Samuel W. K. Wong
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View article: Uncovering distinct protein conformations using coevolutionary information and AlphaFold
Uncovering distinct protein conformations using coevolutionary information and AlphaFold Open
Protein structure prediction has been revolutionized by AlphaFold, yet a key limitation remains: the challenge of characterizing the multiple conformations adopted by proteins that can switch between different folds. Current prevailing app…
View article: Spatio-temporal data fusion for the analysis of in situ and remote sensing data using the INLA-SPDE approach
Spatio-temporal data fusion for the analysis of in situ and remote sensing data using the INLA-SPDE approach Open
We propose a Bayesian hierarchical model to address the challenge of spatial misalignment in spatio-temporal data obtained from in situ and satellite sources. The model is fit using the INLA-SPDE approach, which provides efficient computat…
View article: <b>magi</b>: A Package for Inference of Dynamic Systems from Noisy and Sparse Data via Manifold-Constrained Gaussian Processes
<b>magi</b>: A Package for Inference of Dynamic Systems from Noisy and Sparse Data via Manifold-Constrained Gaussian Processes Open
This article presents the magi software package for the inference of dynamic systems. The focus of magi is on dynamics modeled by nonlinear ordinary differential equations with unknown parameters. While such models are widely used in scien…
View article: A Bayesian Collocation Integral Method for Parameter Estimation in Ordinary Differential Equations
A Bayesian Collocation Integral Method for Parameter Estimation in Ordinary Differential Equations Open
–Inferring the parameters of ordinary differential equations (ODEs) from noisy observations is an important problem in many scientific fields. Currently, most parameter estimation methods that bypass numerical integration tend to rely o…
View article: Particle Gibbs for Likelihood-Free Inference of State Space Models with Application to Stochastic Volatility
Particle Gibbs for Likelihood-Free Inference of State Space Models with Application to Stochastic Volatility Open
State space models (SSMs) are widely used to describe dynamic systems. However, when the likelihood of the observations is intractable, parameter inference for SSMs cannot be easily carried out using standard Markov chain Monte Carlo or se…
View article: Estimating Boltzmann Averages for Protein Structural Quantities Using Sequential Monte Carlo
Estimating Boltzmann Averages for Protein Structural Quantities Using Sequential Monte Carlo Open
Sequential Monte Carlo (SMC) methods are widely used to draw samples from intractable target distributions.Weight degeneracy can hinder the use of SMC when the target distribution is highly constrained.As a motivating application, we consi…
View article: Understanding the Impact of Seasonal Climate Change on Canada's Economy by Region and by Sector
Understanding the Impact of Seasonal Climate Change on Canada's Economy by Region and by Sector Open
To assess the impact of climate change on the Canadian economy, we investigate the relationship between seasonal climate variables and economic growth across provinces and economic sectors. We also provide projections of climate change imp…
View article: A comparative study of compartmental models for COVID-19 transmission in Ontario, Canada
A comparative study of compartmental models for COVID-19 transmission in Ontario, Canada Open
View article: Supplementary Information from Suppression of ACADM-Mediated Fatty Acid Oxidation Promotes Hepatocellular Carcinoma via Aberrant CAV1/SREBP1 Signaling
Supplementary Information from Suppression of ACADM-Mediated Fatty Acid Oxidation Promotes Hepatocellular Carcinoma via Aberrant CAV1/SREBP1 Signaling Open
Supplementary Materials and Methods, Figures and Tables
View article: Supplementary Information from Suppression of ACADM-Mediated Fatty Acid Oxidation Promotes Hepatocellular Carcinoma via Aberrant CAV1/SREBP1 Signaling
Supplementary Information from Suppression of ACADM-Mediated Fatty Acid Oxidation Promotes Hepatocellular Carcinoma via Aberrant CAV1/SREBP1 Signaling Open
Supplementary Materials and Methods, Figures and Tables
View article: Data from Suppression of ACADM-Mediated Fatty Acid Oxidation Promotes Hepatocellular Carcinoma via Aberrant CAV1/SREBP1 Signaling
Data from Suppression of ACADM-Mediated Fatty Acid Oxidation Promotes Hepatocellular Carcinoma via Aberrant CAV1/SREBP1 Signaling Open
Lipid accumulation exacerbates tumor development, as it fuels the proliferative growth of cancer cells. The role of medium-chain acyl-CoA dehydrogenase (ACADM), an enzyme that catalyzes the first step of mitochondrial fatty acid oxidation,…
View article: Data from Suppression of ACADM-Mediated Fatty Acid Oxidation Promotes Hepatocellular Carcinoma via Aberrant CAV1/SREBP1 Signaling
Data from Suppression of ACADM-Mediated Fatty Acid Oxidation Promotes Hepatocellular Carcinoma via Aberrant CAV1/SREBP1 Signaling Open
Lipid accumulation exacerbates tumor development, as it fuels the proliferative growth of cancer cells. The role of medium-chain acyl-CoA dehydrogenase (ACADM), an enzyme that catalyzes the first step of mitochondrial fatty acid oxidation,…
View article: Estimating and Assessing Differential Equation Models with Time-Course Data
Estimating and Assessing Differential Equation Models with Time-Course Data Open
Ordinary differential equation (ODE) models are widely used to describe chemical or biological processes. This Article considers the estimation and assessment of such models on the basis of time-course data. Due to experimental limitations…
View article: A Kriging Metamodel with Adaptive Sampling for Seismic Evaluation of Podium Buildings
A Kriging Metamodel with Adaptive Sampling for Seismic Evaluation of Podium Buildings Open
In this paper, nonlinear time-history dynamic analyses of selected earthquake ground motions are conducted on designated wood-frame podium buildings and the resulting inter-story drifts are analyzed. We aim to construct a reliable region w…
View article: Knots and their effect on the tensile strength of lumber: A case study
Knots and their effect on the tensile strength of lumber: A case study Open
When assessing the strength of sawn lumber for use in engineering applications, the sizes and locations of knots are an important consideration. Knots are the most common visual characteristics of lumber, that result from the growth of tre…
View article: Estimating Boltzmann Averages for Protein Structural Quantities Using Sequential Monte Carlo
Estimating Boltzmann Averages for Protein Structural Quantities Using Sequential Monte Carlo Open
Sequential Monte Carlo (SMC) methods are widely used to draw samples from intractable target distributions. Particle degeneracy can hinder the use of SMC when the target distribution is highly constrained or multimodal. As a motivating app…
View article: A Comparative Study of Compartmental Models for COVID-19 Transmission in Ontario, Canada
A Comparative Study of Compartmental Models for COVID-19 Transmission in Ontario, Canada Open
The number of confirmed COVID-19 cases reached over 1.3 million in Ontario, Canada by June 4, 2022. The continued spread of the virus underlying COVID-19 has been spurred by the emergence of variants since the initial outbreak in December,…
View article: MAGI: A Package for Inference of Dynamic Systems from Noisy and Sparse\n Data via Manifold-constrained Gaussian Processes
MAGI: A Package for Inference of Dynamic Systems from Noisy and Sparse\n Data via Manifold-constrained Gaussian Processes Open
This article presents the MAGI software package for the inference of dynamic\nsystems. The focus of MAGI is on dynamics modeled by nonlinear ordinary\ndifferential equations with unknown parameters. While such models are widely\nused in sc…
View article: MAGI: A Package for Inference of Dynamic Systems from Noisy and Sparse Data via Manifold-constrained Gaussian Processes
MAGI: A Package for Inference of Dynamic Systems from Noisy and Sparse Data via Manifold-constrained Gaussian Processes Open
This article presents the MAGI software package for the inference of dynamic systems. The focus of MAGI is on dynamics modeled by nonlinear ordinary differential equations with unknown parameters. While such models are widely used in scien…
View article: Comparing regional and provincial-wide COVID-19 models with physical distancing in British Columbia
Comparing regional and provincial-wide COVID-19 models with physical distancing in British Columbia Open
We study the effects of physical distancing measures for the spread of COVID-19 in regional areas within British Columbia, using the reported cases of the five provincial Health Authorities. Building on the Bayesian epidemiological model o…
View article: Decomposition of cell activities revealing the role of the cell cycle in driving biofunctional heterogeneity
Decomposition of cell activities revealing the role of the cell cycle in driving biofunctional heterogeneity Open
Heterogeneity of cell phenotypes remains a barrier in progressing cell research and a challenge in conquering cancer-related drug resistance. Cell morphology, the most direct property of cell phenotype, evolves along the progression of the…
View article: Multimodel Bayesian Analysis of Load Duration Effects in Lumber Reliability
Multimodel Bayesian Analysis of Load Duration Effects in Lumber Reliability Open
This paper evaluates the reliability of lumber, accounting for the duration-of-load (DOL) effect under different load profiles based on a multimodel Bayesian approach. Three individual DOL models previously used for reliability assessment …
View article: Conformational variability of loops in the <scp>SARS‐CoV</scp> ‐2 spike protein
Conformational variability of loops in the <span>SARS‐CoV</span> ‐2 spike protein Open
The SARS‐CoV‐2 spike (S) protein facilitates viral infection, and has been the focus of many structure determination efforts. Its flexible loop regions are known to be involved in protein binding and may adopt multiple conformations. This …
View article: Conformational variability of loops in the SARS-CoV-2 spike protein
Conformational variability of loops in the SARS-CoV-2 spike protein Open
The SARS-CoV-2 spike (S) protein facilitates viral infection, and has been the focus of many structure determination efforts. Its flexible loop regions are known to be involved in protein binding and may adopt multiple conformations. This …
View article: Assessing the effectiveness of regional physical distancing measures of COVID-19 in rural regions of British Columbia
Assessing the effectiveness of regional physical distancing measures of COVID-19 in rural regions of British Columbia Open
We study the effects of physical distancing measures for the spread of COVID-19 in regional areas within British Columbia, using the reported cases of the five provincial Health Authorities. Building on the Bayesian epidemiological model o…
View article: Inference of dynamic systems from noisy and sparse data via manifold-constrained Gaussian processes
Inference of dynamic systems from noisy and sparse data via manifold-constrained Gaussian processes Open
Significance Ordinary differential equations are a ubiquitous tool for modeling behaviors in science, such as gene regulation, biological rhythms, epidemics, and ecology. An important problem is to infer and characterize the uncertainty of…
View article: Statistical challenges in the analysis of sequence and structure data for the COVID-19 spike protein
Statistical challenges in the analysis of sequence and structure data for the COVID-19 spike protein Open
As the major target of many vaccines and neutralizing antibodies against SARS-CoV-2, the spike (S) protein is observed to mutate over time. In this paper, we present statistical approaches to tackle some challenges associated with the anal…
View article: <b>BAMBI</b>: An <i>R</i> Package for Fitting Bivariate Angular Mixture Models
<b>BAMBI</b>: An <i>R</i> Package for Fitting Bivariate Angular Mixture Models Open
Statistical analyses of directional or angular data have applications in a variety of fields, such as geology, meteorology and bioinformatics. There is substantial literature on descriptive and inferential techniques for univariate angular…
View article: Statistical Challenges in the Analysis of Sequence and Structure Data for the COVID-19 Spike Protein
Statistical Challenges in the Analysis of Sequence and Structure Data for the COVID-19 Spike Protein Open
As the major target of many vaccines and neutralizing antibodies against SARS-CoV-2, the spike (S) protein is observed to mutate over time. In this paper, we present statistical approaches to tackle some challenges associated with the anal…
View article: Ellipse Detection and Localization with Applications to Knots in Sawn Lumber Images
Ellipse Detection and Localization with Applications to Knots in Sawn Lumber Images Open
While general object detection has seen tremendous progress, localization of elliptical objects has received little attention in the literature. Our motivating application is the detection of knots in sawn timber images, which is an import…