Sun Kim

ORCID

Publication Activity (10 Years)

Years Active: 1994-2024
Publications (10 Years): 89

Top Venues

Publications

Magsarjav Bataa, Siwoo Song, Kunsoo Park, Miran Kim, Jung Hee Cheon, Sun Kim
Finding Highly Similar Regions of Genomic Sequences Through Homomorphic Encryption. J. Comput. Biol. 31 (3) (2024)
Danyeong Lee, Dohoon Lee, Dongmin Bang, Sun Kim
DiSCO: Diffusion Schrödinger Bridge for Molecular Conformer Optimization. AAAI (2024)
Hwiyeol Jo, Taiwoo Park, Nayoung Choi, Changbong Kim, Ohjoon Kwon, Donghyeon Jeon, Hyunwoo Lee, Eui-Hyeon Lee, Kyoungho Shin, Sun Suk Lim, Kyungmi Kim, Jihye Lee, Sun Kim
Taxonomy and Analysis of Sensitive User Queries in Generative AI Search. CoRR (2024)
Yinhua Piao, Sangseon Lee, Yijingxiu Lu, Sun Kim
Improving out-of-distribution generalization in graphs via hierarchical semantic environments. CoRR (2024)
Ohjoon Kwon, Donghyeon Jeon, Nayoung Choi, Gyu-Hwung Cho, Changbong Kim, Hyunwoo Lee, Inho Kang, Sun Kim, Taiwoo Park
SLM as Guardian: Pioneering AI Safety with Small Language Models. CoRR (2024)
Yijingxiu Lu, Yinhua Piao, Sun Kim
Enhancing Drug-Drug Interaction Prediction with Context-Aware Architecture. Tiny Papers @ ICLR (2024)
Nayeon Kim, Yinhua Piao, Sun Kim
Clinical Note Owns its Hierarchy: Multi-Level Hypergraph Neural Networks for Patient-Level Representation Learning. ACL (1) (2023)
Dabin Jeong, Bonil Koo, Minsik Oh, Tae-Bum Kim, Sun Kim
GOAT: Gene-level biomarker discovery from multi-Omics data using graph ATtention neural network for eosinophilic asthma subtype. Bioinform. 39 (10) (2023)
Minwoo Pak, Sangseon Lee, Inyoung Sung, Bonil Koo, Sun Kim
Improved drug response prediction by drug target data integration via network-based profiling. Briefings Bioinform. 24 (2) (2023)
Jeewon Yang, Dohoon Lee, Bonil Koo, Dabin Jeong, Sun Kim
Deep learning-based survival prediction using DNA methylation-derived 3D genomic information. BCB (2023)
Jeonghyeon Gu, Dongmin Bang, Jungseob Yi, Sangseon Lee, Dong Kyu Kim, Sun Kim
A model-agnostic framework to enhance knowledge graph-based drug combination prediction with drug-drug interaction data and supervised contrastive learning. Briefings Bioinform. 24 (5) (2023)
Nayeon Kim, Yinhua Piao, Sun Kim
Clinical Note Owns its Hierarchy: Multi-Level Hypergraph Neural Networks for Patient-Level Representation Learning. CoRR (2023)
Dohoon Lee, Bonil Koo, Jeewon Yang, Sun Kim
Metheor: Ultrafast DNA methylation heterogeneity calculation from bisulfite read alignments. PLoS Comput. Biol. 19 (3) (2023)
Jungwoo Kim, Sangsoo Lim, Sangseon Lee, Changyun Cho, Sun Kim
Embedding of FDA Approved Drugs in Chemical Space Using Cascade Autoencoder with Metric Learning. BigComp (2022)
Youngchun Kwon, Sun Kim, Youn-Suk Choi, Seokho Kang
Generative Modeling to Predict Multiple Suitable Conditions for Chemical Reactions. J. Chem. Inf. Model. 62 (23) (2022)
Yinhua Piao, Sangseon Lee, Dohoon Lee, Sun Kim
Sparse Structure Learning via Graph Neural Networks for Inductive Document Classification. AAAI (2022)
Sangseon Lee, Dohoon Lee, Yinhua Piao, Sun Kim
SPGP: Structure Prototype Guided Graph Pooling. CoRR (2022)
Inyoung Sung, Sangseon Lee, Minwoo Pak, Yunyol Shin, Sun Kim
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. (3) (2022)
Ji Hwan Moon, Sangseon Lee, Minwoo Pak, Benjamin Hur, Sun Kim
MLDEG: A Machine Learning Approach to Identify Differentially Expressed Genes Using Network Property and Network Propagation. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (4) (2022)
MinGyu Choi, Wonseok Shin, Yijingxiu Lu, Sun Kim
Triangular Contrastive Learning on Molecular Graphs. CoRR (2022)
Hyejin Kang, Hongryul Ahn, Kyuri Jo, Minsik Oh, Sun Kim
mirTime: identifying condition-specific targets of microRNA in time-series transcript data using Gaussian process model and spherical vector clustering. Bioinform. 37 (11) (2021)
Sungjoon Park, Dohoon Lee, Youngkuk Kim, Sangsoo Lim, Heejoon Chae, Sun Kim
BioVLAB-Cancer-Pharmacogenomics: tumor heterogeneity and pharmacogenomics analysis of multi-omics data from tumor on the cloud. Bioinform. 38 (1) (2021)
Dohoon Lee, Youngjune Park, Sun Kim
Towards multi-omics characterization of tumor heterogeneity: a comprehensive review of statistical and machine learning approaches. Briefings Bioinform. 22 (3) (2021)
Cheng Wang, Sun Kim, Taiwoo Park, Sajal Choudhary, Sunghyun Park, Young-Bum Kim, Ruhi Sarikaya, Sungjin Lee
Handling Long-Tail Queries with Slice-Aware Conversational Systems. CoRR (2021)
Hongryul Ahn, Inuk Jung, Heejoon Chae, Minsik Oh, Inyoung Kim, Sun Kim
IDEA: Integrating Divisive and Ensemble-Agglomerate hierarchical clustering framework for arbitrary shape data. IEEE BigData (2021)
Sangseon Lee, Taeheon Lee, Yung-Kyun Noh, Sun Kim
Ranked k-Spectrum Kernel for Comparative and Evolutionary Comparison of Exons, Introns, and CpG Islands. IEEE ACM Trans. Comput. Biol. Bioinform. 18 (3) (2021)
Sun Kim
A generalization of the modular equations of higher degrees. J. Comb. Theory, Ser. A 180 (2021)
Minsik Oh, Sungjoon Park, Sun Kim, Heejoon Chae
Machine learning-based analysis of multi-omics data on the cloud for investigating gene regulations. Briefings Bioinform. 22 (1) (2021)
Minsik Oh, Sungjoon Park, Sun Kim, Heejoon Chae
Erratum to: Machine learning-based analysis of multi-omics data on the cloud for investigating gene regulations. Briefings Bioinform. 22 (1) (2021)
Yinhua Piao, Sangseon Lee, Dohoon Lee, Sun Kim
Sparse Structure Learning via Graph Neural Networks for Inductive Document Classification. CoRR (2021)
Rezarta Islamaj, Dongseop Kwon, Sun Kim, Zhiyong Lu
TeamTat: A Collaborative Text Annotation Tool for Creating Gold-Standard Corpora. AMIA (2021)
Inyoung Kim, Sangseon Lee, Youngkuk Kim, Hugh Namkoong, Sun Kim
A probabilistic model for pathway-guided gene set selection. BIBM (2021)
Sangseon Lee, Sangsoo Lim, Taeheon Lee, Inyoung Sung, Sun Kim
Cancer subtype classification and modeling by pathway attention and propagation. Bioinform. 36 (12) (2020)
Qingyu Chen, Kyubum Lee, Shankai Yan, Sun Kim, Chih-Hsuan Wei, Zhiyong Lu
BioConceptVec: Creating and evaluating literature-based biomedical concept embeddings on a large scale. PLoS Comput. Biol. 16 (4) (2020)
Magsarjav Bataa, Siwoo Song, Kunsoo Park, Miran Kim, Jung Hee Cheon, Sun Kim
Homomorphic Computation of Local Alignment. BIBM (2020)
Lana Yeganova, Sun Kim, Qingyu Chen, Grigory Balasanov, W. John Wilbur, Zhiyong Lu
Better synonyms for enriching biomedical search. J. Am. Medical Informatics Assoc. 27 (12) (2020)
Sangsoo Lim, Sangseon Lee, Inuk Jung, SungMin Rhee, Sun Kim
Comprehensive and critical evaluation of individualized pathway activity measurement tools on pan-cancer data. Briefings Bioinform. 21 (1) (2020)
Rezarta Islamaj Dogan, Dongseop Kwon, Sun Kim, Zhiyong Lu
TeamTat: a collaborative text annotation tool. Nucleic Acids Res. 48 (Webserver-Issue) (2020)
Rezarta Islamaj Dogan, Dongseop Kwon, Sun Kim, Zhiyong Lu
TeamTat: a collaborative text annotation tool. CoRR (2020)
Qingyu Chen, Jingcheng Du, Sun Kim, W. John Wilbur, Zhiyong Lu
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. (1) (2020)
Qingyu Chen, Jingcheng Du, Sun Kim, W. John Wilbur, Zhiyong Lu
Evaluation of Five Sentence Similarity Models on Electronic Medical Records. BCB (2019)
Hongryul Ahn, Inuk Jung, Heejoon Chae, Dongwon Kang, Woosuk Jung, Sun Kim
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. (16) (2019)
Qingyu Chen, Jingcheng Du, Sun Kim, W. John Wilbur, Zhiyong Lu
Deep learning with sentence embeddings pre-trained on biomedical corpora improves the performance of finding similar sentences in electronic medical records. CoRR (2019)
Rezarta Islamaj Dogan, Sun Kim, Andrew Chatr-aryamontri, Chih-Hsuan Wei, Donald C. Comeau, Rui Antunes, Sérgio Matos, Qingyu Chen, Aparna Elangovan, Nagesh C. Panyam, Karin Verspoor, Hongfang Liu, Yanshan Wang, Zhuang Liu, Berna Altinel, Zehra Melce Hüsünbeyi, Arzucan Özgür, Aris Fergadis, Chen-Kai Wang, Hong-Jie Dai, Tung Tran, Ramakanth Kavuluru, Ling Luo, Albert Steppi, Jinfeng Zhang, Jinchan Qu, Zhiyong Lu
Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine. Database J. Biol. Databases Curation 2019 (2019)
Yeongjun Jang, Jihae Seo, Insu Jang, Byungwook Lee, Sun Kim, Sanghyuk Lee
CaPSSA: visual evaluation of cancer biomarker genes for patient stratification and survival analysis using mutation and expression data. Bioinform. 35 (24) (2019)
Qingyu Chen, Kyubum Lee, Shankai Yan, Sun Kim, Chih-Hsuan Wei, Zhiyong Lu
BioConceptVec: creating and evaluating literature-based biomedical concept embeddings on a large scale. CoRR (2019)
Alexis Allot, Qingyu Chen, Sun Kim, Roberto Vera Alvarez, Donald C. Comeau, W. John Wilbur, Zhiyong Lu
LitSense: making sense of biomedical literature at sentence level. Nucleic Acids Res. 47 (Webserver-Issue) (2019)
Benjamin Hur, Dongwon Kang, Sangseon Lee, Ji Hwan Moon, Gung Lee, Sun Kim
Venn-diaNet : venn diagram based network propagation analysis framework for comparing multiple biological experiments. BMC Bioinform. (23) (2019)
Sungjoon Park, Minsu Kim, Seokjun Seo, Seungwan Hong, Kyoohyung Han, Keewoo Lee, Jung Hee Cheon, Sun Kim
A secure SNP panel scheme using homomorphically encrypted K-mers without SNP calling on the user side. BMC Genom. 20 (S2) (2019)
Do-Hoon Lee, Sangseon Lee, Sun Kim
PRISM: methylation pattern-based, reference-free inference of subclonal makeup. Bioinform. 35 (14) (2019)
Hongryul Ahn, Seunghyun Son, Sun Kim
DeepFunNet: Deep Learning for Gene Functional Similarity Network Construction. BigComp (2019)
Bruce C. Berndt, Sun Kim, Alexandru Zaharescu
The Circle Problem of Gauss and the Divisor Problem of Dirichlet - Still Unsolved. Am. Math. Mon. 125 (2) (2018)
Qingyu Chen, Sun Kim, W. John Wilbur, Zhiyong Lu
Sentence Similarity Measures Revisited: Ranking Sentences in PubMed Documents. BCB (2018)
Joungmin Choi, Yoonjae Park, Sun Kim, Heejoon Chae
Cloud-BS: A MapReduce-based bisulfite sequencing aligner on cloud. J. Bioinform. Comput. Biol. 16 (6) (2018)
Dongseop Kwon, Sun Kim, Chih-Hsuan Wei, Robert Leaman, Zhiyong Lu
ezTag: tagging biomedical concepts via interactive learning. Nucleic Acids Res. 46 (Webserver-Issue) (2018)
Seokjun Seo, Minsik Oh, Youngjune Park, Sun Kim
DeepFam: deep learning based alignment-free method for protein family modeling and prediction. Bioinform. 34 (13) (2018)
Inyoung Kim, Saemi Choi, Sun Kim
BRCA-Pathway: a structural integration and visualization system of TCGA breast cancer data on KEGG pathways. BMC Bioinform. (1) (2018)
Lana Yeganova, Sun Kim, Grigory Balasanov, W. John Wilbur
Discovering themes in biomedical literature using a projection-based algorithm. BMC Bioinform. 19 (1) (2018)
Hongryul Ahn, Inuk Jung, Heejoon Chae, Dongwon Kang, Woosuk Jung, Sun Kim
HTRgene: Integrating Multiple Heterogeneous Time-series Data to Investigate Cold and Heat Stress Response Signaling Genes in Arabidopsis. BIBM (2018)
Sunil Mohan, Nicolas Fiorini, Sun Kim, Zhiyong Lu
A Fast Deep Learning Model for Textual Relevance in Biomedical Information Retrieval. CoRR (2018)
Sun Kim
Editorial for Selected Papers of a Joint Conferences, Genome Informatics Workshop/International Conference on Bioinformatics (GIW/InCoB) 2015. IEEE ACM Trans. Comput. Biol. Bioinform. 15 (6) (2018)
Inuk Jung, Hyejin Kang, Jang Uk Kim, Hyeonsook Chang, Sun Kim, Woosuk Jung
The mRNA and miRNA transcriptomic landscape of Panax ginseng under the high ambient temperature. BMC Syst. Biol. 12 (S-2) (2018)
SungMin Rhee, Seokjun Seo, Sun Kim
Hybrid Approach of Relation Network and Localized Graph Convolutional Filtering for Breast Cancer Subtype Classification. IJCAI (2018)
Sunil Mohan, Nicolas Fiorini, Sun Kim, Zhiyong Lu
A Fast Deep Learning Model for Textual Relevance in Biomedical Information Retrieval. WWW (2018)
Dongwon Kang, Hongryul Ahn, Sangseon Lee, Chai-Jin Lee, Jihye Hur, Woosuk Jung, Sun Kim
Identifying stress-related genes and predicting stress types in Arabidopsis using logical correlation layer and CMCL loss through time-series data. BIBM (2018)
Rezarta Islamaj Dogan, Sun Kim, Andrew Chatr-aryamontri, Christie S. Chang, Rose Oughtred, Jennifer M. Rust, W. John Wilbur, Donald C. Comeau, Kara Dolinski, Mike Tyers
The BioC-BioGRID corpus: full text articles annotated for curation of protein-protein and genetic interactions. Database J. Biol. Databases Curation 2017 (2017)
Hongryul Ahn, Heejoon Chae, Woosuk Jung, Sun Kim
Integration of heterogeneous time series gene expression data by clustering on time dimension. BigComp (2017)
SungMin Rhee, Sangsoo Lim, Sun Kim
Iterative segmented least square method for functional microRNA-mRNA module discovery in breast cancer. Int. J. Data Min. Bioinform. 17 (1) (2017)
Sangseon Lee, Ji Hwan Moon, Youngjune Park, Sun Kim
Flow maximization analysis of cell cycle pathway activation status in breast cancer subtypes. BigComp (2017)
Sunil Mohan, Nicolas Fiorini, Sun Kim, Zhiyong Lu
Deep Learning for Biomedical Information Retrieval: Learning Textual Relevance from Click Logs. BioNLP (2017)
Ji Hwan Moon, Sangsoo Lim, Kyuri Jo, Sangseon Lee, Seokjun Seo, Sun Kim
PINTnet: construction of condition-specific pathway interaction network by computing shortest paths on weighted PPI. BMC Syst. Biol. 11 (S-2) (2017)
Rezarta Islamaj Dogan, Andrew Chatr-aryamontri, Sun Kim, Chih-Hsuan Wei, Yifan Peng, Donald C. Comeau, Zhiyong Lu
BioCreative VI Precision Medicine Track: creating a training corpus for mining protein-protein interactions affected by mutations. BioNLP (2017)
SungMin Rhee, Seokjun Seo, Sun Kim
Hybrid Approach of Relation Network and Localized Graph Convolutional Filtering for Breast Cancer Subtype Classification. CoRR (2017)
Inuk Jung, Kyuri Jo, Hyejin Kang, Hongryul Ahn, Youngjae Yu, Sun Kim
TimesVector: a vectorized clustering approach to the analysis of time series transcriptome data from multiple phenotypes. Bioinform. 33 (23) (2017)
Sun Kim, Nicolas Fiorini, W. John Wilbur, Zhiyong Lu
Bridging the gap: Incorporating a semantic similarity measure for effectively mapping PubMed queries to documents. J. Biomed. Informatics 75 (2017)
Jinwoo Park, Benjamin Hur, SungMin Rhee, Sangsoo Lim, Min-Su Kim, Kwangsoo Kim, Wonshik Han, Sun Kim
Information theoretic sub-network mining characterizes breast cancer subtypes in terms of cancer core mechanisms. J. Bioinform. Comput. Biol. 14 (5) (2016)
Sun Kim, Lana Yeganova, W. John Wilbur
: searching PubMed abstracts by utilizing MeSH and MeSH-derived topical terms. Bioinform. 32 (19) (2016)
Donald C. Comeau, Rezarta Islamaj Dogan, Sun Kim, Chih-Hsuan Wei, W. John Wilbur, Zhiyong Lu
BioCconvert: A Conversion Tool Between BioC and PubAnnotation. ICBO/BioCreative (2016)
SungMin Rhee, Sangsoo Lim, Sun Kim
Iterative segmented least square method for functional microRNA-mRNA module discovery in breast cancer. BIBM (2016)
Heejoon Chae, Sangseon Lee, Kenneth P. Nephew, Sun Kim
Subtype-specific CpG island shore methylation and mutation patterns in 30 breast cancer cell lines. BMC Syst. Biol. 10 (4) (2016)
Sun Kim, W. John Wilbur, Zhiyong Lu
Bridging the Gap: a Semantic Similarity Measure between Queries and Documents. CoRR (2016)
Soo-Yong Shin, Sun Kim, W. John Wilbur, Dongseop Kwon
BioC viewer: a web-based tool for displaying and merging annotations in BioC. Database J. Biol. Databases Curation 2016 (2016)
Lana Yeganova, Won Kim, Sun Kim, Rezarta Islamaj Dogan, Wanli Liu, Donald C. Comeau, Zhiyong Lu, W. John Wilbur
PubTermVariants: biomedical term variants and their use for PubMed search. BioNLP@ACL (2016)
Jusang Lee, Kyuri Jo, Sunwon Lee, Jaewoo Kang, Sun Kim
Prioritizing biological pathways by recognizing context in time-series gene expression data. BMC Bioinform. 17 (S-17) (2016)
Sun Kim, Rezarta Islamaj Dogan, Andrew Chatr-aryamontri, Christie S. Chang, Rose Oughtred, Jennifer M. Rust, Riza Batista-Navarro, Jacob Carter, Sophia Ananiadou, Sérgio Matos, André Santos, David Campos, José Luís Oliveira, Onkar Singh, Jitendra Jonnagaddala, Hong-Jie Dai, Emily Chia-Yu Su, Yung-Chun Chang, Yu-Chen Su, Chun-Han Chu, Chien Chin Chen, Wen-Lian Hsu, Yifan Peng, Cecilia N. Arighi, Cathy H. Wu, K. Vijay-Shanker, Ferhat Aydin, Zehra Melce Hüsünbeyi, Arzucan Özgür, Soo-Yong Shin, Dongseop Kwon, Kara Dolinski, Mike Tyers, W. John Wilbur, Donald C. Comeau
BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID. Database J. Biol. Databases Curation 2016 (2016)
Kyuri Jo, Inuk Jung, Ji Hwan Moon, Sun Kim
Influence maximization in time bounded network identifies transcription factors regulating perturbed pathways. Bioinform. 32 (12) (2016)
Min-Su Kim, Benjamin Hur, Sun Kim
RDDpred: a condition-specific RNA-editing prediction model from RNA-seq data. BMC Genom. 17 (S-1) (2016)
Inuk Jung, Hongryul Ahn, Seon-Ju Shin, Jukon Kim, Hawk-Bin Kwon, Woosuk Jung, Sun Kim
Clustering and evolutionary analysis of small RNAs identify regulatory siRNA clusters induced under drought stress in rice. BMC Syst. Biol. 10 (4) (2016)
Sun Kim
Networks and models for the integrated analysis of multi omics data. BIBM (2016)
Sun Kim, Zhiyong Lu, W. John Wilbur
Identifying named entities from PubMed®; for enriching semantic categories. BMC Bioinform. 16 (2015)
Sun Kim, Lana Yeganova, W. John Wilbur
Summarizing Topical Contents from PubMed Documents Using a Thematic Analysis. EMNLP (2015)
Heejoon Chae, SungMin Rhee, Kenneth P. Nephew, Sun Kim
BioVLAB-MMIA-NGS: microRNA-mRNA integrated analysis using high-throughput sequencing data. Bioinform. 31 (2) (2015)
Sun Kim, Haibin Liu, Lana Yeganova, W. John Wilbur
Extracting drug-drug interactions from literature using a rich feature-based linear kernel approach. J. Biomed. Informatics 55 (2015)
Bruce C. Berndt, Sun Kim, Alexandru Zaharescu
Weighted divisor sums and Bessel function series, V. J. Approx. Theory 197 (2015)
Dongseop Kwon, Sun Kim, Soo-Yong Shin, Andrew Chatr-aryamontri, W. John Wilbur
Assisting manual literature curation for protein-protein interactions using BioQRator. Database J. Biol. Databases Curation 2014 (2014)
Inuk Jung, Jong Chan Park, Sun Kim
piClust: A density based piRNA clustering algorithm. Comput. Biol. Chem. 50 (2014)
Jaehyun An, Kwangsoo Kim, Sun Kim
An algorithm for identifying differentially expressed genes in multiclass RNA-seq samples. BigComp (2014)
Lana Yeganova, Won Kim, Sun Kim, W. John Wilbur
Retro: concept-based clustering of biomedical topical sets. Bioinform. 30 (22) (2014)
Wanli Liu, Rezarta Islamaj Dogan, Sun Kim, Donald C. Comeau, Won Kim, Lana Yeganova, Zhiyong Lu, W. John Wilbur
Author name disambiguation for PubMed. J. Assoc. Inf. Sci. Technol. 65 (4) (2014)
Sun Kim, Haibin Liu, Lana Yeganova, W. John Wilbur
Extracting drug-drug interactions from literature using a rich feature-based linear kernel approach. AMIA (2014)

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Publication Activity (10 Years)

Top Topics

Top Venues

Sun Kim