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Koji Tsuda, Dr. (Kyoto University, Japan)

Room number:	215
Phone:	+49-7071-601-576
Fax:	+49-7071-601-552
E-Mail:	koji.tsuda

Picture of Tsuda, Koji, Dr. (Kyoto University, Japan)

Koji Tsuda

Position: Senior Research Scientist Unit: Alumni Schölkopf

Publications

Books (1):
•	Schölkopf B , Tsuda K and Vert J-P : Kernel Methods in Computational Biology, 410, MIT Press, Cambridge, MA, USA, (August-2004).
Articles (25):
•	Kam-Thong T , Czamara D , Tsuda K , Borgwardt K , Lewis CM , Erhardt-Lehmann A , Hemmer B , Rieckmann P , Daake M , Weber F , Wolf C , Ziegler A , Pütz B , Holsboer F , Schölkopf B and Müller-Myhsok B (April-2011) EPIBLASTER-fast exhaustive two-locus epistasis detection strategy using graphical processing units European Journal of Human Genetics 19(4) 465-471.
•	Georgii E , Tsuda K and Schölkopf B (February-2011) Multi-way set enumeration in weight tensors Machine Learning 82(2) 123-155.
•	Georgii E , Dietmann S , Uno T , Pagel P and Tsuda K (February-2009) Enumeration of condition-dependent dense modules in protein interaction networks Bioinformatics 25(7) 933-940.
•	Dietmann S , Georgii E , Antonov A , Tsuda K and Mewes H-W (January-2009) The DICS repository: module-assisted analysis of disease-related gene lists Bioinformatics 25(6) 830-831.
•	Saigo H , Nowozin S , Kadowaki T , Kudo T and Tsuda K (November-2008) gBoost: A Mathematical Programming Approach to Graph Classification and Regression Machine Learning 75(1) 69-89.
•	Shin HH , Tsuda K and Schölkopf B (March-2008) Protein Functional Class Prediction With a Combined Graph Expert Systems with Applications 36(2) 3284-3292.
•	Tanaka K and Tsuda K (January-2008) A Quantum-Statistical-Mechanical Extension of Gaussian Mixture Model Journal of Physics: Conference Series 95(012023) 1-9.
•	Steinke F , Seeger M and Tsuda K (November-2007) Experimental design for efficient identification of gene regulatory networks using sparse Bayesian models BMC Systems Biology 1(51) 1-15.
•	Saigo H , Uno T and Tsuda K (September-2007) Mining complex genotypic features for predicting HIV-1 drug resistance Bioinformatics 23(18) 2455-2462.
•	Hamada M , Tsuda K , Kudo T , Kin T and Asai K (October-2006) Mining frequent stem patterns from unaligned RNA sequences Bioinformatics 22(20) 2480-2487.
•	Tabei Y , Tsuda K , Kin T and Asai K (May-2006) SCARNA: Fast and Accurate Structural Alignment of RNA Sequences by Matching Fixed-Length Stem Fragments Bioinformatics 22(14) 1723-1729.
•	Kato T , Murata Y , Miura K , Asai K , Horton PB , Tsuda K and Fujibuchi W (March-2006) Network-based de-noising improves prediction from microarray data BMC Bioinformatics 7(Suppl. 1) S4-S4.
•	Kato T , Tsuda K and Asai K (October-2005) Selective integration of multiple biological data for supervised network inference Bioinformatics 21(10) 2488.
•	Tsuda K , Shin H and Schölkopf B (September-2005) Fast Protein Classification with Multiple Networks Bioinformatics 21(Suppl. 2) 59-65.
•	Tsuda K and Rätsch G (June-2005) Image Reconstruction by Linear Programming IEEE Transactions on Image Processing 14(6) 737-744.
•	Tsuda K , Rätsch G and Warmuth M (June-2005) Matrix Exponentiated Gradient Updates for On-line Learning and Bregman Projection Journal of Machine Learning Research 6 995-1018.
•	Tsuda K and Noble WS (August-2004) Learning kernels from biological networks by maximizing entropy Bioinformatics 20(Suppl. 1) i326-i333.
•	Tsuda K , Akaho S , Kawanabe M and Müller KR (2004) Asymptotic Properties of the Fisher Kernel Neural Computation 16(1) 115-137.
•	Tsuda K , Uda S , Kin T and Asai K (2004) Minimizing the Cross Validation Error to Mix Kernel Matrices of Heterogeneous Biological Data Neural Processing Letters 19 63-72.
•	Tsuda K , Akaho S and Asai K (May-2003) The em Algorithm for Kernel Matrix Completion with Auxiliary Data Journal of Machine Learning Research 4 67-81.
•	Tsuda K , Kawanabe M , Rätsch G , Sonnenburg S and Müller KR (October-2002) A New Discriminative Kernel from Probabilistic Models Neural Computation 14(10) 2397-2414.
•	Tsuda K , Kin T and Asai K (2002) Marginalized kernels for biological sequences Bioinformatics 18(Suppl 1) 268-275.
•	Arita M , Tsuda K and Asai K (2002) Modeling splicing sites with pairwise correlations Bioinformatics 18(Suppl 2) 27-34.
•	Tsuda K , Sugiyama M and Müller KR (2002) Subspace information criterion for non-quadratic regularizers -- model selection for sparse regressors IEEE Trans Neural Networks 13(1) 70-80.
•	Müller K-R , Mika S , Rätsch G , Tsuda K and Schölkopf B (March-2001) An Introduction to Kernel-Based Learning Algorithms IEEE Transactions on Neural Networks 12(2) 181-201.
Conference papers (27):
•	Georgii E , Tsuda K and Schölkopf B (June-2009) Multi-way set enumeration in real-valued tensors In: DMMT '09, KDD 2009 Workshop on Data Mining using Matrices and Tensors, ACM Press, New York, NY, USA, 32-41.
•	Chiappa S , Saigo H and Tsuda K (May-2009) A Bayesian Approach to Graph Regression with Relevant Subgraph Selection In: SDM09, 2009 SIAM International Conference on Data Mining, Society for Industrial and Applied Mathematics, Philadelphia, PA, USA, 295-304.
•	Kashima H , Kato T , Yamanishi Y , Sugiyama M and Tsuda K (May-2009) Link Propagation: A Fast Semi-supervised Learning Algorithm for Link Prediction In: SDM 2009, 2009 SIAM International Conference on Data Mining, Philadelphia, PA, USA, Society for Industrial and Applied Mathematics, 1099-1110.
•	Kashima H , Oyama S , Yamanishi Y and Tsuda K (April-2009) On Pairwise Kernels: An Efficient Alternative and Generalization Analysis In: PAKDD 2009, 13th Pacific Asia Conference on Knowledge Discovery and Data Mining, Springer, Berlin, Germany, 1030-1037.
•	Nowozin S and Tsuda K (December-2008) Frequent Subgraph Retrieval in Geometric Graph Databases In: ICDM 2008, 8th IEEE International Conference on Data Mining, IEEE Computer Society, Los Alamitos, CA, USA, 953-958.
•	Saigo H and Tsuda K (December-2008) Iterative Subgraph Mining for Principal Component Analysis In: ICDM 2008, IEEE International Conference on Data Mining, IEEE Computer Society, Los Alamitos, CA, USA, 1007-1012.
•	Saigo H , Krämer N and Tsuda K (August-2008) Partial Least Squares Regression for Graph Mining In: KDD2008, 14th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, ACM Press, New York, NY, USA, 578-586.
•	Tsuda K and Kurihara K (April-2008) Graph Mining with Variational Dirichlet Process Mixture Models In: SDM 2008, 8th 2008 SIAM International Conference on Data Mining, Society for Industrial and Applied Mathematics, Philadelphia, PA, USA, 432-442.
•	Nowozin S , BakIr G and Tsuda K (October-2007) Discriminative Subsequence Mining for Action Classification In: ICCV 2007, 11th IEEE International Conference on Computer Vision, IEEE Computer Society, Los Alamitos, CA, USA, 1919-1923.
•	Tsuda K (June-2007) Entire Regularization Paths for Graph Data In: ICML 2007, 24th Annual International Conference on Machine Learning, ACM Press, New York, NY, USA, 919-926.
•	Nowozin S , Tsuda K , Uno T , Kudo T and BakIr G (June-2007) Weighted Substructure Mining for Image Analysis In: CVPR 2007, 2007 IEEE Computer Society Conference on Computer Vision and Pattern Recognition, IEEE Computer Society, Los Alamitos, CA, USA, 1-8.
•	Ide T and Tsuda K (April-2007) Change-Point Detection using Krylov Subspace Learning In: SDM 2007, SIAM International Conference on Data Mining, Society for Industrial and Applied Mathematics, Pittsburgh, PA, USA, 515-520.
•	Seeger M , Steinke F and Tsuda K (March-2007) Bayesian Inference and Optimal Design in the Sparse Linear Model In: JMLR Workshop and Conference Proceedings Volume 2: AISTATS 2007, 11th International Conference on Artificial Intelligence and Statistics, JMLR, Cambridge, MA, USA, 444-451.
•	Saigo H , Kadowaki T and Tsuda K (September-2006) A Linear Programming Approach for Molecular QSAR analysis In: MLG 2006, International Workshop on Mining and Learning with Graphs 2006, 85-96.
•	Tsuda K and Kudo T (June-2006) Clustering Graphs by Weighted Substructure Mining In: ICML 2006, 23rd International Conference on Machine Learning, ACM Press, New York, NY, USA, 953-960.
•	Tsuda K , Rätsch G and Warmuth MK (July-2005) Matrix Exponential Gradient Updates for On-line Learning and Bregman Projection In: Advances in Neural Information Processing Systems 17, Eighteenth Annual Conference on Neural Information Processing Systems (NIPS 2004), MIT Press, Cambridge, MA, USA, 1425-1432.
•	Tsuda K (2005) Propagating Distributions on a Hypergraph by Dual Information Regularization ICML Bonn, 921.
•	BakIr G , Zien A and Tsuda K (August-2004) Learning to Find Graph Pre-Images In: Pattern Recognition, 26th DAGM Symposium, Springer, Berlin, Germany, 253-261.
•	Tsuda K and Rätsch G (June-2004) Image Construction by Linear Programming In: Advances in Neural Information Processing Systems 16, Seventeenth Annual Conference on Neural Information Processing Systems (NIPS 2003), MIT Press, Cambridge, MA, USA, 57-64.
•	Kato T , Tsuda K , Tomii K and Asai K (2004) A New Variational Framework for Rigid-Body Alignment Joint IAPR International Workshops on Syntactical and Structural Pattern Recognition (SSPR 2004) and Statistical Pattern Recognition (SPR 2004), 171-179.
•	Shin H , Tsuda K and Schölkopf B (2004) Protein Functional Class Prediction with a Combined Graph Proceedings of the Korean Data Mining Conference, 200-219.
•	Tsuda K , Kawanabe M and Müller KR (October-2003) Clustering with the Fisher score In: Advances in Neural Information Processing Systems 15, Sixteenth Annual Conference on Neural Information Processing Systems (NIPS 2002), MIT Press, Cambridge, MA, USA, 729-736.
•	Kashima H , Tsuda K and Inokuchi A (August-2003) Marginalized Kernels between Labeled Graphs 20th International Conference on Machine Learning, 321-328.
•	Tsuda K , Kawanabe M , Rätsch G , Sonnenburg S and Müller K-R (September-2002) A new discriminative kernel from probabilistic models In: Advances in Neural Information Processing Systems 14, Fifteenth Annual Neural Information Processing Systems Conference (NIPS 2001), MIT Press, Cambridge, MA, USA, 977-984.