Koji Tsuda

Jun-Ichi Ito, Yasuo Tabei, Kana Shimizu, Koji Tsuda, Kentaro Tomii: PoSSuM: a database of similar protein-ligand binding and putative pockets. Nucleic Acids Research 40(Database-Issue): 541-548 (2012)

Kana Shimizu, Koji Tsuda: SlideSort: all pairs similarity search for short reads. Bioinformatics 27(4): 464-470 (2011)

Elisabeth Georgii, Koji Tsuda, Bernhard Schölkopf: Multi-way set enumeration in weight tensors. Machine Learning 82(2): 123-155 (2011)

Koji Tsuda: Graph Classification Methods in Chemoinformatics. Handbook of Statistical Bioinformatics 2011: 335-351

Hiroto Saigo, Koji Tsuda: Matrix Decomposition-based Dimensionality Reduction on Graph Data. Graph Data Management 2011: 260-284

Koji Tsuda, Shin-ichi Minato: Second Workshop on Algorithms for Large-Scale Information Processing in Knowledge Discovery (ALSIP). JSAI-isAI Workshops 2011: 184-185

Yasuo Tabei, Daisuke Okanohara, Shuichi Hirose, Koji Tsuda: LGM: Mining Frequent Subgraphs from Linear Graphs. PAKDD (2) 2011: 26-37

Yasuo Tabei, Koji Tsuda: Kernel-based Similarity Search in Massive Graph Databases with Wavelet Trees. SDM 2011: 154-163

Yasuo Tabei, Daisuke Okanohara, Shuichi Hirose, Koji Tsuda: LGM: Mining Frequent Subgraphs from Linear Graphs. CoRR abs/1102.4480 (2011)

Hiroto Saigo, Masahiro Hattori, Hisashi Kashima, Koji Tsuda: Reaction graph kernels predict EC numbers of unknown enzymatic reactions in plant secondary metabolism. BMC Bioinformatics 11(S-1): 31 (2010)

Hisashi Kashima, Satoshi Oyama, Yoshihiro Yamanishi, Koji Tsuda: Cartesian Kernel: An Efficient Alternative to the Pairwise Kernel. IEICE Transactions 93-D(10): 2672-2679 (2010)

Yasuo Tabei, Takeaki Uno, Masashi Sugiyama, Koji Tsuda: Single versus Multiple Sorting in All Pairs Similarity Search. Journal of Machine Learning Research - Proceedings Track 13: 145-160 (2010)

Koji Tsuda, Hiroto Saigo: Graph Classification. Managing and Mining Graph Data 2010: 337-363

Sabine Dietmann, Elisabeth Georgii, Alexey V. Antonov, Koji Tsuda, Hans-Werner Mewes: The DICS repository: module-assisted analysis of disease-related gene lists. Bioinformatics 25(6): 830-831 (2009)

Elisabeth Georgii, Sabine Dietmann, Takeaki Uno, Philipp Pagel, Koji Tsuda: Enumeration of condition-dependent dense modules in protein interaction networks. Bioinformatics 25(7): 933-940 (2009)

Mitsunori Kayano, Ichigaku Takigawa, Motoki Shiga, Koji Tsuda, Hiroshi Mamitsuka: Efficiently finding genome-wide three-way gene interactions from transcript- and genotype-data. Bioinformatics 25(21): 2735-2743 (2009)

Hisashi Kashima, Yoshihiro Yamanishi, Tsuyoshi Kato, Masashi Sugiyama, Koji Tsuda: Simultaneous inference of biological networks of multiple species from genome-wide data and evolutionary information: a semi-supervised approach. Bioinformatics 25(22): 2962-2968 (2009)

Hyunjung Shin, Koji Tsuda, Bernhard Schölkopf: Protein functional class prediction with a combined graph. Expert Syst. Appl. 36(2): 3284-3292 (2009)

Hiroto Saigo, Sebastian Nowozin, Tadashi Kadowaki, Taku Kudo, Koji Tsuda: gBoost: a mathematical programming approach to graph classification and regression. Machine Learning 75(1): 69-89 (2009)

Elisabeth Georgii, Koji Tsuda, Bernhard Schölkopf: Multi-way set enumeration in real-valued tensors. KDD Workshop on Data Mining using Matrices and Tensors 2009

Yoshinobu Kawahara, Kiyohito Nagano, Koji Tsuda, Jeff A. Bilmes: Submodularity Cuts and Applications. NIPS 2009: 916-924

Hisashi Kashima, Satoshi Oyama, Yoshihiro Yamanishi, Koji Tsuda: On Pairwise Kernels: An Efficient Alternative and Generalization Analysis. PAKDD 2009: 1030-1037

Silvia Chiappa, Hiroto Saigo, Koji Tsuda: A Bayesian Approach to Graphy Regression with Relevant Subgraph Selection. SDM 2009: 295-304

Hisashi Kashima, Tsuyoshi Kato, Yoshihiro Yamanishi, Masashi Sugiyama, Koji Tsuda: Link Propagation: A Fast Semi-supervised Learning Algorithm for Link Prediction. SDM 2009: 1099-1110

Takeaki Uno, Masashi Sugiyama, Koji Tsuda: Efficient Construction of Neighborhood Graphs by the Multiple Sorting Method. CoRR abs/0904.3151 (2009)

Sebastian Nowozin, Koji Tsuda: Frequent Subgraph Retrieval in Geometric Graph Databases. ICDM 2008: 953-958

Hiroto Saigo, Koji Tsuda: Iterative Subgraph Mining for Principal Component Analysis. ICDM 2008: 1007-1012

Hiroto Saigo, Nicole Krämer, Koji Tsuda: Partial least squares regression for graph mining. KDD 2008: 578-586

Koji Tsuda, Kenichi Kurihara: Graph Mining with Variational Dirichlet Process Mixture Models. SDM 2008: 432-442

Hiroto Saigo, Takeaki Uno, Koji Tsuda: Mining complex genotypic features for predicting HIV-1 drug resistance. Bioinformatics 23(18): 2455-2462 (2007)

Gal Chechik, Christina S. Leslie, William Stafford Noble, Gunnar Rätsch, Quaid Morris, Koji Tsuda: NIPS workshop on New Problems and Methods in Computational Biology. BMC Bioinformatics 8(S-10) (2007)

Elisabeth Georgii, Sabine Dietmann, Takeaki Uno, Philipp Pagel, Koji Tsuda: Mining expression-dependent modules in the human interaction network. BMC Bioinformatics 8(S-8) (2007)

Matthias Seeger, Florian Steinke, Koji Tsuda: Bayesian Inference and Optimal Design in the Sparse Linear Model. Journal of Machine Learning Research - Proceedings Track 2: 444-451 (2007)

Sebastian Nowozin, Koji Tsuda, Takeaki Uno, Taku Kudo, Gökhan H. Bakir: Weighted Substructure Mining for Image Analysis. CVPR 2007

Sebastian Nowozin, Gökhan H. Bakir, Koji Tsuda: Discriminative Subsequence Mining for Action Classification. ICCV 2007: 1-8

Koji Tsuda: Entire regularization paths for graph data. ICML 2007: 919-926

Sebastian Nowozin, Koji Tsuda, Takeaki Uno, Taku Kudo, Gökhan H. Bakir: Weighted Substructure Mining for Image Analysis. MLG 2007

Tsuyoshi Idé, Koji Tsuda: Change-Point Detection using Krylov Subspace Learning. SDM 2007

Paolo Frasconi, Kristian Kersting, Koji Tsuda (Eds.): Mining and Learning with Graphs, MLG 2007, Firence, Italy, August 1-3, 2007, Proceedings. 2007

Yasuo Tabei, Koji Tsuda, Taishin Kin, Kiyoshi Asai: SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments. Bioinformatics 22(14): 1723-1729 (2006)

Michiaki Hamada, Koji Tsuda, Taku Kudo, Taishin Kin, Kiyoshi Asai: Mining frequent stem patterns from unaligned RNA sequences. Bioinformatics 22(20): 2480-2487 (2006)

Tsuyoshi Kato, Yukio Murata, Koh Miura, Kiyoshi Asai, Paul Horton, Koji Tsuda, Wataru Fujibuchi: Network-based de-noising improves prediction from microarray data. BMC Bioinformatics 7(S-1) (2006)

Koji Tsuda, Taku Kudo: Clustering graphs by weighted substructure mining. ICML 2006: 953-960

Tsuyoshi Kato, Koji Tsuda, Kiyoshi Asai: Selective integration of multiple biological data for supervised network inference. Bioinformatics 21(10): 2488-2495 (2005)

Koji Tsuda, Gunnar Rätsch, Manfred K. Warmuth: Matrix Exponentiated Gradient Updates for On-line Learning and Bregman Projection. Journal of Machine Learning Research 6: 995-1018 (2005)

Koji Tsuda, Gunnar Rätsch: Image reconstruction by linear programming. IEEE Transactions on Image Processing 14(6): 737-744 (2005)

Koji Tsuda, Hyunjung Shin, Bernhard Schölkopf: Fast protein classification with multiple networks. ECCB/JBI 2005: 65

Koji Tsuda: Propagating distributions on a hypergraph by dual information regularization. ICML 2005: 920-927

Koji Tsuda, Shotaro Akaho, Motoaki Kawanabe, Klaus-Robert Müller: Asymptotic Properties of the Fisher Kernel. Neural Computation 16(1): 115-137 (2004)

Koji Tsuda, Shinsuke Uda, Taishin Kin, Kiyoshi Asai: Minimizing the Cross Validation Error to Mix Kernel Matrices of Heterogeneous Biological Data. Neural Processing Letters 19(1): 63-72 (2004)

Gökhan H. Bakir, Alexander Zien, Koji Tsuda: Learning to Find Graph Pre-images. DAGM-Symposium 2004: 253-261

Koji Tsuda, William Stafford Noble: Learning kernels from biological networks by maximizing entropy. ISMB/ECCB (Supplement of Bioinformatics) 2004: 326-333

Koji Tsuda, Gunnar Rätsch, Manfred K. Warmuth: Matrix Exponential Gradient Updates for On-line Learning and Bregman Projection. NIPS 2004

Tsuyoshi Kato, Koji Tsuda, Kentaro Tomii, Kiyoshi Asai: A New Variational Framework for Rigid-Body Alignment. SSPR/SPR 2004: 171-179

Koji Tsuda, Shotaro Akaho, Kiyoshi Asai: The em Algorithm for Kernel Matrix Completion with Auxiliary Data. Journal of Machine Learning Research 4: 67-81 (2003)

Hisashi Kashima, Koji Tsuda, Akihiro Inokuchi: Marginalized Kernels Between Labeled Graphs. ICML 2003: 321-328

Koji Tsuda, Gunnar Rätsch: Image Reconstruction by Linear Programming. NIPS 2003

Koji Tsuda, Motoaki Kawanabe, Gunnar Rätsch, Sören Sonnenburg, Klaus-Robert Müller: A New Discriminative Kernel from Probabilistic Models. Neural Computation 14(10): 2397-2414 (2002)

Koji Tsuda, Masashi Sugiyama, Klaus-Robert Müller: Subspace information criterion for nonquadratic regularizers-Model selection for sparse regressors. IEEE Transactions on Neural Networks 13(1): 70-80 (2002)

Masanori Arita, Koji Tsuda, Kiyoshi Asai: Modeling splicing sites with pairwise correlations. ECCB 2002: 27-34

Koji Tsuda, Motoaki Kawanabe: The Leave-One-Out Kernel. ICANN 2002: 727-732

Koji Tsuda, Taishin Kin, Kiyoshi Asai: Marginalized kernels for biological sequences. ISMB 2002: 268-275

Koji Tsuda, Motoaki Kawanabe, Klaus-Robert Müller: Clustering with the Fisher Score. NIPS 2002: 729-736

Koji Tsuda, Shotaro Akaho, Kiyoshi Asai: Approximating Incomplete Kernel Matrices by the em Algorithm. CoRR cs.LG/0211007 (2002)

Koji Tsuda: The subspace method in Hilbert space. Systems and Computers in Japan 32(6): 55-61 (2001)

Klaus-Robert Müller, Sebastian Mika, Gunnar Rätsch, Koji Tsuda, Bernhard Schölkopf: An introduction to kernel-based learning algorithms. IEEE Transactions on Neural Networks 12(2): 181-201 (2001)

Shigeru Muraki, Toshiharu Nakai, Yasuyo Kita, Koji Tsuda: An Attempt for Coloring Multichannel MR Imaging Data. IEEE Trans. Vis. Comput. Graph. 7(3): 265-274 (2001)

Volker Roth, Koji Tsuda: Pairwise Coupling for Machine Recognition of Hand-Printed Japanese Characters. CVPR (1) 2001: 1120-1125

Koji Tsuda, Gunnar Rätsch, Sebastian Mika, Klaus-Robert Müller: Learning to Predict the Leave-One-Out Error of Kernel Based Classifiers. ICANN 2001: 331-338

Koji Tsuda, Motoaki Kawanabe, Gunnar Rätsch, Sören Sonnenburg, Klaus-Robert Müller: A New Discriminative Kernel From Probabilistic Models. NIPS 2001: 977-984

Koji Tsuda, Shotaro Akaho: Large Margin Classifier via Semiparametric Inference. IJCNN (2) 2000: 23-28

Koji Tsuda: Subspace classifier in the Hilbert space. Pattern Recognition Letters 20(5): 513-519 (1999)

Koji Tsuda: Support vector classifier with asymetric kernel function. ESANN 1999: 183-188

Hideya Yoshiuchi, Koji Tsuda, Shigenobu Fukushima, Michihiko Minoh: Pattern Recognition Method for Metric Space by Four Points Embedding. IVCNZ 1998: 186-191

Koji Tsuda, Shuji Senda, Michihiko Minoh, Katsuo Ikeda: Sequential fuzzy cluster extraction and its robustness against noise. Systems and Computers in Japan 28(6): 10-17 (1997)

Koji Tsuda, Michihiko Minoh: A Nonparametric Density Model for Classification in a High Dimensional Space. ICDAR 1997: 1082-1087

Koji Tsuda, Michihiko Minoh, Katsuo Ikeda: Extracting straight lines by sequential fuzzy clustering. Pattern Recognition Letters 17(6): 643-649 (1996)

Koji Tsuda, Shuji Senda, Michihiko Minoh, Katsuo Ikeda: Clustering OCR-ed texts for browsing document image database. ICDAR 1995: 171-174