List of works - Koji Tsuda

A New Discriminative Kernel From Probabilistic Models ⬇️

A new discriminative kernel from probabilistic models

scientific article published in October 2002

An interpretable machine learning model for diagnosis of Alzheimer's disease

scholarly article by Diptesh Das et al published 2019 in PeerJ

Asymptotic properties of the Fisher kernel

scientific article published in January 2004

Bayesian optimization package: PHYSBO

scientific article published in 2022

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

scientific article

Clustering with the Fisher Score ⬇️

scientific article published in January 2003

CompRet: a comprehensive recommendation framework for chemical synthesis planning with algorithmic enumeration

publication published on 01 September 2020

Deep-learning-based quality filtering of mechanically exfoliated 2D crystals

scientific article published on 17 December 2019

Dense module enumeration in biological networks

scientific article

Discovering combinatorial interactions in survival data

scientific article

EPIBLASTER-fast exhaustive two-locus epistasis detection strategy using graphical processing units

scientific article

Efficient Search for Energetically Favorable Molecular Conformations against Metastable States via Gray-Box Optimization

scientific article published on 15 July 2021

Efficiently finding genome-wide three-way gene interactions from transcript- and genotype-data

scientific article published on 7 September 2009

Enumeration of condition-dependent dense modules in protein interaction networks

scientific article published on 11 February 2009

Experimental design for efficient identification of gene regulatory networks using sparse Bayesian models

scientific article

Fast protein classification with multiple networks

scientific article published in September 2005

Functional Nanoparticles-Coated Nanomechanical Sensor Arrays for Machine Learning-Based Quantitative Odor Analysis

scholarly article by Kota Shiba et al published 15 August 2018 in ACS sensors

Functional Nanoparticles-Coated Nanomechanical Sensor Arrays for Machine Learning-Based Quantitative Odor Analysis

scholarly article by Kota Shiba et al published 24 August 2018 in ACS sensors

Generating Ampicillin-Level Antimicrobial Peptides with Activity-Aware Generative Adversarial Networks

scientific article published on 28 August 2020

Health checkup and telemedical intervention program for preventive medicine in developing countries: verification study.

scientific article

Hunting for Organic Molecules with Artificial Intelligence: Molecules Optimized for Desired Excitation Energies

scientific article published on 26 September 2018

Hunting for Organic Molecules with Artificial Intelligence: Molecules Optimized for Desired Excitation Energies

scholarly article published 2018

Image Reconstruction by Linear Programming ⬇️

scientific article published in January 2004

Image reconstruction by linear programming.

scientific article published in June 2005

LAMPLINK: detection of statistically significant SNP combinations from GWAS data

scientific article

Learning kernels from biological networks by maximizing entropy

scientific article published in August 2004

Legendre Decomposition for Tensors ⬇️

Li-ion Conductive Li3PO4-Li3BO3-Li2SO4 Mixture: Prevision through Density Functional Molecular Dynamics and Machine Learning

scholarly article published 27 November 2018

MP-LAMP: parallel detection of statistically significant multi-loci markers on cloud platforms

scientific article published on 01 September 2018

Machine Learning Accelerates MD-based Binding-Pose Prediction between Ligands and Proteins

scientific article published on 11 October 2017

Machine learning reveals orbital interaction in materials.

scientific article published on 26 October 2017

Machine-Learning-Assisted Development and Theoretical Consideration for the Al2Fe3Si3 Thermoelectric Material

article

Machine-Learning-Guided Mutagenesis for Directed Evolution of Fluorescent Proteins

scholarly article by Yutaka Saito et al published 21 September 2018 in ACS Synthetic Biology

Machine-learning prediction of the d-band center for metals and bimetals

scholarly article by Ichigaku Takigawa et al published 2016 in RSC Advances

Marginalized kernels for RNA sequence data analysis

scientific article published on January 1, 2002

Marginalized kernels for biological sequences

scientific article published in January 2002

Matrix Exponential Gradient Updates for On-line Learning and Bregman Projection ⬇️

Mining expression-dependent modules in the human interaction network.

scientific article published on 20 November 2007

Mining frequent stem patterns from unaligned RNA sequences

scientific article

Modeling splicing sites with pairwise correlations

scientific article published in January 2002

NIPS workshop on New Problems and Methods in Computational Biology

scientific article

On the performance of methods for finding a switching mechanism in gene expression.

scientific article published in January 2010

PDB‐scale analysis of known and putative ligand‐binding sites with structural sketches ⬇️

scientific article published on November 24, 2011

PoSSuM: a database of similar protein-ligand binding and putative pockets ⬇️

scientific article published on December 1, 2011

Predictive Approaches for Low-Cost Preventive Medicine Program in Developing Countries

Privacy-preserving search for chemical compound databases.

scientific article published on 9 December 2015

Protein functional class prediction with a combined graph

QCforever: A Quantum Chemistry Wrapper for Everyone to Use in Black-Box Optimization

scientific article published in 2022

RNA inverse folding using Monte Carlo tree search

scientific article published on 6 November 2017

ROS-DET: robust detector of switching mechanisms in gene expression ⬇️

scientific article published on April 1, 2011

Reaction graph kernels predict EC numbers of unknown enzymatic reactions in plant secondary metabolism

scientific article

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

scientific article

Selective integration of multiple biological data for supervised network inference

scientific article published on 22 February 2005

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

scientific article

SketchSort: Fast All Pairs Similarity Search for Large Databases of Molecular Fingerprints

scientific article published on 12 July 2011

SlideSort: all pairs similarity search for short reads ⬇️

scientific article published on December 9, 2010

Sparse modeling of EELS and EDX spectral imaging data by nonnegative matrix factorization

scientific article

Statistical significance of combinatorial regulations

scientific article published on 23 July 2013

Structure prediction of boron-doped graphene by machine learning

scientific article published on 01 June 2018

Submodularity Cuts and Applications ⬇️

scientific article published in January 2009

The DICS repository: module-assisted analysis of disease-related gene lists

article

Ultranarrow-Band Wavelength-Selective Thermal Emission with Aperiodic Multilayered Metamaterials Designed by Bayesian Optimization

scientific article published on 22 January 2019

evERdock BAI: Machine-learning-guided selection of protein-protein complex structure

scientific article published on 01 December 2019

List of works by Koji Tsuda

A New Discriminative Kernel From Probabilistic Models ⬇️

A new discriminative kernel from probabilistic models

An interpretable machine learning model for diagnosis of Alzheimer's disease

Asymptotic properties of the Fisher kernel

Bayesian optimization package: PHYSBO

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

Clustering with the Fisher Score ⬇️

CompRet: a comprehensive recommendation framework for chemical synthesis planning with algorithmic enumeration

Deep-learning-based quality filtering of mechanically exfoliated 2D crystals

Dense module enumeration in biological networks

Discovering combinatorial interactions in survival data

EPIBLASTER-fast exhaustive two-locus epistasis detection strategy using graphical processing units

Efficient Search for Energetically Favorable Molecular Conformations against Metastable States via Gray-Box Optimization

Efficiently finding genome-wide three-way gene interactions from transcript- and genotype-data

Enumeration of condition-dependent dense modules in protein interaction networks

Experimental design for efficient identification of gene regulatory networks using sparse Bayesian models

Fast protein classification with multiple networks

Functional Nanoparticles-Coated Nanomechanical Sensor Arrays for Machine Learning-Based Quantitative Odor Analysis

Functional Nanoparticles-Coated Nanomechanical Sensor Arrays for Machine Learning-Based Quantitative Odor Analysis

Generating Ampicillin-Level Antimicrobial Peptides with Activity-Aware Generative Adversarial Networks

Health checkup and telemedical intervention program for preventive medicine in developing countries: verification study.

Hunting for Organic Molecules with Artificial Intelligence: Molecules Optimized for Desired Excitation Energies

Hunting for Organic Molecules with Artificial Intelligence: Molecules Optimized for Desired Excitation Energies

Image Reconstruction by Linear Programming ⬇️

Image reconstruction by linear programming.

LAMPLINK: detection of statistically significant SNP combinations from GWAS data

Learning kernels from biological networks by maximizing entropy

Legendre Decomposition for Tensors ⬇️

Li-ion Conductive Li3PO4-Li3BO3-Li2SO4 Mixture: Prevision through Density Functional Molecular Dynamics and Machine Learning

MP-LAMP: parallel detection of statistically significant multi-loci markers on cloud platforms

Machine Learning Accelerates MD-based Binding-Pose Prediction between Ligands and Proteins

Machine learning reveals orbital interaction in materials.

Machine-Learning-Assisted Development and Theoretical Consideration for the Al2Fe3Si3 Thermoelectric Material

Machine-Learning-Guided Mutagenesis for Directed Evolution of Fluorescent Proteins

Machine-learning prediction of the d-band center for metals and bimetals

Marginalized kernels for RNA sequence data analysis

Marginalized kernels for biological sequences

Matrix Exponential Gradient Updates for On-line Learning and Bregman Projection ⬇️

Mining expression-dependent modules in the human interaction network.

Mining frequent stem patterns from unaligned RNA sequences

Modeling splicing sites with pairwise correlations

NIPS workshop on New Problems and Methods in Computational Biology

On the performance of methods for finding a switching mechanism in gene expression.

PDB‐scale analysis of known and putative ligand‐binding sites with structural sketches ⬇️

PoSSuM: a database of similar protein-ligand binding and putative pockets ⬇️

Predictive Approaches for Low-Cost Preventive Medicine Program in Developing Countries

Privacy-preserving search for chemical compound databases.

Protein functional class prediction with a combined graph

QCforever: A Quantum Chemistry Wrapper for Everyone to Use in Black-Box Optimization

RNA inverse folding using Monte Carlo tree search

ROS-DET: robust detector of switching mechanisms in gene expression ⬇️

Reaction graph kernels predict EC numbers of unknown enzymatic reactions in plant secondary metabolism

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

Selective integration of multiple biological data for supervised network inference

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

SketchSort: Fast All Pairs Similarity Search for Large Databases of Molecular Fingerprints

SlideSort: all pairs similarity search for short reads ⬇️

Sparse modeling of EELS and EDX spectral imaging data by nonnegative matrix factorization

Statistical significance of combinatorial regulations

Structure prediction of boron-doped graphene by machine learning

Submodularity Cuts and Applications ⬇️

The DICS repository: module-assisted analysis of disease-related gene lists

Ultranarrow-Band Wavelength-Selective Thermal Emission with Aperiodic Multilayered Metamaterials Designed by Bayesian Optimization

evERdock BAI: Machine-learning-guided selection of protein-protein complex structure