Development of Causal Structure Mining Method for Large Scale Dimensional Data and Construction of Gene Function Knowledge Base

2009 Fiscal Year Final Research Report

• Project/Area Number: 19200013
• Research Category: Grant-in-Aid for Scientific Research (A)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Intelligent informatics
• Research Institution: Osaka University
• Principal Investigator: WASHIO Takashi Osaka University, 産業科学研究所, 教授 (00192815)
• Co-Investigator(Kenkyū-buntansha): KANO Yutaka 大阪大学, 基礎工学研究科, 教授 (20201436) ; IMOTO Seiya 東京大学, 医科学研究所, 准教授 (10345027) ; OHARA Kouzou 青山学院大学, 理工学部, 准教授 (30294127) ; TERMIER Alexandlre Universite Joseph Fourier, Laboratoired' Informatique de Grenoble, 助教 (60435823)
• Co-Investigator(Renkei-kenkyūsha): INOKUCHI Akihiro 大阪大学, 産業科学研究所, 助教 (70452456) ; SHIMIZU Shohei 大阪大学, 産業科学研究所, 助教 (10509871) ; KAWAHARA Yoshinobu 大阪大学, 産業科学研究所, 助教 (00514796)
• Project Period (FY): 2007 – 2009
• Keywords: 大規模次元 / 因果推論 / データマイニング / 遺伝子機能 / 知識ベース

Research Abstract

Scientists attempt to figure out function of each gene through the analysis of causal relations between gene expressions by using measurement data of the many gene expression variables (large scale dimensional data). However, the analysis of causal relations between dozens or hundreds of variables is hardly performed manually. In spite of this problem, the number of variables to which the computer based causal analysis is applicable is limited to 20-30 in the state of the art. Accordingly, this work developed a novel principle of the statistical causal analysis, and furthermore constructed a knowledge base of the functional relations among expressed genes for the scientists by using our developed approach.

Research Products

• [Journal Article] Estimation of linear non-Gaussian acyclic models for latent factors (2009)
  • Author(s): S. Shimizu, P.O. Hoyer, A. Hyvarinen
  • Journal Title: Neurocomputing Vol.72 Pages: 2024-2027
  • Peer Reviewed
• [Journal Article] ユークリッド距離の高速高精度推定と範囲問合せへの応用 (2009)
  • Author(s): 城戸健太郎, 桑島洋, 鷲尾隆
  • Journal Title: 情報処理学会論文誌 Vol.50,No.5 Pages: 1493-1505
  • Peer Reviewed
• [Journal Article] Unraveling dynamic activities of autocrine pathways that control drug-response transcriptome networks (2009)
  • Author(s): Y. Tamada, H. Araki, S. Imoto, M. Nagasaki, A. Doi, Y. Nakanishi, Y. Tomiyasu, K. Yasuda, B. Dunmore, D. Sanders, S. Humphries, C. Print, D.S. Charnock-Jones, K. Tashiro, S. Kuhara, S. Miyano
  • Journal Title: Pacific Symposium on Biocomputing Vol.14 Pages: 251-263
  • Peer Reviewed
• [Journal Article] Simple computation of maximum likelihood estimates in latent class model with equality and constant constraints (2009)
  • Author(s): K. Takai, Y. Kano
  • Journal Title: Communications in Statistics-Simulation and Computation Vol.38,No.3 Pages: 654-665
  • Peer Reviewed
• [Journal Article] Use of Non-Normality in Structural Equation Modeling: Application to Direction of Causation (2008)
  • Author(s): S. Shimizu, Y. Kano
  • Journal Title: J. of Statistical Planning and Inference Vol.138 Pages: 3483-3491
  • Peer Reviewed
• [Journal Article] Modeling Dynamic Substate Chains among Massive States (2008)
  • Author(s): V.P. Nguyen, T. Washio
  • Journal Title: Intelligent Data Analysis Vol.12,No.3 Pages: 271-291
  • Peer Reviewed
• [Journal Article] DryadeParent, An Efficient and Robust Closed Attribute Tree Mining Algorithm (2008)
  • Author(s): A. Termier, M.-C. Rousset, M. Sebag, K. Ohara, T. Washio, Hiroshi Motoda
  • Journal Title: IEEE Trans. on Knowledge and Data Eng. Vol.20,No.2 Pages: 300-320
  • Peer Reviewed
• [Journal Article] Bayesian learning of biological pathways on genomic data assimilation (2008)
  • Author(s): R. Yoshida, M. Nagasaki, R. Yamaguchi, S. Imoto, S. Miyano, T. Higuchi
  • Journal Title: Bioinformatics Vol.24,No.22 Pages: 592-2601
  • Peer Reviewed
• [Journal Article] Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models (2008)
  • Author(s): O. Hirose, R. Yoshida, S. Imoto, R. Yamaguchi, T. Higuchi, D.S. Charnock-Jones, C. Print, S. Miyano
  • Journal Title: Bioinformatics Vol.24,No.7 Pages: 932-942
  • Peer Reviewed
• [Journal Article] Estimation of nonlinear gene regulatory networks via L1 regularized NVAR from time series gene expression data (2008)
  • Author(s): K. Kojima, A. Fujita, T. Shimamura, S. Imoto, S. Miyano
  • Journal Title: Genome Informatics Vol.20 Pages: 37-51
  • Peer Reviewed
• [Journal Article] Finding optimal Bayesian network given a super-structure (2008)
  • Author(s): E. Perrier, S. Imoto, S. Miyano
  • Journal Title: Journal of Machine Learning Research Vol.9 Pages: 2251-228
  • Peer Reviewed
• [Journal Article] Predicting differences in gene regulatory systems by state space models (2008)
  • Author(s): R. Yamaguchi, S. Imoto, M. Yamauchi, M. Nagasaki, R. Yoshida, T. Shimamura, Y. Hatanaka, K. Ueno, T. Higuchi, N. Gotoh, S. Miyano
  • Journal Title: Genome Informatics Vol.21 Pages: 101-113
  • Peer Reviewed
• [Journal Article] Test of independence in a 2 × 2 contingency table with nonignorable nonresponse via constrained EM algorithm (2008)
  • Author(s): K. Takai, Y. Kano
  • Journal Title: Computational Statistics and Data Analysis Vol.52,No.11 Pages: 5229-5241
  • Peer Reviewed
• [Journal Article] A Classification Method Based on Subspace Clustering and Association Rules (2007)
  • Author(s): T. Washio, K. Nakanishi, H. Motoda
  • Journal Title: New Generation Computing Vol.25 Pages: 235-245
  • Peer Reviewed
• [Journal Article] グラフマイニングとその統計的モデリングへの応用 (2007)
  • Author(s): 鷲尾隆, 樋口知之, 井元清哉, 玉田嘉紀, 佐藤健, 元田浩
  • Journal Title: 予測と発見 Vol.54,No.2 Pages: 315-331
  • Peer Reviewed
• [Journal Article] Finding module-based gene networks with state-space models-Mining high-dimensional and short time-course gene expression data, Special Issue on Signal Processing Methods in Genomics and Proteomics (2007)
  • Author(s): R. Yamaguchi, R. Yoshida, S. Imoto, T. Higuchi, S. Miyano
  • Journal Title: IEEE Signal Processing Magazine Vol.24,No.1 Pages: 37-46
  • Peer Reviewed
• [Presentation] Submodularity cuts and applicastions (2009)
  • Author(s): Y. Kawahara, K. Nagano, K. Tsuda, J. Bilmes
  • Organizer: Proc. of NIPS2009: Advances in Neural Information Processing
  • Place of Presentation: Vancouver (Canada)
  • Year and Date: 2009-12-08
• [Presentation] Consistency of penalized risk of boosting methods in binary classification (2009)
  • Author(s): K. Hayashi, S. Shimizu, Y. Kano
  • Organizer: In New Trends in Psychometrics, Post Proceedings of IMPS2007: the 15th International and 72nd Annual Meeting of the Psychometric Society
  • Place of Presentation: Tower Hall Funabori(Tokyo)
  • Year and Date: 2009-07-11
• [Presentation] Factor prediction in time series factor analysis (2009)
  • Author(s): K. Takai, Y. Kano
  • Organizer: In New Trends in Psychometrics, Post Proceedings of IMPS2007: the 15th International and 72nd Annual Meeting of the Psychometric Society, Psychometric Society
  • Place of Presentation: Tower Hall Funabori(Tokyo)
  • Year and Date: 2009-07-10
• [Presentation] A direct method for estimating a causal ordering in a linear non-Gaussian acyclic model (2009)
  • Author(s): S. Shimizu, A. Hyvinen, Y. Kawahara, T. Washio
  • Organizer: Proc. of UAI2009: 25th Conf. on Uncertainty in Artificial Intelligence, Causality II & Graphical Models
  • Place of Presentation: Montreal(Canada)
  • Year and Date: 2009-06-21
• [Presentation] A Fast Method to Mine Frequent Subsequences from Graph Sequence (2008)
  • Author(s): A. Inokuchi, T. Washio
  • Organizer: Proc. of ICDM2008: 8th IEEE Int. Conf. on Data Mining
  • Place of Presentation: Pisa, Italy
  • Year and Date: 2008-12-17
• [Presentation] Regression with interval output values (2008)
  • Author(s): H. Kashima, K. Yamasaki, A. Inokuchi, H. Saigo
  • Organizer: Proc. of ICPR2008: 19th International Conference on Pattern Recognition 2008
  • Place of Presentation: Tampa, Florida (USA)
  • Year and Date: 2008-12-11
• [Presentation] Scaling with SEM: The Role of Effect and Causal Indicators (Invited) (2008)
  • Author(s): Y. Kano
  • Organizer: IASC2008: the Joint Meeting of 4th World Conference of the IASC and 6th Conference of the Asian Regional Section of the IASC on Computational Statistics & Data Analysis
  • Place of Presentation: Yokohama(Kanagawa)
  • Year and Date: 2008-12-07
• [Presentation] Isomorphism Identification by Using Graph Spectra and Its Application to Graph Mining (2008)
  • Author(s): K. Ohara, T. Washio
  • Organizer: Proc. of IASC2008: the Joint Meeting of 4th World Conf. of the IASC and 6th Conference of the Asian Regional Section of the IASC on Computational Statistics & Data Analysis
  • Place of Presentation: Yokohama(Kanagawa)
  • Year and Date: 2008-12-06
• [Presentation] AIC for Missing Data (2008)
  • Author(s): K. Takai, Y. Kano
  • Organizer: IASC2008: the Joint Meeting of 4th World Conference of the IASC and 6th Conference of the Asian Regional Section of the IASC on Computational Statistics & Data Analysis
  • Place of Presentation: Yokohama(Kanagawa)
  • Year and Date: 2008-12-05
• [Presentation] Partial order-based Bayesian network learning algorithm for estimating gene networks (2008)
  • Author(s): K. Numata, S. Imoto, S. Miyano
  • Organizer: Proc. of IEEE Bioinformatics and Biomedicine 2008
  • Place of Presentation: Philadelphia, Pennsylvania (USA)
  • Year and Date: 2008-12-05
• [Presentation] Feasibility of Graph Sequence Mining based on Admissibility Constraints (2008)
  • Author(s): A. Inokuchi, T. Washio
  • Organizer: Proc. of 3rd International Workshop on Data-Mining and Statistical Science
  • Place of Presentation: Tokyo Institute of Technology
  • Year and Date: 2008-09-25
• [Presentation] Penalized boosting algorithm for mislabeled data (Invited) (2008)
  • Author(s): K. Hayashi, S. Shimizu, Y. Kano
  • Organizer: IMPS2008: the 73rd Annual Meeting of the Psychometric Society
  • Place of Presentation: Greensboro(USA)
  • Year and Date: 2008-06-30
• [Presentation] Test of independence in a 2x2 contingency table with nonignorable nonresponse (2008)
  • Author(s): K. Takai, Y. Kano
  • Organizer: IMPS2008: the 73rd Annual Meeting of the Psychometric Society
  • Place of Presentation: New Hampshire(USA
  • Year and Date: 2008-06-29
• [Presentation] Interval estimations based on normalizing transformations by two approaches (2008)
  • Author(s): Y. Konya, S. Shimizu, Y. Kano
  • Organizer: IMPS2008: the 73rd Annual Meeting of the Psychometric Society
  • Place of Presentation: New Hampshire(USA)
  • Year and Date: 2008-06-29
• [Presentation] Separability of noisy ICA for high dimensional data (2008)
  • Author(s): Y. Kano
  • Organizer: HDM2008: International Conference on Multivariate Statistical Modelling & High Dimensional Data Mining
  • Place of Presentation: Kayseri(Turkey)
  • Year and Date: 2008-06-19
• [Presentation] A Range Query Approach for High Dimensional Euclidean Space Based on EDM Estimation (2008)
  • Author(s): K. Kido, H. Kuwajima, T. Washio
  • Organizer: Proc. of SDM2008: 8th SIAM Int. Conf. on Data Mining
  • Place of Presentation: Atlanta(USA)
  • Year and Date: 2008-04-24
• [Presentation] DIGDAG, a first algorithm to mine closed frequent embedded sub-DAGs (2007)
  • Author(s): A. Termier, Y. Tamada, K. Numata, S. Imoto, T. Washio, Tomoyuki Higuchi
  • Organizer: Proc. of MLG Workshop 2007, Mining and Learning with Graphs
  • Place of Presentation: Firenze(Italy)
  • Year and Date: 2007-08-02