Advanced computation methods for analyzing scientific data

2009 Fiscal Year Final Research Report

• Project/Area Number: 19300045
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Intelligent informatics
• Research Institution: Japan Advanced Institute of Science and Technology
• Principal Investigator: HO Tu・Bao Japan Advanced Institute of Science and Technology, 知識科学研究科, 教授 (60301199)
• Co-Investigator(Kenkyū-buntansha): TAKABAYASHI Katsuhiko 千葉大学, 医学部附属病院, 教授 (90188079) ; KAWASAKI Saori 北陸先端科学技術大学院大学, 知識科学研究科, 助教 (40377437) ; DAM Hieu Chi 北陸先端科学技術大学院大学, 知識科学研究科, 講師 (70397230)
• Project Period (FY): 2007 – 2009
• Keywords: データマイニング / 構造化データ / 知識発見 / 科学データ

Research Abstract

The project objective is twofold. First to establish basic technologies and to develop efficient and effective machine learning/data mining methods for hard problems caused by complexly structured data, in particularly methods in the two directions : (1) kernel methods ; (2) semi-supervised learning for structured prediction. Second is to apply the developed methods for new discovery in medical bioinformatics and materials science. As the result of the project, different methods have been developed and applied to solve problems in biomedicine and materials science.

Research Products

• [Journal Article] MicroRNA expression profiles for classification and analysis of tumor samples (2011)
  • Author(s): Tran, D.H., Ho, T.B., Pham, T.H., Satou, K.
  • Journal Title: IEICE Trans.Information Systems (accepted).
  • Peer Reviewed
• [Journal Article] Privacy Preserving Frequency Mining in 2-Part Fully Distributed Setting (2010)
  • Author(s): Luong, T.D., Ho, T.B.
  • Journal Title: IEICE Trans.Information Systems Vol.E93-D, No.10 Pages: 2701-2708
  • Peer Reviewed
• [Journal Article] Enhancing Privacy in Distributed Data Clustering (2010)
  • Author(s): Luong, T.D., Ho, T.B.
  • Journal Title: Journal of Computer Science and Cybernetics Vol.26, No.2 Pages: 1-15
  • Peer Reviewed
• [Journal Article] Sequence-dependent histone variant positioning signatures (2010)
  • Author(s): Le, N.T., Ho, T.B., Ho, B.H.
  • Journal Title: BMC Genomics Vol.11(Suppl 4) Pages: 1-9
  • Peer Reviewed
• [Journal Article] Computational Discovery of miR-TF Regulatory Modules in Human Genome (2010)
  • Author(s): Tran, D.H., Satou, K., Ho, T.B., Pham, T.H.
  • Journal Title: Bioinformation 4(8) Pages: 371-377
  • Peer Reviewed
• [Journal Article] Ab initio study of the polymerisation of cyclopentasilane (2010)
  • Author(s): Sugiyama, A., Shimoda, T., Dam, H.C.
  • Journal Title: Molecular Physics 108 Pages: 1649-1653
  • Peer Reviewed
• [Journal Article] First principles study of the physisorption of hydrogen molecule on graphene and carbon nanotube surfaces adhered by Pt atom (2010)
  • Author(s): Pham, T.L., Phan, V.D., Sugiyama, A., Shimoda, T., Dam, H.C.
  • Journal Title: Journal of Computational Materials Science 49(1) Pages: S15-S20
  • Peer Reviewed
• [Journal Article] First principles study of the thermally induced polymerization of cyclopentasilane (2010)
  • Author(s): Phan V.D., Pham T.L., A.Sugiyama, T.Shimoda, Dam H.C.
  • Journal Title: Computational Materials Science 49(1) Pages: S21-S24
  • Peer Reviewed
• [Journal Article] Ab initio study of the polymerization of cyclopentasilane (2010)
  • Author(s): Sugiyama, A., Shimoda, T., Dam H.C.
  • Journal Title: Molecular Physics. (accepted)
  • Peer Reviewed
• [Journal Article] Characterizing nucleosome dynamics from genomic and epigenetic information using rule induction learning (2009)
  • Author(s): Le, N.T., Ho, T.B., Tran, D.H.
  • Journal Title: BMC Genomics 10(Suppl.3) Pages: S27
  • Peer Reviewed
• [Journal Article] Augmented Mutual Information for Multiword Extraction (2009)
  • Author(s): Zhang, W., Yoshida, T., Ho, T.B., Tang, X.
  • Journal Title: International Journal of Innovative Computing, Information and Control Vol.5, No.2 Pages: 543-554
  • Peer Reviewed
• [Journal Article] Improving effectiveness of mutual information for substantial multiword expression extraction (2009)
  • Author(s): Zhang, W., Yoshida, T., Tang, X., Ho, T.B.
  • Journal Title: Expert Systems with Applications (Elsevier) Vol.36, No.8 Pages: 10919-10930
  • Peer Reviewed
• [Journal Article] Substrate-mediated interactions of Pt atoms adsorbed on single-wall carbon nanotubes : Density functional calculations (2009)
  • Author(s): Dam H.C., Nguyen T.C., Sugiyama, A., Ozaki, T., Fujiwara, A., Mitani, T., Okada, S.
  • Journal Title: Physical Review B 79(11) Pages: 115426
  • Peer Reviewed
• [Journal Article] A systematic study of influence of ligand substitutions on the electronic structure and magnetic properties of Mn4 single-molecule magnets (2009)
  • Author(s): Nguyen, A.T., Katayama, S., Dam, H.C.
  • Journal Title: Physical Chemistry Chemical Physics 11 Pages: 717-729
  • Peer Reviewed
• [Journal Article] Density functional study of Pt4 clusters adsorbed on a carbonnanotube support (2009)
  • Author(s): Nguyen T.C., A.Sugiyama, A.Fujiwara, T.Mitani, Dam H.C.
  • Journal Title: Physical Review B 79(23) Pages: 235417
  • Peer Reviewed
• [Journal Article] Effects of Carbon supports on Pt nano-cluster catalyst (2009)
  • Author(s): Nguyen, T.C., Fujiwara, A., Mitani, T., Dam, H.C.
  • Journal Title: Computational Materials Science 44 Pages: 163-166
  • Peer Reviewed
• [Journal Article] An Efficient Kernel Matrix Evaluation Measure (2008)
  • Author(s): Nguyen, C.H., Ho, T.B.
  • Journal Title: Pattern Recognition (Elsevier) 41(11) Pages: 3366-3372
  • Peer Reviewed
• [Journal Article] An Integrative Domain-Based Approach to Predicting Protein-Protein Interactions (2008)
  • Author(s): Nguyen, T.P., Ho, T.B.
  • Journal Title: Journal of Bioinformatics and Computational Biology (Imperial College Press.) Vol.6, Issue 6 Pages: 1115-1132
  • Peer Reviewed
• [Journal Article] Finding microRNA regulatory modules in human genome using rule induction (2008)
  • Author(s): Tran, D.H., Satou, K., Ho, T.B.
  • Journal Title: Journal BMC Bioinfor matics (MedCentral.) Vol.9, No.Supp 11 Pages: 1-10
  • Peer Reviewed
• [Journal Article] Prediction of human microRNA hairpin using only positive sample learning (2008)
  • Author(s): Tran, D.H., Pham, T.H., Satou, K., Ho, T.B.
  • Journal Title: Journal of Biomedical Science and Engineering (JBiSE)(Scientific Research Publishing.) Vol.1, Issue 2 Pages: 141-146
  • Peer Reviewed
• [Journal Article] Vietnamese Language Processing : Issues and Challenges (2008)
  • Author(s): Ho, T.B.
  • Journal Title: Special Issue in Journal of Science, Natural Sciences and Technology (Vietnam National University-Hanoi Publishers) Vol.24, N3S Pages: 10-16
  • Peer Reviewed
• [Journal Article] The role of ligands in controlling the electronic structureand magnetic properties of Mn4 single-molecule magnets (2008)
  • Author(s): Nguyen, A.T., Katayama, S., Dam, H.C.
  • Journal Title: Computational Materials Science 44 Pages: 111-116
  • Peer Reviewed
• [Journal Article] Issues and First Phase Development of the English-Vietnamese Translation System EVSMT1.0 (2008)
  • Author(s): Ho, T.B., Pham, N.K., Ha, T.L., Nguyen, P.T.
  • Journal Title: Special Issue in Journal of Science, Natural Sciences and Technology (Vietnam National University-Hanoi Publishers) Vol.24, N3S Pages: 59-66
  • Peer Reviewed
• [Journal Article] Integration of learning methods, medical literature and expert inspection in medical data mining (2007)
  • Author(s): Ho, T.B., Kawasaki, S., Takabayashi, K., Nguyen, C.H.
  • Journal Title: IEICE Trans.Information and Systems Vol.E90-D, No.10 Pages: 1574-1581
  • Peer Reviewed
• [Journal Article] Exploiting Temporal Relations in Mining Hepatitis Data (2007)
  • Author(s): Ho, T.B., Nguyen, C.H., Kawasaki, S., Le,S.Q., Takabayashi, K.
  • Journal Title: Journal of New Generation Computing (Ohmsha, Ltd.and Springer-Verlag) Vol.25, No.3 Pages: 247-262
  • Peer Reviewed
• [Journal Article] Decision making under uncertainty with fuzzy targets (2007)
  • Author(s): Huynh, V.N., Nakamori, Y., M. Ryoke, Ho, T.B.
  • Journal Title: Fuzzy Optimization and Decision Making (Springer) Volume 6, Issue 3 Pages: 255-278
  • Peer Reviewed
• [Journal Article] A hyper-heuristic for descriptive rule induction (2007)
  • Author(s): Pham, T.H., Ho, T.B.
  • Journal Title: International Journal of Data Warehousing and Mining Vol.3, No.1 Pages: 54-66
  • Peer Reviewed
• [Journal Article] An Agent-Based Approach to Solve Dynamic Meeting Scheduling Problems with Preference (2007)
  • Author(s): Ben Hassine, A., Ho, T.B.
  • Journal Title: International Journal of Engineering Applications of Artificial Intelligence (Elsevier Publishers) Volume 20, Issue 6 Pages: 857-873
  • Peer Reviewed
• [Presentation] Simulation-based Data Mining Solution to the Structure of Water Surrounding Proteins. (2011)
  • Author(s): Dam, H.C., Ho, T.B., Sugiyama, A.
  • Organizer: International Join Conference on Artificial Intelligence (IJCAI-2011)
  • Place of Presentation: Barcelona, Spain.
  • Year and Date: 20110702-20110716
• [Presentation] Mining parallel documents across Web sites (2010)
  • Author(s): Pham, N.K., Ho, T.B.
  • Organizer: The Sixth Asia Information Retrieval Societies Conference AIRS 2010
  • Place of Presentation: Taipei, Taiwan.
  • Year and Date: 20101201-20111203
• [Presentation] Discovering Relationship between Hepatitis C Virus NS5A Protein and Interferon/Ribavirin Therapy (2010)
  • Author(s): Kawasaki, S., Ho, T.B., Kanda, T., Yokosuka, O., Takabayashi, K., Le, T.N.
  • Organizer: International Conference on Knowledge, Information and Creativity Support Systems (Best paper award).
  • Place of Presentation: Chiangmai, Thailand
  • Year and Date: 20101125-20101127
• [Presentation] Quantitatively assessing the effect of regulatory factors on nucleosome dynamics (2010)
  • Author(s): Ho, B.H., Le, N.T., Ho, T.B.
  • Organizer: IEEE-RIVF International Conference on Computing and Communication Technologies
  • Place of Presentation: Hanoi, Vietnam.
  • Year and Date: 20101101-20101104
• [Presentation] Support Vector Machine Study for Dynamical Water Classification Problem in Biosystems (2009)
  • Author(s): Sugiyama, A., Mizukami, T., Dam, H.C., Ho, T.B.
  • Organizer: International Conference on Knowledge, Information and Creativity Support Systems (KICSS 2009)(7-16)
  • Place of Presentation: Seoul, Korea
  • Year and Date: 20091125-20091128
• [Presentation] Towards service-oriented knowledge discovery in biomedicine research (2009)
  • Author(s): Ho, T.B., Takabayashi, K., Pham, T.H., Nguyen, T.P., Kawasaki, S., Tran, D.H.
  • Organizer: International Workshop on Third Generation Data Mining, ECML/PKDD 2009 (100-113)
  • Place of Presentation: Bled, Slovenia
  • Year and Date: 20090907-20090911
• [Presentation] An Empirical Study of Vietnamese Noun Phrase Chunking with Discriminative Sequence Models (2009)
  • Author(s): Nguyen, L.M., Nguyen, H.T., Nguyen, P.T., Ho, T.B., Shimazu, A.
  • Organizer: 7th Workshop on Asian Language Resources at 47th Annual Meeting of the Association for Computational Linguistics, ACL-IJCNLP (9-16)
  • Place of Presentation: Singapore, Singapore
  • Year and Date: 20090802-20090807
• [Presentation] Privacy preserving EM-based Clustering (2009)
  • Author(s): Luong, T.D., Ho, T.B.
  • Organizer: IEEE RIVF International Conference on Computing and Communication Technologies (RIVF09, 111-117, IEEE Press.)
  • Place of Presentation: Da Nang, Vietnam
  • Year and Date: 20090713-20090717
• [Presentation] A computational method for classifying and analyzing tumor samples using microRNA expression profiles (2008)
  • Author(s): Tran, D.H., Ho, T.B., Satou, K., Pham, T.H.
  • Organizer: International Conference on Knowledge, Information and Creativity Support Systems (KICSS 2008)(120-127)(Student Best Paper Award).
  • Place of Presentation: Hanoi, Vietnam
  • Year and Date: 20081222-20081223
• [Presentation] A Tree-to-String Phrase-based Model for Statistical Machine Translation (2008)
  • Author(s): Nguyen, P.T., Shimazu, A., Ho, T.B., Nguyen, L.M., Nguyen, V.V.
  • Organizer: Twelfth Conference on Computational Natural Language Learning (143-150)
  • Place of Presentation: Manchester, U.K.
  • Year and Date: 20080816-20080817
• [Presentation] Simple but effective methods of combining kernels for the prediction problem in biology (2008)
  • Author(s): Tanabe, H., Ho, T.B., Nguyen, C.H., Kawasaki, S.
  • Organizer: IEEE RIVF International Conference on Computing and Communication Technologies (RIVF 08,IEEE Press, 71-78)
  • Place of Presentation: Ho Chi Minh City,Vietnam
  • Year and Date: 20080713-20080717
• [Presentation] Estimating Quality of Support Vector Machines Learning Under Probabilistic and Interval Uncertainty : Algorithms and Computational Complexity (2008)
  • Author(s): Nguyen, C.H., Ho, T.B., Kreinovich, V.
  • Organizer: International Workshop on Interval/Probabilistic Uncertainty and Non-Classical Logics (UncLog'08)(Advances in Soft Computing 46, Springer, 57-69)
  • Place of Presentation: Kanazawa, Japan
  • Year and Date: 20080325-20080328
• [Presentation] Prediction of Histone Modifications in DNA sequences (2007)
  • Author(s): Pham, T.H., Ho, T.B., Tran, D.H., Satou, K.
  • Organizer: IEEE 7th International Symposium on Bioinformatics & Bioengineering (IEEE BIBE 2007)(959-966)
  • Place of Presentation: Cambridge-Boston, U.S.A.
  • Year and Date: 20071014-20071017
• [Presentation] Temporal Abstraction and Data Mining with Visualization of Laboratory Data (2007)
  • Author(s): Takabayashi, K., Ho, T.B., Yokoi, H., Nguyen, T.D., Kawasaki, S., Le, S.Q., Suzuki, T., Yokosuka, O.
  • Organizer: Medinfo 2007 Congress (IOI Press, 1304-1308)
  • Place of Presentation: Brisbane, Australia
  • Year and Date: 20070820-20070824
• [Presentation] Combining Domain Fusions and Domain-Domain Interactions to Predict Protein-Protein Interactions (2007)
  • Author(s): Nguyen, T.P., Ho, T.B.
  • Organizer: Workshop on Data Mining in Bioinformatics BIOKDD07 (13th International Conference on Knowledge Discovery and Data Mining ACM SIGKDD 2007, 27-34)
  • Place of Presentation: San Jose, U.S.A.
  • Year and Date: 20070812-20070816
• [Book] Knowledge Technology and Science (Knowledge Discovery (Chapter 4))(Y.Nakamori (Ed.)) (2011)
  • Author(s): Ho, T.B.
  • Total Pages: 57-81
  • Publisher: CRC Press and Taylor & Francis
• [Book] Data Mining : Medical, Health, Social and Biological Applications (Mining multiple biological data for reconstructing signal transduction networks)(D.Holmes (Ed.)) (2011)
  • Author(s): Nguyen, T.P., Ho, T.B.
  • Publisher: Springer (to appear).
• [Book] Advances in Data Warehousing and Mining (Study of protein-protein interactions from multiple data sources)(David Taniar (Ed.)) (2007)
  • Author(s): Ho, T.B., Nguyen, T.P., Tran, T.N.
  • Total Pages: 280-307
  • Publisher: IGC Publishers
• [Book] Handbook of Granular Computing (Rough Document Clustering and the Internet)(Pedrycz, Skowron, Kreinovich (Eds.)) (2007)
  • Author(s): Nguyen, H.S., Ho, T.B.
  • Total Pages: 987-1004
  • Publisher: John Wiley & Sons.
• [Book] In Selected Contributions in Data Analysis and Classification (Finding Rules in Data)(P.Brito, P.Ber-trand, G.Cucumel, F.De Carvalho (Eds.)) (2007)
  • Author(s): Ho, T.B.
  • Total Pages: 387-396
  • Publisher: Springer