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Journal Paper

1. A Variational Bayesian Framework for Clustering with Multiple Graphs
   Motoki Shiga, Hiroshi Mamitsuka
   IEEE Transactions on Knowledge and Data Engineering, (to appear, 2011). [Link]
   
2. A Spectral Approach to Clustering Numerical Vectors as Nodes in a Network
   Motoki Shiga, Ichigaku Takigawa, Hiroshi Mamitsuka
   Pattern Recognition, Vol.44, issue 2, pp.236-251, 2011. [Link]
   
3. On the Performance of Methods for Finding a Switching Mechanism in Gene Expression
   Mitsunori Kayano, Ichigaku Takigawa, Motoki Shiga, Koji Tsuda, Hiroshi Mamitsuka
   Genome Informatics, Vol.24, pp.69-83, 2010. [Link]
   (Proceedings of the 10th Annual International Workshop on Bioinformatics and Systems Biology (IBSB2010))
4. Efficiently Finding Genome-wide Three-way Gene Interactions from Transcript- and Genotype-Data
   Mitsunori Kayano, Ichigaku Takigawa, Motoki Shiga, Koji Tsuda, Hiroshi Mamitsuka
   Bioinformatics, Vol.25, pp.2735-2743, 2009. [PubMed]
   
5. Annotating Gene Functions with Integrative Spectral Clustering on Microarray Expressions and Sequences
   Limin Li, Motoki Shiga, Wai-ki Ching, Hiroshi Mamitsuka
   Genome Informatics, Vol.22, pp.95-120, 2009. [Link]
   (Proceedings of the 9th Annual International Workshop on Bioinformatics and Systems Biology (IBSB2009))
6. Upper Bound for Variational Free Energy of Bayesian Networks
   Kazuho Watanabe, Motoki Shiga, Sumio Watanabe
   Machine Learning, Vol.75, issue 2, pp.199-215, 2009. [Link]
   
7. Clustering Analysis for Combining Multiple Genomic Data
   Motoki Shiga, Ichigaku Takigawa, Hiroshi Mamitsuka
   Seibutsu-butsuri (Biophysics), Vol.48, pp.190-194, 2008. (in Japanese) [Link]
   
8. Mining Significant Tree Patterns in Carbohydrate Sugar Chains
   Kosuke Hashimoto, Ichigaku Takigawa, Motoki Shiga, Minoru Kanehisa, Hiroshi Mamitsuka
   Bioinformatics, Vol.24, i167-i173, 2008. [PubMed]
   (Proceedings of the 7th European Conference on Computational Biology (ECCB2008))
   
9. Annotating Gene Function by Combining Expression Data with a Modular Gene Network
   Motoki Shiga, Ichigaku Takigawa, Hiroshi Mamitsuka
   Bioinformatics, Vol.23, i468-i478, 2007. [PubMed]
   (Proceedings of the 15th Annual International Conference on Intelligent Systems for Molecular Biology & 6th European Conference on Computational Biology (ISMB/ECCB2007))
   
10. An Optimal Entropy Estimator which is an Average over Plural Independent Estimates
    Motoki Shiga, Yasunari Yokota,
    The Transactions of the Institute of Electrical Engineers of Japan (C), Vol.125, No.12, pp.1912-1913, 2005. (in Japanese)
    
11. An Entropy Estimator That Minimizes Mean Squared Error under Condition of Restricted Averaged Squared Bias Error
    Motoki Shiga, Yasunari Yokota
    IEICE Transactions, Vol.J88-A, No.4, pp.519-527, 2005. (in Japanese)
    
12. Effect of Time Division on Estimation Accuracy in Frequency Domain ICA
    Yasunari Yokota, Hideaki Iwata, Motoki Shiga
    IEICE Transactions, Vol.E87-A, No.12, pp.3424-3428, 2004.
    
13. An Entropy Estimator Improving Mean Squared Error
    Motoki Shiga, Yasunari Yokota
    IEICE Transactions, Vol.J86-A, No.9, pp.936-944, 2003. (in Japanese)
    
    

Refereed Conference and Workshop Papers

1. Variational Bayes Learning over Multiple Graphs
   Motoki Shiga, and Hiroshi Mamitsuka
   Proceedings of the IEEE International Workshop on Machine Learning for Signal Processing 2010(MLSP2010),
   pp. 166-171, Kittila, Finland, August 2010. (Acceptance Rate30% (=36/122))
2. On the Performance of Methods for Finding a Switching Mechanism in Gene Expression
   Mitsunori Kayano, Ichigaku Takigawa, Motoki Shiga, Koji Tsuda, Hiroshi Mamitsuka
   Proceedings of the 10th Annual International Workshop on Bioinformatics and Systems Biology (IBSB2010),
   Kyoto, Japan, July 2010. (Genome Informatics, Vol.24, pp.69-83, 2010. [Link])
3. Annotating Gene Functions with Integrative Spectral Clustering on Microarray Expressions and Sequences
   Limin Li, Motoki Shiga, Wai-ki Ching, Hiroshi Mamitsuka
   Proceedings of the 9th Annual International Workshop on Bioinformatics and Systems Biology (IBSB2009),
   Boston, MA, USA, July 2009. (Genome Informatics, Vol.22, pp.95-120, 2009. [Link])
4. Mining Significant Tree Patterns in Carbohydrate Sugar Chains
   Kosuke Hashimoto, Ichigaku Takigawa, Motoki Shiga, Minoru Kanehisa, Hiroshi Mamitsuka
   Proceedings of the 7th European Conference on Computational Biology (ECCB2008)
   Sardinia, Italy, September 2008. (Bioinformatics, Vol. 24, i167-i173, 2008 [PubMed])(Acceptance Rate19% (=36/186) )
   
5. A Spectral Clustering Approach to Optimally Combining Numerical Vectors with a Modular Network
   Motoki Shiga, Ichigaku Takigawa, Hiroshi Mamitsuka
   Proceedings of the 13th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD2007),
   pp.647-656, San Jose, CA, USA, August 2007.[ACM] (Acceptance Rate19% (=111/573)) [Slides], [Poster]
   
6. Annotating Gene Function by Combining Expression Data with a Modular Gene Network
   Motoki Shiga, Ichigaku Takigawa, Hiroshi Mamitsuka
   Proceedings of the 15th Annual International Conference on Intelligent Systems for Molecular Biology & 6th European Conference on Computational Biology (ISMB/ECCB2007)),
   Wien, Austria, July 2007. (Bioinformatics, Vol.23, i468-i478, 2007 [PubMed]) (Acceptance Rate15% (=66/418)) [Slides]
   
7. Upper Bounds for Variational Stochastic Complexities of Bayesian Networks
   Kazuho Watanabe, Motoki Shiga, Sumio Watanabe
   Proceedings of the 7th International Conference on Intelligent Data Engineering and Automated Learning (IDEAL2006),
   Burgos, Spain, September 2006. (Lecture Notes in Computer Science (LNCS), vol. 4424, pp.139-146, 2006)
   
8. An Optimal Entropy Estimator for Discrete Random Variables
   Motoki Shiga, Yasunari Yokota
   Proceedings of the 18th International Joint Conference on Neural Networks, pp.1280-1285, Montreal, Canada, July 2005.
   
9. Error Analysis of Entropy Estimator for A Memory-less Information Source
   Motoki Shiga, Yasunari Yokota
   Proceedings of the International Workshop on Nonlinear Signal and Image Processing 2005 (NSIP2005), pp.99-104, Sapporo, Japan, May 2005.

Book Chapters

1. Mathematical Algorithm for Brain and Neural System Analysis
   Yasunari Yokota, Motoki Shiga （Chapter 7.3（pp.266-277））
   「Neuroinformatics」（Supervising Editor: Shun-ichi Amari, Editor:Shiro Usui）, Ohmsha, 2006. (in Japanese) [Publisher]

• A Study on Entropy Estimation Accuracy for Discrete Information Sources
  Doctor Thesis, Department of Electronics and Information Systems Engineering, Graduate School of Engineering, Gifu University, Japan, March, 2006. (in Japanese)
  
• An Entropy Estimator Improving Mean Squared Error
  Master Thesis, Department of Information Science, Graduate School of Engineering, Gifu University, Japan, March, 2003. (in Japanese)
  
• Rainfall Estimation Based on Maximizing Average Mutual Information between Rainfall and Radar Image
  Undergraduate Thesis, Department of Information Science, Faculty of Engineering, Gifu University, Japan, March, 2001. (in Japanese)
  

Unrefereed Conference and Workshop Papers (*Presenter)

1. Gene Clustering with Multiple Networks by Variational Bayes Learning
   *Motoki Shiga, Hiroshi Mamitsuka
   The 2010 Annual Conference of Japanese Society for Bioinformatics (JSBi2010) (Poster P011), Fukuoka, 13-15 December, 2010.
   
2. Integration of High-throughput Data for Deciphering Histone Code and Predicting Function of Essential Acetyltransferase
   *Yayoi Natsume-Kitatani, Motoki Shiga, Hiroshi Mamitsuka
   The 2010 Annual Conference of Japanese Society for Bioinformatics (JSBi2010) (Poster P017), Fukuoka, 13-15 December, 2010.
   
3. Finding Three-way Gene Interactions from Transcript and Genotype Data
   *Mitsunori Kayano, Ichigaku Takigawa, Motoki Shiga, Koji Tsuda Hiroshi Mamitsuka
   The 2010 Annual Conference of Japanese Society for Bioinformatics (JSBi2010) (Poster P069), Fukuoka, 13-15 December, 2010.
   
4. Annotating Gene Functions by Spectral Clustering for Combining Gene Expressions and Sequences
   Limin Li, *Motoki Shiga, Wai-Ki Ching, and Hiroshi Mamitsuka
   The 20th International Conference on Genome Informatics (GIW) (Poster P042), Yokohama, Japan, 14-16 Dec, 2009.
   
5. Analyzing Histone Codes by a Computational Approach
   *Yayoi Natsume-Kitatani, Motoki Shiga, and Hiroshi Mamitsuka
   The 20th International Conference on Genome Informatics (GIW) (Poster P044), Yokohama, Japan, 14-16 Dec, 2009.
   
6. Genome-Wide Three-Way Gene Interactions from Transcript and Genotype Data
   *Mitsunori Kayano, Ichigaku Takigawa, Motoki Shiga, Koji Tsuda, and Hiroshi Mamitsuka
   The 20th International Conference on Genome Informatics (GIW) (Poster P045), Yokohama, Japan, 14-16 Dec, 2009.
   
7. Association of SNPs with Multiple Genes Using a Nonlinear Regression Model
   *Mitsunori Kayano, Ichigaku Takigawa, Motoki Shiga, Koji Tsuda, and Hiroshi Mamitsuka
   The 2008 Annual Conference of Japanese Society for Bioinformatics (JSBi2008) (Poster P049), Osaka, 15-16 December, 2008.
   
8. Efficiently Finding Significant Substructural Patterns Conserved in Glycans
   *Ichigaku Takigawa, Khosuke Hashimoto, Motoki Shiga, Minoru Kanehisa, and Hiroshi Mamitsuka
   The 2008 Annual Conference of Japanese Society for Bioinformatics (JSBi2008) (Poster P066/ Talk T05), Osaka, 15-16 December, 2008.
   
9. A New Method for Clustering Genes by Optimally Combining Expression Data with a Modular Gene Network
   *Motoki Shiga, Ichigaku Takigawa, Hiroshi Mamitsuka
   The 2007 Annual Conference of Japanese Society for Bioinformatics (JSBi2007) (Poster P037), Tokyo, 17-19 December, 2007.
   
10. Modular Sub-graph Partitioning with Decision Trees
    *Timothy Hancock, Motoki Shiga, Hiroshi Mamitsuka, Danny Coomans
    The 2007 Annual Conference of Japanese Society for Bioinformatics (JSBi2007) (Poster P109), Tokyo, 17-19 December, 2007.
    
11. A Gene Clustering Method Using Gene Expression Data and Gene Networks
    *Motoki Shiga, Ichigaku Takigawa, Hiroshi Mamitsuka
    The 17th International Conference on Genome Informatics (GIW2006) (Poster P022), Yokohama, 18-20 December, 2006.
    

1. Clustering by Combining Numerical Vectors and Network Information
   IBM T. J. Watson Research Center (Host: Dr. Naoki Abe), Yorktown Heights, NY, USA, August 20, 2009
   
2. Gene Clustering Integrating mRNA Expression Profiles and a Gene Network
   Boston College (Host: Professor Peter Clote and Dr. Andy Lorenz), Boston, MA, USA, July 23, 2009
   
3. Annotating Gene Function by Combining Expression Data with a Modular Gene Network
   Departmental Colloquia, Max Planck Institute for Biological Cybernetics,T"ubingen, Germany, July 19, 2007.
   

[ Pathway Engineering Laboratory | Bioinformatics Center | Institute for Chemical Research | Kyoto University ]