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Amanda Bleichrodt

Publications and source records attributed to Amanda Bleichrodt.

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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

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

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