Seiya Imoto
Orcid: 0000-0002-2989-308X
According to our database1,
Seiya Imoto
authored at least 125 papers
between 2002 and 2024.
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Bibliography
2024
Dual-stream multi-dependency graph neural network enables precise cancer survival analysis.
Medical Image Anal., 2024
Histo-Genomic Knowledge Distillation For Cancer Prognosis From Histopathology Whole Slide Images.
CoRR, 2024
2023
Surformer: An interpretable pattern-perceptive survival transformer for cancer survival prediction from histopathology whole slide images.
Comput. Methods Programs Biomed., November, 2023
Investigation of the BERT model on nucleotide sequences with non-standard pre-training and evaluation of different k-mer embeddings.
Bioinform., October, 2023
<i>ggkegg</i>: analysis and visualization of KEGG data utilizing the grammar of graphics.
Bioinform., October, 2023
Zero-shot-capable identification of phage-host relationships with whole-genome sequence representation by contrastive learning.
Briefings Bioinform., September, 2023
iAMPCN: a deep-learning approach for identifying antimicrobial peptides and their functional activities.
Briefings Bioinform., July, 2023
Targeting tumor heterogeneity: multiplex-detection-based multiple instance learning for whole slide image classification.
Bioinform., March, 2023
PFresGO: an attention mechanism-based deep-learning approach for protein annotation by integrating gene ontology inter-relationships.
Bioinform., March, 2023
Gene Regulatory Network-Classifier: Gene Regulatory Network-Based Classifier and Its Applications to Gastric Cancer Drug (5-Fluorouracil) Marker Identification.
J. Comput. Biol., February, 2023
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2023
2022
Uncovering Molecular Mechanisms of Drug Resistance via Network-Constrained Common Structure Identification.
J. Comput. Biol., 2022
Improvement of the Japanese healthcare data system for the effective management of patients with COVID-19: A national survey.
Int. J. Medical Informatics, 2022
Multiplex-detection Based Multiple Instance Learning Network for Whole Slide Image Classification.
CoRR, 2022
PredictiveNetwork: predictive gene network estimation with application to gastric cancer drug response-predictive network analysis.
BMC Bioinform., 2022
Bioinform., 2022
2021
Bioinform., November, 2021
Enhancing breakpoint resolution with deep segmentation model: A general refinement method for read-depth based structural variant callers.
PLoS Comput. Biol., 2021
Halcyon: an accurate basecaller exploiting an encoder-decoder model with monotonic attention.
Bioinform., 2021
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2021
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2021
2020
BMC Bioinform., April, 2020
Ensemble smoothers for inference of hidden states and parameters in combinatorial regulatory model.
J. Frankl. Inst., 2020
Neoantimon: a multifunctional R package for identification of tumor-specific neoantigens.
Bioinform., 2020
Theoretical Foundation of the Performance of Phylogeny-Based Somatic Variant Detection.
Proceedings of the Mathematical and Computational Oncology, 2020
2019
J. Comput. Biol., 2019
ALPHLARD-NT: Bayesian Method for Human Leukocyte Antigen Genotyping and Mutation Calling through Simultaneous Analysis of Normal and Tumor Whole-Genome Sequence Data.
J. Comput. Biol., 2019
Capturing the differences between humoral immunity in the normal and tumor environments from repertoire-seq of B-cell receptors using supervised machine learning.
BMC Bioinform., 2019
Bioinform., 2019
Proceedings of the Mathematical and Computational Oncology - First International Symposium, 2019
2018
Adaptive NetworkProfiler for Identifying Cancer Characteristic-Specific Gene Regulatory Networks.
J. Comput. Biol., 2018
2017
A Novel Adaptive Penalized Logistic Regression for Uncovering Biomarker Associated with Anti-Cancer Drug Sensitivity.
IEEE ACM Trans. Comput. Biol. Bioinform., 2017
Interaction-Based Feature Selection for Uncovering Cancer Driver Genes Through Copy Number-Driven Expression Level.
J. Comput. Biol., 2017
Reconstruction of high read-depth signals from low-depth whole genome sequencing data using deep learning.
Proceedings of the 2017 IEEE International Conference on Bioinformatics and Biomedicine, 2017
2016
Predicting Japanese Kampo formulas by analyzing database of medical records: a preliminary observational study.
BMC Medical Informatics Decis. Mak., 2016
Protein Fold Recognition Using Genetic Algorithm Optimized Voting Scheme and Profile Bigram.
J. Softw., 2016
Int. J. Bioinform. Res. Appl., 2016
A likelihood-free filtering method via approximate Bayesian computation in evaluating biological simulation models.
Comput. Stat. Data Anal., 2016
Proceedings of the Bioinformatics Research and Applications - 12th International Symposium, 2016
2015
J. Comput. Biol., 2015
Genomic data assimilation using a higher moment filtering technique for restoration of gene regulatory networks.
BMC Syst. Biol., 2015
Genomon ITDetector: a tool for somatic internal tandem duplication detection from cancer genome sequencing data.
Bioinform., 2015
Proceedings of the Bioinformatics Research and Applications - 11th International Symposium, 2015
2014
Mach. Vis. Appl., 2014
A feature selection method using fixed-point algorithm for DNA microarray gene expression data.
Int. J. Knowl. Based Intell. Eng. Syst., 2014
An Efficient Data Assimilation Schema for Restoration and Extension of Gene Regulatory Networks Using Time-Course Observation Data.
J. Comput. Biol., 2014
An efficient method of exploring simulation models by assimilating literature and biological observational data.
Biosyst., 2014
HapMuC: somatic mutation calling using heterozygous germ line variants near candidate mutations.
Bioinform., 2014
Proceedings of the 17th International Conference on Information Fusion, 2014
2013
Int. J. Mach. Learn. Cybern., 2013
Multi-omics Approach for Estimating Metabolic Networks Using Low-Order Partial Correlations.
J. Comput. Biol., 2013
A strategy to select suitable physicochemical attributes of amino acids for protein fold recognition.
BMC Bioinform., 2013
Proceedings of the Advances in Bioinformatics and Computational Biology, 2013
Estimation of abrupt changes in sentinel observation data of influenza epidemics in Japan.
Proceedings of the 16th International Conference on Information Fusion, 2013
2012
IEEE ACM Trans. Comput. Biol. Bioinform., 2012
Identifying Gene Pathways Associated with Cancer Characteristics via Sparse Statistical Methods.
IEEE ACM Trans. Comput. Biol. Bioinform., 2012
Int. J. Mach. Learn. Cybern., 2012
J. Bioinform. Comput. Biol., 2012
BMC Syst. Biol., 2012
Identifying regulational alterations in gene regulatory networks by state space representation of vector autoregressive models and variational annealing.
BMC Genom., 2012
Bioinform., 2012
Identifiability of local transmissibility parameters in agent-based pandemic simulation.
Proceedings of the 15th International Conference on Information Fusion, 2012
Analysis of questionnaire for traditional medical and develop decision support system.
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2012
2011
Estimating Genome-Wide Gene Networks Using Nonparametric Bayesian Network Models on Massively Parallel Computers.
IEEE ACM Trans. Comput. Biol. Bioinform., 2011
Proceedings of the Complex Adaptive Systems 2011 Conference, 2011
Neural Networks, 2011
J. Mach. Learn. Res., 2011
Int. J. Knowl. Eng. Soft Data Paradigms, 2011
SiGN-SSM: open source parallel software for estimating gene networks with state space models.
Bioinform., 2011
Proceedings of the Bioinformatics Research and Applications - 7th International Symposium, 2011
Proceedings of the IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, 2011
Proceedings of the 14th International Conference on Information Fusion, 2011
Proceedings of the Advanced Agent Technology, 2011
Proceedings of the Handbook of Statistical Bioinformatics., 2011
2010
Optimal Search on Clustered Structural Constraint for Learning Bayesian Network Structure.
J. Mach. Learn. Res., 2010
Inferring dynamic gene networks under varying conditions for transcriptomic network comparison.
Bioinform., 2010
Model-free unsupervised gene set screening based on information enrichment in expression profiles.
Bioinform., 2010
Searching Optimal Bayesian Network Structure on Constraint Search Space: Super-Structure Approach.
Proceedings of the New Frontiers in Artificial Intelligence, 2010
Proceedings of the Artificial Neural Networks - ICANN 2010, 2010
Proceedings of the 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2010
Discovering functional gene pathways associated with cancer heterogeneity via sparse supervised learning.
Proceedings of the 2010 IEEE International Conference on Bioinformatics and Biomedicine, 2010
Proceedings of the 10th IEEE International Conference on Bioinformatics and Bioengineering, 2010
2009
Network-Based Predictions and Simulations by Biological State Space Models: Search for Drug Mode of Action.
J. Comput. Sci. Technol., 2009
Recursive regularization for inferring gene networks from time-course gene expression profiles.
BMC Syst. Biol., 2009
BMC Bioinform., 2009
Unraveling Dynamic Activities of Autocrine Pathways that Control Drug-Response Transcriptome Networks.
Proceedings of the Biocomputing 2009: Proceedings of the Pacific Symposium, 2009
Proceedings of the Bioinformatics and Computational Biology, 2009
2008
BMC Bioinform., 2008
Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells.
BMC Bioinform., 2008
Bioinform., 2008
Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models.
Bioinform., 2008
Partial Order-Based Bayesian Network Learning Algorithm for Estimating Gene Networks.
Proceedings of the 2008 IEEE International Conference on Bioinformatics and Biomedicine, 2008
Analyzing Time Course Gene Expression Data with Biological and Technical Replicates to Estimate Gene Networks by State Space Models.
Proceedings of the Second Asia International Conference on Modelling and Simulation, 2008
2007
Finding module-based gene networks with state-space models - Mining high-dimensional and short time-course gene expression data.
IEEE Signal Process. Mag., 2007
Proceedings of the Mining and Learning with Graphs, 2007
Proceedings of the Bioinformatics Research and Applications, Third International Symposium, 2007
Computational Genome-Wide Discovery of Aberrant Splice Variations with Exon Expression Profiles.
Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, 2007
A Structure Learning Algorithm for Inference of Gene Networks from Microarray Gene Expression Data Using Bayesian Networks.
Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, 2007
2006
Statistical Model Selection Method to Analyze Combinatorial Effects of Snps and Environmental Factors for Binary Disease.
Int. J. Artif. Intell. Tools, 2006
ArrayCluster: an analytic tool for clustering, data visualization and module finder on gene expression profiles.
Bioinform., 2006
Computational Strategy for Discovering Druggable Gene Networks from Genome-Wide RNA Expression Profiles.
Proceedings of the Biocomputing 2006, 2006
2005
Utilizing Evolutionary Information and Gene Expression Data for Estimating Gene Networks with Bayesian Network Models.
J. Bioinform. Comput. Biol., 2005
Proceedings of the Computational Science and Its Applications, 2005
Estimating Gene Networks from Expression Data and Binding Location Data via Boolean Networks.
Proceedings of the Computational Science and Its Applications, 2005
Estimating gene regulatory networks and protein-protein interactions of <i>Saccharomyces cerevisiae</i> from multiple genome-wide data.
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
Estimating Time-Dependent Gene Networks from Time Series Microarray Data by Dynamic Linear Models with Markov Switching.
Proceedings of the Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference, 2005
2004
Combining Microarrays and Biological Knowledge for Estimating Gene Networks via Bayesian Networks.
J. Bioinform. Comput. Biol., 2004
Proceedings of the Biocomputing 2004, 2004
Using Protein-Protein Interactions for Refining Gene Networks Estimated from Microarray Data by Bayesian Networks.
Proceedings of the Biocomputing 2004, 2004
Predicting the Operon Structure of Bacillus subtilis Using Operon Length, Intergene Distance, and Gene Expression Information.
Proceedings of the Biocomputing 2004, 2004
Proceedings of the Knowledge Exploration in Life Science Informatics, 2004
Predicting gene regulation by sigma factors in Bacillus subtilis from genome-wide data.
Proceedings of the Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004, 2004
A Mixed Factors Model for Dimension Reduction and Extraction of a Group Structure in Gene Expression Data.
Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004
Residual Bootstrapping and Median Filtering for Robust Estimation of Gene Networks from Microarray Data.
Proceedings of the Computational Methods in Systems Biology, International Conference, 2004
Case-Control Study of Binary Disease Trait Considering Interactions between SNPs and Environmental Effects using Logistic Regression.
Proceedings of the 4th IEEE International Symposium on BioInformatics and BioEngineering (BIBE 2004), 2004
2003
J. Bioinform. Comput. Biol., 2003
Bayesian Network and Nonparametric Heteroscedastic Regression for Nonlinear Modeling of Genetic Network.
J. Bioinform. Comput. Biol., 2003
Inferring gene networks from time series microarray data using dynamic Bayesian networks.
Briefings Bioinform., 2003
Inferring Gene Regulatory Networks from Time-Ordered Gene Expression Data of Bacillus Subtilis Using Differential Equations.
Proceedings of the 8th Pacific Symposium on Biocomputing, 2003
Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection.
Proceedings of the European Conference on Computational Biology (ECCB 2003), 2003
Dynamic Bayesian Network and Nonparametric Regression for Nonlinear Modeling of Gene Networks from Time Series Gene Expression Data.
Proceedings of the Computational Methods in Systems Biology, First International Workshop, 2003
2002
Statistical analysis of a small set of time-ordered gene expression data using linear splines.
Bioinform., 2002
Estimation of Genetic Networks and Functional Structures Between Genes by Using Bayesian Networks and Nonparametric Regression.
Proceedings of the 7th Pacific Symposium on Biocomputing, 2002
Inferring Gene Regulatory Networks from Time-Ordered Gene Expression Data Using Differential Equations.
Proceedings of the Discovery Science, 5th International Conference, 2002