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Gerardo Chowell

Publications and source records attributed to Gerardo Chowell.

At least 19 recordsLinked to original sources

Adaptive COVID-19 Trajectory Forecasting Using MAB-Inspired Ensemble Weighting

Forecasting epidemic trajectories is important for public health decision-making, but no single model is consistently reliable across epidemic phases and forecasting settings. We evaluate Multi-Armed Bandit (MAB)-inspired adaptive weighting strategies for combining epidemic forecasting models when component-model performance changes over time. Using U.S. COVID-19 incidence data from three epidemic waves, we compare UCB, EXP3, and epsilon-greedy weighting rules under fixed short-window and growing calibration windows, with both deterministic and stochastic ensemble variants. The model pool includes SIR, SEIR, GLM, Gompertz, Richards, ARIMA, random walk with drift, simple exponential smoothing, Holt's linear trend method, and exponential growth. Adaptive ensembles are compared with individual models and with naive, unweighted, and inverse-WIS weighted ensemble benchmarks. Forecast performance is assessed using RMSE, weighted interval score (WIS), 95% prediction-interval coverage, and mean 95% prediction-interval width. Across waves, calibration windows, and forecast horizons, EXP3Stoch, EXP3Det, and EPSStoch achieved the lowest mean forecast WIS. The main gains were in probabilistic forecast quality, especially WIS and interval coverage, rather than uniformly lower point forecast error. Simple benchmarks, including the unweighted and inverse-WIS ensembles, remained competitive in several settings. These results suggest that MAB-inspired adaptive weighting is a useful complementary tool for epidemic forecasting, especially when model skill is time-varying and forecast uncertainty is substantial.

q-bio.QM

Cruise Ship-Associated Andes Virus Cluster aboard MV Hondius, 2026: A Stochastic Scenario Analysis

In April 2026, the MV Hondius expedition cruise ship became the site of the first documented cruise ship-associated Andes hantavirus (ANDV) cluster, with 13 confirmed and probable cases and 3 deaths among 149 passengers and crew. We applied a stochastic epidemic model to evaluate four embarkation scenarios under reproductive numbers anchored to published ANDV estimates. Scenario D, involving two latent infected persons at embarkation, was most consistent with the observed outbreak, yielding P(final size >= 13) = 11.6% and P(takeoff) = 58.5% at R0 = 2.12. Approximate Bayesian computation provided complementary support for multiple latent infections at embarkation, especially E1(0)=1 and E3(0)=2, but R0 remained weakly identifiable. A day-35 transmission reduction changed takeoff probability little in this counterfactual model. Findings support exposure-history assessment, early onboard surveillance, rapid isolation of symptomatic cases, and postdisembarkation monitoring for travelers from ANDV-endemic regions.

q-bio.PE

Parameter uncertainty in dynamical models: a practical identifiability index

Ordinary differential equation models are widely used to understand and forecast complex dynamical systems, but their predictive value depends on reliable parameter estimation. Structural identifiability assesses whether parameters can be uniquely recovered from ideal observations, whereas practical identifiability depends on finite, noisy and partially observed data. We introduce the Practical Identifiability Index (PII), a marginal uncertainty-width metric based on the logarithmic span of confidence intervals. Expressed on an order-of-magnitude scale, the PII summarises how tightly individual positive-valued parameters are constrained by available observations, enabling comparison across parameters, models, error structures and observation designs. The PII is intended as a complementary diagnostic, not a standalone identifiability test, and should be interpreted alongside coverage, profile likelihoods, posterior summaries, sensitivity analysis or structural identifiability results. Using parametric bootstrap experiments across growth and compartmental epidemic models, we identify consistent principles: uncertainty decreases as calibration windows become more informative, increases with observation noise and parameter coupling, and remains high for latent or indirectly observed processes. Parameters governing early observable dynamics become constrained sooner, while additional observables can improve constraint for latent progression and recovery parameters. The PII provides a simple, reportable summary of marginal parameter uncertainty for dynamical modelling.

q-bio.QM

Cost-Effectiveness of Adult Hepatitis A Vaccination Strategies in Korea Under an Aging Susceptibility Profile

Hepatitis A severity increases sharply with age, while Korea is experiencing a cohort shift in which low seroprevalence adult cohorts are aging into older, higher fatality age groups. This demographic and immunological transition creates an urgent policy question regarding how adult vaccination should be prioritized under resource constraints. We evaluated three adult vaccination scenarios targeting low seroprevalence age groups (S1) 20 to 39 years, (S2) 40 to 59 years, and (S3) 20 to 59 years. Using an age structured dynamic transmission model calibrated to Korean data, we derived dynamically feasible vaccination allocation trajectories under realistic capacity constraints using an optimal control framework and linked these trajectories to long term transmission model simulations. We conducted DALY based cost effectiveness analyses over a lifetime horizon from both healthcare system and societal perspectives, and characterized uncertainty using probabilistic sensitivity analysis (PSA) and cost effectiveness acceptability curves (CEACs). Robustness was examined using one way sensitivity analyses. In the base case, S2 consistently yields the most favorable and robust cost effectiveness profile under both perspectives, with the lowest ICER. S3 achieved the largest reduction in DALYs but requires substantially higher incremental costs, resulting in a higher ICER than S2. S1 produces the smallest DALY reduction and is the least efficient strategy. PSA and CEACs confirm that S2 remains the preferred option across most willingness to pay ranges. S2 offers the most balanced and robustly cost effective strategy in Korea, capturing substantial mortality reduction while limiting additional program costs. S3 may be justified when higher budgets or willingness to pay thresholds are acceptable, but S2 provides the clearest value for money under epidemiological and economic conditions.

q-bio.PE

COVID-19 Forecasting from U.S. Wastewater Surveillance Data: A Retrospective Multi-Model Study (2022-2024)

Accurate and reliable forecasting models are critical for guiding public health responses and policy decisions during pandemics such as COVID-19. Retrospective evaluation of model performance is essential for improving epidemic forecasting capabilities. In this study, we used COVID-19 wastewater data from CDC's National Wastewater Surveillance System to generate sequential weekly retrospective forecasts for the United States from March 2022 through September 2024, both at the national level and for four major regions (Northeast, Midwest, South, and West). We produced 133 weekly forecasts using 11 models, including ARIMA, generalized additive models (GAM), simple linear regression (SLR), Prophet, and the n-sub-epidemic framework (top-ranked, weighted-ensemble, and unweighted-ensemble variants). Forecast performance was assessed using mean absolute error (MAE), mean squared error (MSE), weighted interval score (WIS), and 95% prediction interval coverage. The n-sub-epidemic unweighted ensembles outperformed all other models at 3-4-week horizons, particularly at the national level and in the Midwest and West. ARIMA and GAM performed best at 1-2-week horizons in most regions, whereas Prophet and SLR consistently underperformed across regions and horizons. These findings highlight the value of region-specific modeling strategies and demonstrate the utility of the n-sub-epidemic framework for real-time outbreak forecasting using wastewater surveillance data.

stat.AP

Comparing Bayesian and Frequentist Inference in Biological Models: A Comparative Analysis of Accuracy, Uncertainty, and Identifiability

Mathematical models support inference and forecasting in ecology and epidemiology, but results depend on the estimation framework. We compare Bayesian and Frequentist approaches across three biological models using four datasets: Lotka-Volterra predator-prey dynamics (Hudson Bay), a generalized logistic model (lung injury and 2022 U.S. mpox), and an SEIUR epidemic model (COVID-19 in Spain). Both approaches use a normal error structure to ensure a fair comparison. We first assessed structural identifiability to determine which parameters can theoretically be recovered from the data. We then evaluated practical identifiability and forecasting performance using four metrics: mean absolute error (MAE), mean squared error (MSE), 95 percent prediction interval (PI) coverage, and weighted interval score (WIS). For the Lotka-Volterra model with both prey and predator data, we analyzed three scenarios: prey only, predator only, and both. The Frequentist workflow used QuantDiffForecast (QDF) in MATLAB, which fits ODE models via nonlinear least squares and quantifies uncertainty through parametric bootstrap. The Bayesian workflow used BayesianFitForecast (BFF), which employs Hamiltonian Monte Carlo sampling via Stan to generate posterior distributions and diagnostics such as the Gelman-Rubin R-hat statistic. Results show that Frequentist inference performs best when data are rich and fully observed, while Bayesian inference excels when latent-state uncertainty is high and data are sparse, as in the SEIUR COVID-19 model. Structural identifiability clarifies these patterns: full observability benefits both frameworks, while limited observability constrains parameter recovery. This comparison provides guidance for choosing inference frameworks based on data richness, observability, and uncertainty needs.

q-bio.QM

Comparative study of Bayesian and Frequentist methods for epidemic forecasting: Insights from simulated and historical data

Accurate epidemic forecasting is critical for effective public health interventions. This study compares Bayesian and Frequentist estimation frameworks within deterministic compartmental epidemic models, focusing on nonlinear least squares optimization versus Bayesian inference using MCMC sampling via Stan. We compare forecasting performance under shared modeling structure and error assumptions for specific implementations of both approaches. We assess performance on simulated datasets (with R0 values of 2 and 1.5) and historical datasets including the 1918 influenza pandemic, 1896-97 Bombay plague, and COVID-19 pandemic. Evaluation metrics include Mean Absolute Error, Root Mean Squared Error, Weighted Interval Score, and 95% prediction interval coverage. Forecasting performance depends on epidemic phase and dataset characteristics, with no method consistently outperforming across all contexts. Frequentist methods perform well at peak and post-peak phases but are less accurate pre-peak. Bayesian methods, particularly with uniform priors, offer better early-epidemic accuracy and stronger uncertainty quantification, especially valuable when data are sparse or noisy. Frequentist methods often yield more accurate point forecasts with lower error metrics, though their interval estimates may be less robust. We examine how prior choice influences Bayesian forecasts and how extending forecasting horizons affects convergence. These findings offer practical guidance for choosing estimation strategies tailored to epidemic phase and data quality, supporting more effective public health interventions.

q-bio.QM

A Tutorial on Structural Identifiability of Epidemic Models Using StructuralIdentifiability.jl

Structural identifiability is the theoretical ability to uniquely recover model parameters from ideal, noise-free data and is a prerequisite for reliable parameter estimation in epidemic modeling. Despite its importance for calibration and inference, structural identifiability analysis remains underused and inconsistently applied in infectious disease modeling. This paper presents a user-oriented methodological tutorial demonstrating how global structural identifiability analysis can be systematically integrated into epidemic modeling workflows. We provide a reproducible framework for conducting structural identifiability analysis of ordinary differential equation models using the Julia package StructuralIdentifiability.jl. The workflow is illustrated across commonly used epidemic models, including SEIR variants with asymptomatic and presymptomatic transmission, vector-borne disease models, and systems incorporating hospitalization and disease-induced mortality. We also introduce a visual communication strategy that embeds identifiability results directly into compartmental diagrams, facilitating interpretation and interdisciplinary communication. Our results show that identifiability depends critically on model structure, the choice of observed variables, and assumptions about initial conditions, and that identifiable parameter combinations may exist even when individual parameters are not globally identifiable. Emphasizing transparent implementation, interpretation, and communication, this work provides practical guidance and comparative insights across model classes. The tutorial is designed as both a reference and a teaching resource for researchers and educators seeking to incorporate structural identifiability analysis into epidemic model development. All code and annotated diagrams are publicly available to ensure reproducibility and reuse.

q-bio.QM

Structural and Practical Identifiability of Phenomenological Growth Models for Epidemic Forecasting

Phenomenological models are highly effective tools for forecasting disease dynamics using real world data, particularly in scenarios where detailed knowledge of disease mechanisms is limited. However, their reliability depends on the model parameters' structural and practical identifiability. In this study, we systematically analyze the identifiability of six commonly used growth models in epidemiology:the generalized growth model, the generalized logistic model, the Richards model, the generalized Richards model, the Gompertz model, and a modified SEIR model with inhomogeneous mixing. To address challenges posed by non-integer power exponents in these models, we reformulate them by introducing additional state variables. This enables rigorous structural identifiability analysis using the StructuralIdentifiability.jl package in JULIA. We validate the structural identifiability results by performing parameter estimation and forecasting using the GrowthPredict MATLAB toolbox. This toolbox is designed to fit and forecast time series trajectories based on phenomenological growth models. We applied it to three epidemiological datasets: weekly incidence data for monkeypox, COVID 19, and Ebola. Additionally, we assess practical identifiability through Monte Carlo simulations to evaluate parameter estimation robustness under varying levels of observational noise. Our results confirm that all six models are structurally identifiable under the proposed reformulation. Furthermore, practical identifiability analyses demonstrate that parameter estimates remain robust across different noise levels, though sensitivity varies by model and dataset. These findings provide critical insights into the strengths and limitations of phenomenological models to characterize epidemic trajectories, emphasizing their adaptability to real world challenges and their role in informing public health interventions.

q-bio.QM

BayesianFitForecast: A User-Friendly R Toolbox for Parameter Estimation and Forecasting with Ordinary Differential Equations

Background: Mathematical models based on ordinary differential equations (ODEs) are essential tools across various scientific disciplines, including biology, ecology, and healthcare informatics. They are used to simulate complex dynamic systems and inform decision-making. In this paper, we introduce BayesianFitForecast, an R toolbox specifically developed to streamline Bayesian parameter estimation and forecasting in ODE models, making it particularly relevant to health informatics and public health decision-making. The toolbox is available at https://github.com/gchowell/BayesianFitForecast/. Results: This toolbox enables automatic generation of Stan files, allowing users to configure models, define priors, and analyze results with minimal programming expertise. To demonstrate the versatility and robustness of BayesianFitForecast, we apply it to the analysis of the 1918 influenza pandemic in San Francisco, comparing Poisson and negative binomial error structures within the SEIR model. We also test it by fitting multiple time series of state variables using simulated data. BayesianFitForecast provides robust tools for evaluating model performance, including convergence diagnostics, posterior distributions, credible intervals, and performance metrics. Conclusion: By improving the accessibility of advanced Bayesian methods, this toolbox significantly broadens the application of Bayesian inference methods to dynamical systems critical for healthcare and epidemiological forecasting. A tutorial video demonstrating the toolbox's functionality is available at https://youtu.be/jnxMjz3V3n8.

q-bio.QM

Assembling ensembling: An adventure in approaches across disciplines

When discussing model ensembling or ensemble modeling, a term arises across numerous disciplines, what is meant by it can vary drastically. The very meaning of 'ensemble' - a collection together - conjures different ideas even within disciplines when approaching phenomena. For example, one might think of a set of descriptions of a phenomenon in the world, perhaps a time series or a snapshot of multivariate space, and perhaps that set is comprised of data-independent descriptions, or perhaps it is quite intentionally fit *to* data, or even a suite of data sets with a common theme or intention. Recently, ensemble models have appeared widely across applications, for disease forecasting, environmental suitability modeling, and more. In this piece, we present a typology of the scope of potential perspectives across disciplines to disambiguate terms, concepts, and processes associated with 'ensembles' and 'ensembling'. We do not provide an exhaustive review nor do we recommend that all disciplines must adopt a common suite of terms, but instead focus on facilitating communication, awareness, identification of gaps, and adoption of tools to avoid independent efforts to reinvent the wheel across disciplines. To anchor our discussion, we provide a Shiny App to contain the typology, with a living collection, or compendium, of example publications about ensembles.

cs.DL

Structural identifiability analysis of epidemic models based on differential equations: A tutorial-based primer

The successful application of epidemic models hinges on our ability to estimate model parameters from limited observations reliably. An often-overlooked step before estimating model parameters consists of ensuring that the model parameters are structurally identifiable from the observed states of the system. In this tutorial-based primer, intended for a diverse audience, including students training in dynamic systems, we review and provide detailed guidance for conducting structural identifiability analysis of differential equation epidemic models based on a differential algebra approach using DAISY (Differential Algebra for Identifiability of SYstems) and \textit{Mathematica} (Wolfram Research). This approach aims to uncover any existing parameter correlations that preclude their estimation from the observed variables. We demonstrate this approach through examples, including tutorial videos of compartmental epidemic models previously employed to study transmission dynamics and control. We show that the lack of structural identifiability may be remedied by incorporating additional observations from different model states, assuming that the system's initial conditions are known, using prior information to fix some parameters involved in parameter correlations, or modifying the model based on existing parameter correlations. We also underscore how the results of structural identifiability analysis can help enrich compartmental diagrams of differential-equation models by indicating the observed state variables and the results of the structural identifiability analysis.

q-bio.QM

A large-scale COVID-19 Twitter chatter dataset for open scientific research -- an international collaboration

As the COVID-19 pandemic continues its march around the world, an unprecedented amount of open data is being generated for genetics and epidemiological research. The unparalleled rate at which many research groups around the world are releasing data and publications on the ongoing pandemic is allowing other scientists to learn from local experiences and data generated in the front lines of the COVID-19 pandemic. However, there is a need to integrate additional data sources that map and measure the role of social dynamics of such a unique world-wide event into biomedical, biological, and epidemiological analyses. For this purpose, we present a large-scale curated dataset of over 152 million tweets, growing daily, related to COVID-19 chatter generated from January 1st to April 4th at the time of writing. This open dataset will allow researchers to conduct a number of research projects relating to the emotional and mental responses to social distancing measures, the identification of sources of misinformation, and the stratified measurement of sentiment towards the pandemic in near real time.

cs.SI

A dynamic modeling tool for estimating healthcare demand from the COVID19 epidemic and evaluating population-wide interventions

Objectives. Public health officials need tools to assist with anticipating the healthcare resources required to confront the SARS-COV-2 pandemic. We built a modeling tool to aid practicing public health officials with estimating healthcare demand from the pandemic in their jurisdictions and to evaluate the potential impacts of population-wide social-distancing interventions. Methods. The tool uses a SEIR compartmental model to project the local spread of the pandemic. Users input case counts, healthcare resources, and select intervention strategies to evaluate. Outputs include the number of infections and deaths with and without intervention, and the demand for hospital and critical care beds and ventilators relative to existing capacity. We illustrate the tool using data from three regions of Chile. Results. Our scenarios indicate a surge in COVID-19 patients could overwhelm Chilean hospitals by June, peaking in July or August at 6 to 50 times the current supply of beds and ventilators. A lockdown strategy or combination of case isolation, home quarantine, social distancing of individuals greater than 70 years, and telework interventions may keep treatment demand below capacity. Conclusions. Aggressive interventions can avert substantial morbidity and mortality from COVID-19. Our tool permits rapid evaluation of locally-applicable policy scenarios and updating of results as new data become available.

q-bio.PE

Characterizing the reproduction number of epidemics with early sub-exponential growth dynamics

Early estimates of the transmission potential of emerging and re-emerging infections are increasingly used to inform public health authorities on the level of risk posed by outbreaks. Existing methods to estimate the reproduction number generally assume exponential growth in case incidence in the first few disease generations, before susceptible depletion sets in. In reality, outbreaks can display sub-exponential (i.e., polynomial) growth in the first few disease generations, owing to clustering in contact patterns, spatial effects, inhomogeneous mixing, reactive behavior changes, or other mechanisms. Here, we introduce the generalized growth model to characterize the early growth profile of outbreaks and estimate the effective reproduction number, with no need for explicit assumptions about the shape of epidemic growth. We demonstrate this phenomenologic approach using analytical results and simulations from mechanistic models, and provide validation against a range of empirical disease datasets. Our results suggest that sub-exponential growth in the early phase of an epidemic is the rule rather the exception. For empirical outbreaks, the generalized-growth model consistently outperforms the exponential model for a variety of directly and indirectly transmitted diseases datasets with model estimates supporting sub-exponential growth dynamics. The rapid decline in effective reproduction number predicted by analytical results and observed in real and synthetic datasets within 3-5 disease generations contrasts with the expectation of invariant reproduction number in epidemics obeying exponential growth. Overall, our approach promotes a more reliable and data-driven characterization of the early epidemic phase, which is important for accurate estimation of the reproduction number and prediction of disease impact.

q-bio.QM

Prevention and control of Zika fever as a mosquito-borne and sexually transmitted disease

The ongoing Zika virus (ZIKV) epidemic poses a major global public health emergency. It is known that ZIKV is spread by \textit{Aedes} mosquitoes, recent studies show that ZIKV can also be transmitted via sexual contact and cases of sexually transmitted ZIKV have been confirmed in the U.S., France, and Italy. How sexual transmission affects the spread and control of ZIKV infection is not well-understood. We presented a mathematical model to investigate the impact of mosquito-borne and sexual transmission on spread and control of ZIKV and used the model to fit the ZIKV data in Brazil, Colombia, and El Salvador. Based on the estimated parameter values, we calculated the median and confidence interval of the basic reproduction number R0=2.055 (95% CI: 0.523-6.300), in which the distribution of the percentage of contribution by sexual transmission is 3.044 (95% CI: 0.123-45.73). Our study indicates that R0 is most sensitive to the biting rate and mortality rate of mosquitoes while sexual transmission increases the risk of infection and epidemic size and prolongs the outbreak. In order to prevent and control the transmission of ZIKV, it must be treated as not only a mosquito-borne disease but also a sexually transmitted disease.

q-bio.PE

A generalized-growth model to characterize the early ascending phase of infectious disease outbreaks

A better characterization of the early growth dynamics of an epidemic is needed to dissect the important drivers of disease transmission. We introduce a 2-parameter generalized-growth model to characterize the ascending phase of an outbreak and capture epidemic profiles ranging from sub-exponential to exponential growth. We test the model against empirical outbreak data representing a variety of viral pathogens and provide simulations highlighting the importance of sub-exponential growth for forecasting purposes. We applied the generalized-growth model to 20 infectious disease outbreaks representing a range of transmission routes. We uncovered epidemic profiles ranging from very slow growth (p=0.14 for the Ebola outbreak in Bomi, Liberia (2014)) to near exponential (p>0.9 for the smallpox outbreak in Khulna (1972), and the 1918 pandemic influenza in San Francisco). The foot-and-mouth disease outbreak in Uruguay displayed a profile of slower growth while the growth pattern of the HIV/AIDS epidemic in Japan was approximately linear. The West African Ebola epidemic provided a unique opportunity to explore how growth profiles vary by geography; analysis of the largest district-level outbreaks revealed substantial growth variations (mean p=0.59, range: 0.14-0.97). Our findings reveal significant variation in epidemic growth patterns across different infectious disease outbreaks and highlights that sub-exponential growth is a common phenomenon. Sub-exponential growth profiles may result from heterogeneity in contact structures or risk groups, reactive behavior changes, or the early onset of interventions strategies, and consideration of "deceleration parameters" may be useful to refine existing mathematical transmission models and improve disease forecasts.

q-bio.QM

The Western Africa Ebola virus disease epidemic exhibits both global exponential and local polynomial growth rates

Background: While many infectious disease epidemics are initially characterized by an exponential growth in time, we show that district-level Ebola virus disease (EVD) outbreaks in West Africa follow slower polynomial-based growth kinetics over several generations of the disease. Methods: We analyzed epidemic growth patterns at three different spatial scales (regional, national, and subnational) of the Ebola virus disease epidemic in Guinea, Sierra Leone and Liberia by compiling publicly available weekly time series of reported EVD case numbers from the patient database available from the World Health Organization website for the period 05-Jan to 17-Dec 2014. Results: We found significant differences in the growth patterns of EVD cases at the scale of the country, district, and other subnational administrative divisions. The national cumulative curves of EVD cases in Guinea, Sierra Leone, and Liberia show periods of approximate exponential growth. In contrast, local epidemics are asynchronous and exhibit slow growth patterns during 3 or more EVD generations, which can be better approximated by a polynomial than an exponential. Conclusions: The slower than expected growth pattern of local EVD outbreaks could result from a variety of factors, including behavior changes, success of control interventions, or intrinsic features of the disease such as a high level of clustering. Quantifying the contribution of each of these factors could help refine estimates of final epidemic size and the relative impact of different mitigation efforts in current and future EVD outbreaks.

q-bio.PE