Koji Tsuda

Orcid: 0000-0002-4288-1606

According to our database1, Koji Tsuda authored at least 127 papers between 1995 and 2024.

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Bibliography

2024
Preference-Optimized Pareto Set Learning for Blackbox Optimization.
CoRR, 2024

Molecule Graph Networks with Many-body Equivariant Interactions.
CoRR, 2024

2023
Revealing factors influencing polymer degradation with rank-based machine learning.
Patterns, December, 2023

Efficient model selection for predictive pattern mining model by safe pattern pruning.
Patterns, December, 2023

Interpretable Fragment-Based Molecule Design with Self-Learning Entropic Population Annealing.
Adv. Intell. Syst., October, 2023

On a linear fused Gromov-Wasserstein distance for graph structured data.
Pattern Recognit., June, 2023

3D-Sensitive Encoding of Pharmacophore Features.
J. Chem. Inf. Model., April, 2023

Feature Importance Measurement based on Decision Tree Sampling.
CoRR, 2023

NIMS-OS: An automation software to implement a closed loop between artificial intelligence and robotic experiments in materials science.
CoRR, 2023

2022
QCforever: A Quantum Chemistry Wrapper for Everyone to Use in Black-Box Optimization.
J. Chem. Inf. Model., 2022

Bayesian optimization package: PHYSBO.
Comput. Phys. Commun., 2022

Fast and More Powerful Selective Inference for Sparse High-Order Interaction Model.
Proceedings of the Thirty-Sixth AAAI Conference on Artificial Intelligence, 2022

2021
Molecular generation by Fast Assembly of (Deep)SMILES fragments.
J. Cheminformatics, 2021

A generative model for molecule generation based on chemical reaction trees.
CoRR, 2021

Continuous black-box optimization with quantum annealing and random subspace coding.
CoRR, 2021

2020
Efficient query autocompletion with edit distance-based error tolerance.
VLDB J., 2020

CompRet: a comprehensive recommendation framework for chemical synthesis planning with algorithmic enumeration.
J. Cheminformatics, 2020

2019
Leveraging Legacy Data to Accelerate Materials Design via Preference Learning.
CoRR, 2019

2018
Improving the Accuracy of Protein-Ligand Binding Mode Prediction Using a Molecular Dynamics-Based Pocket Generation Approach.
J. Comput. Chem., 2018

Transductive Boltzmann Machines.
CoRR, 2018

Legendre Tensor Decomposition.
CoRR, 2018

MP-LAMP: parallel detection of statistically significant multi-loci markers on cloud platforms.
Bioinform., 2018

Machine learning accelerates MD-based binding pose prediction between ligands and proteins.
Bioinform., 2018

DenseZDD: A Compact and Fast Index for Families of Sets.
Algorithms, 2018

Legendre Decomposition for Tensors.
Proceedings of the Advances in Neural Information Processing Systems 31: Annual Conference on Neural Information Processing Systems 2018, 2018

2017
ChemTS: An Efficient Python Library for de novo Molecular Generation.
CoRR, 2017

RNA inverse folding using Monte Carlo tree search.
BMC Bioinform., 2017

Selective Inference for Sparse High-Order Interaction Models.
Proceedings of the 34th International Conference on Machine Learning, 2017

Tensor Balancing on Statistical Manifold.
Proceedings of the 34th International Conference on Machine Learning, 2017

2016
CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data.
BMC Bioinform., 2016

LAMPLINK: detection of statistically significant SNP combinations from GWAS data.
Bioinform., 2016

Significant Pattern Mining with Confounding Variables.
Proceedings of the Advances in Knowledge Discovery and Data Mining, 2016

Safe Pattern Pruning: An Efficient Approach for Predictive Pattern Mining.
Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 2016

Information decomposition on structured space.
Proceedings of the IEEE International Symposium on Information Theory, 2016

2015
Privacy-preserving search for chemical compound databases.
BMC Bioinform., December, 2015

Redesigning pattern mining algorithms for supercomputers.
CoRR, 2015

Superset Generation on Decision Diagrams.
Proceedings of the WALCOM: Algorithms and Computation - 9th International Workshop, 2015

Privacy-Preserving Statistical Analysis by Exact Logistic Regression.
Proceedings of the 2015 IEEE Symposium on Security and Privacy Workshops, 2015

BDD construction for all solutions SAT and efficient caching mechanism.
Proceedings of the 30th Annual ACM Symposium on Applied Computing, 2015

Predictive Approaches for Low-Cost Preventive Medicine Program in Developing Countries.
Proceedings of the 21th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 2015

2014
Distribution Loss Minimization With Guaranteed Error Bound.
IEEE Trans. Smart Grid, 2014

Oblivious Evaluation of Non-deterministic Finite Automata with Application to Privacy-Preserving Virus Genome Detection.
Proceedings of the 13th Workshop on Privacy in the Electronic Society, 2014

Statistically significant subgraphs for genome-wide association study.
Proceedings of the 1st ECML/PKDD Workshop on Statistically Sound Data Mining, 2014

A Fast Method of Statistical Assessment for Combinatorial Hypotheses Based on Frequent Itemset Enumeration.
Proceedings of the Machine Learning and Knowledge Discovery in Databases, 2014

Online matrix prediction for sparse loss matrices.
Proceedings of the Sixth Asian Conference on Machine Learning, 2014

2013
Efficient Error-tolerant Query Autocompletion.
Proc. VLDB Endow., 2013

Fast Iterative Mining Using Sparsity-Inducing Loss Functions.
IEICE Trans. Inf. Syst., 2013

Discovering combinatorial interactions in survival data.
Bioinform., 2013

Compact Complete Inverted Files for Texts and Directed Acyclic Graphs Based on Sequence Binary Decision Diagrams .
Proceedings of the Prague Stringology Conference 2013, Prague, Czech Republic, 2013

Fast Westfall-Young permutation procedure for combinatorial regulation discovery.
Proceedings of the 2013 IEEE International Conference on Bioinformatics and Biomedicine, 2013

2012
PoSSuM: a database of similar protein-ligand binding and putative pockets.
Nucleic Acids Res., 2012

Data Mining for Biologists.
Int. J. Knowl. Discov. Bioinform., 2012

2011
Multi-way set enumeration in weight tensors.
Mach. Learn., 2011

SlideSort: all pairs similarity search for short reads.
Bioinform., 2011

Kernel-based Similarity Search in Massive Graph Databases with Wavelet Trees.
Proceedings of the Eleventh SIAM International Conference on Data Mining, 2011

LGM: Mining Frequent Subgraphs from Linear Graphs.
Proceedings of the Advances in Knowledge Discovery and Data Mining, 2011

Second Workshop on Algorithms for Large-Scale Information Processing in Knowledge Discovery (ALSIP).
Proceedings of the New Frontiers in Artificial Intelligence, 2011

Matrix Decomposition-based Dimensionality Reduction on Graph Data.
Proceedings of the Graph Data Management: Techniques and Applications., 2011

Graph Classification Methods in Chemoinformatics.
Proceedings of the Handbook of Statistical Bioinformatics., 2011

2010
Graph Classification.
Proceedings of the Managing and Mining Graph Data, 2010

Single versus Multiple Sorting in All Pairs Similarity Search.
Proceedings of the 2nd Asian Conference on Machine Learning, 2010

Cartesian Kernel: An Efficient Alternative to the Pairwise Kernel.
IEICE Trans. Inf. Syst., 2010

Reaction graph kernels predict EC numbers of unknown enzymatic reactions in plant secondary metabolism.
BMC Bioinform., 2010

2009
gBoost: a mathematical programming approach to graph classification and regression.
Mach. Learn., 2009

Protein functional class prediction with a combined graph.
Expert Syst. Appl., 2009

Efficient Construction of Neighborhood Graphs by the Multiple Sorting Method
CoRR, 2009

Efficiently finding genome-wide three-way gene interactions from transcript- and genotype-data.
Bioinform., 2009

Simultaneous inference of biological networks of multiple species from genome-wide data and evolutionary information: a semi-supervised approach.
Bioinform., 2009

Enumeration of condition-dependent dense modules in protein interaction networks.
Bioinform., 2009

The DICS repository: module-assisted analysis of disease-related gene lists.
Bioinform., 2009

Link Propagation: A Fast Semi-supervised Learning Algorithm for Link Prediction.
Proceedings of the SIAM International Conference on Data Mining, 2009

A Bayesian Approach to Graphy Regression with Relevant Subgraph Selection.
Proceedings of the SIAM International Conference on Data Mining, 2009

On Pairwise Kernels: An Efficient Alternative and Generalization Analysis.
Proceedings of the Advances in Knowledge Discovery and Data Mining, 2009

Submodularity Cuts and Applications.
Proceedings of the Advances in Neural Information Processing Systems 22: 23rd Annual Conference on Neural Information Processing Systems 2009. Proceedings of a meeting held 7-10 December 2009, 2009

Multi-way set enumeration in real-valued tensors.
Proceedings of the 2nd ACM SIGKDD Workshop on Data Mining using Matrices and Tensors, 2009

2008
Graph Mining with Variational Dirichlet Process Mixture Models.
Proceedings of the SIAM International Conference on Data Mining, 2008

Partial least squares regression for graph mining.
Proceedings of the 14th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 2008

Iterative Subgraph Mining for Principal Component Analysis.
Proceedings of the 8th IEEE International Conference on Data Mining (ICDM 2008), 2008

Frequent Subgraph Retrieval in Geometric Graph Databases.
Proceedings of the 8th IEEE International Conference on Data Mining (ICDM 2008), 2008

2007
Bayesian Inference and Optimal Design in the Sparse Linear Model.
Proceedings of the Eleventh International Conference on Artificial Intelligence and Statistics, 2007

Experimental design for efficient identification of gene regulatory networks using sparse Bayesian models.
BMC Syst. Biol., 2007

Mining expression-dependent modules in the human interaction network.
BMC Bioinform., 2007

NIPS workshop on New Problems and Methods in Computational Biology.
BMC Bioinform., 2007

Mining complex genotypic features for predicting HIV-1 drug resistance.
Bioinform., 2007

Change-Point Detection using Krylov Subspace Learning.
Proceedings of the Seventh SIAM International Conference on Data Mining, 2007

Entire regularization paths for graph data.
Proceedings of the Machine Learning, 2007

Discriminative Subsequence Mining for Action Classification.
Proceedings of the IEEE 11th International Conference on Computer Vision, 2007

Weighted Substructure Mining for Image Analysis.
Proceedings of the 2007 IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR 2007), 2007

2006
Network-based de-noising improves prediction from microarray data.
BMC Bioinform., 2006

SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments.
Bioinform., 2006

Mining frequent stem patterns from unaligned RNA sequences.
Bioinform., 2006

Clustering graphs by weighted substructure mining.
Proceedings of the Machine Learning, 2006

Prediction of Protein Function from Networks.
Proceedings of the Semi-Supervised Learning, 2006

2005
Image reconstruction by linear programming.
IEEE Trans. Image Process., 2005

Matrix Exponentiated Gradient Updates for On-line Learning and Bregman Projection.
J. Mach. Learn. Res., 2005

Selective integration of multiple biological data for supervised network inference.
Bioinform., 2005

Propagating distributions on a hypergraph by dual information regularization.
Proceedings of the Machine Learning, 2005

Fast protein classification with multiple networks.
Proceedings of the ECCB/JBI'05 Proceedings, Fourth European Conference on Computational Biology/Sixth Meeting of the Spanish Bioinformatics Network (Jornadas de BioInformática), Palacio de Congresos, Madrid, Spain, September 28, 2005

2004
Minimizing the Cross Validation Error to Mix Kernel Matrices of Heterogeneous Biological Data.
Neural Process. Lett., 2004

Asymptotic Properties of the Fisher Kernel.
Neural Comput., 2004

A New Variational Framework for Rigid-Body Alignment.
Proceedings of the Structural, 2004

Matrix Exponential Gradient Updates for On-line Learning and Bregman Projection.
Proceedings of the Advances in Neural Information Processing Systems 17 [Neural Information Processing Systems, 2004

Learning kernels from biological networks by maximizing entropy.
Proceedings of the Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004, 2004

Learning to Find Graph Pre-images.
Proceedings of the Pattern Recognition, 26th DAGM Symposium, August 30, 2004

2003
The em Algorithm for Kernel Matrix Completion with Auxiliary Data.
J. Mach. Learn. Res., 2003

Marginalized Kernels Between Labeled Graphs.
Proceedings of the Machine Learning, 2003

2002
Subspace information criterion for nonquadratic regularizers-Model selection for sparse regressors.
IEEE Trans. Neural Networks, 2002

A New Discriminative Kernel from Probabilistic Models.
Neural Comput., 2002

Approximating Incomplete Kernel Matrices by the em Algorithm
CoRR, 2002

Clustering with the Fisher Score.
Proceedings of the Advances in Neural Information Processing Systems 15 [Neural Information Processing Systems, 2002

Marginalized kernels for biological sequences.
Proceedings of the Tenth International Conference on Intelligent Systems for Molecular Biology, 2002

The Leave-One-Out Kernel.
Proceedings of the Artificial Neural Networks, 2002

Modeling splicing sites with pairwise correlations.
Proceedings of the European Conference on Computational Biology (ECCB 2002), 2002

2001
An Attempt for Coloring Multichannel MR Imaging Data.
IEEE Trans. Vis. Comput. Graph., 2001

An introduction to kernel-based learning algorithms.
IEEE Trans. Neural Networks, 2001

The subspace method in Hilbert space.
Syst. Comput. Jpn., 2001

Learning to Predict the Leave-One-Out Error of Kernel Based Classifiers.
Proceedings of the Artificial Neural Networks, 2001

Pairwise Coupling for Machine Recognition of Hand-Printed Japanese Characters.
Proceedings of the 2001 IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR 2001), 2001

2000
Large Margin Classifier via Semiparametric Inference.
Proceedings of the IEEE-INNS-ENNS International Joint Conference on Neural Networks, 2000

1999
Subspace classifier in the Hilbert space.
Pattern Recognit. Lett., 1999

Subspace classifier in reproducing kernel Hilbert space.
Proceedings of the International Joint Conference Neural Networks, 1999

Support vector classifier with asymetric kernel function.
Proceedings of the 7th European Symposium on Artificial Neural Networks, 1999

1998
Pattern Recognition Method for Metric Space by Four Points Embedding.
Proceedings of the Image and Vision Computing New Zealand, International Conference, 1998

1997
Sequential fuzzy cluster extraction and its robustness against noise.
Syst. Comput. Jpn., 1997

A Nonparametric Density Model for Classification in a High Dimensional Space.
Proceedings of the 4th International Conference Document Analysis and Recognition (ICDAR '97), 1997

1996
Extracting straight lines by sequential fuzzy clustering.
Pattern Recognit. Lett., 1996

1995
Clustering OCR-ed texts for browsing document image database.
Proceedings of the Third International Conference on Document Analysis and Recognition, 1995


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