Byung-Jun Yoon

157 papers A* 5A 4B 3Misc 10Journal 94Unranked 39

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Iterative Decoding of Stabilizer Codes under Radiation-Induced Correlated Noise. CoRR Anuj K. Nayak, Paul Baity, Peter J. Love, Nicholas Jeon, Byung-Jun Yoon, Adolfy Hoisie, Lav R. Varshney
2026	J	`jnl`	Variable rate neural compression for sparse detector data. Patterns Yi Huang, Yeonju Go, Jin Huang, Shuhang Li, Xihaier Luo, Thomas Marshall, Joseph D. Osborn, Christopher Pinkenburg, Yihui Ren, Evgeny Shulga, Shinjae Yoo, Byung-Jun Yoon
2025	—	`conf`	A Dual Graph Encoder Approach to Structure-Based TCR-pMHC Binding Prediction. BCB A. N. M. Nafiz Abeer, Xiaoning Qian, Byung-Jun Yoon
2025	J	`jnl`	An Effective Pipeline for Training Variational Autoencoders for Synthesizable and Optimized Molecular Design. IEEE Access Fardeen H. Mozumder, Byung-Jun Yoon
2025	J	`jnl`	C-LoRA: Contextual Low-Rank Adaptation for Uncertainty Estimation in Large Language Models. CoRR Amir Hossein Rahmati, Sanket R. Jantre, Weifeng Zhang, Yucheng Wang, Byung-Jun Yoon, Nathan M. Urban, Xiaoning Qian
2025	J	`jnl`	Comparative Performance Evaluation of Large Language Models for Extracting Molecular Interactions and Pathway Knowledge. J. Comput. Biol. Gilchan Park, Byung-Jun Yoon, Xihaier Luo, Vanessa López-Marrero, Shinjae Yoo, Shantenu Jha
2025	J	`jnl`	Cost-effective Reduced-Order Modeling via Bayesian Active Learning. CoRR Amir Hossein Rahmati, Nathan M. Urban, Byung-Jun Yoon, Xiaoning Qian
2025	—	`conf`	Enhancing Future Link Prediction in Quantum Computing Semantic Networks through LLM-Initiated Node Features. COLING (Industry) Gilchan Park, Paul Baity, Byung-Jun Yoon, Adolfy Hoisie
2025	J	`jnl`	Forward Target Propagation: A Forward-Only Approach to Global Error Credit Assignment via Local Losses. CoRR Nazmus Saadat As-Saquib, A. N. M. Nafiz Abeer, Hung-Ta Chien, Byung-Jun Yoon, Suhas Kumar, Su-In Yi
2025	A*	`conf`	Pareto Prompt Optimization. ICLR Guang Zhao, Byung-Jun Yoon, Gilchan Park, Shantenu Jha, Shinjae Yoo, Xiaoning Qian
2025	—	`conf`	Scale-Invariant Implicit Neural Representations For Object Counting. CVPR Workshops Siyuan Xu, Yucheng Wang, Xihaier Luo, Byung-Jun Yoon, Xiaoning Qian
2025	J	`jnl`	Uncertainty-Aware Adaptation of Large Language Models for Protein-Protein Interaction Analysis. CoRR Sanket R. Jantre, Tianle Wang, Gilchan Park, Kriti Chopra, Nicholas Jeon, Xiaoning Qian, Nathan M. Urban, Byung-Jun Yoon
2024	—	`conf`	Calibration of Compartmental Epidemiological Models via Graybox Bayesian Optimization. BHI Puhua Niu, Byung-Jun Yoon, Xiaoning Qian
2024	J	`jnl`	Efficient Compression of Sparse Accelerator Data Using Implicit Neural Representations and Importance Sampling. CoRR Xihaier Luo, Samuel Lurvey, Yi Huang, Yihui Ren, Jin Huang, Byung-Jun Yoon
2024	J	`jnl`	Enhancing Future Link Prediction in Quantum Computing Semantic Networks through LLM-Initiated Node Features. CoRR Gilchan Park, Paul Baity, Byung-Jun Yoon, Adolfy Hoisie
2024	J	`jnl`	Enhancing Generative Molecular Design via Uncertainty-guided Fine-tuning of Variational Autoencoders. CoRR A. N. M. Nafiz Abeer, Sanket R. Jantre, Nathan M. Urban, Byung-Jun Yoon
2024	J	`jnl`	Epidemiological Model Calibration via Graybox Bayesian Optimization. CoRR Puhua Niu, Byung-Jun Yoon, Xiaoning Qian
2024	A*	`conf`	Hierarchical Neural Operator Transformer with Learnable Frequency-aware Loss Prior for Arbitrary-scale Super-resolution. ICML Xihaier Luo, Xiaoning Qian, Byung-Jun Yoon
2024	J	`jnl`	Hierarchical Neural Operator Transformer with Learnable Frequency-aware Loss Prior for Arbitrary-scale Super-resolution. CoRR Xihaier Luo, Xiaoning Qian, Byung-Jun Yoon
2024	—	`conf`	Implicit Neural Representations for Simultaneous Reduction and Continuous Reconstruction of Multi-Altitude Climate Data. MLSP Alif Bin Abdul Qayyum, Xihaier Luo, Nathan M. Urban, Xiaoning Qian, Byung-Jun Yoon
2024	J	`jnl`	Implicit Neural Representations for Simultaneous Reduction and Continuous Reconstruction of Multi-Altitude Climate Data. CoRR Alif Bin Abdul Qayyum, Xihaier Luo, Nathan M. Urban, Xiaoning Qian, Byung-Jun Yoon
2024	Misc	`conf`	Learning Active Subspaces for Effective and Scalable Uncertainty Quantification in Deep Neural Networks. ICASSP Sanket R. Jantre, Nathan M. Urban, Xiaoning Qian, Byung-Jun Yoon
2024	—	`conf`	Leveraging Active Subspaces to Capture Epistemic Model Uncertainty in Deep Generative Models for Molecular Design. MLSP A. N. M. Nafiz Abeer, Sanket R. Jantre, Nathan M. Urban, Byung-Jun Yoon
2024	J	`jnl`	Leveraging Active Subspaces to Capture Epistemic Model Uncertainty in Deep Generative Models for Molecular Design. CoRR A. N. M. Nafiz Abeer, Sanket R. Jantre, Nathan M. Urban, Byung-Jun Yoon
2024	J	`jnl`	LoRA-BERT: a Natural Language Processing Model for Robust and Accurate Prediction of long non-coding RNAs. CoRR Nicholas Jeon, Xiaoning Qian, Lamin SaidyKhan, Paul de Figueiredo, Byung-Jun Yoon
2024	A	`conf`	Multi-fidelity Bayesian Optimization with Multiple Information Sources of Input-dependent Fidelity. UAI Mingzhou Fan, Byung-Jun Yoon, Edward R. Dougherty, Nathan M. Urban, Francis J. Alexander, Raymundo Arróyave, Xiaoning Qian
2024	J	`jnl`	Multi-modal Representation Learning for Cross-modal Prediction of Continuous Weather Patterns from Discrete Low-Dimensional Data. CoRR Alif Bin Abdul Qayyum, Xihaier Luo, Nathan M. Urban, Xiaoning Qian, Byung-Jun Yoon
2024	J	`jnl`	Multi-objective latent space optimization of generative molecular design models. Patterns A. N. M. Nafiz Abeer, Nathan M. Urban, M. Ryan Weil, Francis J. Alexander, Byung-Jun Yoon
2024	J	`jnl`	Neural machine translation of clinical procedure codes for medical diagnosis and uncertainty quantification. CoRR Pei-Hung Chung, Shuhan He, Norawit Kijpaisalratana, Abdel-badih el Ariss, Byung-Jun Yoon
2024	J	`jnl`	Pathway-Guided Optimization of Deep Generative Molecular Design Models for Cancer Therapy. CoRR Alif Bin Abdul Qayyum, Susan D. Mertins, Amanda K. Paulson, Nathan M. Urban, Byung-Jun Yoon
2024	J	`jnl`	Pathway-based analyses of gene expression profiles at low doses of ionizing radiation. Frontiers Bioinform. 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
2024	B	`conf`	Privacy-Preserving Federated Learning for Science: Challenges and Research Directions. IEEE Big Data Kibaek Kim, Krishnan Raghavan, Olivera Kotevska, Matthieu Dorier, Ravi K. Madduri, Minseok Ryu, Todd S. Munson, Robert Ross, Thomas Flynn, Ai Kagawa, Byung-Jun Yoon, Christian Engelmann, Farzad Yousefian
2024	A	`conf`	Uncertainty-aware Continuous Implicit Neural Representations for Remote Sensing Object Counting. AISTATS Siyuan Xu, Yucheng Wang, Mingzhou Fan, Byung-Jun Yoon, Xiaoning Qian
2024	J	`jnl`	Understanding Uncertainty-based Active Learning Under Model Mismatch. CoRR Amir Hossein Rahmati, Mingzhou Fan, Ruida Zhou, Nathan M. Urban, Byung-Jun Yoon, Xiaoning Qian
2024	J	`jnl`	Variable Rate Neural Compression for Sparse Detector Data. CoRR Yi Huang, Yeonju Go, Jin Huang, Shuhang Li, Xihaier Luo, Thomas Marshall, Joseph D. Osborn, Christopher Pinkenburg, Yihui Ren, Evgeny Shulga, Shinjae Yoo, Byung-Jun Yoon
2024	—	`conf`	When Uncertainty-Based Active Learning May Fail? ICPR (1) Amir Hossein Rahmati, Mingzhou Fan, Ruida Zhou, Nathan M. Urban, Byung-Jun Yoon, Xiaoning Qian
2023	J	`jnl`	A Rigorous Uncertainty-Aware Quantification Framework Is Essential for Reproducible and Replicable Machine Learning Workflows. CoRR Line Pouchard, Kristofer G. Reyes, Francis J. Alexander, Byung-Jun Yoon
2023	J	`jnl`	Accelerating scientific discoveries through data-driven innovations. Patterns Francis J. Alexander, Meifeng Lin, Xiaoning Qian, Byung-Jun Yoon
2023	—	`conf`	Automated Extraction of Molecular Interactions and Pathway Knowledge using Large Language Model, Galactica: Opportunities and Challenges. BioNLP@ACL Gilchan Park, Byung-Jun Yoon, Xihaier Luo, Vanessa López-Marrero, Patrick R. Johnstone, Shinjae Yoo, Francis J. Alexander
2023	J	`jnl`	Comparative Performance Evaluation of Large Language Models for Extracting Molecular Interactions and Pathway Knowledge. CoRR Gilchan Park, Byung-Jun Yoon, Xihaier Luo, Vanessa López-Marrero, Patrick R. Johnstone, Shinjae Yoo, Francis J. Alexander
2023	J	`jnl`	Comprehensive analysis of gene expression profiles to radiation exposure reveals molecular signatures of low-dose radiation response. CoRR Xihaier Luo, Sean McCorkle, Gilchan Park, Vanessa López-Marrero, Shinjae Yoo, Edward R. Dougherty, Xiaoning Qian, Francis J. Alexander, Byung-Jun Yoon
2023	—	`conf`	Enhancing Cryo-EM Particle Picking Through Consistency Model-based Latent Space Denoiser. BCB Alif Bin Abdul Qayyum, Xiaoning Qian, Byung-Jun Yoon
2023	J	`jnl`	Geometric Affinity Propagation for Clustering With Network Knowledge. IEEE Trans. Knowl. Data Eng. Omar Maddouri, Xiaoning Qian, Byung-Jun Yoon
2023	J	`jnl`	Knowledge-driven learning, optimization, and experimental design under uncertainty for materials discovery. Patterns Xiaoning Qian, Byung-Jun Yoon, Raymundo Arróyave, Xiaofeng Qian, Edward R. Dougherty
2023	J	`jnl`	Learning Active Subspaces for Effective and Scalable Uncertainty Quantification in Deep Neural Networks. CoRR Sanket R. Jantre, Nathan M. Urban, Xiaoning Qian, Byung-Jun Yoon
2023	J	`jnl`	Neural message-passing for objective-based uncertainty quantification and optimal experimental design. Eng. Appl. Artif. Intell. Qihua Chen, Xuejin Chen, Hyun-Myung Woo, Byung-Jun Yoon
2023	J	`jnl`	Optimal decision-making in high-throughput virtual screening pipelines. Patterns Hyun-Myung Woo, Xiaoning Qian, Li Tan, Shantenu Jha, Francis J. Alexander, Edward R. Dougherty, Byung-Jun Yoon
2023	—	`ed.`	Proceedings of the 14th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, BCB 2023, Houston, TX, USA, September 3-6, 2023 BCB May D. Wang, Byung-Jun Yoon
2023	J	`jnl`	Sensitivity Analysis of Genome-Scale Metabolic Flux Prediction. J. Comput. Biol. Puhua Niu, Maria J. Soto, Shuai Huang, Byung-Jun Yoon, Edward R. Dougherty, Francis J. Alexander, Ian Blaby, Xiaoning Qian
2022	Misc	`conf`	Adaptive Group Testing with Mismatched Models. ICASSP Mingzhou Fan, Byung-Jun Yoon, Francis J. Alexander, Edward R. Dougherty, Xiaoning Qian
2022	—	`conf`	Comprehensive analysis of gene expression profiles to radiation exposure reveals molecular signatures of low-dose radiation response. BIBM Xihaier Luo, Sean McCorkle, Gilchan Park, Vanessa López-Marrero, Shinjae Yoo, Edward R. Dougherty, Xiaoning Qian, Francis J. Alexander, Byung-Jun Yoon
2022	J	`jnl`	Deep graph representations embed network information for robust disease marker identification. Bioinform. Omar Maddouri, Xiaoning Qian, Byung-Jun Yoon
2022	J	`jnl`	Looking back on forward-looking COVID models. Patterns Paul Chong, Byung-Jun Yoon, Debbie Lai, Michael Carlson, Jarone Lee, Shuhan He
2022	J	`jnl`	Multi-Objective Latent Space Optimization of Generative Molecular Design Models. CoRR A. N. M. Nafiz Abeer, Nathan M. Urban, M. Ryan Weil, Francis J. Alexander, Byung-Jun Yoon
2022	J	`jnl`	Neural Message Passing for Objective-Based Uncertainty Quantification and Optimal Experimental Design. CoRR Qihua Chen, Hyun-Myung Woo, Xuejin Chen, Byung-Jun Yoon
2022	J	`jnl`	Robust importance sampling for error estimation in the context of optimal Bayesian transfer learning. Patterns Omar Maddouri, Xiaoning Qian, Francis J. Alexander, Edward R. Dougherty, Byung-Jun Yoon
2021	—	`conf`	AI-Enabled High-Throughput Wireless Telemetry for Effective Photodynamic Therapy. ACSCC Woo Seok Kim, Hyun-Myung Woo, M. Ibrahim Khot, Sungcheol Hong, David G. Jayne, Byung-Jun Yoon, Sung Il Park
2021	J	`jnl`	Accelerating Optimal Experimental Design for Robust Synchronization of Uncertain Kuramoto Oscillator Model Using Machine Learning. IEEE Trans. Signal Process. Hyun-Myung Woo, Youngjoon Hong, Bongsuk Kwon, Byung-Jun Yoon
2021	A	`conf`	Bayesian Active Learning by Soft Mean Objective Cost of Uncertainty. AISTATS Guang Zhao, Edward R. Dougherty, Byung-Jun Yoon, Francis J. Alexander, Xiaoning Qian
2021	J	`jnl`	Co-design Center for Exascale Machine Learning Technologies (ExaLearn). Int. J. High Perform. Comput. Appl. 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 Ramakrishnaiah, 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
2021	A*	`conf`	Efficient Active Learning for Gaussian Process Classification by Error Reduction. NeurIPS Guang Zhao, Edward R. Dougherty, Byung-Jun Yoon, Francis J. Alexander, Xiaoning Qian
2021	J	`jnl`	Geometric Affinity Propagation for Clustering with Network Knowledge. CoRR Omar Maddouri, Xiaoning Qian, Byung-Jun Yoon
2021	J	`jnl`	MONACO: accurate biological network alignment through optimal neighborhood matching between focal nodes. Bioinform. Hyun-Myung Woo, Byung-Jun Yoon
2021	J	`jnl`	Optimal Decision Making in High-Throughput Virtual Screening Pipelines. CoRR Hyun-Myung Woo, Xiaoning Qian, Li Tan, Shantenu Jha, Francis J. Alexander, Edward R. Dougherty, Byung-Jun Yoon
2021	J	`jnl`	Optimal Experimental Design for Uncertain Systems Based on Coupled Differential Equations. IEEE Access Youngjoon Hong, Bongsuk Kwon, Byung-Jun Yoon
2021	A*	`conf`	Physics-constrained Automatic Feature Engineering for Predictive Modeling in Materials Science. AAAI Ziyu Xiang, Mingzhou Fan, Guillermo Vázquez Tovar, William Trehern, Byung-Jun Yoon, Xiaofeng Qian, Raymundo Arróyave, Xiaoning Qian
2021	J	`jnl`	Quantifying the Multi-Objective Cost of Uncertainty. IEEE Access Byung-Jun Yoon, Xiaoning Qian, Edward R. Dougherty
2021	J	`jnl`	Robust Importance Sampling for Error Estimation in the Context of Optimal Bayesian Transfer Learning. CoRR Omar Maddouri, Xiaoning Qian, Francis J. Alexander, Edward R. Dougherty, Byung-Jun Yoon
2021	A*	`conf`	Uncertainty-aware Active Learning for Optimal Bayesian Classifier. ICLR Guang Zhao, Edward R. Dougherty, Byung-Jun Yoon, Francis J. Alexander, Xiaoning Qian
2020	J	`jnl`	ClusterM: a scalable algorithm for computational prediction of conserved protein complexes across multiple protein interaction networks. BMC Genom. Yijie Wang, Hyundoo Jeong, Byung-Jun Yoon, Xiaoning Qian
2020	Misc	`conf`	Machine Learning Enabled Adaptive Wireless Power Transmission System for Neuroscience Study. ACSSC Hyun-Myung Woo, Woo Seok Kim, Sungcheol Hong, Vivekanand Jeevakumar, Clay M. Smithhart, Theodore J. Price, Byung-Jun Yoon, Sung Il Park
2020	J	`jnl`	Model-Based Robust Filtering and Experimental Design for Stochastic Differential Equation Systems. IEEE Trans. Signal Process. Guang Zhao, Xiaoning Qian, Byung-Jun Yoon, Francis J. Alexander, Edward R. Dougherty
2020	Misc	`conf`	Network-Based RNA Structural Alignment Through Optimal Local Neighborhood Matching. ACSSC Hyun-Myung Woo, Byung-Jun Yoon
2020	J	`jnl`	Optimal Experimental Design for Uncertain Systems Based on Coupled Differential Equations. CoRR Youngjoon Hong, Bongsuk Kwon, Byung-Jun Yoon
2020	J	`jnl`	Quantifying the multi-objective cost of uncertainty. CoRR Byung-Jun Yoon, Xiaoning Qian, Edward R. Dougherty
2019	J	`jnl`	RNAdetect: efficient computational detection of novel non-coding RNAs. Bioinform. Chun-Chi Chen, Xiaoning Qian, Byung-Jun Yoon
2019	J	`jnl`	Selected research articles from the 2018 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC). BMC Bioinform. Byung-Jun Yoon, Xiaoning Qian, Tamer Kahveci, Ranadip Pal
2019	J	`jnl`	TOPAS: network-based structural alignment of RNA sequences. Bioinform. Chun-Chi Chen, Hyundoo Jeong, Xiaoning Qian, Byung-Jun Yoon
2018	—	`conf`	Comprehensive Updates in Network Synthesis Models to Create An Improved Benchmark for Network Alignment Algorithms. BCB Hyun-Myung Woo, Hyundoo Jeong, Byung-Jun Yoon
2018	J	`jnl`	Computational Prediction of Pathogenic Network Modules in Fusarium verticillioides. IEEE ACM Trans. Comput. Biol. Bioinform. Mansuck Kim, Huan Zhang, Charles Woloshuk, Won-Bo Shim, Byung-Jun Yoon
2018	J	`jnl`	Examining De Novo Transcriptome Assemblies via a Quality Assessment Pipeline. IEEE ACM Trans. Comput. Biol. Bioinform. Noushin Ghaffari, Osama A. Arshad, Hyundoo Jeong, John Thiltges, Michael F. Criscitiello, Byung-Jun Yoon, Aniruddha Datta, Charles D. Johnson
2018	J	`jnl`	Selected research articles from the 2017 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC). BMC Bioinform. Byung-Jun Yoon, Xiaoning Qian, Tamer Kahveci, Ranadip Pal
2017	—	`conf`	CNB-MAC'17: The Fourth International Workshop on Computational Network Biology: Modeling, Analysis, and Control. BCB Byung-Jun Yoon, Xiaoning Qian, Tamer Kahveci
2017	J	`jnl`	CUFID-query: accurate network querying through random walk based network flow estimation. BMC Bioinform. Hyundoo Jeong, Xiaoning Qian, Byung-Jun Yoon
2017	J	`jnl`	Effective computational detection of piRNAs using n-gram models and support vector machine. BMC Bioinform. Chun-Chi Chen, Xiaoning Qian, Byung-Jun Yoon
2017	J	`jnl`	Optimal hybrid sequencing and assembly: Feasibility conditions for accurate genome reconstruction and cost minimization strategy. Comput. Biol. Chem. Chun-Chi Chen, Noushin Ghaffari, Xiaoning Qian, Byung-Jun Yoon
2017	J	`jnl`	SEQUOIA: significance enhanced network querying through context-sensitive random walk and minimization of network conductance. BMC Syst. Biol. Hyundoo Jeong, Byung-Jun Yoon
2017	J	`jnl`	Selected research articles from the 2016 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC). BMC Bioinform. Byung-Jun Yoon, Xiaoning Qian, Tamer Kahveci
2016	Misc	`conf`	Co-segmentation of multiple images through random walk on graphs. ICASSP Yijie Wang, Byung-Jun Yoon, Xiaoning Qian
2016	J	`jnl`	Effective comparative analysis of protein-protein interaction networks by measuring the steady-state network flow using a Markov model. BMC Bioinform. Hyundoo Jeong, Xiaoning Qian, Byung-Jun Yoon
2016	J	`jnl`	Incorporating topological information for predicting robust cancer subnetwork markers in human protein-protein interaction network. BMC Bioinform. Navadon Khunlertgit, Byung-Jun Yoon
2016	—	`ch.`	Inference of gene regulatory networks: validation and uncertainty. Big Data over Networks Xiaoning Qian, Byung-Jun Yoon, Edward R. Dougherty
2016	—	`conf`	SEQUOIA: Significance enhanced network querying through context-sensitive random walk and minimization of network conductance. BCB Hyundoo Jeong, Byung-Jun Yoon
2015	J	`jnl`	Accurate multiple network alignment through context-sensitive random walk. BMC Syst. Biol. Hyundoo Jeong, Byung-Jun Yoon
2015	J	`jnl`	Computational identification of genetic subnetwork modules associated with maize defense response to Fusarium verticillioides. BMC Bioinform. Mansuck Kim, Huan Zhang, Charles Woloshuk, Won-Bo Shim, Byung-Jun Yoon
2015	—	`conf`	Computational identification of key functional genes associated with BCB Mansuck Kim, Huan Zhang, Charles Woloshuk, Won-Bo Shim, Byung-Jun Yoon
2015	J	`jnl`	Discrete optimal Bayesian classification with error-conditioned sequential sampling. Pattern Recognit. Ariana Broumand, Mohammad Shahrokh Esfahani, Byung-Jun Yoon, Edward R. Dougherty
2015	J	`jnl`	Effective Estimation of Node-to-Node Correspondence Between Different Graphs. IEEE Signal Process. Lett. Hyundoo Jeong, Byung-Jun Yoon
2015	J	`jnl`	Efficient experimental design for uncertainty reduction in gene regulatory networks. BMC Bioinform. Roozbeh Dehghannasiri, Byung-Jun Yoon, Edward R. Dougherty
2015	J	`jnl`	Erratum to: Efficient experimental design for uncertainty reduction in gene regulatory networks. BMC Bioinform. Roozbeh Dehghannasiri, Byung-Jun Yoon, Edward R. Dougherty
2015	—	`conf`	Identifying molecular complexes in biological networks through context sensitive network querying. BCB Hyundoo Jeong, Byung-Jun Yoon
2015	J	`jnl`	Optimal Experimental Design for Gene Regulatory Networks in the Presence of Uncertainty. IEEE ACM Trans. Comput. Biol. Bioinform. Roozbeh Dehghannasiri, Byung-Jun Yoon, Edward R. Dougherty
2014	—	`conf`	A novel context-sensitive random walk model for estimating node correspondence between two biological networks. BCB Hyundoo Jeong, Byung-Jun Yoon
2014	—	`conf`	Computational identification of functional network modules associated with the pathogenicity of BCB Mansuck Kim, Huan Zhang, Charles Woloshuk, Won-Bo Shim, Byung-Jun Yoon
2014	—	`conf`	Computationally efficient experimental design strategy for reducing gene network uncertainty. GlobalSIP Roozbeh Dehghannasiri, Byung-Jun Yoon, Edward R. Dougherty
2014	—	`conf`	De novo transcriptome assemblies and annotation for pacifie whiteleg shrimp. GlobalSIP Noushin Ghaffari, Osama A. Arshad, Hyundoo Jeong, John Thiltges, Michael F. Criscitiello, Byung-Jun Yoon, Aniruddha Datta, Charles D. Johnson
2014	J	`jnl`	Sequence alignment by passing messages. BMC Genom. Byung-Jun Yoon
2014	—	`conf`	Simultaneous identification of robust synergistic subnetwork markers for effective cancer prognosis. BCB Navadon Khunlertgit, Byung-Jun Yoon
2014	J	`jnl`	Simultaneous identification of robust synergistic subnetwork markers for effective cancer prognosis. EURASIP J. Bioinform. Syst. Biol. Navadon Khunlertgit, Byung-Jun Yoon
2013	—	`conf`	Automated image analysis and inference of gene function from high - Content screens. EUSIPCO Priyanka J. Raja, Justin Jacob, Byung-Jun Yoon, Geoffrey Bartholomeusz, Arvind Rao
2013	J	`jnl`	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. Mohammad Shahrokh Esfahani, Jason M. Knight, Amin Zollanvari, Byung-Jun Yoon, Edward R. Dougherty
2013	—	`conf`	Designing experiments for optimal reduction of uncertainty in gene regulatory networks. GENSiPS Roozbeh Dehghannasiri, Byung-Jun Yoon, Edward R. Dougherty
2013	—	`conf`	Finding robust subnetwork markers that improve cross-dataset performance of cancer classification. GlobalSIP Navadon Khunlertgit, Byung-Jun Yoon
2013	J	`jnl`	Identification of Robust Pathway Markers for Cancer through Rank-Based Pathway Activity Inference. Adv. Bioinformatics Navadon Khunlertgit, Byung-Jun Yoon
2013	J	`jnl`	Quantifying the Objective Cost of Uncertainty in Complex Dynamical Systems. IEEE Trans. Signal Process. Byung-Jun Yoon, Xiaoning Qian, Edward R. Dougherty
2012	J	`jnl`	Comparative Analysis of Biological Networks: Hidden Markov model and Markov chain-based approach. IEEE Signal Process. Mag. Byung-Jun Yoon, Xiaoning Qian, Sayed Mohammad Ebrahim Sahraeian
2012	—	`conf`	Fast DNA barcode generating algorithm using Radix Coding method. GENSiPS Amir Nikooienejad, Richard Metz, Byung-Jun Yoon, Charles D. Johnson
2012	—	`conf`	Finding robust pathway markers for cancer classification. GENSiPS Navadon Khunlertgit, Byung-Jun Yoon
2012	B	`conf`	RESQUE: Network Reduction Using Semi-Markov Random Walk Scores for Efficient Querying of Biological Networks (Extended Abstract). RECOMB Sayed Mohammad Ebrahim Sahraeian, Byung-Jun Yoon
2012	J	`jnl`	RESQUE: Network reduction using semi-Markov random walk scores for efficient querying of biological networks. Bioinform. Sayed Mohammad Ebrahim Sahraeian, Byung-Jun Yoon
2012	Misc	`conf`	Structural intervention of gene regulatory networks by general rank-k matrix perturbation. ICASSP Xiaoning Qian, Byung-Jun Yoon, Edward R. Dougherty
2011	J	`jnl`	A Novel Low-Complexity HMM Similarity Measure. IEEE Signal Process. Lett. Sayed Mohammad Ebrahim Sahraeian, Byung-Jun Yoon
2011	J	`jnl`	Comparative analysis of protein interaction networks reveals that conserved pathways are susceptible to HIV-1 interception. BMC Bioinform. Xiaoning Qian, Byung-Jun Yoon
2011	Misc	`conf`	Contour-based hidden Markov model to segment 2D ultrasound images. ICASSP Xiaoning Qian, Byung-Jun Yoon
2011	—	`conf`	Designing enhanced classifiers using prior process knowledge: Regularized maximum-likelihood. GENSiPS Mohammad Shahrokh Esfahani, Amin Zollanvari, Byung-Jun Yoon, Edward R. Dougherty
2011	—	`conf`	Efficient combinatorial drug optimization through stochastic search. GENSiPS Mansuck Kim, Byung-Jun Yoon
2011	J	`jnl`	Enhanced stochastic optimization algorithm for finding effective multi-target therapeutics. BMC Bioinform. Byung-Jun Yoon
2011	J	`jnl`	Enhancing the accuracy of HMM-based conserved pathway prediction using global correspondence scores. BMC Bioinform. Xiaoning Qian, Sayed Mohammad Ebrahim Sahraeian, Byung-Jun Yoon
2011	Misc	`conf`	Fast network querying algorithm for searching large-scale biological networks. ICASSP Sayed Mohammad Ebrahim Sahraeian, Byung-Jun Yoon
2011	—	`conf`	Finding effective subnetwork markers for cancer by passing messages. GENSiPS Byung-Jun Yoon
2011	J	`jnl`	PicXAA-R: Efficient structural alignment of multiple RNA sequences using a greedy approach. BMC Bioinform. Sayed Mohammad Ebrahim Sahraeian, Byung-Jun Yoon
2011	J	`jnl`	PicXAA-Web: a web-based platform for non-progressive maximum expected accuracy alignment of multiple biological sequences. Nucleic Acids Res. Sayed Mohammad Ebrahim Sahraeian, Byung-Jun Yoon
2011	—	`conf`	Probabilistic consistency transformation for multiple alignment of biological networks. GENSiPS Sayed Mohammad Ebrahim Sahraeian, Byung-Jun Yoon
2011	J	`jnl`	Probabilistic reconstruction of the tumor progression process in gene regulatory networks in the presence of uncertainty. BMC Bioinform. Mohammad Shahrokh Esfahani, Byung-Jun Yoon, Edward R. Dougherty
2011	—	`conf`	Session TA8a1: Signal processing methods for representation, analysis, and control of biological systems. ACSCC Byung-Jun Yoon, Xiaoning Qian
2011	—	`conf`	Uncertainty-based essentiality in gene regulatory networks. GENSiPS Xiaoning Qian, Byung-Jun Yoon, Edward R. Dougherty
2010	J	`jnl`	Identification of diagnostic subnetwork markers for cancer in human protein-protein interaction network. BMC Bioinform. Junjie Su, Byung-Jun Yoon, Edward R. Dougherty
2010	Misc	`conf`	Identifying reliable subnetwork markers in protein-protein interaction network for classification of breast cancer metastasis. ICASSP Junjie Su, Byung-Jun Yoon
2010	Misc	`conf`	Shape matching based on graph alignment using hidden Markov models. ICASSP Xiaoning Qian, Byung-Jun Yoon
2009	J	`jnl`	Efficient Alignment of RNAs with Pseudoknots Using Sequence Alignment Constraints. EURASIP J. Bioinform. Syst. Biol. Byung-Jun Yoon
2009	J	`jnl`	Querying Pathways in Protein Interaction Networks Based on Hidden Markov Models. J. Comput. Biol. Xiaoning Qian, Sing-Hoi Sze, Byung-Jun Yoon
2008	B	`conf`	Coding Overcomplete Representations of Audio Using the MCLT. DCC Byung-Jun Yoon, Henrique S. Malvar
2008	J	`jnl`	Fast Structural Alignment of RNAs by Optimizing the Adjoining Order of Profile-csHMMs. IEEE J. Sel. Top. Signal Process. Byung-Jun Yoon, P. P. Vaidyanathan
2008	J	`jnl`	Structural Alignment of RNAs Using Profile-csHMMs and Its Application to RNA Homology Search: Overview and New Results. IEEE Trans. Autom. Control. Byung-Jun Yoon, Palghat P. Vaidyanathan
2007	J	`jnl`	Computational identification and analysis of noncoding RNAs - Unearthing the buried treasures in the genorne. IEEE Signal Process. Mag. Byung-Jun Yoon, P. P. Vaidyanathan
2007	—	`conf`	Fast Search of Sequences with Complex Symbol Correlations using Profile Context-Sensitive HMMS and Pre-Screening Filters. ICASSP (1) Byung-Jun Yoon, P. P. Vaidyanathan
2007	—	`conf`	Robust Adaptive Beamforming Algorithm using Instantaneous Direction of Arrival with Enhanced Noise Suppression Capability. ICASSP (1) Byung-Jun Yoon, Ivan Tashev, Alex Acero
2006	J	`jnl`	A practical approach for the design of nonuniform lapped transforms. IEEE Signal Process. Lett. Byung-Jun Yoon, Henrique S. Malvar
2006	J	`jnl`	Context-Sensitive Hidden Markov Models for Modeling Long-Range Dependencies in Symbol Sequences. IEEE Trans. Signal Process. Byung-Jun Yoon, P. P. Vaidyanathan
2006	—	`conf`	Profile Context-Sensitive HMMs for Probabilistic Modeling of Sequences With Complex Correlations. ICASSP (3) Byung-Jun Yoon, P. P. Vaidyanathan
2005	J	`jnl`	A multirate DSP model for estimation of discrete probability density functions. IEEE Trans. Signal Process. Byung-Jun Yoon, P. P. Vaidyanathan
2005	—	`conf`	Optimal alignment algorithm for context-sensitive hidden Markov models. ICASSP (4) Byung-Jun Yoon, P. P. Vaidyanathan
2004	—	`conf`	Discrete pdf estimation in the presence of noise. ISCAS (3) Byung-Jun Yoon, Palghat P. Vaidyanathan
2004	J	`jnl`	The role of signal-processing concepts in genomics and proteomics. J. Frankl. Inst. P. P. Vaidyanathan, Byung-Jun Yoon
2004	—	`conf`	Wavelet-based denoising by customized thresholding. ICASSP (2) Byung-Jun Yoon, Palghat P. Vaidyanathan
2003	—	`conf`	Discrete probability density estimation using multirate DSP models. ICASSP (6) Palghat P. Vaidyanathan, Byung-Jun Yoon
2003	A	`conf`	Discrete probability density estimation using multirate DSP models. ICME Palghat P. Vaidyanathan, Byung-Jun Yoon