Seiya Imoto

According to our database1, Seiya Imoto authored at least 123 papers between 2002 and 2023.

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Bibliography

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

Imputing time-series microbiome abundance profiles with diffusion model.
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

Identification of bacteriophage genome sequences with representation learning.
Bioinform., 2022

2021
HEAL: an automated deep learning framework for cancer histopathology image analysis.
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

On the application of BERT models for nanopore methylation detection.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2021

Discovering microbe functionality in human disease with a gene-ontology-aware model.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2021

2020
Nanopore basecalling from a perspective of instance segmentation.
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
Robust Sample-Specific Stability Selection with Effective Error Control.
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

A Bayesian model integration for mutation calling through data partitioning.
Bioinform., 2019

Accurate and Flexible Bayesian Mutation Call from Multi-regional Tumor Samples.
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

Binary contingency table method for analysing gene mutation in cancer genome.
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

OVarCall: Bayesian Mutation Calling Method Utilizing Overlapping Paired-End Reads.
Proceedings of the Bioinformatics Research and Applications - 12th International Symposium, 2016

2015
Sparse Overlapping Group Lasso for Integrative Multi-Omics Analysis.
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

Binary Contingency Table Method for Analyzing Gene Mutation in Cancer Genome.
Proceedings of the Bioinformatics Research and Applications - 11th International Symposium, 2015

2014
A feature selection method using improved regularized linear discriminant analysis.
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

Parameter estimation in multi-compartment SIR model.
Proceedings of the 17th International Conference on Information Fusion, 2014

2013
Principal component analysis using QR decomposition.
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

Multilayer Cluster Heat Map Visualizing Biological Tensor Data.
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
A Top-r Feature Selection Algorithm for Microarray Gene Expression Data.
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

Connection between traditional medicine and disease.
SIGHIT Rec., 2012

Null space based feature selection method for gene expression data.
Int. J. Mach. Learn. Cybern., 2012

A between-Class Overlapping Filter-Based Method for transcriptome Data Analysis.
J. Bioinform. Comput. Biol., 2012

Computational gene network analysis reveals TNF-induced angiogenesis.
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

Statistical model-based testing to evaluate the recurrence of genomic aberrations.
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

Clustering for Visual Analogue Scale Data in Symbolic Data Analysis.
Proceedings of the Complex Adaptive Systems 2011 Conference, 2011

Estimating exogenous variables in data with more variables than observations.
Neural Networks, 2011

Parallel Algorithm for Learning Optimal Bayesian Network Structure.
J. Mach. Learn. Res., 2011

Transform of visual analogue scale data and their clustering.
Int. J. Knowl. Eng. Soft Data Paradigms, 2011

SiGN-SSM: open source parallel software for estimating gene networks with state space models.
Bioinform., 2011

Comprehensive Pharmacogenomic Pathway Screening by Data Assimilation.
Proceedings of the Bioinformatics Research and Applications - 7th International Symposium, 2011

Poster: Comprehensive pharmacogenomic pathway screening by data assimilation.
Proceedings of the IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, 2011

Estimation of macroscopic parameter in agent-based pandemic simulation.
Proceedings of the 14th International Conference on Information Fusion, 2011

Parallel Agent-Based Simulator for Influenza Pandemic.
Proceedings of the Advanced Agent Technology, 2011

Computational Drug Target Pathway Discovery: A Bayesian Network Approach.
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

Discovery of Exogenous Variables in Data with More Variables Than Observations.
Proceedings of the Artificial Neural Networks - ICANN 2010, 2010

Network profiling analysis for generating modulator-dependent gene networks.
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

Identifying Hidden Confounders in Gene Networks by Bayesian Networks.
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

Gene set-based module discovery in the breast cancer transcriptome.
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

Gene Networks Viewed through Two Models.
Proceedings of the Bioinformatics and Computational Biology, 2009

2008
ExonMiner: Web service for analysis of GeneChip Exon array data.
BMC Bioinform., 2008

Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells.
BMC Bioinform., 2008

Bayesian learning of biological pathways on genomic data assimilation.
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

DIGDAG, a First Algorithm to Mine Closed Frequent Embedded Sub-DAGs.
Proceedings of the Mining and Learning with Graphs, 2007

Statistical Absolute Evaluation of Gene Ontology Terms with Gene Expression Data.
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

A Penalized Likelihood Estimation on Transcriptional Module-Based Clustering.
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

Finding Optimal Models for Small Gene Networks.
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

Functional Data Analysis of the Dynamics of Gene Regulatory Networks.
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
Use of Gene Networks for Identifying and Validating Drug Targets.
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


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