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Hamed Karami

Publications and source records attributed to Hamed Karami.

10 recordsLinked to original sources
arXiv2026

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.

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arXiv2026

Intersection Arrays of Completely Regular Codes of Covering Radius One in Generalized Petersen Graphs

We determine all possible intersection arrays of completely regular codes of covering radius one in the generalized Petersen graphs \(GP(n,k)\), where \(n\geq 3\) and \(1\leq k<n/2\). In the equivalent language of perfect colorings, this amounts to enumerating all quotient matrices of perfect \(2\)-colorings, up to interchanging the two colors. Since \(GP(n,k)\) is cubic, there are only six possible nontrivial quotient matrices. For each of them, we give necessary and sufficient arithmetic conditions on \(n\) and \(k\) for its existence. The feasible cases are realized by explicit periodic colorings. The nonexistence part is obtained by reducing the local coloring conditions to cyclic systems of linear equations and applying a Fourier argument on roots of unity. Together with the previously known cases \(GP(n,2)\) and \(GP(n,3)\), the results give a complete arithmetic classification of quotient matrices, and hence of covering-radius-one completely regular code parameters, in the generalized Petersen family.

math.CO↗
arXiv2026

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.

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arXiv2026

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.

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arXiv2025

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↗
arXiv2025

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↗
arXiv2025

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.

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arXiv2024

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.

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