv237

    • NAID

      120005980853

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] BMExpert: Mining MEDLINE for Finding Experts in Biomedical Domains Based on Language Model.2015

    • Author(s)
      Wang, B., Chen, X., Mamitsuka, H. and Zhu, S.
    • Journal Title

      IEEE/ACM Transactions on Computational Biology and Bioinformatics

      Volume: 12 Issue: 6 Pages: 1286-1294

    • DOI

      10.1109/tcbb.2015.2430338

    • NAID

      120006654074

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] MeSHSim: An R/Bioconductor Package for Measuring Semantic Similarity over MeSH Headings and MEDLINE Documents2015

    • Author(s)
      Zhou, J., Shui, Y., Peng, S., Li, X., Mamitsuka, H. and Zhu, S.
    • Journal Title

      Journal of Bioinformatics and Computational Biology

      Volume: 13 Issue: 06 Pages: 1542002-1542002

    • DOI

      10.1142/s0219720015420020

    • NAID

      120006654075

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Evaluation of Serum-based Cancer Biomarkers: A Brief Review from a Clinical and Computational Viewpoint2015

    • Author(s)
      Yotsukura, S. and Mamitsuka, H.
    • Journal Title

      Critical Reviews in Oncology/Hematology

      Volume: 93 Issue: 2 Pages: 103-115

    • DOI

      10.1016/j.critrevonc.2014.10.002

    • Related Report
      2015 Annual Research Report 2014 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] NetPathMiner:R/Bioconductor Package for Network Path Mining through Gene Expression2014

    • Author(s)
      Mohamed, A., Hancock, T., Nguyen, C. H. and Mamitsuka, H.
    • Journal Title

      Bioinformatics

      Volume: 30 Issue: 21 Pages: 3139-3141

    • DOI

      10.1093/bioinformatics/btu501

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Detecting Differentially Coexpressed Genes from Labeled Expression Data:A Brief Review2014

    • Author(s)
      Kayano, M., Shiga, M. and Mamitsuka, H.
    • Journal Title

      IEEE/ACM Transactions on Computational Biology and Bioinformatics

      Volume: 11 Issue: 1 Pages: 154-167

    • DOI

      10.1109/tcbb.2013.2297921

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Selecting Graph Cut Solutions via Global Graph Similarity2014

    • Author(s)
      Nguyen, C. H., Wicker, N. and Mamitsuka, H.
    • Journal Title

      IEEE Transactions on Neural Networks and Learning Systems

      Volume: 25 Issue: 7 Pages: 1407-1412

    • DOI

      10.1109/tnnls.2013.2292975

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Similarity-based machine learning methods for predicting drug.target interactions : a brief review2013

    • Author(s)
      Ding H, Takigawa I, Mamitsuka H, Zhu S
    • Journal Title

      Briefings in Bioinformatics

      Volume: (印刷中・先行オンライン出版済) Issue: 5 Pages: 737-747

    • DOI

      10.1093/bib/bbt056

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Multiple Graph Label Propagation by Sparse Integration2013

    • Author(s)
      Karasuyama, M. and Mamitsuka, H.
    • Journal Title

      IEEE Transactions on Neural Networks and Learning Systems

      Volume: 24 Issue: 12 Pages: 1999-2012

    • DOI

      10.1109/tnnls.2013.2271327

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A New Dissimilarity Measure for Comparing Labeled Graphs2013

    • Author(s)
      Wicker, N., Nguyen, C. H. and Mamitsuka, H.
    • Journal Title

      Linear Algebra and its Applications

      Volume: 438 Issue: 5 Pages: 2331-2338

    • DOI

      10.1016/j.laa.2012.10.021

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Efficient Semi-supervised MEDLINE Document Clustering with MeSH Semantic and Global Content Constraints2013

    • Author(s)
      Gu, J., Feng, W., Zeng, J., Mamitsuka, H. and Zhu, S.
    • Journal Title

      IEEE Transactions on Cybernetics

      Volume: 43 Issue: 4 Pages: 1265-1276

    • DOI

      10.1109/tsmcb.2012.2227998

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Fast Algorithms for Finding a Minimum Repetition Representation of Strings and Trees2013

    • Author(s)
      Nakamura, A., Saito, T., Takigawa, I., Kudo, M. and Mamitsuka, H.
    • Journal Title

      Discrete Applied Mathematics

      Volume: 161 Issue: 10-11 Pages: 1556-1575

    • DOI

      10.1016/j.dam.2012.12.013

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Graph mining: procedure, application to drug discovery and recent advances2013

    • Author(s)
      Ichigaku Takigawa, Hiroshi Mamitsuka
    • Journal Title

      Drug Discovery Today

      Volume: 18: 1-2 Issue: 1-2 Pages: 50-57

    • DOI

      10.1016/j.drudis.2012.07.016

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] SIBIC : A Web Server for Generating Gene Set Seiworks Based on Blelusters Obtained by Maximal Frequent Itemsel Mining2013

    • Author(s)
      Keiichio Takahashi. Ichigaku Takigawa and Hiroshi Mamitsuka
    • Journal Title

      PLOS ONE

      Volume: 8(12) Issue: 12 Pages: e82890-e82890

    • DOI

      10.1371/journal.pone.0082890

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] An In Silico Model for Interpreting Polypharmacological Relationships in Drug-Target Networks2013

    • Author(s)
      Ichigaku Takigawa, Koji Tsuda, Hiroshi Mamitsuka
    • Journal Title

      Methods in Molecular Biology (In Silico Models for Drug Discovery)

      Volume: 993 Pages: 67-80

    • DOI

      10.1007/978-1-62703-342-8_5

    • ISBN
      9781627033411, 9781627033428
    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Identifying Pathways of Coordinated Gene Expression2013

    • Author(s)
      Timothy Hancock, Ichigaku Takigawa, Hiroshi Mamitsuka
    • Journal Title

      Methods in Molecular Biology (Data Mining for Systems Biology)

      Volume: 939 Pages: 69-85

    • DOI

      10.1007/978-1-62703-107-3_7

    • ISBN
      9781627031066, 9781627031073
    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Latent Feature Kernels for Link Prediction on Sparse Graphs2012

    • Author(s)
      Nguhen, C. H. and Mamitsuka, H.
    • Journal Title

      LEEE Transactions on Neural Networks and Learning Systems

      Volume: 23 Issue: 11 Pages: 1793-1804

    • DOI

      10.1109/tnnls.2012.2215337

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Boosted Network Classifiers for Local Feature Selection2012

    • Author(s)
      Hancock. T. and Mami tsuka, H.
    • Journal Title

      IEEE Transactions on Neural Networks and Learning Systels

      Volume: 23 Issue: 11 Pages: 1767-1778

    • DOI

      10.1109/tnnls.2012.2214057

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A Variational Bayesian Framework for Clustering with Multiple Graphs2012

    • Author(s)
      Shiga, M. and Mam i tsuka, H.
    • Journal Title

      IEEE Transactions on Knowledge and Data Engineering

      Volume: 24 Issue: 4 Pages: 577-590

    • DOI

      10.1109/tkde.2010.272

    • NAID

      120004007455

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Presentation] Collaborative matrix factorization for predicting drug-target interactions2015

    • Author(s)
      Mamitsuka, H.
    • Organizer
      CIM Workshop on Machine Learning
    • Place of Presentation
      Uppsala, Sweden
    • Year and Date
      2015-10-08
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] Instance-wise Weighted Nonnegative Matrix Factorization for Aggregating Partitions with Locally Reliable Clusters.2015

    • Author(s)
      Zheng, X., Zhu, S., Gao, J. and Mamitsuka, H.
    • Organizer
      24th International Joint Conference on Artificial Intelligence (IJCAI 2015)
    • Place of Presentation
      Buenos Aires, Argentina
    • Year and Date
      2015-07-25
    • Related Report
      2015 Annual Research Report
  • [Presentation] MeSHLabeler: Improving the Accuracy of Large-scale MeSH indexing by Integrating Diverse Evidence2015

    • Author(s)
      Liu, K., Peng, S., Wu, J., Zhai, C., Mamitsuka H. and Zhu S.
    • Organizer
      23rd International Conference on Intelligent Systems for Molecular Biology (ISMB/ECCB 2015)
    • Place of Presentation
      Dublin, Ireland
    • Year and Date
      2015-07-10
    • Related Report
      2015 Annual Research Report
  • [Presentation] Learning kernel-based feature representation for gene essentiality prediction2014

    • Author(s)
      Karasuyama, M. and Mamitsuka, H.
    • Organizer
      DREAM Challenges and Cytoscape Workshops
    • Place of Presentation
      San Diego, CA, USA
    • Year and Date
      2014-11-09 – 2014-11-14
    • Related Report
      2014 Annual Research Report
  • [Presentation] Collaborative Matrix Factorization for Predicting Drug-Target Interactions2014

    • Author(s)
      Mamitsuka, H.
    • Organizer
      Trends in Machine Learning
    • Place of Presentation
      Kyoto University, Japan
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Manifold-based Similarity Adaptation for Label Propagation2013

    • Author(s)
      Karasuyama, M. and Mamitsuka, H.
    • Organizer
      Twenty-Seventh Annual Conference on Neural Information Processing Systems (NIPS 2013)
    • Place of Presentation
      Lake Tahoe, NV, USA
    • Related Report
      2013 Annual Research Report
  • [Presentation] Collaborative Matrix Factorization with Multiple Similarities for Predicting Drug-Target Interactions2013

    • Author(s)
      Zheng, X., Ding, H., Mamitsuka, H. and Zhu, S.
    • Organizer
      Nineteenth ACM SIGKDD International Conference On Knowledge Discovery and Data Mining (KDD 2013)
    • Place of Presentation
      Chicago, IL, USA
    • Related Report
      2013 Annual Research Report
  • [Presentation] Variational Bayes Co-clustering with Auxiliary Information2013

    • Author(s)
      Shiga, M. and Mamitsuka, H.
    • Organizer
      4th MultiClust Workshop on Multiple Clusterings, Multi-view Data, and Multi-source Knowledge-driven Clustering (MultiClust 2013)
    • Place of Presentation
      Chicago, IL, USA
    • Related Report
      2013 Annual Research Report
  • [Presentation] Machine Learning for Bioinformatics2013

    • Author(s)
      Mamitsuka, H.
    • Organizer
      FASEB Science and Research Conference, The Biology of Calpains in Health and Disease
    • Place of Presentation
      Saxtons River, VT, USA
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Mining Significant Substructure Pairs from Drug-Target Network2013

    • Author(s)
      馬見塚 拓
    • Organizer
      日本バイオインフォマティクス学会第17回創薬インフォマティクス研究会
    • Place of Presentation
      産業技術総合研究所臨海副都心センター別館
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Mining Metabolic Pathways through Gene Expression2013

    • Author(s)
      Mamitsuka, H.
    • Organizer
      Kyoto University--Koc University Symposium ``New Frontiers in Health Sciences & Technologies''
    • Place of Presentation
      Kyoto University, Japan
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Efficiently Detecting Switching Mechanisms in Gene Expression2013

    • Author(s)
      Mamitsuka, H.
    • Organizer
      23rd International Conference on Genome Informatics (GIW 2013)
    • Place of Presentation
      Matrix, Biopolis, Singpore
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Book] Data Mining for Systems Biology: Methods and Protocols2013

    • Author(s)
      Mamitsuka, H., DeLisi, C., and Kanehisa, M.
    • Total Pages
      279
    • Publisher
      Springer
    • Related Report
      2013 Annual Research Report
  • [Remarks] DREAMチャレンジ 遺伝子エッセンシャリティー予測で第1位を達成

    • URL

      http://www.kuicr.kyoto-u.ac.jp/announce/2014/news_141114.html

    • Related Report
      2014 Annual Research Report

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Published: 2012-04-24   Modified: 2022-01-31  

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