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  • New paper – Improving outbreak forecasts through model augmentation

    The Fox lab had our latest forecasting work published in PNAS a couple of weeks ago! https://www.pnas.org/doi/10.1073/pnas.2508575122

    This paper has been about 4 years in the making beginning a couple of years in to the COVID-19 pandemic when our group at UT Austin (where I was a research associate) and Graham (Casey) was a postdoc. We noticed that models were tending to overshoot the peaks of the pandemic waves, but realized there weren’t obvious ways for correcting this behavior, particularly in empirical forecast models (e.g. ARIMA and ML approaches).

    The team came up with a great solution which was to integrate epidemiological dynamics into forecasts, something we called “epimodulation.” The basic idea is that the model has the ability to enforce a peak directly on a forecast without changing the underlying forecast model. There’s a single parameter, theta, that controls these dynamics and we use cross-validation on historical forecast performance to estimate it. Here’s the principal in action:

    On this ARIMA forecast for this hypothetical time-series you can see that the two forecasts are the same for the first peak, but then the model learns that actually the ARIMA seems to be overpredicting peaks, so during the second peak the epimodulation adjustment causes a peak to occur much sooner and makes that forecast more closely match the actual data. In Panel B you can see estimates of Theta over time, beginning at zero before any forecasts have been made and then increasing as the model learns the relationship between the ARIMA forecast model and the ultimate data.

    So we wanted to test this on real data and we deployed 5 different models for multiple years of both COVID-19 and influenza (COVID shown below). What you basically can see is that epimodulation reduced the mean absolute error of all forecast models for almost every date (Panel B), forecast horizon (Panel C), and location (Panel D) for every model we tested. Epimodulation had the biggest impact during epidemiological peaks as we had hoped. What surprised us was that epimodulation almost never hurt the forecast performance.

    Okay so you might be thinking that we tried it on 5 different forecast models but none of them may have been particularly good. So we then tested it to see how it might improve the COVID-19 ensemble forecasts, which are generally thought of as the “gold standard” forecast model to try and beat. Our results showed that we could improve that performance by 5-10% over the whole time period. It might seem small, but this is a simple way to get a high single digit forecast improvement out of the best forecast model right now!

    We are really excited about this model and are hoping to deploy it in real-time for forecast models this upcoming season! Also, we think this is a really interesting research avenue that can be improved more. Maybe we can correct model tendencies to miss when epidemics begin increasing, or maybe we can design epimodulation to be more intelligent, knowing the exact theta to use based on the seasonality timing or other features within the data. We hope many other people will be interested and start exploring other ways to modulate the forecasts of other models to correct for their inherent biases!

    If you’re interested in it, check out the paper here (it will be open access in 6 months): https://www.pnas.org/doi/10.1073/pnas.2508575122

    We also have an open access preprint of the paper here, which is only missing some of the additional results we made during the revision process: https://arxiv.org/abs/2506.16410

    To close, here’s a picture of Nefertiti (Toobss) from our writer’s retreat long weekend where we hammered out most of the draft of this paper before celebrating with an insane powder ski day at Pajarito!

  • The Fox Lab has moved to NAU in Flagstaff, AZ

    This semester the Fox lab officially moved from the University of Georgia to Northern Arizona University in Flagstaff, AZ! Leaving the University of Georgia is extremely bittersweet. I had the privilege of working with incredible colleagues and students, and Athens is truly a special place that felt like home. At the same time, I’m excited to begin a new chapter at NAU, where I’ll continue to grow my research and teaching in a new environment surrounded by inspiring people and landscapes. For those who have followed my adventures the past few years you know that the Southwest has always held a special place in my heart and I am excited to be full-time in the middle of it!

    The good news is that I’m maintaining and hoping to build on my UGA connections. I should be back in Athens regularly, as I will continue to mentor all of my wonderful students until they finish their degrees. This move puts our lab very much in a transition phase, where our work will wind down at UGA and slowly ramp up here at NAU over the next few years. It feels a bit like starting over, which has provided a lot of time for introspection to think about our work the past few years and the direction the lab will take moving forward.

    So that brings us to NAU. Here, I am housed in the School of Informatics, Computing, and Cyber Systems (SICCS) and have a tight connection with the Center for Community Health and Engaged Research (CHER). There is also the Pathogen and Microbiome Institute (PMI) that I am hoping to build close ties with over time. While other options may be open in the future, in the short-term I will be able to take PhD students through the Informatics program in SICCS, which will provide the computational, data science, and ML/AI instruction that will power our research moving forward.

    Over the past few years the Fox Lab has really dove head first into the field of outbreak forecasting. Designing behavior-powered forecast models, optimizing ensemble forecasting approaches and the design of forecasting hubs, augmenting model forecasts with epidemiological dynamics, developing new and winning respiratory virus forecast models, and expanding our forecasting efforts internationally to Paraguay and additional Southern Hemisphere countries through grants from CSTE and CDC (papers forthcoming). We’ll continue tackling diverse and impactful modeling questions, but I’m particularly eager to lean further into forecasting—broadening our efforts to new diseases and regions while building the models and infrastructure that will drive the next generation of predictive science.

    Leaving Athens isn’t easy, but change brings new energy and perspective. I can’t wait to see what we’ll build together at NAU, and I’m so thankful to everyone who’s been part of the journey so far. For those looking to get involved, keep an eye out—PhD and postdoc positions will be opening soon! As always, feel free to reach out to me at my new email address even without a posting: spencer.fox@nau.edu.

    30 km and a huge major life decision later, still standing (barely) and smiling in Flagstaff.

  • New paper – Optimizing Disease Outbreak Forecast Ensembles

    The Fox lab had our first “lab” paper come out this year that was started and finished during my tenure here at UGA! In the paper, myself and my collaborators (Lauren Meyers from UT, and Evan, Nick, and Minsu from UMass Amherst) investigated how the size of ensembles impacted their performance using data from all of the recent collaborative forecast hub data: https://wwwnc.cdc.gov/eid/article/30/9/24-0026-f2

    Background

    The background for this project came as Nick, Evan, and I were chatting at the CSTE Forecast conference in 2022 about forecasting. There was a question that came up repeatedly that year if we really needed dozens of teams to be producing weekly forecasts for COVID-19, because in the end we tend to only broadcast a single ensemble forecast. Since all of the collaborative hubs have publicly available data, we mapped out a project to actually investigate it.

    Methods

    We gathered all of the forecasts for all recent collaborative forecast efforts (millions and millions of data points), constructed random ensembles of varying sizes, and scored their performance. A key limitation is that we chose to run the analysis with a subset of models that had regularly forecasted during the time periods we chosen, meaning that our sample size wasn’t that large for many of the hubs AND that our analysis likely focuses on some of the better forecast models (many models that don’t perform well come in and out, so the consistent models tend to be some of the better ones submitted).

    Results

    We have three results from our primary analysis: (1) adding models always improves and reduces variability of the average forecast performance, (2) performance gains level off after 4-5 models are included, and (3) you want to include at least four models in your ensemble to beat baseline forecasts. All of these conclusions can be seen in Figure 2 of the manuscript (Panel B of this version):

    After running these analyses, one can see that there are some randomly assembled ensembles for almost all of these efforts that beat the published ensemble that is composed of all submitted forecasts (some of the grey shaded regions are below the horizontal purple line and lower numbers are better in these). We set out to see if we could develop a simple way to select these models and found that generally ensembles of models that perform well in one season perform well in others (The Ensemble rank line in this figure):

    While I think this is a really amazing finding, I didn’t feel comfortable having this as the key finding in the paper, for two reasons:

    1. We didn’t investigate more sophisticated ensemble weighting methodologies that likely will outperform these ones
    2. This approach will not work if the submitted models change season to season. For example, this past season the Flusion model performed amazingly, but would not have been included in this ensemble, because we were basing everything on performance from the previous season. I would love to pursue a method to make a real-time version of this ensemble that would address this issue and see if it outperforms other approaches.

    Conclusions

    Hub organizers should target a minimum of 4 validated forecast models to ensure robust performance compared with baseline models. Adding more models reduces the variability in expected ensemble performance but might come with diminishing returns in average forecast skill. As public health officials and researchers look to expand collaborative forecast efforts, and as funding agencies allocate budgets across methodological and applied forecast efforts, our results can be used to identify target participation rates, assemble appropriate forecast models, and further improve ensemble forecast performance.

    The project was largely built on infrastructure made available through the hubverse ecosystem, and I think these data have a lot of potential for project you’re interested in the topic or methodology, you can find the code to recreate the analysis here: https://github.com/sjfox/ensemble-size

  • Hiring in Fall 2024!

    We’re hiring! We’re looking for an additional postdoc to join our group!! Are you interested? Here are some quick hits about it:

    1. The position and project focus are flexible. I want you to be excited about the projects you’re working on, so the interview process will involve learning about your interests and discussing possible projects that would make sense based on our overlap. Currently our lab focuses on forecasting infectious disease dynamics and a wide-range of infectious disease modeling projects. Check out some of our latest publications and reach out to hear more about what we’re working on: https://scholar.google.com/citations?hl=en&user=qZ0DYksAAAAJ&view_op=list_works&sortby=pubdate
    2. The position will pay $57-67k/year for two years, and I will have additional funds that we can use to support conference travel, equipment, and other scientific expenses.
    3. The UGA benefits are good! Healthcare, dental, vision options. Retirement matching, subsidized child care, etc. For more information see here: https://hr.uga.edu/Current_Employees/Benefits/benefits/
    4. I am very flexible about the work arrangement and would be happy for the postdoc to be in-person or fully remote. This flexibility also extends to start dates, vacations, etc.

    The link to the job advertisement can be found here, but feel free to email me directly with any questions or concerns before applying: https://www.ugajobsearch.com/postings/392752

    Please don’t hesitate to reach out if you have any questions about the position or our group!

    A photo of the State Botanical Garden that is just south of the main UGA campus, one of the great outdoors spaces nearby!

  • The Fox lab, est. 2022

    This summer I excitedly accepted a position at the University of Georgia as an Assistant Professor jointly appointed in the Department of Epidemiology & Biostatistics and the Institute of Bioinformatics. I also have an appointment with the Center for the Ecology of Infectious Diseases and am hoping to receive a courtesy appointment with the Odum School of Ecology (tbd).

    I’m sad to leave my position as Associate Director of the UT COVID-19 Modeling Consortium, but I’m excited (and honestly a bit anxious overall) about starting my own research lab at UGA. Luckily we were already working over Zoom, so my collaboration with Lauren and team at UT is just moving time zones!

    I’ll be looking for PhD students and postdoctoral researchers soon, so stay tuned!

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