Papers & Talks

†: (co-)1st author  ·  *: (co-)corresponding author  ·  Note: Where no author is designated as the first author (†), names are listed in alphabetical order by last name, as is standard practice in mathematical journals.

Preprints & In Preparation

18. Ella Buelling^†, Wolfram Liebermeister*, Hyukpyo Hong*
    Connections between structural sensitivity analysis and metabolic control analysis In Prep
17. Hyukpyo Hong, Seewoo Lee
    Necessary and sufficient conditions of the existence of a finite dimensional invariant subspace for polynomial ODEs In Prep
16. Geonhee Ryu^†, Hyukpyo Hong*, Daewook Kim*
    Non-autonomous dynamics learning via Koopman-based Neural Networks In Prep
15. Seewoo Lee^†, Byung-Hak Hwang^†, Hyojae Lim, Jihoon Hyun, Ilkyoo Choi, Yeachan Park, Jineon Baek, Hyukpyo Hong, Keewoo Lee, Jaeseong Heo, Hyungryul Baik, Chul-hee Lee*, Kyu-Hwan Lee
    LEAN-GAP: A Dataset of Formalized Graduate Algebra Problems arXiv Submitted
14. Hyukpyo Hong^†, Qin Li, Matthew Colbrook, Hanbaek Lyu*
    Finding Koopman Invariant Subspaces via Personalized PageRank arXiv Submitted
13. Hyukpyo Hong^†*, Diego Rojas La Luz^†, Gheorghe Craciun*
    Ubiquitous asymptotic robustness in biochemical systems arXiv Under Review

Published & Accepted

12. Dongju Lim^†, Kyeong Tae Ko^†, Hyukpyo Hong, Hyojung Lee, Boseung Choi, Won Chang, Sunhwa Choi*, Jae Kyoung Kim*
    A history-dependent approach for accurate initial condition estimation in epidemic models Journal
    PLoS Computational Biology, 2025
11. Hyukpyo Hong^†, Seokhwan Moon^†, Yuji Hirono^†*, Jae Kyoung Kim*
    Topological criterion for robust perfect adaptation of reaction fluxes in biological networks arXiv Journal
    iScience, 2025
10. Hyukpyo Hong^†, Eunjin Eom^†, Hyojung Lee, Sunhwa Choi*, Boseung Choi*, Jae Kyoung Kim*
    Overcoming bias in estimating epidemiological parameters with realistic history-dependent disease spread dynamics Journal
    Nature Communications, 2024
9. Hyeontae Jo^†, Hyukpyo Hong^†, Hyung Ju Hwang, Won Chang, Jae Kyoung Kim*
   Density physics-informed neural networks reveal sources of cell heterogeneity in signal transduction bioRxiv Journal
   Patterns, 2023
8. Hyukpyo Hong^†, Mark Jayson Cortez, Yu-Yu Cheng, Hang J. Kim, Boseung Choi*, Krešimir Josić*, Jae Kyoung Kim*
   Inferring delays in partially observed gene regulation processes bioRxiv Journal
   Bioinformatics, 2023
7. Hyukpyo Hong, Bryan S. Hernandez, Jinsu Kim, Jae Kyoung Kim*
   Computational translation framework identifies biochemical reaction networks with special topologies and their long-term dynamics arXiv Journal
   SIAM Journal on Applied Mathematics, 2023
6. Hyukpyo Hong^†, Ji Yun Noh^†, Hyojung Lee, Sunhwa Choi, Boseung Choi, Jae Kyoung Kim*, Eui-Cheol Shin*
   Modeling incorporating the severity-reducing long-term immunity: higher viral transmission paradoxically reduces severe COVID-19 during endemic transition medRxiv Journal
   Immune Network, 2022
5. Dae Wook Kim^†, Hyukpyo Hong^†, Jae Kyoung Kim*
   Systematic inference identifies a major source of heterogeneity in cell signaling dynamics: the rate-limiting step number Journal
   Science Advances, 2022
4. Jaehyoung Hong^†, Su Jung Choi^†, Se Ho Park, Hyukpyo Hong, Victoria Booth, Eun Yeon Joo*, Jae Kyoung Kim*
   Personalized sleep-wake patterns aligned with circadian rhythm relieve daytime sleepiness bioRxiv Journal
   iScience, 2021
3. Yun Min Song^†, Hyukpyo Hong^†, Jae Kyoung Kim*
   Universally valid reduction of multiscale stochastic biochemical systems with simple non-elementary propensities bioRxiv Journal
   PLoS Computational Biology, 2021
2. Mark Jayson Cortez^†, Hyukpyo Hong, Boseung Choi*, Jae Kyoung Kim*, Krešimir Josić*
   Hierarchical Bayesian models for inference in biochemical reactions with delays bioRxiv Journal
   Bioinformatics, 2021
1. Hyukpyo Hong^†, Jinsu Kim^†, M. Ali Al-Radhawi, Eduardo D. Sontag, Jae Kyoung Kim*
   Derivation of stationary distributions of biochemical reaction networks via structure transformation bioRxiv Journal
   Communications Biology, 2021

1. Hyukpyo Hong, Boseung Choi, Jae Kyoung Kim*
   Beyond the Michaelis-Menten: Bayesian inference for enzyme kinetic analysis Link
   Computational Methods for Estimating the Kinetics Parameters of Biological Systems, Methods in Molecular Biology

SMB: Society for Mathematical Biology · KSMB: Korean SMB · SIAM: Society for Industrial and Applied Mathematics · KSIAM: Korean SIAM · KMS: Korean Mathematical Society

• 2026-04-28 Formal reaction kinetics and related questions, Online Link video
  Ubiquitous Asymptotic Robustness in Biochemical Systems
• 2026-02-26 Mathematics of Reaction Networks (MoRN) Seminar, Online Link video
  Ubiquitous Asymptotic Robustness in Biochemical Systems
• 2025-11-21 Duke University Math Bio Seminar, Durham, NC, USA
  Identifying major sources of heterogeneity in antibiotic cell responses via Bayesian inference and Physics-informed neural networks
• 2025-11-20 NC State Univ. TPB Cluster, Durham, NC, USA
  Bridging Mathematical Theory and Biological Challenges: From intracellular networks to human-scale dynamics
• 2025-11-19 NC State Univ. Dept. of Mathematics, Durham, NC, USA
  Leveraging Koopman Operator Theory and Graph Representation for Deeper Insight into Complex Dynamical Systems
• 2025-11-13 Seminar at Seoul National University, Seoul, Korea
  Finite-Dimensional Representations of the Koopman Operator: Equation- and Data-Driven Approaches
• 2025-10-31 UW–Madison Applied and Computational Mathematics Seminar, Madison, WI, USA Link
  Finite-Dimensional Representations of the Koopman Operator: Equation- and Data-Driven Approaches
• 2025-10-28 Midwest Mathematical Biology Seminar, Online Link
  Ubiquitous Asymptotic Robustness in Biochemical Systems
• 2025-10-01 Seminar at Korea University, Seoul, Korea
  Leveraging Koopman Operator Theory and Graph Representation for Deeper Insight into Complex Dynamical Systems
• 2025-09-27 2025 GLSIAM Meeting, Chicago, IL, USA
  Digital biomarker of cognitive impairment: fractal patterns of human activity data
• 2025-07-17 SMB Annual Meeting, Edmonton, Canada
  Inferring delay distributions in partially observed biological processes
• 2025-07-08 SIAM Conference on Applied Algebraic Geometry, Madison, WI, USA
  Ubiquitous Asymptotic Robustness in Biochemical Systems
• 2025-06-20 Pusan National University Math Seminar, Busan, Korea
  Parameter inference in Markovian and non-Markovian models
• 2025-06-04 KAIST Brain & Cognitive Sciences Seminar, Daejeon, Korea
  Digital biomarker of cognitive impairment: fractal patterns of human activity data
• 2025-06-02 Konkuk University Math Seminar, Seoul, Korea
  Parameter inference in Markovian and non-Markovian models
• 2025-05-17 KSIAM Spring Conference, Seoul, Korea
  KSIAM Next Generation Researcher Award speech
• 2025-05-15 SIAM Conference on Applied Dynamical Systems, Denver, CO, USA
  Network Translation of a Stochastic Reaction Network to Reveal Stationary Distributions
• 2025-03-03 Computational and Applied Math / Data Science Seminar, Arizona State University, Online
  Koopman representation: Linear representation of nonlinear dynamics
• 2024-10-25 Applied Math Seminar at the University of Cincinnati, Cincinnati, OH, USA
  Koopman representation: Linear representation of nonlinear dynamics
• 2024-10-07 Seminar at the University of the Philippines Diliman, Online
  Accurate epidemiological parameters estimation with realistic history-dependent disease spread dynamics
• 2024-08-01 Seminar at Pusan National University, Busan, Korea
  Analysis of dynamical systems using ``easier'' representations
• 2024-07-31 Biomedical Mathematics Seminar at Institute for Basic Science, Daejeon, Korea
  Koopman representation: Linear representation--not an approximation--of nonlinear dynamics
• 2024-07-04 SMB Annual Meeting, Seoul, Korea
  Density-PINNs reveal that multiple pathways reduce cell-to-cell heterogeneity in antibiotic responses
• 2024-07-02 SMB Annual Meeting, Seoul, Korea
  Inferring delays in partially observed gene regulation processes
• 2024-06-04 Data Computational Sciences Special Lecture at Korea University, Sejong Campus, Sejong, Korea
  How to sample random numbers from a target distribution
• 2024-06-03 Data Science Seminar at Sogang University, Seoul, Korea
  Analysis of dynamical systems using ``easier'' representations
• 2024-05-23 CM2LA Seminar at POSTECH, Pohang, Korea
  Analysis of dynamical systems using ``easier'' representations
• 2024-04-25 Mathematical Biology Seminar at UIUC, Champaign, IL, USA
  Analyzing long-term behavior of dynamical systems using ``easy-to-handle'' representations
• 2023-08-17 ICIAM 2023 Satellite Workshop: Stochastic Modeling and Data Analysis for Biological Systems, Daejeon, Korea
  Network translation allows for revealing long-term dynamics of stochastic reaction networks
• 2023-07-17 SMB Annual Meeting, Columbus, OH, USA
  Network translation allows for revealing long-term dynamics of stochastic reaction networks
• 2023-06-27 The 8th CIJK International Conference on Mathematical and Theoretical Biology, Jeju, Korea
  Things we have been overlooking in infectious disease modeling
• 2023-05-19 KSIAM Spring Conference, Special session, Pyeongchang, Korea
  Increasing viral transmission paradoxically reduces severe COVID-19 during endemic transition
• 2022-12-19 Mini-workshop on Recent Trends in Pure and Applied Mathematics, Daejeon, Korea
  Inferring delays in partially observed gene regulatory networks
• 2022-11-21 Population Approach Group Korea Annual Meeting, Seoul, Korea
  Increasing viral transmission paradoxically reduces severe COVID-19 during endemic transition
• 2022-10-19 Global KMS International Conference, Seoul, Korea
  Systematic inference identifies a major source of heterogeneity in non-Markovian cell signaling dynamics
• 2022-06-25 KSMB Annual Meeting, Yeosu, Korea
  Increasing viral transmission paradoxically reduces severe COVID-19 during endemic transition
• 2022-06-22 BRIC Webinar, Online Link
  Systematic inference for cell signalling pathways identifies a key determinant of cell-to-cell variability
• 2022-05-28 KSIAM Spring Conference, Daejeon, Korea
  Systematic inference for cell signalling pathways identifies a key determinant of cell-to-cell variability
• 2021-08-27 KSMB Annual Meeting, Online, Korea
  Inference of stochastic dynamics in biochemical reaction networks
• 2021-06-16 SMB Annual Meeting, Online
  Inference of stochastic dynamics in biochemical reaction networks
• 2021-05-27 SIAM Conference on Applications of Dynamical Systems, Online
  Derivation of stationary distributions of stochastic chemical reaction networks via network translation
• 2021-05-13 Seminar on the Mathematics of Reaction Networks, Online Link video
  Derivation of stationary distributions of stochastic chemical reaction networks via network translation
• 2020-10-24 KMS Annual Meeting, Minisymposium, Online
  Derivation of stationary distributions of biochemical reaction networks via structure transformation

• 2024-06-27 KSMB-SMB Satellite Workshop, Daejeon, Korea (Poster)
  Inferring delays in partially observed gene regulation processes
• 2024-06-10 SPT Workshop on Reaction Networks, Cagliari, Italy (Poster)
  Network translation allows for revealing long-term dynamics of stochastic reaction networks
• 2023-07-14 Dynamical Systems in the Life Sciences, Columbus, OH, USA (Poster)
  Systematic inference identifies a major source of heterogeneity in non-Markovian cell signaling dynamics
• 2022-12-06 Workshop on Non-equilibrium Phenomena in Physics and Biology, Gyeongju, Korea (Poster)
  Network translation allows for revealing long-term dynamics of stochastic reaction networks
• 2022-11-26 KSIAM Annual Conference, Jeju, Korea
  Increasing viral transmission paradoxically reduces severe COVID-19 during endemic transition
• 2022-10-11 International Conference on Systems Biology, Berlin, Germany
  Systematic inference identifies a major source of heterogeneity in non-Markovian cell signaling dynamics: the rate-limiting step number
• 2022-07-14 SIAM Conference on the Life Sciences, Pittsburgh, USA
  Systematic inference identifies a major source of heterogeneity in non-Markovian cell signaling dynamics: the rate-limiting step number
• 2022-05-17 SRBR Biennial Conference, Jacksonville, USA (Poster)
  Personalized sleep-wake patterns aligned with circadian rhythm relieve daytime sleepiness
• 2021-12-17 KSMB Winter Conference, Jeju, Korea (Poster)
  Derivation of stationary distributions of stochastic chemical reaction networks via network translation
• 2021-12-04 KSIAM Annual Conference, Busan, Korea (Poster)
  Derivation of stationary distributions of stochastic chemical reaction networks via network translation
• 2021-09-28 Non-equilibrium collective phenomena workshop, Gyeongju, Korea (Poster)
  Derivation of stationary distributions of stochastic chemical reaction networks via network translation
• 2021-06-26 KSIAM Spring Conference, Gangneung, Korea
  Derivation of stationary distributions of biochemical reaction networks via structure transformation
• 2020-11-13 KSIAM Annual Conference, Online (Poster)
  Derivation of stationary distributions of biochemical reaction networks via structure transformation
• 2020-08-20 SMB Annual Meeting, Online
  Derivation of stationary distributions of biochemical reaction networks via structure transformation
• 2019-07-23 SMB Annual Meeting, Montréal, Canada (Poster)
  Product-form stationary distributions for non-complex balanced networks
• 2019-07-08 Chemical Reaction Networks Workshop, Torino, Italy
  Product-form stationary distributions for non-complex balanced networks
• 2019-05-18 KSIAM Spring Conference, Seoul, Korea
  Product-form stationary distributions for non-complex balanced networks
• 2019-05-11 A3 Workshop on Mathematical Life Science, Beijing, China
  Product-form stationary distributions for non-complex balanced networks

• 2026-05-26 Alumni Career Talk, KAIST Department of Mathematical Sciences Slides
  Preparing for a Postdoc Abroad: A Three-Year Retrospective
  Slides are available but written in Korean.
• 2023-06-20 KAIST Math Graduate Student Seminar, KAIST Department of Mathematical Sciences
  Preparation for Postdoc Positions
• 2022-09-16 Science Slam-D Public Lecture, Yongsan High School, Daejeon, Korea
  Mathematics Meets Biology: Discovering the Optimal Sleep Pattern through Mathematical Modeling
  Hosted by NST, IBS, Daejeon MBC (TV network), and Hello DD (Press). Delivered for high school students.
• 2021-04-27 Mobile Science Classroom, National Research Foundation of Korea Link
  Mathematical Biology: Bridging Mathematics and the Life Sciences
  Delivered for middle school students.