# overview
Dr. Yoon's main theoretical interests include objective-based uncertainty quantification, optimal experimental design (OED), machine learning, and signal processing. Application areas of interest include bioinformatics, computational network biology, and AI-driven drug/materials discovery.

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Networking And Information Technology R&d

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1.1 Normal Biological Development And Functioning

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3102 Bioinformatics And Computational Biology

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Mean Objective Cost Of Uncertainty (mocu)

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4007 Control Engineering, Mechatronics And Robotics

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Networking And Information Technology R&d

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Networking And Information Technology R&d

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4.1 Discovery And Preclinical Testing Of Markers And Technologies

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3102 Bioinformatics And Computational Biology

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4.1 Discovery And Preclinical Testing Of Markers And Technologies

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Mean Objective Cost Of Uncertainty (mocu)

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3102 Bioinformatics And Computational Biology

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4603 Computer Vision And Multimedia Computation

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Approximate Mean Objective Cost Of Uncertainty (mocu)

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Networking And Information Technology R&d

# keywords[]
1.1 Normal Biological Development And Functioning

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3102 Bioinformatics And Computational Biology

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3102 Bioinformatics And Computational Biology

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Multiple Network Alignment And Clustering

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Mean Objective Cost Of Uncertainty (mocu)

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Mean Multi-objective Cost Of Uncertainty (multi-objective Mocu)

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1.1 Normal Biological Development And Functioning

# keywords[]
Networking And Information Technology R&d

# keywords[]
Mean Objective Cost Of Uncertainty (mocu)

# keywords[]
4603 Computer Vision And Multimedia Computation

# keywords[]
Mean Objective Cost Of Uncertainty (mocu)

# keywords[]
3102 Bioinformatics And Computational Biology

# keywords[]
Mean Objective Cost Of Uncertainty (mocu)

# educationAndTraining[].organization.label
California Institute of Technology - (Pasadena, California, United States)

# educationAndTraining[].name
B.S.E. Bachelor of Science in Engineering

# educationAndTraining[].organization.label
Seoul National University - (Seoul, South Korea)

# educationAndTraining[].organization.label
California Institute of Technology - (Pasadena, California, United States)

# awardsAndHonors[].label
Faculty Early Career Development (CAREER) Program

# publications[].label
Finding effective subnetwork markers for cancer by passing messages

# publications[].label
Fast Search of Sequences with Complex Symbol Correlations using Profile Context-Sensitive HMMS and Pre-Screening Filters

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Structural Alignment of RNAs Using Profile-csHMMs and Its Application to RNA Homology Search: Overview and New Results

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Effective Annotation of Noncoding RNA Families Using Profile Context-Sensitive HMMs

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Selected research articles from the 2017 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC).

# publications[].label
Comparative Analysis of Biological Networks: Hidden Markov model and Markov chain-based approach

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
AI-Driven Battery-Free Dual-Channel Wireless Optogenetics for High-Throughput Automation of Behavioral Analysis

# publications[].label
Designing Experiments for Optimal Reduction of Uncertainty in Gene Regulatory Networks

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Accurate and reliable cancer classification based on probabilistic inference of pathway activity.

# publications[].label
The role of signal-processing concepts in genomics and proteomics

# publications[].label
Effective Estimation of Node-to-Node Correspondence Between Different Graphs

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Optimal Experimental Design for Uncertain Systems Based on Coupled Differential Equations

# publications[].label
STRUCTURAL INTERVENTION OF GENE REGULATORY NETWORKS BY GENERAL RANK-K MATRIX PERTURBATION

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Autism Spectrum Disorder: A Neuro-Immunometabolic Hypothesis of the Developmental Origins.

# publications[].label
Probabilistic reconstruction of the tumor progression process in gene regulatory networks in the presence of uncertainty.

# publications[].label
CO-SEGMENTATION OF MULTIPLE IMAGES THROUGH RANDOM WALK ON GRAPHS

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Identification of CpG islands using a bank of IIR lowpass filters

# publications[].label
A network synthesis model for generating protein interaction network families.

# publications[].label
Identification of diagnostic subnetwork markers for cancer in human protein-protein interaction network.

# publications[].label
Optimal Experimental Design for Gene Regulatory Networks in the Presence of Uncertainty.

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Discrete pdf estimation in the presence of noise

# publications[].label
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.

# publications[].label
Finding Robust Subnetwork Markers that Improve Cross-Dataset Performance of Cancer Classification

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
CONTOUR-BASED HIDDEN MARKOV MODEL TO SEGMENT 2D ULTRASOUND IMAGES

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Identification of differentially expressed miRNAs in chicken lung and trachea with avian influenza virus infection by a deep sequencing approach.

# publications[].label
Profile context-sensitive HMMS for probabilistic modeling of sequences with complex correlations

# publications[].label
Computationally Efficient Experimental Design Strategy for Reducing Gene Network Uncertainty

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Probabilistic consistency transformation for multiple alignment of biological networks

# publications[].label
Rna secondary structure prediction using context-sensitive hidden markov models

# publications[].label
Selected research articles from the 2018 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC).

# publications[].label
A Novel Low-Complexity HMM Similarity Measure

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Systematic computational network-based analysis to predict subnetwork modules associated with pathogenicity and fumonisins in Fusarium verticillioides

# publications[].label
Geometric Affinity Propagation for Clustering With Network Knowledge

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Identification of differentially expressed miRNAs in chicken lung and trachea with avian influenza virus infection by a deep sequencing approach (vol 11, pg 373, 2010)

# publications[].label
Fast DNA Barcode Generating Algorithm Using Radix Coding Method

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Adaptive reference update (ARU) algorithm. A stochastic search algorithm for efficient optimization of multi-drug cocktails.

# publications[].label
PicXAA: greedy probabilistic construction of maximum expected accuracy alignment of multiple sequences.

# publications[].label
SMETANA: accurate and scalable algorithm for probabilistic alignment of large-scale biological networks.

# publications[].label
TRIMER: Transcription Regulation Integrated with MEtabolic Regulation

# publications[].label
Sensitivity analysis of genome-scale metabolic flux prediction

# publications[].label
Incorporating topological information for predicting robust cancer subnetwork markers in human protein-protein interaction network.

# publications[].label
Identification of Robust Pathway Markers for Cancer through Rank-Based Pathway Activity Inference.

# publications[].label
Coding Overcomplete Representations of Audio using the MCLT

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
ClusterM: a scalable algorithm for computational prediction of conserved protein complexes across multiple protein interaction networks.

# publications[].label
Efficient combinatorial drug optimization through stochastic search

# publications[].label
Quantifying the multi-objective cost of uncertainty

# publications[].label
UNCERTAINTY-BASED ESSENTIALITY IN GENE REGULATORY NETWORKS

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Optimal Alignment Algorithm for Context-Sensitive Hidden Markov Models

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
SIMPLE ALIGNMENT CONSTRAINTS FOR EFFICIENT ALIGNMENT OF RNA SEQUENCES USING FAMILY-SPECIFIC MODELS

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Effective identification of conserved pathways in biological networks using hidden Markov models.

# publications[].label
Optimal Experimental Design for Uncertain Systems Based on Coupled Differential Equations

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Discrete Probability Density Estimation Using Multirate DSP Models

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
PicXAA: A Probabilistic Scheme for Finding the Maximum Expected Accuracy Alignment of Multiple Biological Sequences

# publications[].label
Erratum to: Efficient experimental design for uncertainty reduction in gene regulatory networks.

# publications[].label
A Practical Approach for the Design of Nonuniform Lapped Transforms

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Evaluation of Rice Varieties for Resistance for Autumn Decline in Arkansas

# publications[].label
Selected research articles from the 2016 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC).

# publications[].label
Deep graph representations embed network information for robust disease marker identification.

# publications[].label
TOPAS: network-based structural alignment of RNA sequences.

# publications[].label
Enhancing our understanding of Fusarium maize stalk rot pathogenesis through gene association subnetwork module analyses

# publications[].label
Discrete Probability Density Estimation Using Multirate DSP Models

# publications[].label
Fast Structural Alignment of RNAs by Optimizing the Adjoining Order of Profile-csHMMs

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
AI-driven high-throughput automation of behavioral analysis and dual-channel wireless optogenetics for multiplexing brain dynamics

# publications[].label
Enhanced stochastic optimization algorithm for finding effective multi-target therapeutics.

# publications[].label
Examining De Novo Transcriptome Assemblies via a Quality Assessment Pipeline.

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
CUFID-query: accurate network querying through random walk based network flow estimation.

# publications[].label
SEQUOIA: significance enhanced network querying through context-sensitive random walk and minimization of network conductance.

# publications[].label
Fast Structural Similarity Search of Noncoding RNAs Based on Matched Filtering of Stem Patterns

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Computational identification of genetic subnetwork modules associated with maize defense response to Fusarium verticillioides.

# publications[].label
An overview of the role of context-sensitive HMMS in the prediction of ncrna genes

# publications[].label
PicXAA-R: efficient structural alignment of multiple RNA sequences using a greedy approach.

# publications[].label
Comparative analysis of protein interaction networks reveals that conserved pathways are susceptible to HIV-1 interception.

# publications[].label
De novo Transcriptome Assemblies and Annotation for Pacific Whiteleg Shrimp

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
A Rigorous Uncertainty-Aware Quantification Framework Is Essential for Reproducible and Replicable Machine Learning Workflows

# publications[].label
Designing Enhanced Classifiers Using Prior Process Knowledge: Regularized Maximum-Likelihood

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Robust Adaptive Beamforming Algorithm using Instantaneous Direction of Arrival with Enhanced Noise Suppression Capability

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Digital filters for gene prediction applications

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].publisher
Association for Computing Machinery (ACM)

# publications[].label
SHAPE MATCHING BASED ON GRAPH ALIGNMENT USING HIDDEN MARKOV MODELS

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Hidden Markov Models and their Applications in Biological Sequence Analysis.

# publications[].label
HMM with auxiliary memory: A new tool for modeling RNA secondary structures

# publications[].label
Efficient Active Learning for Gaussian Process Classification by Error Reduction

# publications[].publisher
Association for Computing Machinery (ACM)

# publications[].label
Efficient alignment of RNAs with pseudoknots using sequence alignment constraints.

# publications[].label
Simultaneous identification of robust synergistic subnetwork markers for effective cancer prognosis.

# publications[].label
AUTOMATED IMAGE ANALYSIS AND INFERENCE OF GENE FUNCTION FROM HIGH - CONTENT SCREENS

# publications[].label
Discrete optimal Bayesian classification with error-conditioned sequential sampling

# publications[].label
Optimal hybrid sequencing and assembly: Feasibility conditions for accurate genome reconstruction and cost minimization strategy.

# publications[].label
Special Issue on Genomic Signal Processing FOREWORD

# publications[].label
Bayesian Active Learning by Soft Mean Objective Cost of Uncertainty

# publications[].label
TRIMER: Transcription Regulation Integrated with Metabolic Regulation.

# publications[].label
Efficient experimental design for uncertainty reduction in gene regulatory networks.

# publications[].label
Accelerating Optimal Experimental Design for Robust Synchronization of Uncertain Kuramoto Oscillator Model Using Machine Learning

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Context-Sensitive Hidden Markov Models for Modeling Long-Range Dependencies in Symbol Sequences

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
A SIMPLE METHOD FOR FINDING STRUCTURALLY SIMILAR RNAS USING TWO-DIMENSIONAL DISCRETE CONVOLUTION

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Computational Prediction of Pathogenic Network Modules in Fusarium verticillioides.

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Comparison of Global and United States Social Determinants in COVID-19 Vaccination Rates

# publications[].label
Computational identification and analysis of noncoding RNAs - Unearthing the buried treasures in the genorne

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Effective computational detection of piRNAs using n-gram models and support vector machine.

# publications[].label
FAST NETWORK QUERYING ALGORITHM FOR SEARCHING LARGE-SCALE BIOLOGICAL NETWORKS

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
AI-enabled, implantable, multichannel wireless telemetry for photodynamic therapy.

# publications[].label
Identifying new genetic targets for maize ear rot and mycotoxin control through computational subnetwork module analyses

# publications[].label
Accurate multiple network alignment through context-sensitive random walk.

# publications[].label
Quantifying the Multi-Objective Cost of Uncertainty

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Modeling and Identification of Alternative Folding in Regulatory RNAS using Context-Sensitive HMMS

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Querying pathways in protein interaction networks based on hidden Markov models.

# publications[].label
Model-Based Robust Filtering and Experimental Design for Stochastic Differential Equation Systems

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Robust importance sampling for error estimation in the context of optimal Bayesian transfer learning.

# publications[].label
Effective comparative analysis of protein-protein interaction networks by measuring the steady-state network flow using a Markov model.

# publications[].label
IDENTIFYING RELIABLE SUBNETWORK MARKERS IN PROTEIN-PROTEIN INTERACTION NETWORK FOR CLASSIFICATION OF BREAST CANCER METASTASIS

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Improved estimation of discrete probability density functions using multirate models

# publications[].label
Finding Robust Pathway Markers for Cancer Classification

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
PicXAA: a probabilistic scheme for finding the maximum expected accuracy alignment of multiple biological sequences.

# publications[].label
Enhancing the accuracy of HMM-based conserved pathway prediction using global correspondence scores.

# publications[].label
Computational and functional analyses of MADS-box transcription factor-mediated regulation of fumonisin biosynthesis in Fusarium verticillioides

# publications[].label
A Multirate DSP Model for Estimation of Discrete Probability Density Functions

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Quantifying the Objective Cost of Uncertainty in Complex Dynamical Systems

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
RESQUE: Network Reduction Using Semi-Markov Random Walk Scores for Efficient Querying of Biological Networks (Extended Abstract)

# publications[].label
RESQUE: network reduction using semi-Markov random walk scores for efficient querying of biological networks.

# publications[].label
PicXAA-Web: a web-based platform for non-progressive maximum expected accuracy alignment of multiple biological sequences.

# researcherOn[].label
Elements: Software: Autonomous, Robust, and Optimal In-Silico Experimental Design Platform for Accelerating Innovations in Materials Discovery

# researcherOn[].awardedBy.label
National Science Foundation - (Arlington, Virginia, United States)

# researcherOn[].label
Brookhaven Science Associates - Joint Assignment Agreement

# researcherOn[].awardedBy.label
Brookhaven National Laboratory - (Upton, New York, United States)

# researcherOn[].label
EAGER: Identifying Blockmodel Functional Modules across Multiple Networks

# researcherOn[].awardedBy.label
National Science Foundation - (Arlington, Virginia, United States)

# researcherOn[].label
FFATA:  CAREER: Models and Algorithms for Comparative Analysis of Biological Networks

# researcherOn[].awardedBy.label
National Science Foundation - (Arlington, Virginia, United States)

# researcherOn[].label
International Workshop on Computational Network Biology: Modeling,-Analysis, and Control (CNB-MAC 2016)

# researcherOn[].awardedBy.label
National Science Foundation - (Arlington, Virginia, United States)

# researcherOn[].label
International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC 2015)

# researcherOn[].awardedBy.label
National Science Foundation - (Arlington, Virginia, United States)

# streetAddress
Texas A&M University; Electrical Engineering; 3128 TAMU

# etdChairOf[].label
Khunlertgit, Navadon (2016-11). Improvement of Reproducibility in Cancer Classification Based on Pathway Markers and Subnetwork Markers. Doctoral Dissertation.

# etdChairOf[].label
Sahraeian, Sayed 1983- (2013-01). Probabilistic Approaches in Comparative Analysis of Biological Networks and Sequences. Doctoral Dissertation.

# etdChairOf[].label
Nikooienejad, Amir (2013-07). Presence / Absence Marker Discovery in RAD Markers for Multiplexed Samples in the Context of Next-Generation Sequencing. Master's Thesis.

# etdChairOf[].label
Su, Junjie (2012-02). Accurate and Reliable Cancer Classi cation Based on Pathway-Markers and Subnetwork-Markers. Master's Thesis.

# etdChairOf[].label
Kim, Mansuck (2016-02). Computational Identification of Functional Modules and Hub Genes Involved in Pathogenicity-Associated or Defense Response on Fusarium Verticillioides-Maize Interactions. Doctoral Dissertation.