Discrete probability density estimation using multirate DSP models. - Palghat P. Vaidyanathan; Byung-Jun Yoon (ICASSP (6), 2003)

Wavelet-based denoising by customized thresholding. - Byung-Jun Yoon; Palghat P. Vaidyanathan (ICASSP (2), 2004)

Discrete pdf estimation in the presence of noise. - Byung-Jun Yoon; Palghat P. Vaidyanathan (ISCAS (3), 2004)

The role of signal-processing concepts in genomics and proteomics. - P. P. Vaidyanathan; Byung-Jun Yoon (J. Frankl. Inst., 2004)

Optimal alignment algorithm for context-sensitive hidden Markov models. - Byung-Jun Yoon; P. P. Vaidyanathan (ICASSP (4), 2005)

A multirate DSP model for estimation of discrete probability density functions. - Byung-Jun Yoon; P. P. Vaidyanathan (IEEE Trans. Signal Process., 2005)

Profile Context-Sensitive HMMs for Probabilistic Modeling of Sequences With Complex Correlations. - Byung-Jun Yoon; P. P. Vaidyanathan (ICASSP (3), 2006)

A practical approach for the design of nonuniform lapped transforms. - Byung-Jun Yoon; Henrique S. Malvar (IEEE Signal Process. Lett., 2006)

Context-Sensitive Hidden Markov Models for Modeling Long-Range Dependencies in Symbol Sequences. - Byung-Jun Yoon; P. P. Vaidyanathan (IEEE Trans. Signal Process., 2006)

Robust Adaptive Beamforming Algorithm using Instantaneous Direction of Arrival with Enhanced Noise Suppression Capability. - Byung-Jun Yoon; Ivan Tashev; Alex Acero (ICASSP (1), 2007)

Fast Search of Sequences with Complex Symbol Correlations using Profile Context-Sensitive HMMS and Pre-Screening Filters. - Byung-Jun Yoon; P. P. Vaidyanathan (ICASSP (1), 2007)

Computational identification and analysis of noncoding RNAs - Unearthing the buried treasures in the genorne. - Byung-Jun Yoon; P. P. Vaidyanathan (IEEE Signal Process. Mag., 2007)

Coding Overcomplete Representations of Audio Using the MCLT. - Byung-Jun Yoon; Henrique S. Malvar (DCC, 2008)

Fast Structural Alignment of RNAs by Optimizing the Adjoining Order of Profile-csHMMs. - Byung-Jun Yoon; P. P. Vaidyanathan (IEEE J. Sel. Top. Signal Process., 2008)

Structural Alignment of RNAs Using Profile-csHMMs and Its Application to RNA Homology Search: Overview and New Results. - Byung-Jun Yoon; Palghat P. Vaidyanathan (IEEE Trans. Autom. Control., 2008)

Efficient Alignment of RNAs with Pseudoknots Using Sequence Alignment Constraints. - Byung-Jun Yoon (EURASIP J. Bioinform. Syst. Biol., 2009)

Querying Pathways in Protein Interaction Networks Based on Hidden Markov Models. - Xiaoning Qian; Sing-Hoi Sze; Byung-Jun Yoon (J. Comput. Biol., 2009)

Shape matching based on graph alignment using hidden Markov models. - Xiaoning Qian; Byung-Jun Yoon (ICASSP, 2010)

Identifying reliable subnetwork markers in protein-protein interaction network for classification of breast cancer metastasis. - Junjie Su; Byung-Jun Yoon (ICASSP, 2010)

Identification of diagnostic subnetwork markers for cancer in human protein-protein interaction network. - Junjie Su; Byung-Jun Yoon; Edward R. Dougherty (BMC Bioinform., 2010)

Session TA8a1: Signal processing methods for representation, analysis, and control of biological systems. - Byung-Jun Yoon; Xiaoning Qian (ACSCC, 2011)

Designing enhanced classifiers using prior process knowledge: Regularized maximum-likelihood. - Mohammad Shahrokh Esfahani; Amin Zollanvari; Byung-Jun Yoon; Edward R. Dougherty (GENSiPS, 2011)

Efficient combinatorial drug optimization through stochastic search. - Mansuck Kim; Byung-Jun Yoon (GENSiPS, 2011)

Uncertainty-based essentiality in gene regulatory networks. - Xiaoning Qian; Byung-Jun Yoon; Edward R. Dougherty (GENSiPS, 2011)

Probabilistic consistency transformation for multiple alignment of biological networks. - Sayed Mohammad Ebrahim Sahraeian; Byung-Jun Yoon (GENSiPS, 2011)

Finding effective subnetwork markers for cancer by passing messages. - Byung-Jun Yoon (GENSiPS, 2011)

Contour-based hidden Markov model to segment 2D ultrasound images. - Xiaoning Qian; Byung-Jun Yoon (ICASSP, 2011)

Fast network querying algorithm for searching large-scale biological networks. - Sayed Mohammad Ebrahim Sahraeian; Byung-Jun Yoon (ICASSP, 2011)

Probabilistic reconstruction of the tumor progression process in gene regulatory networks in the presence of uncertainty. - Mohammad Shahrokh Esfahani; Byung-Jun Yoon; Edward R. Dougherty (BMC Bioinform., 2011)

Enhancing the accuracy of HMM-based conserved pathway prediction using global correspondence scores. - Xiaoning Qian; Sayed Mohammad Ebrahim Sahraeian; Byung-Jun Yoon (BMC Bioinform., 2011)

Comparative analysis of protein interaction networks reveals that conserved pathways are susceptible to HIV-1 interception. - Xiaoning Qian; Byung-Jun Yoon (BMC Bioinform., 2011)

PicXAA-R: Efficient structural alignment of multiple RNA sequences using a greedy approach. - Sayed Mohammad Ebrahim Sahraeian; Byung-Jun Yoon (BMC Bioinform., 2011)

Enhanced stochastic optimization algorithm for finding effective multi-target therapeutics. - Byung-Jun Yoon (BMC Bioinform., 2011)

PicXAA-Web: a web-based platform for non-progressive maximum expected accuracy alignment of multiple biological sequences. - Sayed Mohammad Ebrahim Sahraeian; Byung-Jun Yoon (Nucleic Acids Res., 2011)

A Novel Low-Complexity HMM Similarity Measure. - Sayed Mohammad Ebrahim Sahraeian; Byung-Jun Yoon (IEEE Signal Process. Lett., 2011)

Finding robust pathway markers for cancer classification. - Navadon Khunlertgit; Byung-Jun Yoon (GENSiPS, 2012)

Fast DNA barcode generating algorithm using Radix Coding method. - Amir Nikooienejad; Richard Metz; Byung-Jun Yoon; Charles D. Johnson (GENSiPS, 2012)

Structural intervention of gene regulatory networks by general rank-k matrix perturbation. - Xiaoning Qian; Byung-Jun Yoon; Edward R. Dougherty (ICASSP, 2012)

RESQUE: Network Reduction Using Semi-Markov Random Walk Scores for Efficient Querying of Biological Networks (Extended Abstract). - Sayed Mohammad Ebrahim Sahraeian; Byung-Jun Yoon (RECOMB, 2012)

RESQUE: Network reduction using semi-Markov random walk scores for efficient querying of biological networks. - Sayed Mohammad Ebrahim Sahraeian; Byung-Jun Yoon (Bioinform., 2012)

Comparative Analysis of Biological Networks: Hidden Markov model and Markov chain-based approach. - Byung-Jun Yoon; Xiaoning Qian; Sayed Mohammad Ebrahim Sahraeian (IEEE Signal Process. Mag., 2012)

Automated image analysis and inference of gene function from high - Content screens. - Priyanka J. Raja; Justin Jacob; Byung-Jun Yoon; Geoffrey Bartholomeusz; Arvind Rao (EUSIPCO, 2013)

Designing experiments for optimal reduction of uncertainty in gene regulatory networks. - Roozbeh Dehghannasiri; Byung-Jun Yoon; Edward R. Dougherty (GENSiPS, 2013)

Finding robust subnetwork markers that improve cross-dataset performance of cancer classification. - Navadon Khunlertgit; Byung-Jun Yoon (GlobalSIP, 2013)

Identification of Robust Pathway Markers for Cancer through Rank-Based Pathway Activity Inference. - Navadon Khunlertgit; Byung-Jun Yoon (Adv. Bioinformatics, 2013)

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. - Mohammad Shahrokh Esfahani; Jason M. Knight; Amin Zollanvari; Byung-Jun Yoon; Edward R. Dougherty (Pattern Recognit., 2013)

Quantifying the Objective Cost of Uncertainty in Complex Dynamical Systems. - Byung-Jun Yoon; Xiaoning Qian; Edward R. Dougherty (IEEE Trans. Signal Process., 2013)

A novel context-sensitive random walk model for estimating node correspondence between two biological networks. - Hyundoo Jeong; Byung-Jun Yoon (BCB, 2014)

Computational identification of functional network modules associated with the pathogenicity of Fusarium verticillioides. - Mansuck Kim; Huan Zhang; Charles Woloshuk; Won-Bo Shim; Byung-Jun Yoon (BCB, 2014)

Computationally efficient experimental design strategy for reducing gene network uncertainty. - Roozbeh Dehghannasiri; Byung-Jun Yoon; Edward R. Dougherty (GlobalSIP, 2014)

De novo transcriptome assemblies and annotation for pacifie whiteleg shrimp. - Noushin Ghaffari; Osama A. Arshad; Hyundoo Jeong; John Thiltges; Michael F. Criscitiello; Byung-Jun Yoon; Aniruddha Datta; Charles D. Johnson (GlobalSIP, 2014)

Sequence alignment by passing messages. - Byung-Jun Yoon (BMC Genom., 2014)

Simultaneous identification of robust synergistic subnetwork markers for effective cancer prognosis. - Navadon Khunlertgit; Byung-Jun Yoon (EURASIP J. Bioinform. Syst. Biol., 2014)

Identifying molecular complexes in biological networks through context sensitive network querying. - Hyundoo Jeong; Byung-Jun Yoon (BCB, 2015)

Computational identification of key functional genes associated with fusarium verticillioides pathogenicity. - Mansuck Kim; Huan Zhang; Charles Woloshuk; Won-Bo Shim; Byung-Jun Yoon (BCB, 2015)

Erratum to: Efficient experimental design for uncertainty reduction in gene regulatory networks. - Roozbeh Dehghannasiri; Byung-Jun Yoon; Edward R. Dougherty (BMC Bioinform., 2015)

Accurate multiple network alignment through context-sensitive random walk. - Hyundoo Jeong; Byung-Jun Yoon (BMC Syst. Biol., 2015)

Discrete optimal Bayesian classification with error-conditioned sequential sampling. - Ariana Broumand; Mohammad Shahrokh Esfahani; Byung-Jun Yoon; Edward R. Dougherty (Pattern Recognit., 2015)

Effective Estimation of Node-to-Node Correspondence Between Different Graphs. - Hyundoo Jeong; Byung-Jun Yoon (IEEE Signal Process. Lett., 2015)

Optimal Experimental Design for Gene Regulatory Networks in the Presence of Uncertainty. - Roozbeh Dehghannasiri; Byung-Jun Yoon; Edward R. Dougherty (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

Efficient experimental design for uncertainty reduction in gene regulatory networks. - Roozbeh Dehghannasiri; Byung-Jun Yoon; Edward R. Dougherty (BMC Bioinform., 2015)

Computational identification of genetic subnetwork modules associated with maize defense response to Fusarium verticillioides. - Mansuck Kim; Huan Zhang; Charles Woloshuk; Won-Bo Shim; Byung-Jun Yoon (BMC Bioinform., 2015)

Inference of gene regulatory networks: validation and uncertainty. - Xiaoning Qian; Byung-Jun Yoon; Edward R. Dougherty (Big Data over Networks, 2016)

Co-segmentation of multiple images through random walk on graphs. - Yijie Wang 003; Byung-Jun Yoon; Xiaoning Qian (ICASSP, 2016)

Effective comparative analysis of protein-protein interaction networks by measuring the steady-state network flow using a Markov model. - Hyundoo Jeong; Xiaoning Qian; Byung-Jun Yoon (BMC Bioinform., 2016)

Incorporating topological information for predicting robust cancer subnetwork markers in human protein-protein interaction network. - Navadon Khunlertgit; Byung-Jun Yoon (BMC Bioinform., 2016)

CNB-MAC'17: The Fourth International Workshop on Computational Network Biology: Modeling, Analysis, and Control. - Byung-Jun Yoon; Xiaoning Qian; Tamer Kahveci (BCB, 2017)

Effective computational detection of piRNAs using n-gram models and support vector machine. - Chun-Chi Chen; Xiaoning Qian; Byung-Jun Yoon (BMC Bioinform., 2017)

CUFID-query: accurate network querying through random walk based network flow estimation. - Hyundoo Jeong; Xiaoning Qian; Byung-Jun Yoon (BMC Bioinform., 2017)

Selected research articles from the 2016 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC). - Byung-Jun Yoon; Xiaoning Qian; Tamer Kahveci (BMC Bioinform., 2017)

SEQUOIA: significance enhanced network querying through context-sensitive random walk and minimization of network conductance. - Hyundoo Jeong; Byung-Jun Yoon (BMC Syst. Biol., 2017)

Optimal hybrid sequencing and assembly: Feasibility conditions for accurate genome reconstruction and cost minimization strategy. - Chun-Chi Chen; Noushin Ghaffari; Xiaoning Qian; Byung-Jun Yoon (Comput. Biol. Chem., 2017)

Comprehensive Updates in Network Synthesis Models to Create An Improved Benchmark for Network Alignment Algorithms. - Hyun-Myung Woo; Hyundoo Jeong; Byung-Jun Yoon (BCB, 2018)

Selected research articles from the 2017 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC). - Byung-Jun Yoon; Xiaoning Qian; Tamer Kahveci; Ranadip Pal (BMC Bioinform., 2018)

Examining De Novo Transcriptome Assemblies via a Quality Assessment Pipeline. - Noushin Ghaffari; Osama A. Arshad; Hyundoo Jeong; John Thiltges; Michael F. Criscitiello; Byung-Jun Yoon; Aniruddha Datta; Charles D. Johnson (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

Computational Prediction of Pathogenic Network Modules in Fusarium verticillioides. - Mansuck Kim; Huan Zhang; Charles Woloshuk; Won-Bo Shim; Byung-Jun Yoon (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

TOPAS: network-based structural alignment of RNA sequences. - Chun-Chi Chen; Hyundoo Jeong; Xiaoning Qian; Byung-Jun Yoon (Bioinform., 2019)

RNAdetect: efficient computational detection of novel non-coding RNAs. - Chun-Chi Chen; Xiaoning Qian; Byung-Jun Yoon (Bioinform., 2019)

Selected research articles from the 2018 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC). - Byung-Jun Yoon; Xiaoning Qian; Tamer Kahveci; Ranadip Pal (BMC Bioinform., 2019)

Machine Learning Enabled Adaptive Wireless Power Transmission System for Neuroscience Study. - Hyun-Myung Woo; Woo Seok Kim; Sungcheol Hong; Vivekanand Jeevakumar; Clay M. Smithhart; Theodore J. Price; Byung-Jun Yoon; Sung Il Park (ACSSC, 2020)

Network-Based RNA Structural Alignment Through Optimal Local Neighborhood Matching. - Hyun-Myung Woo; Byung-Jun Yoon (ACSSC, 2020)

ClusterM: a scalable algorithm for computational prediction of conserved protein complexes across multiple protein interaction networks. - Yijie Wang 003; Hyundoo Jeong; Byung-Jun Yoon; Xiaoning Qian (BMC Genom., 2020)

Model-Based Robust Filtering and Experimental Design for Stochastic Differential Equation Systems. - Guang Zhao; Xiaoning Qian; Byung-Jun Yoon; Francis J. Alexander; Edward R. Dougherty (IEEE Trans. Signal Process., 2020)

Physics-constrained Automatic Feature Engineering for Predictive Modeling in Materials Science. - Ziyu Xiang; Mingzhou Fan; Guillermo Vázquez Tovar; William Trehern; Byung-Jun Yoon; Xiaofeng Qian; Raymundo Arróyave; Xiaoning Qian (AAAI, 2021)

AI-Enabled High-Throughput Wireless Telemetry for Effective Photodynamic Therapy. - Woo Seok Kim; Hyun-Myung Woo; M. Ibrahim Khot; Sungcheol Hong; David G. Jayne; Byung-Jun Yoon; Sung Il Park (ACSCC, 2021)

Bayesian Active Learning by Soft Mean Objective Cost of Uncertainty. - Guang Zhao; Edward R. Dougherty; Byung-Jun Yoon; Francis J. Alexander; Xiaoning Qian (AISTATS, 2021)

Uncertainty-aware Active Learning for Optimal Bayesian Classifier. - Guang Zhao; Edward R. Dougherty; Byung-Jun Yoon; Francis J. Alexander; Xiaoning Qian (ICLR, 2021)

Efficient Active Learning for Gaussian Process Classification by Error Reduction. - Guang Zhao; Edward R. Dougherty; Byung-Jun Yoon; Francis J. Alexander; Xiaoning Qian (NeurIPS, 2021)

Optimal Experimental Design for Uncertain Systems Based on Coupled Differential Equations. - Youngjoon Hong; Bongsuk Kwon; Byung-Jun Yoon (IEEE Access, 2021)

Quantifying the Multi-Objective Cost of Uncertainty. - Byung-Jun Yoon; Xiaoning Qian; Edward R. Dougherty (IEEE Access, 2021)

MONACO: accurate biological network alignment through optimal neighborhood matching between focal nodes. - Hyun-Myung Woo; Byung-Jun Yoon (Bioinform., 2021)

Co-design Center for Exascale Machine Learning Technologies (ExaLearn). - Francis J. Alexander; James A. Ang; Jenna A. Bilbrey; Jan Balewski; Tiernan Casey; Ryan Chard; Jong Choi 001; Sutanay Choudhury; Bert J. Debusschere; Anthony M. DeGennaro; Nikoli Dryden; J. Austin Ellis; et al. (Int. J. High Perform. Comput. Appl., 2021)

Accelerating Optimal Experimental Design for Robust Synchronization of Uncertain Kuramoto Oscillator Model Using Machine Learning. - Hyun-Myung Woo; Youngjoon Hong; Bongsuk Kwon; Byung-Jun Yoon (IEEE Trans. Signal Process., 2021)

Comprehensive analysis of gene expression profiles to radiation exposure reveals molecular signatures of low-dose radiation response. - Xihaier Luo; Sean McCorkle; Gilchan Park; Vanessa López-Marrero; Shinjae Yoo; Edward R. Dougherty; Xiaoning Qian; Francis J. Alexander; Byung-Jun Yoon (BIBM, 2022)

Adaptive Group Testing with Mismatched Models. - Mingzhou Fan; Byung-Jun Yoon; Francis J. Alexander; Edward R. Dougherty; Xiaoning Qian (ICASSP, 2022)

Deep graph representations embed network information for robust disease marker identification. - Omar Maddouri; Xiaoning Qian; Byung-Jun Yoon (Bioinform., 2022)

Looking back on forward-looking COVID models. - Paul Chong; Byung-Jun Yoon; Debbie Lai; Michael Carlson; Jarone Lee; Shuhan He (Patterns, 2022)

Robust importance sampling for error estimation in the context of optimal Bayesian transfer learning. - Omar Maddouri; Xiaoning Qian; Francis J. Alexander; Edward R. Dougherty; Byung-Jun Yoon (Patterns, 2022)

Enhancing Cryo-EM Particle Picking Through Consistency Model-based Latent Space Denoiser. - Alif Bin Abdul Qayyum; Xiaoning Qian; Byung-Jun Yoon (BCB, 2023)

Automated Extraction of Molecular Interactions and Pathway Knowledge using Large Language Model, Galactica: Opportunities and Challenges. - Gilchan Park; Byung-Jun Yoon; Xihaier Luo; Vanessa López-Marrero; Patrick R. Johnstone; Shinjae Yoo; Francis J. Alexander (BioNLP@ACL, 2023)

A Rigorous Uncertainty-Aware Quantification Framework Is Essential for Reproducible and Replicable Machine Learning Workflows. - Line Pouchard; Kristofer G. Reyes; Francis J. Alexander; Byung-Jun Yoon (CoRR, 2023)

Comparative Performance Evaluation of Large Language Models for Extracting Molecular Interactions and Pathway Knowledge. - Gilchan Park; Byung-Jun Yoon; Xihaier Luo; Vanessa López-Marrero; Patrick R. Johnstone; Shinjae Yoo; Francis J. Alexander (CoRR, 2023)

Neural message-passing for objective-based uncertainty quantification and optimal experimental design. - Qihua Chen; Xuejin Chen; Hyun-Myung Woo; Byung-Jun Yoon (Eng. Appl. Artif. Intell., 2023)

Sensitivity Analysis of Genome-Scale Metabolic Flux Prediction. - Puhua Niu; Maria J. Soto; Shuai Huang 001; Byung-Jun Yoon; Edward R. Dougherty; Francis J. Alexander; Ian Blaby; Xiaoning Qian (J. Comput. Biol., 2023)

Accelerating scientific discoveries through data-driven innovations. - Francis J. Alexander; Meifeng Lin; Xiaoning Qian; Byung-Jun Yoon (Patterns, 2023)

Knowledge-driven learning, optimization, and experimental design under uncertainty for materials discovery. - Xiaoning Qian; Byung-Jun Yoon; Raymundo Arróyave; Xiaofeng Qian; Edward R. Dougherty (Patterns, 2023)

Optimal decision-making in high-throughput virtual screening pipelines. - Hyun-Myung Woo; Xiaoning Qian; Li Tan; Shantenu Jha; Francis J. Alexander; Edward R. Dougherty; Byung-Jun Yoon (Patterns, 2023)

Geometric Affinity Propagation for Clustering With Network Knowledge. - Omar Maddouri; Xiaoning Qian; Byung-Jun Yoon (IEEE Trans. Knowl. Data Eng., 2023)

Uncertainty-aware Continuous Implicit Neural Representations for Remote Sensing Object Counting. - Siyuan Xu; Yucheng Wang; Mingzhou Fan; Byung-Jun Yoon; Xiaoning Qian (AISTATS, 2024)

Calibration of Compartmental Epidemiological Models via Graybox Bayesian Optimization. - Puhua Niu; Byung-Jun Yoon; Xiaoning Qian (BHI, 2024)

Privacy-Preserving Federated Learning for Science: Challenges and Research Directions. - Kibaek Kim; Krishnan Raghavan; Olivera Kotevska; Matthieu Dorier; Ravi K. Madduri; Minseok Ryu; Todd S. Munson; Robert Ross; Thomas Flynn 001; Ai Kagawa; Byung-Jun Yoon; Christian Engelmann; et al. (IEEE Big Data, 2024)

Learning Active Subspaces for Effective and Scalable Uncertainty Quantification in Deep Neural Networks. - Sanket R. Jantre; Nathan M. Urban; Xiaoning Qian; Byung-Jun Yoon (ICASSP, 2024)

Hierarchical Neural Operator Transformer with Learnable Frequency-aware Loss Prior for Arbitrary-scale Super-resolution. - Xihaier Luo; Xiaoning Qian; Byung-Jun Yoon (ICML, 2024)

When Uncertainty-Based Active Learning May Fail? - Amir Hossein Rahmati; Mingzhou Fan; Ruida Zhou; Nathan M. Urban; Byung-Jun Yoon; Xiaoning Qian (ICPR (1), 2024)

Leveraging Active Subspaces to Capture Epistemic Model Uncertainty in Deep Generative Models for Molecular Design. - A. N. M. Nafiz Abeer; Sanket R. Jantre; Nathan M. Urban; Byung-Jun Yoon (MLSP, 2024)

Implicit Neural Representations for Simultaneous Reduction and Continuous Reconstruction of Multi-Altitude Climate Data. - Alif Bin Abdul Qayyum; Xihaier Luo; Nathan M. Urban; Xiaoning Qian; Byung-Jun Yoon (MLSP, 2024)

Multi-fidelity Bayesian Optimization with Multiple Information Sources of Input-dependent Fidelity. - Mingzhou Fan; Byung-Jun Yoon; Edward R. Dougherty; Nathan M. Urban; Francis J. Alexander; Raymundo Arróyave; Xiaoning Qian (UAI, 2024)

Multi-modal Representation Learning for Cross-modal Prediction of Continuous Weather Patterns from Discrete Low-Dimensional Data. - Alif Bin Abdul Qayyum; Xihaier Luo; Nathan M. Urban; Xiaoning Qian; Byung-Jun Yoon (CoRR, 2024)

Neural machine translation of clinical procedure codes for medical diagnosis and uncertainty quantification. - Pei-Hung Chung; Shuhan He; Norawit Kijpaisalratana; Abdel-badih el Ariss; Byung-Jun Yoon (CoRR, 2024)

Enhancing Generative Molecular Design via Uncertainty-guided Fine-tuning of Variational Autoencoders. - A. N. M. Nafiz Abeer; Sanket R. Jantre; Nathan M. Urban; Byung-Jun Yoon (CoRR, 2024)

Understanding Uncertainty-based Active Learning Under Model Mismatch. - Amir Hossein Rahmati; Mingzhou Fan; Ruida Zhou; Nathan M. Urban; Byung-Jun Yoon; Xiaoning Qian (CoRR, 2024)

Pathway-Guided Optimization of Deep Generative Molecular Design Models for Cancer Therapy. - Alif Bin Abdul Qayyum; Susan D. Mertins; Amanda K. Paulson; Nathan M. Urban; Byung-Jun Yoon (CoRR, 2024)

LoRA-BERT: a Natural Language Processing Model for Robust and Accurate Prediction of long non-coding RNAs. - Nicholas Jeon; Xiaoning Qian; Lamin SaidyKhan; Paul de Figueiredo; Byung-Jun Yoon (CoRR, 2024)

Variable Rate Neural Compression for Sparse Detector Data. - Yi Huang 019; Yeonju Go; Jin Huang; Shuhang Li; Xihaier Luo; Thomas Marshall; Joseph D. Osborn; Christopher Pinkenburg; Yihui Ren 001; Evgeny Shulga; Shinjae Yoo; Byung-Jun Yoon (CoRR, 2024)

Efficient Compression of Sparse Accelerator Data Using Implicit Neural Representations and Importance Sampling. - Xihaier Luo; Samuel Lurvey; Yi Huang 019; Yihui Ren 001; Jin Huang; Byung-Jun Yoon (CoRR, 2024)

Epidemiological Model Calibration via Graybox Bayesian Optimization. - Puhua Niu; Byung-Jun Yoon; Xiaoning Qian (CoRR, 2024)

Pathway-based analyses of gene expression profiles at low doses of ionizing radiation. - 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 (Frontiers Bioinform., 2024)

Multi-objective latent space optimization of generative molecular design models. - A. N. M. Nafiz Abeer; Nathan M. Urban; M. Ryan Weil; Francis J. Alexander; Byung-Jun Yoon (Patterns, 2024)

Enhancing Future Link Prediction in Quantum Computing Semantic Networks through LLM-Initiated Node Features. - Gilchan Park; Paul Baity; Byung-Jun Yoon; Adolfy Hoisie (COLING (Industry), 2025)

Scale-Invariant Implicit Neural Representations For Object Counting. - Siyuan Xu; Yucheng Wang; Xihaier Luo; Byung-Jun Yoon; Xiaoning Qian (CVPR Workshops, 2025)

Pareto Prompt Optimization. - Guang Zhao; Byung-Jun Yoon; Gilchan Park; Shantenu Jha; Shinjae Yoo; Xiaoning Qian (ICLR, 2025)

An Effective Pipeline for Training Variational Autoencoders for Synthesizable and Optimized Molecular Design. - Fardeen H. Mozumder; Byung-Jun Yoon (IEEE Access, 2025)

Comparative Performance Evaluation of Large Language Models for Extracting Molecular Interactions and Pathway Knowledge. - Gilchan Park; Byung-Jun Yoon; Xihaier Luo; Vanessa López-Marrero; Shinjae Yoo; Shantenu Jha (J. Comput. Biol., 2025)

Uncertainty-Aware Adaptation of Large Language Models for Protein-Protein Interaction Analysis. - Sanket R. Jantre; Tianle Wang 001; Gilchan Park; Kriti Chopra; Nicholas Jeon; Xiaoning Qian; Nathan M. Urban; Byung-Jun Yoon (CoRR, 2025)

C-LoRA: Contextual Low-Rank Adaptation for Uncertainty Estimation in Large Language Models. - Amir Hossein Rahmati; Sanket R. Jantre; Weifeng Zhang; Yucheng Wang; Byung-Jun Yoon; Nathan M. Urban; Xiaoning Qian (CoRR, 2025)

Forward Target Propagation: A Forward-Only Approach to Global Error Credit Assignment via Local Losses. - Nazmus Saadat As-Saquib; A. N. M. Nafiz Abeer; Hung-Ta Chien; Byung-Jun Yoon; Suhas Kumar; Su-in Yi (CoRR, 2025)

Cost-effective Reduced-Order Modeling via Bayesian Active Learning. - Amir Hossein Rahmati; Nathan M. Urban; Byung-Jun Yoon; Xiaoning Qian (CoRR, 2025)