Hyokyeong Lee's homepage

My research interests are mathematical modeling of biological problems using statistical machine learning and numerical optimization, and developing new machine learning methods with theoretical foundations. I have developed novel methods by composing machine learning and optimization or respectively to solve various real-world problems.


  • Kernel-based learning for linearly inseparable data

  • Structure learning of graphical models

  • Cancer genomics

  • Genome-wide association study

  • Computational drug discovery

  • Publications


  • Hyokyeong Lee. Oil Field Optimization: Optimization and Machine Learning Approaches. Scholars' Press. 2014. ISBN-13: 978-3-639-70862-2, ISBN-10: 3639708628. Available from Amazon.com

  • Journal publications

  • Hyokyeong Lee and Liang Chen. Inference of kinship using spatial distributions of SNPs for genome-wide association studies, BMC Genomics, Under review.

  • Hyokyeong Lee, Asher Moody-Davis, Utsab Saha, Brian M. Suzuki, Daniel Asarnow, Steven Chen, Michelle Arkin, Conor R. Caffrey, and Rahul Singh. Quantification and Clustering of Phenotypic Screening Data using Time-Series Analysis for Chemotherapy of Schistosomiasis, BMC Genomics, 13(Suppl 1):S4, 2012.

  • Hyokyeong Lee, Ke-Thia Yao, Olu Ogbonnaya Okpani, Aiichiro Nakano, Iraj Ershaghi. Hybrid Constrained Nonlinear Optimization to Infer Injector-Producer Relationship in Oil Fields. International Journal of Computational Science, vol. 4, no. 1, pp. 1-22, 2010.

  • Carole Beal, Lei Qu, Hyokyeong Lee. Mathematics motivation and achievement as predictors of high school students guessing and help-seeking with instructional software, Journal of Computer Assisted Learning, 2009.

  • Conference publications

  • Hyokyeong Lee and Rahul Singh. Unsupervised Kernel Parameter Estimation by Constrained Nonlinear Optimization for Clustering Nonlinear Biological Data, IEEE International Conference on Bioinformatics and Biomedicine, Philadelphia, USA, Oct 4 - 7, 2012.

  • Hyokyeong Lee and Rahul Singh. Symbolic Representation and Clustering of Bio-Medical Time-Series Data Using Non-Parametric Segmentation and Cluster Ensemble, IEEE International Conference on Computer-Based Medical System, 2012.

  • Hyokyeong Lee, Ke-Thia Yao, Aiichiro Nakano. Dynamic Structure Learning of Factor Graphs and Estimating Parameters of a Constrained Nonlinear Predictive Model for Oilfield Optimization. International Conference on Artificial Intelligence, Las Vegas, USA, July 12-15, 2010.

  • Hyokyeong Lee, Ke-Thia Yao, Olu Ogbonnaya Okpani. Aiichiro Nakano, Iraj Ershaghi. Identifying Injector-Producer Relationship in Waterflood using Hybrid Constrained Nonlinear Optimization, SPE Western Regional Meeting. Anaheim, California, USA, May 27-29, 2010.

  • Ali Khodaei, Hyokyeong Lee, Farnoush Banaei-Kashani, Cyrus Shahabi, Iraj Ershaghi. A Mutual Information-Based Metric for Identification of Nonlinear Injector-Producer Relationships in Waterfloods, SPE Western Regional Meeting, San Jose, California, March 24-26, 2009.

  • Carole Beal, Lei Qu, Hyokyeong Lee. Classifying learner engagement through integration of multiple data sources, The Twenty-First National Conference on Artificial Intelligence, Boston, Massachusetts, 2006.

  • Hyokyeong Lee, Carole Beal, Erin Shaw. Assessing Student Motivation with Online Self-report Instruments in Web-Based Intelligent Tutoring System, American Educational Research Association Annual Meeting, San Francisco, 2006.

  • Carole Beal and Hyokyeong Lee. Creating a pedagogical model that uses student self reports of motivation and mood to adapt ITS instruction, Workshop on motivation and affect in educational software, 2005.

  • Carole Beal, Erin Shaw, Yuan-Chun Chui, Hyokyeong Lee, Hannes Vilhjalmsson, Lei Qu. Enhancing ITS instruction with integrated assessments of learner mood, motivation and gender, 12th International Conference on Artificial Intelligence in Education, 2005.

  • Paola Rizzo, Hyokyeong Lee, Erin Shaw, W. Lewis Johnson, Ning Wang, and Richard E. Mayer. A Semi-Automated Wizard of Oz Interface for Modeling Tutorial Strategies, 10th International Conference on User Modeling, 2005.

  • Sunhee Choi and Hyokyeong Lee. Cognitive and Motivational Effects of Animated Pedagogical Agent in Learning English as a Second Language, 12th International Conference on Artificial Intelligence in Education, 2005.

  • Workshop publication

  • W. Lewis Johnson, Paola Rizzo, Hyokyeong Lee, Ning Wang, and Erin Shaw. Modeling Motivational and Social Aspects of Tutorial Dialog, Workshop on Modelling Human Teaching Tactics and Strategies, 2004.

  • Invited Talks

  • Guest lecture for Smart Oilfield Data Mining course, Petroleum Engineering, University of Southern California, Fall 2011, Fall 2013

  • My role model

  • Christopher M. Bishop

  • What my heart tells me:

  • I love computational biology and machine learning research, and will dedicate the rest of my life to them.
  • Whenever a research problem challenges me, my heart starts beating.

  • What I believe

  • I believe only mathematics.

  • The secret of health for both mind and body is not to mourn for the past, not to worry about the future, or not to anticipate troubles, but to live the present moment wisely and earnestly. -- The Buddha