Koji Tsuda

ORCID

Publication Activity (10 Years)

Years Active: 1995-2024
Publications (10 Years): 38

Top Venues

Publications

Zetian Mao, Jiawen Li, Chen Liang, Diptesh Das, Masato Sumita, Koji Tsuda
Molecule Graph Networks with Many-body Equivariant Interactions. CoRR (2024)
Jiawen Li, Masato Sumita, Ryo Tamura, Koji Tsuda
Interpretable Fragment-Based Molecule Design with Self-Learning Entropic Population Annealing. Adv. Intell. Syst. 5 (10) (2023)
Chao Huang, Diptesh Das, Koji Tsuda
Feature Importance Measurement based on Decision Tree Sampling. CoRR (2023)
Francois Berenger, Koji Tsuda
3D-Sensitive Encoding of Pharmacophore Features. J. Chem. Inf. Model. 63 (8) (2023)
Ryo Tamura, Koji Tsuda, Shoichi Matsuda
NIMS-OS: An automation software to implement a closed loop between artificial intelligence and robotic experiments in materials science. CoRR (2023)
Takumi Yoshida, Hiroyuki Hanada, Kazuya Nakagawa, Kouichi Taji, Koji Tsuda, Ichiro Takeuchi
Efficient model selection for predictive pattern mining model by safe pattern pruning. Patterns 4 (12) (2023)
Weilin Yuan, Yusuke Hibi, Ryo Tamura, Masato Sumita, Yasuyuki Nakamura, Masanobu Naito, Koji Tsuda
Revealing factors influencing polymer degradation with rank-based machine learning. Patterns 4 (12) (2023)
Takumi Yoshida, Hiroyuki Hanada, Kazuya Nakagawa, Kouichi Taji, Koji Tsuda, Ichiro Takeuchi
Efficient Model Selection for Predictive Pattern Mining Model by Safe Pattern Pruning. CoRR (2023)
Dai Hai Nguyen, Koji Tsuda
On a linear fused Gromov-Wasserstein distance for graph structured data. Pattern Recognit. 138 (2023)
Masato Sumita, Kei Terayama, Ryo Tamura, Koji Tsuda
QCforever: A Quantum Chemistry Wrapper for Everyone to Use in Black-Box Optimization. J. Chem. Inf. Model. 62 (18) (2022)
Diptesh Das, Vo Nguyen Le Duy, Hiroyuki Hanada, Koji Tsuda, Ichiro Takeuchi
Fast and More Powerful Selective Inference for Sparse High-Order Interaction Model. AAAI (2022)
Yuichi Motoyama, Ryo Tamura, Kazuyoshi Yoshimi, Kei Terayama, Tsuyoshi Ueno, Koji Tsuda
Bayesian optimization package: PHYSBO. Comput. Phys. Commun. 278 (2022)
Dai Hai Nguyen, Koji Tsuda
On a linear fused Gromov-Wasserstein distance for graph structured data. CoRR (2022)
Dai Hai Nguyen, Koji Tsuda
A generative model for molecule generation based on chemical reaction trees. CoRR (2021)
Syun Izawa, Koki Kitai, Shu Tanaka, Ryo Tamura, Koji Tsuda
Continuous black-box optimization with quantum annealing and random subspace coding. CoRR (2021)
Francois Berenger, Koji Tsuda
Molecular generation by Fast Assembly of (Deep)SMILES fragments. J. Cheminformatics 13 (1) (2021)
Diptesh Das, Vo Nguyen Le Duy, Hiroyuki Hanada, Koji Tsuda, Ichiro Takeuchi
Fast and More Powerful Selective Inference for Sparse High-order Interaction Model. CoRR (2021)
Ryosuke Shibukawa, Shoichi Ishida, Kazuki Yoshizoe, Kunihiro Wasa, Kiyosei Takasu, Yasushi Okuno, Kei Terayama, Koji Tsuda
CompRet: a comprehensive recommendation framework for chemical synthesis planning with algorithmic enumeration. J. Cheminformatics 12 (1) (2020)
Jianbin Qin, Chuan Xiao, Sheng Hu, Jie Zhang, Wei Wang, Yoshiharu Ishikawa, Koji Tsuda, Kunihiko Sadakane
Efficient query autocompletion with edit distance-based error tolerance. VLDB J. 29 (4) (2020)
Xiaolin Sun, Zhufeng Hou, Masato Sumita, Shinsuke Ishihara, Ryo Tamura, Koji Tsuda
Leveraging Legacy Data to Accelerate Materials Design via Preference Learning. CoRR (2019)
Kei Terayama, Hiroaki Iwata, Mitsugu Araki, Yasushi Okuno, Koji Tsuda
Machine learning accelerates MD-based binding pose prediction between ligands and proteins. Bioinform. 34 (5) (2018)
Mitsugu Araki, Hiroaki Iwata, Biao Ma, Atsuto Fujita, Kei Terayama, Yukari Sagae, Fumie Ono, Koji Tsuda, Narutoshi Kamiya, Yasushi Okuno
Improving the Accuracy of Protein-Ligand Binding Mode Prediction Using a Molecular Dynamics-Based Pocket Generation Approach. J. Comput. Chem. 39 (32) (2018)
Mahito Sugiyama, Hiroyuki Nakahara, Koji Tsuda
Legendre Tensor Decomposition. CoRR (2018)
Kazuki Yoshizoe, Aika Terada, Koji Tsuda
MP-LAMP: parallel detection of statistically significant multi-loci markers on cloud platforms. Bioinform. 34 (17) (2018)
Shuhei Denzumi, Jun Kawahara, Koji Tsuda, Hiroki Arimura, Shin-ichi Minato, Kunihiko Sadakane
DenseZDD: A Compact and Fast Index for Families of Sets. Algorithms 11 (8) (2018)
Mahito Sugiyama, Hiroyuki Nakahara, Koji Tsuda
Legendre Decomposition for Tensors. NeurIPS (2018)
Mahito Sugiyama, Koji Tsuda, Hiroyuki Nakahara
Transductive Boltzmann Machines. CoRR (2018)
Mahito Sugiyama, Hiroyuki Nakahara, Koji Tsuda
Tensor Balancing on Statistical Manifold. CoRR (2017)
Xiufeng Yang, Jinzhe Zhang, Kazuki Yoshizoe, Kei Terayama, Koji Tsuda
ChemTS: An Efficient Python Library for de novo Molecular Generation. CoRR (2017)
Xiufeng Yang, Kazuki Yoshizoe, Akito Taneda, Koji Tsuda
RNA inverse folding using Monte Carlo tree search. BMC Bioinform. 18 (1) (2017)
Mahito Sugiyama, Hiroyuki Nakahara, Koji Tsuda
Tensor Balancing on Statistical Manifold. ICML (2017)
Shinya Suzumura, Kazuya Nakagawa, Yuta Umezu, Koji Tsuda, Ichiro Takeuchi
Selective Inference for Sparse High-Order Interaction Models. ICML (2017)
Aika Terada, Ryo Yamada, Koji Tsuda, Jun Sese
LAMPLINK: detection of statistically significant SNP combinations from GWAS data. Bioinform. 32 (22) (2016)
Mahito Sugiyama, Hiroyuki Nakahara, Koji Tsuda
Information decomposition on structured space. ISIT (2016)
Aika Terada, David duVerle, Koji Tsuda
Significant Pattern Mining with Confounding Variables. PAKDD (1) (2016)
Kazuya Nakagawa, Shinya Suzumura, Masayuki Karasuyama, Koji Tsuda, Ichiro Takeuchi
Safe Pattern Pruning: An Efficient Approach for Predictive Pattern Mining. KDD (2016)
Mahito Sugiyama, Hiroyuki Nakahara, Koji Tsuda
Information Decomposition on Structured Space. CoRR (2016)
David A. duVerle, Sohiya Yotsukura, Seitaro Nomura, Hiroyuki Aburatani, Koji Tsuda
CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data. BMC Bioinform. 17 (2016)
Takahisa Toda, Shogo Takeuchi, Koji Tsuda, Shin-ichi Minato
Superset Generation on Decision Diagrams. WALCOM (2015)
Yukino Baba, Hisashi Kashima, Yasunobu Nohara, Eiko Kai, Partha Pratim Ghosh, Rafiqul Islam Maruf, Ashir Ahmed, Masahiro Kuroda, Sozo Inoue, Tatsuo Hiramatsu, Michio Kimura, Shuji Shimizu, Kunihisa Kobayashi, Koji Tsuda, Masashi Sugiyama, Mathieu Blondel, Naonori Ueda, Masaru Kitsuregawa, Naoki Nakashima
Predictive Approaches for Low-Cost Preventive Medicine Program in Developing Countries. KDD (2015)
Kazuki Yoshizoe, Aika Terada, Koji Tsuda
Redesigning pattern mining algorithms for supercomputers. CoRR (2015)
Takahisa Toda, Koji Tsuda
BDD construction for all solutions SAT and efficient caching mechanism. SAC (2015)
Kana Shimizu, Koji Nuida, Hiromi Arai, Shigeo Mitsunari, Nuttapong Attrapadung, Michiaki Hamada, Koji Tsuda, Takatsugu Hirokawa, Jun Sakuma, Goichiro Hanaoka, Kiyoshi Asai
Privacy-preserving search for chemical compound databases. BMC Bioinform. 16 (S18) (2015)
David A. duVerle, Shohei Kawasaki, Yoshiji Yamada, Jun Sakuma, Koji Tsuda
Privacy-Preserving Statistical Analysis by Exact Logistic Regression. IEEE Symposium on Security and Privacy Workshops (2015)
Ken-ichiro Moridomi, Kohei Hatano, Eiji Takimoto, Koji Tsuda
Online matrix prediction for sparse loss matrices. ACML (2014)
Jun Sese, Aika Terada, Yuki Saito, Koji Tsuda
Statistically significant subgraphs for genome-wide association study. SSDM@ECML/PKDD (2014)
Shin-ichi Minato, Takeaki Uno, Koji Tsuda, Aika Terada, Jun Sese
A Fast Method of Statistical Assessment for Combinatorial Hypotheses Based on Frequent Itemset Enumeration. ECML/PKDD (2) (2014)
Hirohito Sasakawa, Hiroki Harada, David duVerle, Hiroki Arimura, Koji Tsuda, Jun Sakuma
Oblivious Evaluation of Non-deterministic Finite Automata with Application to Privacy-Preserving Virus Genome Detection. WPES (2014)
Shuhei Denzumi, Jun Kawahara, Koji Tsuda, Hiroki Arimura, Shin-ichi Minato, Kunihiko Sadakane
DenseZDD: A Compact and Fast Index for Families of Sets. SEA (2014)
Takeru Inoue, Keiji Takano, Takayuki Watanabe, Jun Kawahara, Ryo Yoshinaka, Akihiro Kishimoto, Koji Tsuda, Shin-ichi Minato, Yasuhiro Hayashi
Distribution Loss Minimization With Guaranteed Error Bound. IEEE Trans. Smart Grid 5 (1) (2014)
Aika Terada, Koji Tsuda, Jun Sese
Fast Westfall-Young permutation procedure for combinatorial regulation discovery. BIBM (2013)
Shuhei Denzumi, Koji Tsuda, Hiroki Arimura, Shin-ichi Minato
Compact Complete Inverted Files for Texts and Directed Acyclic Graphs Based on Sequence Binary Decision Diagrams . Stringology (2013)
Chuan Xiao, Jianbin Qin, Wei Wang, Yoshiharu Ishikawa, Koji Tsuda, Kunihiko Sadakane
Efficient Error-tolerant Query Autocompletion. Proc. VLDB Endow. 6 (6) (2013)
David duVerle, Ichiro Takeuchi, Yuko Murakami-Tonami, Kenji Kadomatsu, Koji Tsuda
Discovering combinatorial interactions in survival data. Bioinform. 29 (23) (2013)
Hiroto Saigo, Hisashi Kashima, Koji Tsuda
Fast Iterative Mining Using Sparsity-Inducing Loss Functions. IEICE Trans. Inf. Syst. (8) (2013)
Koji Tsuda
Data Mining for Biologists. Int. J. Knowl. Discov. Bioinform. 3 (4) (2012)
Jun-Ichi Ito, Yasuo Tabei, Kana Shimizu, Koji Tsuda, Kentaro Tomii
PoSSuM: a database of similar protein-ligand binding and putative pockets. Nucleic Acids Res. 40 (Database-Issue) (2012)
Yasuo Tabei, Koji Tsuda
Kernel-based Similarity Search in Massive Graph Databases with Wavelet Trees. SDM (2011)
Yasuo Tabei, Daisuke Okanohara, Shuichi Hirose, Koji Tsuda
LGM: Mining Frequent Subgraphs from Linear Graphs CoRR (2011)
Elisabeth Georgii, Koji Tsuda, Bernhard Schölkopf
Multi-way set enumeration in weight tensors. Mach. Learn. 82 (2) (2011)
Koji Tsuda, Shin-ichi Minato
Second Workshop on Algorithms for Large-Scale Information Processing in Knowledge Discovery (ALSIP). JSAI-isAI Workshops (2011)
Kana Shimizu, Koji Tsuda
SlideSort: all pairs similarity search for short reads. Bioinform. 27 (4) (2011)
Yasuo Tabei, Daisuke Okanohara, Shuichi Hirose, Koji Tsuda
LGM: Mining Frequent Subgraphs from Linear Graphs. PAKDD (2) (2011)
Yasuo Tabei, Takeaki Uno, Masashi Sugiyama, Koji Tsuda
Single versus Multiple Sorting in All Pairs Similarity Search. ACML (2010)
Hisashi Kashima, Satoshi Oyama, Yoshihiro Yamanishi, Koji Tsuda
Cartesian Kernel: An Efficient Alternative to the Pairwise Kernel. IEICE Trans. Inf. Syst. (10) (2010)
Hiroto Saigo, Masahiro Hattori, Hisashi Kashima, Koji Tsuda
Reaction graph kernels predict EC numbers of unknown enzymatic reactions in plant secondary metabolism. BMC Bioinform. 11 (S-1) (2010)
Takeaki Uno, Masashi Sugiyama, Koji Tsuda
Efficient Construction of Neighborhood Graphs by the Multiple Sorting Method CoRR (2009)
Mitsunori Kayano, Ichigaku Takigawa, Motoki Shiga, Koji Tsuda, Hiroshi Mamitsuka
Efficiently finding genome-wide three-way gene interactions from transcript- and genotype-data. Bioinform. 25 (21) (2009)
Silvia Chiappa, Hiroto Saigo, Koji Tsuda
A Bayesian Approach to Graphy Regression with Relevant Subgraph Selection. SDM (2009)
Hisashi Kashima, Satoshi Oyama, Yoshihiro Yamanishi, Koji Tsuda
On Pairwise Kernels: An Efficient Alternative and Generalization Analysis. PAKDD (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)
Hiroto Saigo, Sebastian Nowozin, Tadashi Kadowaki, Taku Kudo, Koji Tsuda
gBoost: a mathematical programming approach to graph classification and regression. Mach. Learn. 75 (1) (2009)
Elisabeth Georgii, Sabine Dietmann, Takeaki Uno, Philipp Pagel, Koji Tsuda
Enumeration of condition-dependent dense modules in protein interaction networks. Bioinform. 25 (7) (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. Bioinform. 25 (22) (2009)
Hisashi Kashima, Tsuyoshi Kato, Yoshihiro Yamanishi, Masashi Sugiyama, Koji Tsuda
Link Propagation: A Fast Semi-supervised Learning Algorithm for Link Prediction. SDM (2009)
Sabine Dietmann, Elisabeth Georgii, Alexey V. Antonov, Koji Tsuda, Hans-Werner Mewes
The DICS repository: module-assisted analysis of disease-related gene lists. Bioinform. 25 (6) (2009)
Hyunjung Shin, Koji Tsuda, Bernhard Schölkopf
Protein functional class prediction with a combined graph. Expert Syst. Appl. 36 (2) (2009)
Hiroto Saigo, Koji Tsuda
Iterative Subgraph Mining for Principal Component Analysis. ICDM (2008)
Sebastian Nowozin, Koji Tsuda
Frequent Subgraph Retrieval in Geometric Graph Databases. ICDM (2008)
Hiroto Saigo, Nicole Krämer, Koji Tsuda
Partial least squares regression for graph mining. KDD (2008)
Koji Tsuda, Kenichi Kurihara
Graph Mining with Variational Dirichlet Process Mixture Models. SDM (2008)
Matthias W. Seeger, Florian Steinke, Koji Tsuda
Bayesian Inference and Optimal Design in the Sparse Linear Model. AISTATS (2007)
Hiroto Saigo, Takeaki Uno, Koji Tsuda
Mining complex genotypic features for predicting HIV-1 drug resistance. Bioinform. 23 (18) (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 Bioinform. 8 (S-10) (2007)
Elisabeth Georgii, Sabine Dietmann, Takeaki Uno, Philipp Pagel, Koji Tsuda
Mining expression-dependent modules in the human interaction network. BMC Bioinform. 8 (S-8) (2007)
Sebastian Nowozin, Gökhan H. Bakir, Koji Tsuda
Discriminative Subsequence Mining for Action Classification. ICCV (2007)
Sebastian Nowozin, Koji Tsuda, Takeaki Uno, Taku Kudo, Gökhan H. Bakir
Weighted Substructure Mining for Image Analysis. MLG (2007)
Florian Steinke, Matthias W. Seeger, Koji Tsuda
Experimental design for efficient identification of gene regulatory networks using sparse Bayesian models. BMC Syst. Biol. 1 (2007)
Koji Tsuda
Entire regularization paths for graph data. ICML (2007)
Tsuyoshi Idé, Koji Tsuda
Change-Point Detection using Krylov Subspace Learning. SDM (2007)
Sebastian Nowozin, Koji Tsuda, Takeaki Uno, Taku Kudo, Gökhan H. Bakir
Weighted Substructure Mining for Image Analysis. CVPR (2007)
Yasuo Tabei, Koji Tsuda, Taishin Kin, Kiyoshi Asai
SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments. Bioinform. 22 (14) (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 Bioinform. 7 (S-1) (2006)
Michiaki Hamada, Koji Tsuda, Taku Kudo, Taishin Kin, Kiyoshi Asai
Mining frequent stem patterns from unaligned RNA sequences. Bioinform. 22 (20) (2006)
Koji Tsuda, Taku Kudo
Clustering graphs by weighted substructure mining. ICML (2006)
Koji Tsuda, Gunnar Rätsch, Manfred K. Warmuth
Matrix Exponentiated Gradient Updates for On-line Learning and Bregman Projection. J. Mach. Learn. Res. 6 (2005)
Tsuyoshi Kato, Koji Tsuda, Kiyoshi Asai
Selective integration of multiple biological data for supervised network inference. Bioinform. 21 (10) (2005)
Koji Tsuda, Gunnar Rätsch
Image reconstruction by linear programming. IEEE Trans. Image Process. 14 (6) (2005)
Koji Tsuda, Hyunjung Shin, Bernhard Schölkopf
Fast protein classification with multiple networks. ECCB/JBI (2005)

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Publication Activity (10 Years)

Top Topics

Top Venues

Koji Tsuda