Our team develops statistical methods and analytical tools to help people make sense of data. Building on close collaborative relationships with public health practitioners from across the world -- from Denver to San Juan to Bangkok -- we use modern statistical and machine learning tools to gain insights into complex disease systems.
We build software packages, maintain code repositories, develop SQL databases, create interactive data visualizations, and run computationally intensive simulation studies. We use the R programming language for most of our work, but also use some C, C++, and Python.
Check out our work on GitHub.
Our team develops models for understanding complex and dynamic systems of infectious disease. We have developed real-time forecasts of dengue fever in Thailand, estimated the duration of cross-protection between serotypes of dengue, and predicted the trajectory of the flu season in the US.
Posted on 17 September, 2018
Last week, I attended a Pandemic Influenza Exercise at the US CDC. To be clear, there is NOT a pandemic occuring right now, but the CDC ran this exercise where hundreds of staff members and outside observers and participants came together to practice going through the motions of a public health response to a major pandemic. As someone who is usually sheltered from this everyday aspect of public health decision-making, this was a fascinating window into understanding the careful, if time-pressured, scientific deliberation that underlies the response to public health emergencies.
Posted on 28 November, 2017
In March 2017, a group of influenza forecasters who have participated in the CDC FluSight challenge in past seasons established the FluSight Network, a multi-institution and multi-disciplinary consortium of forecasting teams. This group worked throughout 2017 to create a public, real-time collaborative ensemble forecasting model that provides updated forecasts of influenza in the US each week.
Posted on 24 May, 2017
Here are the slides for my presentation today at the annual MIDAS conference in Atlanta, GA. The talk summarizes recent work led by post-doc Evan Ray on creating interpretable “feature-weighted density ensembles” for infectious disease forecasting. The paper is currently under review, but the preprint is available on arXiv. Check out the 2017-2018 real-time influenza forecasts from this model available on our flusight app. And here are some slices of the feature-dependent weighting functions for predicting peak incidence for influenza in the U.S.
Posted on 14 May, 2017
I wrote a response to Siddhartha Mukherjee’s article “A.I. vs. M.D.” that appeared in the New Yorker last month. While I submitted it as a letter to the editor, they didn’t publish it. In retrospect, perhaps it was a bit long-winded for their curt and pithy letters section. Mukherjee’s article was published on the heels of Evan submitting his latest work on improving the consistency of infectious disease prediction using interpretable model averaging methods. What follows is the letter I submitted.
Posted on 30 November, 2016
We updated our U.S. influenza forecasts on Tuesday, November 29th. (We tend to update the forecasts on Mondays, but the CDC data release was delayed this week due to Thanksgiving last week.) Overall, the data and the short-term forecasts for flu are showing regional circulation of flu that is a bit below the CDC-defined baseline levels. The two exceptions are in HHS Region 2 (NY and NJ) which is right at its baseline level, according to the most recent data from the CDC (reported through November 19th), and HHS Region 4 (the southeastern corner of the US) which already has risen above its baseline. Region 4 has historically had somewhat earlier seasons than the rest of the US. Check out our interactive FluSight app for more details on each region.