Refereed papers
- Zhaoran Hou and Samuel WK Wong (2025). Particle Gibbs for likelihood-free inference of stochastic volatility models. Statistics and Computing, 35, article 34. [PDF]
- Yuxuan Zhao and Samuel WK Wong (2024). Inference for Delay Differential Equations Using Manifold-Constrained Gaussian Processes. Statistica Sinica, to appear.
- Shiyu He and Samuel WK Wong (2024). Spatio-temporal data fusion for the analysis of in situ and remote sensing data using the INLA-SPDE approach. Spatial Statistics, 64, 100863.
- Mingwei Xu, Samuel WK Wong, and Peijun Sang (2024). A Bayesian Collocation Integral Method for Parameter Estimation in Ordinary Differential Equations. Journal of Computational and Graphical Statistics, 33(3), 845-854.
- Zhaoran Hou and Samuel WK Wong (2024). Estimating Boltzmann Averages for Protein Structural Quantities Using Sequential Monte Carlo. Statistica Sinica, 34, 1263-1280.
- Samuel WK Wong, Shihao Yang, SC Kou (2024). magi: A Package for Inference of Dynamic Systems from Noisy and Sparse Data via Manifold-Constrained Gaussian Processes. Journal of Statistical Software, 109(4), 1-47. [CRAN]
- Yuxuan Zhao and Samuel WK Wong (2023). A Comparative Study of Compartmental Models for COVID-19 Transmission in Ontario, Canada. Scientific Reports, 13, 15050.
- Samuel WK Wong, Shihao Yang, SC Kou (2023). Estimating and Assessing Differential Equation Models with Time-Course Data. Journal of Physical Chemistry B, 127(11), 2362-2374.
- Shuxian Fan, Samuel WK Wong, James V Zidek (2023). Knots and their effect on the tensile strength of lumber: A case study. Journal of Quality Technology, 55(4), 510-522.
- Yuying Huang, Zhiyong Chen, Samuel WK Wong (2023). A Kriging Metamodel with Adaptive Sampling for Seismic Evaluation of Podium Buildings. In 14th International Conference on Application of Statistics and Probability in Civil Engineering (ICASP14), Dublin, Ireland.
- Saptarshi Chakraborty and Samuel WK Wong (2023). On the circular correlation coefficients for bivariate von Mises distributions on a torus. Statistical Papers, 64(2), 643-675.
- Samuel WK Wong and Zongjun Liu (2022). Conformational variability of loops in the SARS-CoV-2 spike protein. Proteins: Structure, Function, and Bioinformatics, 90(3), 691-703.
- Geoffrey McGregor, Jennifer Tippett, Andy TS Wan, Mengxiao Wang, Samuel WK Wong (2022). Comparing regional and provincial-wide COVID-19 models with physical distancing in British Columbia. AIMS Mathematics, 7(4), 6743-6778 (Mathematics in Science and Industry, special issue on COVID-19).
- Yunfeng Yang, Martin Lysy, and Samuel WK Wong (2022). Multimodel Bayesian Analysis of Load Duration Effects in Lumber Reliability. In 13th International Conference on Structural Safety & Reliability (ICOSSAR 2021-2022), pages 399-407, Shanghai, China.
- Saptarshi Chakraborty, Tian Lan, Yiider Tseng, Samuel WK Wong (2022). Bayesian analysis of coupled cellular and nuclear trajectories for cell migration. Biometrics, 78(3), 1209-1220.
- Tian Lan, Meng Yu, Weisheng Chen, Jun Yin, Hsiang-Tsun Chang, Shan Tang, Ye Zhao, Spyros Svoronos, Samuel WK Wong, Yiider Tseng (2021). Decomposition of cell activities revealing the role of the cell cycle in driving biofunctional heterogeneity. Scientific Reports, 11, 23431.
- Saptarshi Chakraborty and Samuel WK Wong (2021). BAMBI: An R package for Fitting Bivariate Angular Mixture Models. Journal of Statistical Software, 99(11), 1-69.
- Shihao Yang, Samuel WK Wong, SC Kou (2021). Inference of dynamic systems from noisy and sparse data via manifold-constrained Gaussian processes. Proceedings of the National Academy of Sciences, 118 (15), e2020397118. [software]
- Shiyu He and Samuel WK Wong (2021). Statistical challenges in the analysis of sequence and structure data for the COVID-19 spike protein. Journal of Data Science, 19(2), 314-333.
- Shenyi Pan, Shuxian Fan, Samuel WK Wong, James V Zidek, Helge Rhodin (2021). Ellipse Detection and Localization with Applications to Knots in Sawn Lumber Images. Proceedings of the IEEE/CVF Winter Conference on Applications of Computer Vision (WACV), 3892-3901.
- Samuel WK Wong (2020). Calibrating wood products for load duration and rate: A statistical look at three damage models. Wood Science and Technology, 54(6), 1511-1528.
- Katherine Kempfert and Samuel WK Wong (2020). Where Does Haydn End and Mozart Begin? Composer Classification of String Quartets. Journal of New Music Research, 49(5), 457-476.
- Samuel WK Wong (2020). Assessing the impacts of mutations to the structure of COVID-19 spike protein via sequential Monte Carlo. Journal of Data Science, 18(3), 511-525 (special issue on COVID-19).
- Edsel Ing, Joseph Kam, Jasmine Cheng, Samuel WK Wong, Marcela H Strungaru, Allan Slomovic, Lawrence Weisbrod, Nurhan Torun (2020). The Incidence of Non-Arteritic Ischemic Optic Neuropathy Following Topical Clear Corneal Cataract Surgery: Survey and Meta-analysis. Canadian Journal of Ophthalmology, 55(1), 87-92.
- Katherine Kempfert, Yishi Wang, Cuixian Chen, Samuel WK Wong (2020). A Comparison Study on Nonlinear Dimension Reduction Methods with Kernel Variations: Visualization, Optimization and Classification. Intelligent Data Analysis, 24(2), 267-290.
- Seong-Hwan Jun, Samuel WK Wong, James V Zidek, Alexandre Bouchard-Côté (2019). Sequential Decision Model for Inference and Prediction on Non-Uniform Hypergraphs with Application to Knot Matching from Computational Forestry. Annals of Applied Statistics, 13(3), 1678-1707.
- Samuel WK Wong and James V Zidek (2019). The duration of load effect in lumber as stochastic degradation. IEEE Transactions on Reliability, 68(2), 410-419.
- Ing EB, Miller NR, Nguyen A, Su W, Bursztyn LLCD, Poole M, Kansal V, Toren A, Albreiki D, Mouhanna JG, Muladzanov A, Bernier M, Gans M, Lee D, Wendel C, Sheldon C, Shields M, Bellan L, Lee-Wing M, Mohadjery Y, Nijhawan N, Tyndel F, Sundaram A, ten Hove MW, Chen J, Rodriguez A, Hu A, Khalidi N, Ing R, Wong SWK, Torun N (2019). Neural Network and Logistic Regression Diagnostic Prediction Models for Giant Cell Arteritis: Development and Validation. Clinical Ophthalmology, 13, 421-430.
- Chun-Hao Yang, James V Zidek, Samuel WK Wong (2019). Bayesian analysis of accumulated damage models in lumber reliability. Technometrics, 61(2), 233-245.
- Tian Lan, Shen-Hsiu Hung, Xudong Su, Samuel WK Wong, Yiider Tseng (2018). Integrating transient cellular and nuclear motions to comprehensively describe cell migration patterns. Scientific Reports, 8, 1488.
- Samuel WK Wong, Jun S Liu, SC Kou (2018). Exploring the conformational space for protein folding with sequential Monte Carlo. Annals of Applied Statistics, 12, 1628-1654. [ Linux binary ]
- Samuel WK Wong, James V Zidek (2018). Dimensional and statistical foundations for accumulated damage models. Wood Science and Technology, 52(1), 45-65.
- Xulin Chen, Samuel W. K. Wong, and Philip A. Stansly (2018). Oviposition Behavior of Tamarixia radiata: Effects of Host Density and Exposure Time. Ecological Entomology, 43, 55-59.
- Samuel WK Wong, Jun S Liu, Samuel Kou (2017). Fast de novo discovery of low-energy protein loop conformations. Proteins: Structure, Function, and Bioinformatics, 85(8), 1402-1412.
- Seong-Hwan Jun, Samuel WK Wong, James V Zidek, Alexandre Bouchard-Côté (2017). Sequential Graph Matching with Sequential Monte Carlo. Proceedings of Machine Learning Research (AISTATS), 54, 1075-1084.
- Samuel WK Wong, Conroy Lum, Lang Wu, James V Zidek (2016). Quantifying uncertainty in lumber grading and strength prediction: a Bayesian approach. Technometrics, 58(2), 236-243.
- Xulin Chen, Samuel W. K. Wong, and Philip A. Stansly (2016). Functional Response of Tamarixia radiata (Hymenoptera: Eulophidae) to Densities of Its Host, Diaphorina citri (Hemiptera: Psylloidea). Annals of the Entomological Society of America, 109(3), 432-437.
- Ke Tang, Samuel WK Wong, Jun S Liu, Jinfeng Zhang, Jie Liang (2015). Conformational Sampling and Structure Prediction of Multiple Interacting Loops in Soluble and ß-Barrel Membrane Proteins Using Multi-Loop Distance-Guided Chain Growth Monte Carlo Method. Bioinformatics, 31(16), 2646-2652.
- Allan W MacAfee and Samuel WK Wong (2007). Extreme Value Analysis of Tropical Cyclone Trapped-Fetch Waves. Journal of Applied Meteorology and Climatology, 46(10), 1501-1522.
Preprints
- Yuxuan Zhao and Samuel WK Wong. Manifold-Constrained Gaussian Processes for Inference of Mixed-effects Ordinary Differential Equations with Application to Pharmacokinetics.
- Yuying Huang and Samuel WK Wong. Fully Bayesian Sequential Design for Mean Response Surface Prediction of Heteroscedastic Stochastic Simulations. [arXiv]
- Yongkai Chen, Samuel WK Wong, SC Kou. SMICE: enhanced conformational sampling using AlphaFold and coevolutionary information.
- Tyler Verhaar and Samuel WK Wong. Multimodal Protein Language Models for Flexibility Prediction and Loop Design.
- Mingwei Xu, Samuel WK Wong, and Peijun Sang. A Bayesian Collocation Integral Method for System Identification of Ordinary Differential Equations.
- Shiyu He, Trang Bui, Yuying Huang, Wenling Zhang, Jie Jian, Samuel WK Wong, Tony S Wirjanto. Understanding the Impact of Seasonal Climate Change on Canada's Economy by Region and Sector. [arXiv]
- Samuel WK Wong. Monte Carlo sampling of flexible protein structures: an application to the SARS-CoV-2 omicron variant. [arXiv]
Software packages
- MAGI: MAnifold-constrained Gaussian process Inference for dynamic systems.
- PETALS: Method for sampling and prediction of protein loop segments.
- BAMBI: R package for Bivariate Angular Mixture Models.
- abcADM: Accumulated damage models via approximate Bayesian computation. [C++ Github]
- compas: Conformational Manipulations of Protein Atomic Structures.