Yoshihiro Yamanishi
Orcid: 0000-0003-2279-8773
According to our database1,
Yoshihiro Yamanishi
authored at least 64 papers
between 2003 and 2024.
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Bibliography
2024
<i>De Novo</i> Generation of Chemical Structures of Inhibitor and Activator Candidates for Therapeutic Target Proteins by a Transformer-Based Variational Autoencoder and Bayesian Optimization.
J. Chem. Inf. Model., 2024
Proceedings of the Thirty-Eighth AAAI Conference on Artificial Intelligence, 2024
2023
EarlGAN: An enhanced actor-critic reinforcement learning agent-driven GAN for de novo drug design.
Pattern Recognit. Lett., November, 2023
SpotGAN: A Reverse-Transformer GAN Generates Scaffold-Constrained Molecules with Property Optimization.
Proceedings of the Machine Learning and Knowledge Discovery in Databases: Research Track, 2023
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2023
2022
Pathway trajectory analysis with tensor imputation reveals drug-induced single-cell transcriptomic landscape.
Nat. Comput. Sci., 2022
Scaffold-Retained Structure Generator to Exhaustively Create Molecules in an Arbitrary Chemical Space.
J. Chem. Inf. Model., 2022
Epigenetic landscape of drug responses revealed through large-scale ChIP-seq data analyses.
BMC Bioinform., 2022
TRANSDIRE: data-driven direct reprogramming by a pioneer factor-guided trans-omics approach.
Bioinform., 2022
Transformer-based Objective-reinforced Generative Adversarial Network to Generate Desired Molecules.
Proceedings of the Thirty-First International Joint Conference on Artificial Intelligence, 2022
2021
TRIOMPHE: Transcriptome-Based Inference and Generation of Molecules with Desired Phenotypes by Machine Learning.
J. Chem. Inf. Model., 2021
Lean-Docking: Exploiting Ligands' Predicted Docking Scores to Accelerate Molecular Docking.
J. Chem. Inf. Model., 2021
2020
BMC Bioinform., April, 2020
Ranking Molecules with Vanishing Kernels and a Single Parameter: Active Applicability Domain Included.
J. Chem. Inf. Model., 2020
Network-based characterization of disease-disease relationships in terms of drugs and therapeutic targets.
Bioinform., 2020
2019
IEEE ACM Trans. Comput. Biol. Bioinform., 2019
A Distance-Based Boolean Applicability Domain for Classification of High Throughput Screening Data.
J. Chem. Inf. Model., 2019
Network-based characterization of drug-protein interaction signatures with a space-efficient approach.
BMC Syst. Biol., 2019
Predicting drug-induced transcriptome responses of a wide range of human cell lines by a novel tensor-train decomposition algorithm.
Bioinform., 2019
2018
2016
Simultaneous prediction of enzyme orthologs from chemical transformation patterns for <i>de novo</i> metabolic pathway reconstruction.
Bioinform., 2016
Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 2016
2015
Mining Discriminative Patterns from Graph Data with Multiple Labels and Its Application to Quantitative Structure-Activity Relationship (QSAR) Models.
J. Chem. Inf. Model., 2015
J. Chem. Inf. Model., 2015
Systematic Drug Repositioning for a Wide Range of Diseases with Integrative Analyses of Phenotypic and Molecular Data.
J. Chem. Inf. Model., 2015
Large-Scale Prediction of Beneficial Drug Combinations Using Drug Efficacy and Target Profiles.
J. Chem. Inf. Model., 2015
Metabolome-scale <i>de novo</i> pathway reconstruction using regioisomer-sensitive graph alignments.
Bioinform., 2015
2014
DINIES: drug-target interaction network inference engine based on supervised analysis.
Nucleic Acids Res., 2014
Metabolome-scale prediction of intermediate compounds in multistep metabolic pathways with a recursive supervised approach.
Bioinform., 2014
2013
Nucleic Acids Res., 2013
BMC Syst. Biol., 2013
KCF-S: KEGG Chemical Function and Substructure for improved interpretability and prediction in chemical bioinformatics.
BMC Syst. Biol., 2013
Inferring protein domains associated with drug side effects based on drug-target interaction network.
BMC Syst. Biol., 2013
Supervised <i>de novo</i> reconstruction of metabolic pathways from metabolome-scale compound sets.
Bioinform., 2013
Succinct interval-splitting tree for scalable similarity search of compound-protein pairs with property constraints.
Proceedings of the 19th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 2013
2012
Nucleic Acids Res., 2012
Drug Side-Effect Prediction Based on the Integration of Chemical and Biological Spaces.
J. Chem. Inf. Model., 2012
Drug target prediction using adverse event report systems: a pharmacogenomic approach.
Bioinform., 2012
Identification of chemogenomic features from drug-target interaction networks using interpretable classifiers.
Bioinform., 2012
2011
Extracting Sets of Chemical Substructures and Protein Domains Governing Drug-Target Interactions.
J. Chem. Inf. Model., 2011
BMC Bioinform., 2011
2010
IEICE Trans. Inf. Syst., 2010
Drug-target interaction prediction from chemical, genomic and pharmacological data in an integrated framework.
Bioinform., 2010
2009
E-zyme: predicting potential EC numbers from the chemical transformation pattern of substrate-product pairs.
Bioinform., 2009
Simultaneous inference of biological networks of multiple species from genome-wide data and evolutionary information: a semi-supervised approach.
Bioinform., 2009
Bioinform., 2009
Proceedings of the SIAM International Conference on Data Mining, 2009
Proceedings of the Advances in Knowledge Discovery and Data Mining, 2009
2008
Proceedings of the Advances in Neural Information Processing Systems 21, 2008
Prediction of drug-target interaction networks from the integration of chemical and genomic spaces.
Proceedings of the Proceedings 16th International Conference on Intelligent Systems for Molecular Biology (ISMB), 2008
2007
Proceedings of the Algebraic Biology, Second International Conference, 2007
2006
Partial correlation coefficient between distance matrices as a new indicator of protein-protein interactions.
Bioinform., 2006
2005
The inference of protein-protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationships.
Bioinform., 2005
Supervised enzyme network inference from the integration of genomic data and chemical information.
Proceedings of the Proceedings Thirteenth International Conference on Intelligent Systems for Molecular Biology 2005, 2005
2004
Proceedings of the Advances in Neural Information Processing Systems 17 [Neural Information Processing Systems, 2004
Proceedings of the Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004, 2004
2003
Extraction of correlated gene clusters from multiple genomic data by generalized kernel canonical correlation analysis.
Proceedings of the Eleventh International Conference on Intelligent Systems for Molecular Biology, June 29, 2003