Colombia announced the first case of severe acute respiratory syndrome coronavirus 2 on March 6, ... more Colombia announced the first case of severe acute respiratory syndrome coronavirus 2 on March 6, 2020. Since then, the country has reported a total of 5,002,387 cases and 127,258 deaths as of October 31, 2021. The aggressive transmission dynamics of SARS-CoV-2 motivate an investigation of COVID-19 at the national and regional levels in Colombia. We utilize the case incidence and mortality data to estimate the transmission potential and generate short-term forecasts of the COVID-19 pandemic to inform the public health policies using previously validated mathematical models. The analysis is augmented by the examination of geographic heterogeneity of COVID-19 at the departmental level along with the investigation of mobility and social media trends. Overall, the national and regional reproduction numbers show sustained disease transmission during the early phase of the pandemic, exhibiting sub-exponential growth dynamics. Whereas the most recent estimates of reproduction number indicat...
The development of the technology makes it possible to measure large amount of genes expressions ... more The development of the technology makes it possible to measure large amount of genes expressions simultaneously. Since biological functions are mostly coordinated by multiple genes, called “gene pathway”, it is interesting to identify differential gene pathways which are associated with clinical phenotype. Principal component analysis has been proposed to identify differential gene pathways in several literatures, while sparse principal component analysis (SPCA) has not drawn any attention. We proposed to use SPCA to identify differential gene pathways. The results show that, comparing to PCA, SPCA could identify more differential expressed gene pathways, especially when the higher-order interactions among genes are considered.
The COVID-19 pandemic reached Latin America in February 2020, with the first case in Chile identi... more The COVID-19 pandemic reached Latin America in February 2020, with the first case in Chile identified on March 3rd, 2020. Since then Chile has accumulated a total of 14365 cases as of April 28th, 2020. We estimate the reproduction number during the early transmission phase in Chile and study the effectiveness of control interventions by conducting short-term forecasts based on early transmission dynamics of COVID-19. The incidence curve displays sub-exponential growth dynamics with the scaling of growth parameter, p, estimated at 0.8 (95% CI: 0.7, 0.8) and the reproduction number estimated at 1.6 (95% CI: 1.5, 1.6). The sub-epidemic model indicates a stationary wave of stable epidemic size. Our current findings point to sustained transmission of SARS-CoV-2 in Chile. While the social distancing interventions have slowed the virus spread, the number of new COVID-19 cases continue to accrue, underscoring the need for persistent social distancing efforts to control the epidemic.
Various regularized linear discriminant analysis (LDA) methods have been proposed to address the ... more Various regularized linear discriminant analysis (LDA) methods have been proposed to address the problems of the classic methods in high-dimensional settings. Asymptotic optimality has been established for some of these methods in high dimension when there are only two classes. A major difficulty in proving asymptotic optimality for multiclass classification is that the classification boundary is typically complicated and no explicit formula for classification error generally exists when the number of classes is greater than two. For the Fisher's LDA, one additional difficulty is that the covariance matrix is also involved in the linear constraints. The main purpose of this paper is to establish asymptotic consistency and asymptotic optimality for our sparse Fisher's LDA with thresholded linear constraints in the high-dimensional settings for arbitrary number of classes. To address the first difficulty above, we provide asymptotic optimality and the corresponding convergence...
Modern techniques generate highly densely observed functional data that exhibit complex local var... more Modern techniques generate highly densely observed functional data that exhibit complex local variation patterns. To build the scalar-on-function or function-onfunction linear regression model for such data, we consider general coefficient functions that can be smooth, nonsmooth, or even discontinuous. The usual smoothness measures, such as the integral of a squared derivative, may not be suitable to differentiate the roughness of these functions. We propose a family of new roughness measures based on the moduli of continuity and wavelet transformation for these general functions. Using new roughness measures, we propose new regularization and estimation methods for the scalar-on-function and function-on-function models with highly densely observed functional variables. Simulation studies and real data applications illustrate that the new methods have good performance for various coefficient functions and predictor curves. Compared to the smoothness regularization and sparsity regul...
Since the detection of the first case of COVID-19 in Chile on March 3rd, 2020, a total of 513,188... more Since the detection of the first case of COVID-19 in Chile on March 3rd, 2020, a total of 513,188 cases, including ~14,302 deaths have been reported in Chile as of November 2nd, 2020. Here, we estimate the reproduction number throughout the epidemic in Chile and study the effectiveness of control interventions especially the effectiveness of lockdowns by conducting short-term forecasts based on the early transmission dynamics of COVID-19. Chile’s incidence curve displays early sub-exponential growth dynamics with the deceleration of growth parameter,p, estimated at 0.8 (95% CI: 0.7, 0.8) and the reproduction number,R, estimated at 1.8 (95% CI: 1.6, 1.9). Our findings indicate that the control measures at the start of the epidemic significantly slowed down the spread of the virus. However, the relaxation of restrictions and spread of the virus in low-income neighborhoods in May led to a new surge of infections, followed by the reimposition of lockdowns in Greater Santiago and other m...
BackgroundEnsemble modeling aims to boost the forecasting performance by systematically integrati... more BackgroundEnsemble modeling aims to boost the forecasting performance by systematically integrating the predictive accuracy across individual models. Here we introduce a simple-yet-powerful ensemble methodology for forecasting the trajectory of dynamic growth processes that are defined by a system of non-linear differential equations with applications to infectious disease spread.MethodsWe propose and assess the performance of two ensemble modeling schemes with different parametric bootstrapping procedures for trajectory forecasting and uncertainty quantification. Specifically, we conduct sequential probabilistic forecasts to evaluate their forecasting performance using simple dynamical growth models with good track records including the Richards model, the generalized-logistic growth model, and the Gompertz model. We first test and verify the functionality of the method using simulated data from phenomenological models and a mechanistic transmission model. Next, the performance of ...
The ongoing COVID-19 epidemic continues to spread within and outside of China, despite several so... more The ongoing COVID-19 epidemic continues to spread within and outside of China, despite several social distancing measures implemented by the Chinese government. Limited epidemiological data are available, and recent changes in case definition and reporting further complicate our understanding of the impact of the epidemic, particularly in the epidemic’s epicenter. Here we use previously validated phenomenological models to generate short-term forecasts of cumulative reported cases in Guangdong and Zhejiang, China. Using daily reported cumulative case data up until 13 February 2020 from the National Health Commission of China, we report 5- and 10-day ahead forecasts of cumulative case reports. Specifically, we generate forecasts using a generalized logistic growth model, the Richards growth model, and a sub-epidemic wave model, which have each been previously used to forecast outbreaks due to different infectious diseases. Forecasts from each of the models suggest the outbreaks may b...
Lack of a gold standard for latent TB infection has precluded direct measurement of test characte... more Lack of a gold standard for latent TB infection has precluded direct measurement of test characteristics of the tuberculin skin test and interferon-γ release assays (QuantiFERON Gold In-Tube and T-SPOT.TB). We estimated test sensitivity/specificity and latent TB infection prevalence in a prospective, US-based cohort of 10 740 participants at high risk for latent infection. Bayesian latent class analysis was used to estimate test sensitivity/specificity and latent TB infection prevalence among subgroups based on age, foreign birth outside the USA and HIV infection. Latent TB infection prevalence varied from 4.0% among foreign-born, HIV-seronegative persons aged <5 years to 34.0% among foreign-born, HIV-seronegative persons aged ≥5 years. Test sensitivity ranged from 45.8% for the T-SPOT.TB among foreign-born, HIV-seropositive persons aged ≥5 years to 80.7% for the tuberculin skin test among foreign-born, HIV-seronegative persons aged ≥5 years. The skin test was less specific than ...
Journal of health care for the poor and underserved, 2017
Cross-sectional research suggests that neighborhood characteristics and transportation access sha... more Cross-sectional research suggests that neighborhood characteristics and transportation access shape unmet need for medical care. This longitudinal analysis explores relationships of changes in neighborhood socioeconomic disadvantage and trans- portation access to unmet need for medical care. We analyzed seven waves of data from African American adults (N = 172) relocating from severely distressed public housing complexes in Atlanta, Georgia. Surveys yielded individual-level data and admin- istrative data characterized census tracts. We used hierarchical generalized linear models to explore relationships. Unmet need declined from 25% pre-relocation to 12% at Wave 7. Post-relocation reductions in neighborhood disadvantage were inversely associated with reductions in unmet need over time (OR = 0.71, 95% CI = 0.51-0.99). More frequent transportation barriers predicted unmet need (OR = 1.16, 95% CI = 1.02-1.31). These longitudinal findings support the importance of neighborhood environme...
Colombia announced the first case of severe acute respiratory syndrome coronavirus 2 on March 6, ... more Colombia announced the first case of severe acute respiratory syndrome coronavirus 2 on March 6, 2020. Since then, the country has reported a total of 5,002,387 cases and 127,258 deaths as of October 31, 2021. The aggressive transmission dynamics of SARS-CoV-2 motivate an investigation of COVID-19 at the national and regional levels in Colombia. We utilize the case incidence and mortality data to estimate the transmission potential and generate short-term forecasts of the COVID-19 pandemic to inform the public health policies using previously validated mathematical models. The analysis is augmented by the examination of geographic heterogeneity of COVID-19 at the departmental level along with the investigation of mobility and social media trends. Overall, the national and regional reproduction numbers show sustained disease transmission during the early phase of the pandemic, exhibiting sub-exponential growth dynamics. Whereas the most recent estimates of reproduction number indicat...
The development of the technology makes it possible to measure large amount of genes expressions ... more The development of the technology makes it possible to measure large amount of genes expressions simultaneously. Since biological functions are mostly coordinated by multiple genes, called “gene pathway”, it is interesting to identify differential gene pathways which are associated with clinical phenotype. Principal component analysis has been proposed to identify differential gene pathways in several literatures, while sparse principal component analysis (SPCA) has not drawn any attention. We proposed to use SPCA to identify differential gene pathways. The results show that, comparing to PCA, SPCA could identify more differential expressed gene pathways, especially when the higher-order interactions among genes are considered.
The COVID-19 pandemic reached Latin America in February 2020, with the first case in Chile identi... more The COVID-19 pandemic reached Latin America in February 2020, with the first case in Chile identified on March 3rd, 2020. Since then Chile has accumulated a total of 14365 cases as of April 28th, 2020. We estimate the reproduction number during the early transmission phase in Chile and study the effectiveness of control interventions by conducting short-term forecasts based on early transmission dynamics of COVID-19. The incidence curve displays sub-exponential growth dynamics with the scaling of growth parameter, p, estimated at 0.8 (95% CI: 0.7, 0.8) and the reproduction number estimated at 1.6 (95% CI: 1.5, 1.6). The sub-epidemic model indicates a stationary wave of stable epidemic size. Our current findings point to sustained transmission of SARS-CoV-2 in Chile. While the social distancing interventions have slowed the virus spread, the number of new COVID-19 cases continue to accrue, underscoring the need for persistent social distancing efforts to control the epidemic.
Various regularized linear discriminant analysis (LDA) methods have been proposed to address the ... more Various regularized linear discriminant analysis (LDA) methods have been proposed to address the problems of the classic methods in high-dimensional settings. Asymptotic optimality has been established for some of these methods in high dimension when there are only two classes. A major difficulty in proving asymptotic optimality for multiclass classification is that the classification boundary is typically complicated and no explicit formula for classification error generally exists when the number of classes is greater than two. For the Fisher's LDA, one additional difficulty is that the covariance matrix is also involved in the linear constraints. The main purpose of this paper is to establish asymptotic consistency and asymptotic optimality for our sparse Fisher's LDA with thresholded linear constraints in the high-dimensional settings for arbitrary number of classes. To address the first difficulty above, we provide asymptotic optimality and the corresponding convergence...
Modern techniques generate highly densely observed functional data that exhibit complex local var... more Modern techniques generate highly densely observed functional data that exhibit complex local variation patterns. To build the scalar-on-function or function-onfunction linear regression model for such data, we consider general coefficient functions that can be smooth, nonsmooth, or even discontinuous. The usual smoothness measures, such as the integral of a squared derivative, may not be suitable to differentiate the roughness of these functions. We propose a family of new roughness measures based on the moduli of continuity and wavelet transformation for these general functions. Using new roughness measures, we propose new regularization and estimation methods for the scalar-on-function and function-on-function models with highly densely observed functional variables. Simulation studies and real data applications illustrate that the new methods have good performance for various coefficient functions and predictor curves. Compared to the smoothness regularization and sparsity regul...
Since the detection of the first case of COVID-19 in Chile on March 3rd, 2020, a total of 513,188... more Since the detection of the first case of COVID-19 in Chile on March 3rd, 2020, a total of 513,188 cases, including ~14,302 deaths have been reported in Chile as of November 2nd, 2020. Here, we estimate the reproduction number throughout the epidemic in Chile and study the effectiveness of control interventions especially the effectiveness of lockdowns by conducting short-term forecasts based on the early transmission dynamics of COVID-19. Chile’s incidence curve displays early sub-exponential growth dynamics with the deceleration of growth parameter,p, estimated at 0.8 (95% CI: 0.7, 0.8) and the reproduction number,R, estimated at 1.8 (95% CI: 1.6, 1.9). Our findings indicate that the control measures at the start of the epidemic significantly slowed down the spread of the virus. However, the relaxation of restrictions and spread of the virus in low-income neighborhoods in May led to a new surge of infections, followed by the reimposition of lockdowns in Greater Santiago and other m...
BackgroundEnsemble modeling aims to boost the forecasting performance by systematically integrati... more BackgroundEnsemble modeling aims to boost the forecasting performance by systematically integrating the predictive accuracy across individual models. Here we introduce a simple-yet-powerful ensemble methodology for forecasting the trajectory of dynamic growth processes that are defined by a system of non-linear differential equations with applications to infectious disease spread.MethodsWe propose and assess the performance of two ensemble modeling schemes with different parametric bootstrapping procedures for trajectory forecasting and uncertainty quantification. Specifically, we conduct sequential probabilistic forecasts to evaluate their forecasting performance using simple dynamical growth models with good track records including the Richards model, the generalized-logistic growth model, and the Gompertz model. We first test and verify the functionality of the method using simulated data from phenomenological models and a mechanistic transmission model. Next, the performance of ...
The ongoing COVID-19 epidemic continues to spread within and outside of China, despite several so... more The ongoing COVID-19 epidemic continues to spread within and outside of China, despite several social distancing measures implemented by the Chinese government. Limited epidemiological data are available, and recent changes in case definition and reporting further complicate our understanding of the impact of the epidemic, particularly in the epidemic’s epicenter. Here we use previously validated phenomenological models to generate short-term forecasts of cumulative reported cases in Guangdong and Zhejiang, China. Using daily reported cumulative case data up until 13 February 2020 from the National Health Commission of China, we report 5- and 10-day ahead forecasts of cumulative case reports. Specifically, we generate forecasts using a generalized logistic growth model, the Richards growth model, and a sub-epidemic wave model, which have each been previously used to forecast outbreaks due to different infectious diseases. Forecasts from each of the models suggest the outbreaks may b...
Lack of a gold standard for latent TB infection has precluded direct measurement of test characte... more Lack of a gold standard for latent TB infection has precluded direct measurement of test characteristics of the tuberculin skin test and interferon-γ release assays (QuantiFERON Gold In-Tube and T-SPOT.TB). We estimated test sensitivity/specificity and latent TB infection prevalence in a prospective, US-based cohort of 10 740 participants at high risk for latent infection. Bayesian latent class analysis was used to estimate test sensitivity/specificity and latent TB infection prevalence among subgroups based on age, foreign birth outside the USA and HIV infection. Latent TB infection prevalence varied from 4.0% among foreign-born, HIV-seronegative persons aged <5 years to 34.0% among foreign-born, HIV-seronegative persons aged ≥5 years. Test sensitivity ranged from 45.8% for the T-SPOT.TB among foreign-born, HIV-seropositive persons aged ≥5 years to 80.7% for the tuberculin skin test among foreign-born, HIV-seronegative persons aged ≥5 years. The skin test was less specific than ...
Journal of health care for the poor and underserved, 2017
Cross-sectional research suggests that neighborhood characteristics and transportation access sha... more Cross-sectional research suggests that neighborhood characteristics and transportation access shape unmet need for medical care. This longitudinal analysis explores relationships of changes in neighborhood socioeconomic disadvantage and trans- portation access to unmet need for medical care. We analyzed seven waves of data from African American adults (N = 172) relocating from severely distressed public housing complexes in Atlanta, Georgia. Surveys yielded individual-level data and admin- istrative data characterized census tracts. We used hierarchical generalized linear models to explore relationships. Unmet need declined from 25% pre-relocation to 12% at Wave 7. Post-relocation reductions in neighborhood disadvantage were inversely associated with reductions in unmet need over time (OR = 0.71, 95% CI = 0.51-0.99). More frequent transportation barriers predicted unmet need (OR = 1.16, 95% CI = 1.02-1.31). These longitudinal findings support the importance of neighborhood environme...
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Papers by Ruiyan Luo