Sun Kim
Orcid: 0000-0001-5385-9546
According to our database1,
Sun Kim
authored at least 172 papers
between 1994 and 2024.
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Bibliography
2024
J. Comput. Biol., 2024
Proceedings of the Second Tiny Papers Track at ICLR 2024, 2024
Proceedings of the 2024 Conference on Empirical Methods in Natural Language Processing: EMNLP 2024, 2024
Improving Out-of-Distribution Generalization in Graphs via Hierarchical Semantic Environments.
Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, 2024
Proceedings of the Thirty-Eighth AAAI Conference on Artificial Intelligence, 2024
2023
GOAT: Gene-level biomarker discovery from multi-Omics data using graph ATtention neural network for eosinophilic asthma subtype.
Bioinform., October, 2023
A model-agnostic framework to enhance knowledge graph-based drug combination prediction with drug-drug interaction data and supervised contrastive learning.
Briefings Bioinform., September, 2023
Metheor: Ultrafast DNA methylation heterogeneity calculation from bisulfite read alignments.
PLoS Comput. Biol., March, 2023
Improved drug response prediction by drug target data integration via network-based profiling.
Briefings Bioinform., March, 2023
Deep learning-based survival prediction using DNA methylation-derived 3D genomic information.
Proceedings of the 14th ACM International Conference on Bioinformatics, 2023
Clinical Note Owns its Hierarchy: Multi-Level Hypergraph Neural Networks for Patient-Level Representation Learning.
Proceedings of the 61st Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers), 2023
2022
MLDEG: A Machine Learning Approach to Identify Differentially Expressed Genes Using Network Property and Network Propagation.
IEEE ACM Trans. Comput. Biol. Bioinform., 2022
J. Chem. Inf. Model., 2022
AutoCoV: tracking the early spread of COVID-19 in terms of the spatial and temporal patterns from embedding space by K-mer based deep learning.
BMC Bioinform., 2022
Embedding of FDA Approved Drugs in Chemical Space Using Cascade Autoencoder with Metric Learning.
Proceedings of the IEEE International Conference on Big Data and Smart Computing, 2022
Sparse Structure Learning via Graph Neural Networks for Inductive Document Classification.
Proceedings of the Thirty-Sixth AAAI Conference on Artificial Intelligence, 2022
2021
Ranked k-Spectrum Kernel for Comparative and Evolutionary Comparison of Exons, Introns, and CpG Islands.
IEEE ACM Trans. Comput. Biol. Bioinform., 2021
BioVLAB-Cancer-Pharmacogenomics: tumor heterogeneity and pharmacogenomics analysis of multi-omics data from tumor on the cloud.
Bioinform., 2021
mirTime: identifying condition-specific targets of microRNA in time-series transcript data using Gaussian process model and spherical vector clustering.
Bioinform., 2021
Erratum to: Machine learning-based analysis of multi-omics data on the cloud for investigating gene regulations.
Briefings Bioinform., 2021
Machine learning-based analysis of multi-omics data on the cloud for investigating gene regulations.
Briefings Bioinform., 2021
Towards multi-omics characterization of tumor heterogeneity: a comprehensive review of statistical and machine learning approaches.
Briefings Bioinform., 2021
IDEA: Integrating Divisive and Ensemble-Agglomerate hierarchical clustering framework for arbitrary shape data.
Proceedings of the 2021 IEEE International Conference on Big Data (Big Data), 2021
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2021
Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021
2020
Deep learning with sentence embeddings pre-trained on biomedical corpora improves the performance of finding similar sentences in electronic medical records.
BMC Medical Informatics Decis. Mak., April, 2020
BioConceptVec: Creating and evaluating literature-based biomedical concept embeddings on a large scale.
PLoS Comput. Biol., 2020
J. Am. Medical Informatics Assoc., 2020
Bioinform., 2020
Comprehensive and critical evaluation of individualized pathway activity measurement tools on pan-cancer data.
Briefings Bioinform., 2020
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2020
2019
Nucleic Acids Res., 2019
A secure SNP panel scheme using homomorphically encrypted K-mers without SNP calling on the user side.
BMC Genom., 2019
Venn-diaNet : venn diagram based network propagation analysis framework for comparing multiple biological experiments.
BMC Bioinform., 2019
HTRgene: a computational method to perform the integrated analysis of multiple heterogeneous time-series data: case analysis of cold and heat stress response signaling genes in Arabidopsis.
BMC Bioinform., 2019
Bioinform., 2019
CaPSSA: visual evaluation of cancer biomarker genes for patient stratification and survival analysis using mutation and expression data.
Bioinform., 2019
Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine.
Database J. Biol. Databases Curation, 2019
Proceedings of the IEEE International Conference on Big Data and Smart Computing, 2019
Proceedings of the 10th ACM International Conference on Bioinformatics, 2019
2018
Editorial for Selected Papers of a Joint Conferences, Genome Informatics Workshop/International Conference on Bioinformatics (GIW/InCoB) 2015.
IEEE ACM Trans. Comput. Biol. Bioinform., 2018
Am. Math. Mon., 2018
Nucleic Acids Res., 2018
J. Bioinform. Comput. Biol., 2018
The mRNA and miRNA transcriptomic landscape of Panax ginseng under the high ambient temperature.
BMC Syst. Biol., 2018
BMC Bioinform., 2018
BRCA-Pathway: a structural integration and visualization system of TCGA breast cancer data on KEGG pathways.
BMC Bioinform., 2018
DeepFam: deep learning based alignment-free method for protein family modeling and prediction.
Bioinform., 2018
A Fast Deep Learning Model for Textual Relevance in Biomedical Information Retrieval.
Proceedings of the 2018 World Wide Web Conference on World Wide Web, 2018
Hybrid Approach of Relation Network and Localized Graph Convolutional Filtering for Breast Cancer Subtype Classification.
Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, 2018
Identifying stress-related genes and predicting stress types in Arabidopsis using logical correlation layer and CMCL loss through time-series data.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018
HTRgene: Integrating Multiple Heterogeneous Time-series Data to Investigate Cold and Heat Stress Response Signaling Genes in Arabidopsis.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018
Proceedings of the 2018 ACM International Conference on Bioinformatics, 2018
2017
Bridging the gap: Incorporating a semantic similarity measure for effectively mapping PubMed queries to documents.
J. Biomed. Informatics, 2017
Iterative segmented least square method for functional microRNA-mRNA module discovery in breast cancer.
Int. J. Data Min. Bioinform., 2017
PINTnet: construction of condition-specific pathway interaction network by computing shortest paths on weighted PPI.
BMC Syst. Biol., 2017
TimesVector: a vectorized clustering approach to the analysis of time series transcriptome data from multiple phenotypes.
Bioinform., 2017
The BioC-BioGRID corpus: full text articles annotated for curation of protein-protein and genetic interactions.
Database J. Biol. Databases Curation, 2017
Deep Learning for Biomedical Information Retrieval: Learning Textual Relevance from Click Logs.
Proceedings of the BioNLP 2017, Vancouver, Canada, August 4, 2017, 2017
BioCreative VI Precision Medicine Track: creating a training corpus for mining protein-protein interactions affected by mutations.
Proceedings of the BioNLP 2017, Vancouver, Canada, August 4, 2017, 2017
Flow maximization analysis of cell cycle pathway activation status in breast cancer subtypes.
Proceedings of the 2017 IEEE International Conference on Big Data and Smart Computing, 2017
Integration of heterogeneous time series gene expression data by clustering on time dimension.
Proceedings of the 2017 IEEE International Conference on Big Data and Smart Computing, 2017
2016
Information theoretic sub-network mining characterizes breast cancer subtypes in terms of cancer core mechanisms.
J. Bioinform. Comput. Biol., 2016
CoRR, 2016
Clustering and evolutionary analysis of small RNAs identify regulatory siRNA clusters induced under drought stress in rice.
BMC Syst. Biol., 2016
Subtype-specific CpG island shore methylation and mutation patterns in 30 breast cancer cell lines.
BMC Syst. Biol., 2016
BMC Genom., 2016
Prioritizing biological pathways by recognizing context in time-series gene expression data.
BMC Bioinform., 2016
<i>Meshable</i>: searching PubMed abstracts by utilizing MeSH and MeSH-derived topical terms.
Bioinform., 2016
Influence maximization in time bounded network identifies transcription factors regulating perturbed pathways.
Bioinform., 2016
Database J. Biol. Databases Curation, 2016
BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID.
Database J. Biol. Databases Curation, 2016
Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016
Proceedings of the 15th Workshop on Biomedical Natural Language Processing, 2016
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016
2015
Extracting drug-drug interactions from literature using a rich feature-based linear kernel approach.
J. Biomed. Informatics, 2015
BMC Bioinform., 2015
BioVLAB-MMIA-NGS: microRNA-mRNA integrated analysis using high-throughput sequencing data.
Bioinform., 2015
Proceedings of the 2015 Conference on Empirical Methods in Natural Language Processing, 2015
2014
J. Comb. Theory A, 2014
Assisting manual literature curation for protein-protein interactions using BioQRator.
Database J. Biol. Databases Curation, 2014
An algorithm for identifying differentially expressed genes in multiclass RNA-seq samples.
Proceedings of the International Conference on Big Data and Smart Computing, BIGCOMP 2014, 2014
2013
The Rogers-Ramanujan-Gordon identities, the generalized Göllnitz-Gordon identities, and parity questions.
J. Comb. Theory A, 2013
Genome-Wide Analysis and Modeling of DNA methylation susceptibility in 30 Breast Cancer Cell Lines by using CPG Flanking Sequences.
J. Bioinform. Comput. Biol., 2013
Designing discriminative spatial filter vectors in motor imagery brain-computer interface.
Int. J. Imaging Syst. Technol., 2013
Health Inf. Sci. Syst., 2013
Bioinform., 2013
Towards simultaneous clustering and motif-modeling for a large number of protein family.
Proceedings of the 2013 IEEE International Conference on Bioinformatics and Biomedicine, 2013
2012
A novel k-mer mixture logistic regression for methylation susceptibility modeling of CpG dinucleotides in human gene promoters.
BMC Bioinform., 2012
J. Biomed. Semant., 2012
GeneclusterViz: a tool for conserved gene cluster visualization, exploration and analysis.
Bioinform., 2012
PIE <i>the search</i>: searching PubMed literature for protein interaction information.
Bioinform., 2012
Prioritizing PubMed articles for the Comparative Toxicogenomic Database utilizing semantic information.
Database J. Biol. Databases Curation, 2012
Proceedings of the IEEE International Conference on Systems, Man, and Cybernetics, 2012
Classifying Gene Sentences in Biomedical Literature by Combining High-Precision Gene Identifiers.
Proceedings of the 2012 Workshop on Biomedical Natural Language Processing, 2012
2011
Sequence-Based enzyme catalytic Domain Prediction Using Clustering and Aggregated Mutual Information Content.
J. Bioinform. Comput. Biol., 2011
The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text.
BMC Bioinform., 2011
BMC Bioinform., 2011
Proceedings of the 2011 TeraGrid Conference - Extreme Digital Discovery, 2011
Proceedings of the 10th International Conference on Machine Learning and Applications and Workshops, 2011
BioVLAB-MMIA: A Reconfigurable Cloud Computing Environment for microRNA and mRNA Integrated Analysis.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2011
2010
Bioinform., 2010
Artif. Intell. Medicine, 2010
Gene cluster profile vectors: A novel method to infer functional coupling using both gene proximity and co-occurrence profiles.
Proceedings of the 2010 IEEE International Conference on Bioinformatics and Biomedicine, 2010
EGGSlicer: predicting biologically meaningful gene sets from gene clusters using gene ontology information.
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, 2010
2009
MicroRNA and mRNA integrated analysis (MMIA): a web tool for examining biological functions of microRNA expression.
Nucleic Acids Res., 2009
J. Comb. Theory A, 2009
Ensembled support vector machines for human papillomavirus risk type prediction from protein secondary structures.
Comput. Biol. Medicine, 2009
Computational analysis of microRNA profiles and their target genes suggests significant involvement in breast cancer antiestrogen resistance.
Bioinform., 2009
Proceedings of the 27th Annual International Conference on Design of Communication, 2009
Evolutionary hypernetwork classifiers for protein-proteininteraction sentence filtering.
Proceedings of the Genetic and Evolutionary Computation Conference, 2009
Evolving hypernetwork models of binary time series for forecasting price movements on stock markets.
Proceedings of the IEEE Congress on Evolutionary Computation, 2009
2008
Nucleic Acids Res., 2008
BMC Bioinform., 2008
BMC Bioinform., 2008
Enriched transcription factor binding sites in hypermethylated gene promoters in drug resistant cancer cells.
Bioinform., 2008
Bioinform., 2008
Proceedings of the Biocomputing 2008, 2008
Proceedings of the Fourth International Conference on e-Science, 2008
2007
A Study of Residue Correlation within Protein Sequences and Its Application to Sequence Classification.
EURASIP J. Bioinform. Syst. Biol., 2007
dPattern: transcription factor binding site (TFBS) discovery in human genome using a discriminative pattern analysis.
Bioinform., 2007
Proceedings of the Sixth International Conference on Machine Learning and Applications, 2007
Proceedings of the IEEE Congress on Evolutionary Computation, 2007
EGGS: Extraction of Gene Clusters Using Genome Context Based Sequence Matching Techniques.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2007
Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, 2007
Proceedings of the Analysis of Biological Data: A Soft Computing Approach, 2007
2006
Int. J. Data Min. Bioinform., 2006
EURASIP J. Adv. Signal Process., 2006
REFINEMENT: A search framework for the identification of interferon-responsive elements in DNA sequences - a case study with ISRE and GAS.
Comput. Biol. Chem., 2006
Bioinform., 2006
A mixture model-based discriminate analysis for identifying ordered transcription factor binding site pairs in gene promoters directly regulated by estrogen receptor-alpha.
Bioinform., 2006
Bioinform., 2006
An Approximate de Bruijn Graph Approach to Multiple Local Alignment and Motif Discovery in Protein Sequences.
Proceedings of the Data Mining and Bioinformatics, First International Workshop, 2006
A Tree Kernel-Based Method for Protein-Protein Interaction Mining from Biomedical Literature.
Proceedings of the Knowledge Discovery in Life Science Literature, 2006
Proceedings of the Advances in Neural Networks - ISNN 2006, Third International Symposium on Neural Networks, Chengdu, China, May 28, 2006
Proceedings of the Workshops Proceedings of the 6th IEEE International Conference on Data Mining (ICDM 2006), 2006
Human Papillomavirus Risk Type Classification from Protein Sequences Using Support Vector Machines.
Proceedings of the Applications of Evolutionary Computing, 2006
Proceedings of the IEEE International Conference on Evolutionary Computation, 2006
2005
GAME: A simple and efficient whole genome alignment method using maximal exact match filtering.
Comput. Biol. Chem., 2005
Proceedings of the 5th international workshop on Bioinformatics, 2005
An Application of Support Vector Machines for Customer Churn Analysis: Credit Card Case.
Proceedings of the Advances in Natural Computation, First International Conference, 2005
Proceedings of the Data Integration in the Life Sciences, Second InternationalWorkshop, 2005
Proceedings of the Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference Workshops & Poster Abstracts, 2005
Proceedings of the Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference, 2005
Proceedings of the Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference Workshops & Poster Abstracts, 2005
2004
Proceedings of the 2004 ACM Symposium on Applied Computing (SAC), 2004
Proceedings of the Comparative Genomics, 2004
Multi-objective Evolutionary Probe Design Based on Thermodynamic Criteria for HPV Detection.
Proceedings of the PRICAI 2004: Trends in Artificial Intelligence, 2004
2003
Appl. Intell., 2003
Motif Discovery from Large Number of Sequences: A Case Study with Disease Resistance Genes in Arabidopsos thaliana.
Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Scienes, 2003
Graph Theoretic Sequence Clustering Algorithms and Their Applications to Genome Comparison.
Proceedings of the Computational Biology and Genome Informatics, 2003
2001
Proceedings of the ACM SIGKDD Workshop on Data Mining in Bioinformatics (BIOKDD 2001), 2001
Proceedings of the 2001 Congress on Evolutionary Computation, 2001
2000
Proceedings of the International Workshop on Text and Web Mining, 2000
1999
ACM J. Exp. Algorithmics, 1999
J. Comput. Biol., 1999
1994
Proceedings of the 12th National Conference on Artificial Intelligence, Seattle, WA, USA, July 31, 1994