Byung-Jun Yoon

ORCID

Publication Activity (10 Years)

Years Active: 2003-2024
Publications (10 Years): 63

Top Venues

Publications

Siyuan Xu, Yucheng Wang, Mingzhou Fan, Byung-Jun Yoon, Xiaoning Qian
Uncertainty-aware Continuous Implicit Neural Representations for Remote Sensing Object Counting. AISTATS (2024)
Xihaier Luo, Seyednami Niyakan, Patrick R. Johnstone, Sean McCorkle, Gilchan Park, Vanessa López-Marrero, Shinjae Yoo, Edward R. Dougherty, Xiaoning Qian, Francis J. Alexander, Shantenu Jha, Byung-Jun Yoon
Pathway-based analyses of gene expression profiles at low doses of ionizing radiation. Frontiers Bioinform. 4 (2024)
Pei-Hung Chung, Shuhan He, Norawit Kijpaisalratana, Abdel-badih el Ariss, Byung-Jun Yoon
Neural machine translation of clinical procedure codes for medical diagnosis and uncertainty quantification. CoRR (2024)
Alif Bin Abdul Qayyum, Xihaier Luo, Nathan M. Urban, Xiaoning Qian, Byung-Jun Yoon
Multi-modal Representation Learning for Cross-modal Prediction of Continuous Weather Patterns from Discrete Low-Dimensional Data. CoRR (2024)
Sanket R. Jantre, Nathan M. Urban, Xiaoning Qian, Byung-Jun Yoon
Learning Active Subspaces for Effective and Scalable Uncertainty Quantification in Deep Neural Networks. ICASSP (2024)
Xihaier Luo, Xiaoning Qian, Byung-Jun Yoon
Hierarchical Neural Operator Transformer with Learnable Frequency-aware Loss Prior for Arbitrary-scale Super-resolution. CoRR (2024)
A. N. M. Nafiz Abeer, Sanket R. Jantre, Nathan M. Urban, Byung-Jun Yoon
Enhancing Generative Molecular Design via Uncertainty-guided Fine-tuning of Variational Autoencoders. CoRR (2024)
A. N. M. Nafiz Abeer, Sanket R. Jantre, Nathan M. Urban, Byung-Jun Yoon
Leveraging Active Subspaces to Capture Epistemic Model Uncertainty in Deep Generative Models for Molecular Design. CoRR (2024)
Line Pouchard, Kristofer G. Reyes, Francis J. Alexander, Byung-Jun Yoon
A Rigorous Uncertainty-Aware Quantification Framework Is Essential for Reproducible and Replicable Machine Learning Workflows. CoRR (2023)
Qihua Chen, Xuejin Chen, Hyun-Myung Woo, Byung-Jun Yoon
Neural message-passing for objective-based uncertainty quantification and optimal experimental design. Eng. Appl. Artif. Intell. 123 (Part A) (2023)
Alif Bin Abdul Qayyum, Xiaoning Qian, Byung-Jun Yoon
Enhancing Cryo-EM Particle Picking Through Consistency Model-based Latent Space Denoiser. BCB (2023)
Xihaier Luo, Sean McCorkle, Gilchan Park, Vanessa López-Marrero, Shinjae Yoo, Edward R. Dougherty, Xiaoning Qian, Francis J. Alexander, Byung-Jun Yoon
Comprehensive analysis of gene expression profiles to radiation exposure reveals molecular signatures of low-dose radiation response. CoRR (2023)
Francis J. Alexander, Meifeng Lin, Xiaoning Qian, Byung-Jun Yoon
Accelerating scientific discoveries through data-driven innovations. Patterns 4 (11) (2023)
Puhua Niu, Maria J. Soto, Shuai Huang, Byung-Jun Yoon, Edward R. Dougherty, Francis J. Alexander, Ian Blaby, Xiaoning Qian
Sensitivity Analysis of Genome-Scale Metabolic Flux Prediction. J. Comput. Biol. 30 (7) (2023)
Hyun-Myung Woo, Xiaoning Qian, Li Tan, Shantenu Jha, Francis J. Alexander, Edward R. Dougherty, Byung-Jun Yoon
Optimal decision-making in high-throughput virtual screening pipelines. Patterns 4 (11) (2023)
Xiaoning Qian, Byung-Jun Yoon, Raymundo Arróyave, Xiaofeng Qian, Edward R. Dougherty
Knowledge-driven learning, optimization, and experimental design under uncertainty for materials discovery. Patterns 4 (11) (2023)
Sanket R. Jantre, Nathan M. Urban, Xiaoning Qian, Byung-Jun Yoon
Learning Active Subspaces for Effective and Scalable Uncertainty Quantification in Deep Neural Networks. CoRR (2023)
Gilchan Park, Byung-Jun Yoon, Xihaier Luo, Vanessa López-Marrero, Patrick R. Johnstone, Shinjae Yoo, Francis J. Alexander
Comparative Performance Evaluation of Large Language Models for Extracting Molecular Interactions and Pathway Knowledge. CoRR (2023)
Gilchan Park, Byung-Jun Yoon, Xihaier Luo, Vanessa López-Marrero, Patrick R. Johnstone, Shinjae Yoo, Francis J. Alexander
Automated Extraction of Molecular Interactions and Pathway Knowledge using Large Language Model, Galactica: Opportunities and Challenges. BioNLP@ACL (2023)
Omar Maddouri, Xiaoning Qian, Byung-Jun Yoon
Geometric Affinity Propagation for Clustering With Network Knowledge. IEEE Trans. Knowl. Data Eng. 35 (11) (2023)
Paul Chong, Byung-Jun Yoon, Debbie Lai, Michael Carlson, Jarone Lee, Shuhan He
Looking back on forward-looking COVID models. Patterns 3 (7) (2022)
A. N. M. Nafiz Abeer, Nathan Urban, M. Ryan Weil, Francis J. Alexander, Byung-Jun Yoon
Multi-Objective Latent Space Optimization of Generative Molecular Design Models. CoRR (2022)
Qihua Chen, Hyun-Myung Woo, Xuejin Chen, Byung-Jun Yoon
Neural Message Passing for Objective-Based Uncertainty Quantification and Optimal Experimental Design. CoRR (2022)
Xihaier Luo, Sean McCorkle, Gilchan Park, Vanessa López-Marrero, Shinjae Yoo, Edward R. Dougherty, Xiaoning Qian, Francis J. Alexander, Byung-Jun Yoon
Comprehensive analysis of gene expression profiles to radiation exposure reveals molecular signatures of low-dose radiation response. BIBM (2022)
Omar Maddouri, Xiaoning Qian, Byung-Jun Yoon
Deep graph representations embed network information for robust disease marker identification. Bioinform. 38 (4) (2022)
Omar Maddouri, Xiaoning Qian, Francis J. Alexander, Edward R. Dougherty, Byung-Jun Yoon
Robust importance sampling for error estimation in the context of optimal Bayesian transfer learning. Patterns 3 (3) (2022)
Mingzhou Fan, Byung-Jun Yoon, Francis J. Alexander, Edward R. Dougherty, Xiaoning Qian
Adaptive Group Testing with Mismatched Models. ICASSP (2022)
Hyun-Myung Woo, Byung-Jun Yoon
MONACO: accurate biological network alignment through optimal neighborhood matching between focal nodes. Bioinform. 37 (10) (2021)
Omar Maddouri, Xiaoning Qian, Francis J. Alexander, Edward R. Dougherty, Byung-Jun Yoon
Robust Importance Sampling for Error Estimation in the Context of Optimal Bayesian Transfer Learning. CoRR (2021)
Ziyu Xiang, Mingzhou Fan, Guillermo Vázquez Tovar, William Trehern, Byung-Jun Yoon, Xiaofeng Qian, Raymundo Arróyave, Xiaoning Qian
Physics-constrained Automatic Feature Engineering for Predictive Modeling in Materials Science. AAAI (2021)
Guang Zhao, Edward R. Dougherty, Byung-Jun Yoon, Francis J. Alexander, Xiaoning Qian
Efficient Active Learning for Gaussian Process Classification by Error Reduction. NeurIPS (2021)
Omar Maddouri, Xiaoning Qian, Byung-Jun Yoon
Geometric Affinity Propagation for Clustering with Network Knowledge. CoRR (2021)
Guang Zhao, Edward R. Dougherty, Byung-Jun Yoon, Francis J. Alexander, Xiaoning Qian
Bayesian Active Learning by Soft Mean Objective Cost of Uncertainty. AISTATS (2021)
Byung-Jun Yoon, Xiaoning Qian, Edward R. Dougherty
Quantifying the Multi-Objective Cost of Uncertainty. IEEE Access 9 (2021)
Francis J. Alexander, James Ang, Jenna A. Bilbrey, Jan Balewski, Tiernan Casey, Ryan Chard, Jong Choi, Sutanay Choudhury, Bert J. Debusschere, Anthony M. DeGennaro, Nikoli Dryden, J. Austin Ellis, Ian T. Foster, Cristina Garcia-Cardona, Sayan Ghosh, Peter Harrington, Yunzhi Huang, Shantenu Jha, Travis Johnston, Ai Kagawa, Ramakrishnan Kannan, Neeraj Kumar, Zhengchun Liu, Naoya Maruyama, Satoshi Matsuoka, Erin McCarthy, Jamaludin Mohd-Yusof, Peter Nugent, Yosuke Oyama, Thomas Proffen, David Pugmire, Sivasankaran Rajamanickam, Vinay Ramakrishniah, Malachi Schram, Sudip K. Seal, Ganesh Sivaraman, Christine Sweeney, Li Tan, Rajeev Thakur, Brian Van Essen, Logan T. Ward, Paul M. Welch, Michael Wolf, Sotiris S. Xantheas, Kevin G. Yager, Shinjae Yoo, Byung-Jun Yoon
Co-design Center for Exascale Machine Learning Technologies (ExaLearn). Int. J. High Perform. Comput. Appl. 35 (6) (2021)
Hyun-Myung Woo, Xiaoning Qian, Li Tan, Shantenu Jha, Francis J. Alexander, Edward R. Dougherty, Byung-Jun Yoon
Optimal Decision Making in High-Throughput Virtual Screening Pipelines. CoRR (2021)
Hyun-Myung Woo, Youngjoon Hong, Bongsuk Kwon, Byung-Jun Yoon
Accelerating Optimal Experimental Design for Robust Synchronization of Uncertain Kuramoto Oscillator Model Using Machine Learning. IEEE Trans. Signal Process. 69 (2021)
Youngjoon Hong, Bongsuk Kwon, Byung-Jun Yoon
Optimal Experimental Design for Uncertain Systems Based on Coupled Differential Equations. IEEE Access 9 (2021)
Woo Seok Kim, Hyun-Myung Woo, M. Ibrahim Khot, Sungcheol Hong, David G. Jayne, Byung-Jun Yoon, Sung Il Park
AI-Enabled High-Throughput Wireless Telemetry for Effective Photodynamic Therapy. ACSCC (2021)
Guang Zhao, Edward R. Dougherty, Byung-Jun Yoon, Francis J. Alexander, Xiaoning Qian
Uncertainty-aware Active Learning for Optimal Bayesian Classifier. ICLR (2021)
Byung-Jun Yoon, Xiaoning Qian, Edward R. Dougherty
Quantifying the multi-objective cost of uncertainty. CoRR (2020)
Guang Zhao, Xiaoning Qian, Byung-Jun Yoon, Francis J. Alexander, Edward R. Dougherty
Model-Based Robust Filtering and Experimental Design for Stochastic Differential Equation Systems. IEEE Trans. Signal Process. 68 (2020)
Hyun-Myung Woo, Byung-Jun Yoon
Network-Based RNA Structural Alignment Through Optimal Local Neighborhood Matching. ACSSC (2020)
Hyun-Myung Woo, Woo Seok Kim, Sungcheol Hong, Vivekanand Jeevakumar, Clay M. Smithhart, Theodore J. Price, Byung-Jun Yoon, Sung Il Park
Machine Learning Enabled Adaptive Wireless Power Transmission System for Neuroscience Study. ACSSC (2020)
Yijie Wang, Hyundoo Jeong, Byung-Jun Yoon, Xiaoning Qian
ClusterM: a scalable algorithm for computational prediction of conserved protein complexes across multiple protein interaction networks. BMC Genom. 21 (S-10) (2020)
Youngjoon Hong, Bongsuk Kwon, Byung-Jun Yoon
Optimal Experimental Design for Uncertain Systems Based on Coupled Differential Equations. CoRR (2020)
Chun-Chi Chen, Hyundoo Jeong, Xiaoning Qian, Byung-Jun Yoon
TOPAS: network-based structural alignment of RNA sequences. Bioinform. 35 (17) (2019)
Chun-Chi Chen, Xiaoning Qian, Byung-Jun Yoon
RNAdetect: efficient computational detection of novel non-coding RNAs. Bioinform. 35 (7) (2019)
Byung-Jun Yoon, Xiaoning Qian, Tamer Kahveci, Ranadip Pal
Selected research articles from the 2018 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC). BMC Bioinform. (12) (2019)
Noushin Ghaffari, Osama A. Arshad, Hyundoo Jeong, John Thiltges, Michael F. Criscitiello, Byung-Jun Yoon, Aniruddha Datta, Charles D. Johnson
Examining De Novo Transcriptome Assemblies via a Quality Assessment Pipeline. IEEE ACM Trans. Comput. Biol. Bioinform. 15 (2) (2018)
Hyun-Myung Woo, Hyundoo Jeong, Byung-Jun Yoon
Comprehensive Updates in Network Synthesis Models to Create An Improved Benchmark for Network Alignment Algorithms. BCB (2018)
Byung-Jun Yoon, Xiaoning Qian, Tamer Kahveci, Ranadip Pal
Selected research articles from the 2017 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC). BMC Bioinform. (3) (2018)
Mansuck Kim, Huan Zhang, Charles Woloshuk, Won-Bo Shim, Byung-Jun Yoon
Computational Prediction of Pathogenic Network Modules in Fusarium verticillioides. IEEE ACM Trans. Comput. Biol. Bioinform. 15 (2) (2018)
Byung-Jun Yoon, Xiaoning Qian, Tamer Kahveci
Selected research articles from the 2016 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC). BMC Bioinform. 18 (S-4) (2017)
Byung-Jun Yoon, Xiaoning Qian, Tamer Kahveci
CNB-MAC'17: The Fourth International Workshop on Computational Network Biology: Modeling, Analysis, and Control. BCB (2017)
Hyundoo Jeong, Xiaoning Qian, Byung-Jun Yoon
CUFID-query: accurate network querying through random walk based network flow estimation. BMC Bioinform. 18 (14) (2017)
Chun-Chi Chen, Noushin Ghaffari, Xiaoning Qian, Byung-Jun Yoon
Optimal hybrid sequencing and assembly: Feasibility conditions for accurate genome reconstruction and cost minimization strategy. Comput. Biol. Chem. 69 (2017)
Hyundoo Jeong, Byung-Jun Yoon
SEQUOIA: significance enhanced network querying through context-sensitive random walk and minimization of network conductance. BMC Syst. Biol. 11 (3) (2017)
Chun-Chi Chen, Xiaoning Qian, Byung-Jun Yoon
Effective computational detection of piRNAs using n-gram models and support vector machine. BMC Bioinform. 18 (14) (2017)
Hyundoo Jeong, Byung-Jun Yoon
SEQUOIA: Significance enhanced network querying through context-sensitive random walk and minimization of network conductance. BCB (2016)
Yijie Wang, Byung-Jun Yoon, Xiaoning Qian
Co-segmentation of multiple images through random walk on graphs. ICASSP (2016)
Hyundoo Jeong, Xiaoning Qian, Byung-Jun Yoon
Effective comparative analysis of protein-protein interaction networks by measuring the steady-state network flow using a Markov model. BMC Bioinform. 17 (S-13) (2016)
Navadon Khunlertgit, Byung-Jun Yoon
Incorporating topological information for predicting robust cancer subnetwork markers in human protein-protein interaction network. BMC Bioinform. 17 (S-13) (2016)
Roozbeh Dehghannasiri, Byung-Jun Yoon, Edward R. Dougherty
Optimal Experimental Design for Gene Regulatory Networks in the Presence of Uncertainty. IEEE ACM Trans. Comput. Biol. Bioinform. 12 (4) (2015)
Mansuck Kim, Huan Zhang, Charles Woloshuk, Won-Bo Shim, Byung-Jun Yoon
Computational identification of genetic subnetwork modules associated with maize defense response to Fusarium verticillioides. BMC Bioinform. 16 (S13) (2015)
Mansuck Kim, Huan Zhang, Charles Woloshuk, Won-Bo Shim, Byung-Jun Yoon
pathogenicity. BCB (2015)
Ariana Broumand, Mohammad Shahrokh Esfahani, Byung-Jun Yoon, Edward R. Dougherty
Discrete optimal Bayesian classification with error-conditioned sequential sampling. Pattern Recognit. 48 (11) (2015)
Roozbeh Dehghannasiri, Byung-Jun Yoon, Edward R. Dougherty
Erratum to: Efficient experimental design for uncertainty reduction in gene regulatory networks. BMC Bioinform. 16 (2015)
Hyundoo Jeong, Byung-Jun Yoon
Effective Estimation of Node-to-Node Correspondence Between Different Graphs. IEEE Signal Process. Lett. 22 (6) (2015)
Hyundoo Jeong, Byung-Jun Yoon
Accurate multiple network alignment through context-sensitive random walk. BMC Syst. Biol. 9 (S-1) (2015)
Hyundoo Jeong, Byung-Jun Yoon
Identifying molecular complexes in biological networks through context sensitive network querying. BCB (2015)
Roozbeh Dehghannasiri, Byung-Jun Yoon, Edward R. Dougherty
Efficient experimental design for uncertainty reduction in gene regulatory networks. BMC Bioinform. 16 (S13) (2015)
Noushin Ghaffari, Osama A. Arshad, Hyundoo Jeong, John Thiltges, Michael F. Criscitiello, Byung-Jun Yoon, Aniruddha Datta, Charles D. Johnson
De novo transcriptome assemblies and annotation for pacifie whiteleg shrimp. GlobalSIP (2014)
Mansuck Kim, Huan Zhang, Charles Woloshuk, Won-Bo Shim, Byung-Jun Yoon
. BCB (2014)
Roozbeh Dehghannasiri, Byung-Jun Yoon, Edward R. Dougherty
Computationally efficient experimental design strategy for reducing gene network uncertainty. GlobalSIP (2014)
Hyundoo Jeong, Byung-Jun Yoon
A novel context-sensitive random walk model for estimating node correspondence between two biological networks. BCB (2014)
Navadon Khunlertgit, Byung-Jun Yoon
Simultaneous identification of robust synergistic subnetwork markers for effective cancer prognosis. EURASIP J. Bioinform. Syst. Biol. 2014 (2014)
Byung-Jun Yoon
Sequence alignment by passing messages. BMC Genom. 15 (S-1) (2014)
Navadon Khunlertgit, Byung-Jun Yoon
Simultaneous identification of robust synergistic subnetwork markers for effective cancer prognosis. BCB (2014)
Mohammad Shahrokh Esfahani, Jason M. Knight, Amin Zollanvari, Byung-Jun Yoon, Edward R. Dougherty
Classifier design given an uncertainty class of feature distributions via regularized maximum likelihood and the incorporation of biological pathway knowledge in steady-state phenotype classification. Pattern Recognit. 46 (10) (2013)
Priyanka J. Raja, Justin Jacob, Byung-Jun Yoon, Geoffrey Bartholomeusz, Arvind Rao
Automated image analysis and inference of gene function from high - Content screens. EUSIPCO (2013)
Navadon Khunlertgit, Byung-Jun Yoon
Finding robust subnetwork markers that improve cross-dataset performance of cancer classification. GlobalSIP (2013)
Navadon Khunlertgit, Byung-Jun Yoon
Identification of Robust Pathway Markers for Cancer through Rank-Based Pathway Activity Inference. Adv. Bioinformatics 2013 (2013)
Byung-Jun Yoon, Xiaoning Qian, Edward R. Dougherty
Quantifying the Objective Cost of Uncertainty in Complex Dynamical Systems. IEEE Trans. Signal Process. 61 (9) (2013)
Roozbeh Dehghannasiri, Byung-Jun Yoon, Edward R. Dougherty
Designing experiments for optimal reduction of uncertainty in gene regulatory networks. GENSiPS (2013)
Xiaoning Qian, Byung-Jun Yoon, Edward R. Dougherty
Structural intervention of gene regulatory networks by general rank-k matrix perturbation. ICASSP (2012)
Sayed Mohammad Ebrahim Sahraeian, Byung-Jun Yoon
RESQUE: Network reduction using semi-Markov random walk scores for efficient querying of biological networks. Bioinform. 28 (16) (2012)
Navadon Khunlertgit, Byung-Jun Yoon
Finding robust pathway markers for cancer classification. GENSiPS (2012)
Byung-Jun Yoon, Xiaoning Qian, Sayed Mohammad Ebrahim Sahraeian
Comparative Analysis of Biological Networks: Hidden Markov model and Markov chain-based approach. IEEE Signal Process. Mag. 29 (1) (2012)
Amir Nikooienejad, Richard Metz, Byung-Jun Yoon, Charles D. Johnson
Fast DNA barcode generating algorithm using Radix Coding method. GENSiPS (2012)
Sayed Mohammad Ebrahim Sahraeian, Byung-Jun Yoon
RESQUE: Network Reduction Using Semi-Markov Random Walk Scores for Efficient Querying of Biological Networks (Extended Abstract). RECOMB (2012)
Xiaoning Qian, Byung-Jun Yoon
Contour-based hidden Markov model to segment 2D ultrasound images. ICASSP (2011)
Byung-Jun Yoon
Finding effective subnetwork markers for cancer by passing messages. GENSiPS (2011)
Xiaoning Qian, Sayed Mohammad Ebrahim Sahraeian, Byung-Jun Yoon
Enhancing the accuracy of HMM-based conserved pathway prediction using global correspondence scores. BMC Bioinform. 12 (S-10) (2011)
Sayed Mohammad Ebrahim Sahraeian, Byung-Jun Yoon
Fast network querying algorithm for searching large-scale biological networks. ICASSP (2011)
Byung-Jun Yoon
Enhanced stochastic optimization algorithm for finding effective multi-target therapeutics. BMC Bioinform. 12 (S-1) (2011)
Xiaoning Qian, Byung-Jun Yoon
Comparative analysis of protein interaction networks reveals that conserved pathways are susceptible to HIV-1 interception. BMC Bioinform. 12 (S-1) (2011)
Mohammad Shahrokh Esfahani, Amin Zollanvari, Byung-Jun Yoon, Edward R. Dougherty
Designing enhanced classifiers using prior process knowledge: Regularized maximum-likelihood. GENSiPS (2011)
Byung-Jun Yoon, Xiaoning Qian
Session TA8a1: Signal processing methods for representation, analysis, and control of biological systems. ACSCC (2011)
Sayed Mohammad Ebrahim Sahraeian, Byung-Jun Yoon
PicXAA-R: Efficient structural alignment of multiple RNA sequences using a greedy approach. BMC Bioinform. 12 (S-1) (2011)

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Publication Activity (10 Years)

Top Topics

Top Venues

Byung-Jun Yoon