arXiv subjects

Evan L. Ray

Publications and source records attributed to Evan L. Ray.

10 recordsLinked to original sources

arXiv2026

Collaborative estimation and evaluation of SARS-CoV-2 variant nowcasting in the United States

The ability to estimate and predict pathogen variant dynamics can inform public health responses, including planning for increased transmission or severity, shifts in population immunity, or changes to vaccine or therapeutic effectiveness. The COVID-19 pandemic demonstrated the importance of monitoring SARS-CoV-2 variant evolution through viral genome sequencing, enabling predictive models to estimate variant frequencies in the recent past, present, and short-term future. Collaborative forecasting Hubs provided a valuable way to centralize predictive modeling of epidemiological indicators such as cases, hospitalizations, and deaths during the pandemic; however, none existed for variant dynamics. Here, we discuss the creation of the United States SARS-CoV-2 Variant Nowcast Hub, designed to solicit estimates of the relative abundance of a specified set of SARS-CoV-2 variants at the U.S. state level. We discuss the design decisions and challenges in building the Hub and its scoring procedures. Using submissions from the Hub's first respiratory virus season (nowcast dates October 9th, 2024 to June 4th, 2025), we evaluate five individual models and a baseline model. We found that the baseline model, which pools sequences across the U.S., performs well overall, with most individual models performing similarly or slightly worse. Locations with lower sequencing volumes exhibited greater variability in model performance. Models submitted for a single location outperformed those submitted for all locations, potentially due to greater timeliness and magnitude of local data. Much remains to be investigated regarding relative model performance across different phases of variant emergence, and we conclude by proposing future directions within and beyond this Hub.

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arXiv2026

modelimportance: An R package for evaluating model importance within a multi-model ensemble

Ensemble forecasts are commonly used to support decision-making and policy planning across various fields because they often offer improved accuracy and stability compared to individual models. As each model has its own unique characteristics, understanding and measuring the value of each constituent model can support the construction of effective ensembles. The R package modelimportance provides tools to quantify how each component model contributes to the accuracy of ensemble performance for both point and probabilistic forecasts. The package supports multiple ensemble methods and multiple model importance metrics. Additionally, the software offers customizable options for handling missing values. These features enable the package to serve as a versatile tool for researchers and practitioners. It helps not only in constructing an effective ensemble model across a wide range of forecasting tasks, but also in understanding the role of each model within the ensemble and gaining insights into individual models themselves. This package follows the 'hubverse' framework, which is a collection of open-source software, tools and data standards developed to promote collaborative modeling hub efforts and simplify their setup and operation. Doing so enables seamless integration and flexibility with other forecasting tools and systems, allowing many analyses to be performed on existing hubs.

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arXiv2026

Comparison of probabilistic nowcasts and forecasts of SARS-CoV-2 variant proportions made by hierarchical multinomial linear regression models

Nowcasting and forecasting of infectious diseases have become increasingly important since the SARS-CoV-2 pandemic. In particular, methods for modeling the composition of circulating variants at a given time have seen more use in part due to a large increase in the frequency of genomic sequencing conducted as a part of routine surveillance. However, methods must take into account that locations have different amounts of data and sometimes have different trends. We discuss hierarchical multinomial logistic regression (HMLR), a commonly used method for forecasting SARS-CoV-2 variants, which allows for data sharing across locations. We show how it has been used in the literature, and define a class of HMLR models for SARS-CoV-2 variant nowcasting and forecasting. We rigorously test a subset of this class of models using the framework of the US SARS-CoV-2 Variant Nowcast Hub, a collaborative modeling project that launched in 2024. We created two years of weekly predictions based on retrospective datasets, with the prediction dates ranging from Wednesday, August 3, 2022, to Wednesday, August 7, 2024. We tested 12 HMLR models against a baseline model on these datasets. We found that the HMLR models outperformed the baseline both in terms of probabilistic accuracy, as measured by the energy score, as well as point accuracy, as measured by the Brier score. Overall, we find that HMLR models perform best with respect to the baseline model in locations with more data, and more complex HMLR models also showed more improvement in those high-data locations; however, there was no one best model across all metrics, and simpler HMLR models perform better in low-data locations. We find that HMLR models perform well in practice for nowcasting and forecasting SARS-CoV-2 variants.

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arXiv2024

Beyond forecast leaderboards: Measuring individual model importance based on contribution to ensemble accuracy

Ensemble forecasts often outperform forecasts from individual standalone models, and have been used to support decision-making and policy planning in various fields. As collaborative forecasting efforts to create effective ensembles grow, so does interest in understanding individual models' relative importance in the ensemble. To this end, we propose two practical methods that measure the difference between ensemble performance when a given model is or is not included in the ensemble: a leave-one-model-out algorithm and a leave-all-subsets-of-models-out algorithm, which is based on the Shapley value. We explore the relationship between these metrics, forecast accuracy, and the similarity of errors, both analytically and through simulations. We illustrate this measure of the value a component model adds to an ensemble in the presence of other models using US COVID-19 death probabilistic forecasts. This study offers valuable insight into individual models' unique features within an ensemble, which standard accuracy metrics alone cannot reveal.

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arXiv2024

Flusion: Integrating multiple data sources for accurate influenza predictions

Over the last ten years, the US Centers for Disease Control and Prevention (CDC) has organized an annual influenza forecasting challenge with the motivation that accurate probabilistic forecasts could improve situational awareness and yield more effective public health actions. Starting with the 2021/22 influenza season, the forecasting targets for this challenge have been based on hospital admissions reported in the CDC's National Healthcare Safety Network (NHSN) surveillance system. Reporting of influenza hospital admissions through NHSN began within the last few years, and as such only a limited amount of historical data are available for this signal. To produce forecasts in the presence of limited data for the target surveillance system, we augmented these data with two signals that have a longer historical record: 1) ILI+, which estimates the proportion of outpatient doctor visits where the patient has influenza; and 2) rates of laboratory-confirmed influenza hospitalizations at a selected set of healthcare facilities. Our model, Flusion, is an ensemble that combines gradient boosting quantile regression models with a Bayesian autoregressive model. The gradient boosting models were trained on all three data signals, while the autoregressive model was trained on only the target signal; all models were trained jointly on data for multiple locations. Flusion was the top-performing model in the CDC's influenza prediction challenge for the 2023/24 season. In this article we investigate the factors contributing to Flusion's success, and we find that its strong performance was primarily driven by the use of a gradient boosting model that was trained jointly on data from multiple surveillance signals and locations. These results indicate the value of sharing information across locations and surveillance signals, especially when doing so adds to the pool of available training data.

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arXiv2023

Evaluating infectious disease forecasts with allocation scoring rules

Recent years have seen increasing efforts to forecast infectious disease burdens, with a primary goal being to help public health workers make informed policy decisions. However, there has only been limited discussion of how predominant forecast evaluation metrics might indicate the success of policies based in part on those forecasts. We explore one possible tether between forecasts and policy: the allocation of limited medical resources so as to minimize unmet need. We use probabilistic forecasts of disease burden in each of several regions to determine optimal resource allocations, and then we score forecasts according to how much unmet need their associated allocations would have allowed. We illustrate with forecasts of COVID-19 hospitalizations in the US, and we find that the forecast skill ranking given by this allocation scoring rule can vary substantially from the ranking given by the weighted interval score. We see this as evidence that the allocation scoring rule detects forecast value that is missed by traditional accuracy measures and that the general strategy of designing scoring rules that are directly linked to policy performance is a promising direction for epidemic forecast evaluation.

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arXiv2022

Comparison of Combination Methods to Create Calibrated Ensemble Forecasts for Seasonal Influenza in the U.S

The characteristics of influenza seasons varies substantially from year to year, posing challenges for public health preparation and response. Influenza forecasting is used to inform seasonal outbreak response, which can in turn potentially reduce the societal impact of an epidemic. The United States Centers for Disease Control and Prevention, in collaboration with external researchers, has run an annual prospective influenza forecasting exercise, known as the FluSight challenge. A subset of participating teams has worked together to produce a collaborative multi-model ensemble, the FluSight Network ensemble. Uniting theoretical results from the forecasting literature with domain-specific forecasts from influenza outbreaks, we applied parametric forecast combination methods that simultaneously optimize individual model weights and calibrate the ensemble via a beta transformation. We used the beta-transformed linear pool and the finite beta mixture model to produce ensemble forecasts retrospectively for the 2016/2017 to 2018/2019 influenza seasons in the U.S. We compared their performance to methods currently used in the FluSight challenge, namely the equally weighted linear pool and the linear pool. Ensemble forecasts produced from methods with a beta transformation were shown to outperform those from the equally weighted linear pool and the linear pool for all week-ahead targets across in the test seasons based on average log scores. We observed improvements in overall accuracy despite the beta-transformed linear pool or beta mixture methods' modest under-prediction across all targets and seasons. Combination techniques that explicitly adjust for known calibration issues in linear pooling should be considered to improve ensemble probabilistic scores in outbreak settings.

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arXiv2022

Comparing trained and untrained probabilistic ensemble forecasts of COVID-19 cases and deaths in the United States

The U.S. COVID-19 Forecast Hub aggregates forecasts of the short-term burden of COVID-19 in the United States from many contributing teams. We study methods for building an ensemble that combines forecasts from these teams. These experiments have informed the ensemble methods used by the Hub. To be most useful to policy makers, ensemble forecasts must have stable performance in the presence of two key characteristics of the component forecasts: (1) occasional misalignment with the reported data, and (2) instability in the relative performance of component forecasters over time. Our results indicate that in the presence of these challenges, an untrained and robust approach to ensembling using an equally weighted median of all component forecasts is a good choice to support public health decision makers. In settings where some contributing forecasters have a stable record of good performance, trained ensembles that give those forecasters higher weight can also be helpful.

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arXiv2020

Evaluating epidemic forecasts in an interval format

For practical reasons, many forecasts of case, hospitalization and death counts in the context of the current COVID-19 pandemic are issued in the form of central predictive intervals at various levels. This is also the case for the forecasts collected in the COVID-19 Forecast Hub (https://covid19forecasthub.org/). Forecast evaluation metrics like the logarithmic score, which has been applied in several infectious disease forecasting challenges, are then not available as they require full predictive distributions. This article provides an overview of how established methods for the evaluation of quantile and interval forecasts can be applied to epidemic forecasts in this format. Specifically, we discuss the computation and interpretation of the weighted interval score, which is a proper score that approximates the continuous ranked probability score. It can be interpreted as a generalization of the absolute error to probabilistic forecasts and allows for a decomposition into a measure of sharpness and penalties for over- and underprediction.

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arXiv2017

Prediction of infectious disease epidemics via weighted density ensembles

Accurate and reliable predictions of infectious disease dynamics can be valuable to public health organizations that plan interventions to decrease or prevent disease transmission. A great variety of models have been developed for this task, using different model structures, covariates, and targets for prediction. Experience has shown that the performance of these models varies; some tend to do better or worse in different seasons or at different points within a season. Ensemble methods combine multiple models to obtain a single prediction that leverages the strengths of each model. We considered a range of ensemble methods that each form a predictive density for a target of interest as a weighted sum of the predictive densities from component models. In the simplest case, equal weight is assigned to each component model; in the most complex case, the weights vary with the region, prediction target, week of the season when the predictions are made, a measure of component model uncertainty, and recent observations of disease incidence. We applied these methods to predict measures of influenza season timing and severity in the United States, both at the national and regional levels, using three component models. We trained the models on retrospective predictions from 14 seasons (1997/1998 - 2010/2011) and evaluated each model's prospective, out-of-sample performance in the five subsequent influenza seasons. In this test phase, the ensemble methods showed overall performance that was similar to the best of the component models, but offered more consistent performance across seasons than the component models. Ensemble methods offer the potential to deliver more reliable predictions to public health decision makers.

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