Overview
The workshop will focus on training students in foundational and emerging quantitative tools and applied skills for disease ecology. Quantitative tools that will be covered in this workshop potentially include (i) modeling vector and host abundance and time-dependent data and (ii) AI applications to disease ecology and evolution. Students will choose one of these quantitative tracks and learn the relevant skills through group project-based work. The applied part of the workshop will narrow in on applications of disease ecology in public health, policy, conservation, management, and decision-making through discussions and case studies with experts. Workshop leaders will include scientists, both academic and non-academic, with experience translating their work in a variety of contexts.
General Structure and Content of the AI and Infectious Disease Workshop
Instructors: Pranav Pandit and Pranav Kulkarni from UC Davis and Valya Kuskova and Nuno Moniz from the University of Notre Dame
*Meals will be provided
Arrival Day (Fri, June 13): Please join for a 6:00 pm welcome dinner on campus. Optional.
Day 1 (Sat., June 14, 9:00-12:00):
Introduction to AI/Machine Learning (ML) and Python
Unsupervised Learning: Clustering
Group coding exercise
Day 1 (Sat., June 14, 1:00-5:00):
Introduction to Supervised Learning
Tree-based Supervised Machine Learning
Group coding exercise
Day 2 (Sun., June 15, 9:00-12:00):
Introduction to Regression-based Machine Learning
Machine Learning Autoregressive Models: applied to infectious disease time series
Group coding exercise
Day 2 (Sun., June 15, 1:00-3:30):
Machine Learning Models: testing for environmental signals on infectious disease risk
Group coding exercises
(Sun., June 15, 3:45-5:00)
Discussion: Panel discussion, issues with AI-ML in disease ecology
Day 3 (Mon., June 16, 9:00-12:00):
Machine learning-based Species Distribution Models
Group coding exercises
Workshop ends at 1PM after lunch.
Requisite Knowledge/Skills for the AI and Infectious Disease Workshop
Participants should have a foundational understanding of ecology and infectious disease dynamics, along with basic proficiency in coding with Python and R. Prior experience with data analysis and visualization using libraries such as Pandas, ggplot2, and Matplotlib will be beneficial. While no advanced machine learning background is required, familiarity with statistical modeling, regression analysis, and GIS tools (for species distribution modeling) will enhance the learning experience. The workshop will include more running of code than writing of code in both Python and R, so participants should be comfortable working with Jupyter Notebooks and RStudio and have some exposure to data manipulation techniques. You will need your own laptop with Python installed ahead of the workshop.
In the next few days, we will have tutorials and documentation files that will help trainees get up to speed on basic skills before the workshop.
Content of the Modeling Vector and Host Abundance and Time-dependent Data Workshop
Instructors: Leah Johnson from Virginia Tech, Sadie Ryan from the University of Florida, Sam Rund from the University of Notre Dame
Details
When: The workshop begins Saturday, June 14th at 9:00 am and will end on Monday, June 16th at 1:00 pm. Workshop participants should plan to arrive on-campus on Friday, June 13th. Optional Welcome Dinner on Friday night. Dorm check-in begins at 3:00 pm
Who: The workshop will prioritize students in the 3rd year or later of their PhD program or postdoctoral scholars who completed their PhD less than 2 years ago, but others may apply and will be considered on a case-by-case basis. Approximately 30 students will receive scholarships to cover the costs of workshop attendance, and there will be space available for approximately additional students who can fund their own costs through their own programs or advisors. If there are spots available, more junior PhD students may be considered based upon their coding experience.
Where: The workshop will be held on-campus at the University of Notre Dame.
Workshop Fee: There is no fee to attend the workshop. However, participants who do not receive a travel award will be responsible for the cost of housing and travel. On the submission form, you may indicate if you need a travel award in order to attend (see details below). If you are able to secure travel and housing funding elsewhere, please do not apply for a travel award to save resources for applicants who really need the funding. We expect all workshop attendees to stay on for the EEID conference Monday, June 16th through Thursday, June 19th. Attendees will be responsible for covering their own conference registration and housing fees during the conference (exceptions may be made on a case-by-case basis and a limited number of scholarships to cover the costs of conference attendance may be available for students in need).
Meals: Complimentary meals (Friday dinner through Monday lunch) will be provided to all workshop participants.
Housing: On-campus housing is available at the University of Notre Dame. Dorm style (single and double occupancy, shared bath) is available for workshop participants. Travel awards will cover the cost of double occupancy accommodation. Workshop participants should plan to check in to on campus housing on Friday, June 13th and stay for the conference which ends midday, June 16th.
Travel Awards: Individuals accepted into the workshop are eligible to receive a travel award. We anticipate we will be able to offer travel awards for ~20 participants.
The travel award includes:
- Round trip economy class airfare, up to $600, from your home city to South Bend, IN, arriving Friday, June 13 and departing on Thursday, June 19, 2025. Information about booking airfare will be provided upon acceptance of travel award. A limited number of larger airfare awards will be available for international participants.
- Vouchers to use for ground transportation to/from the South Bend airport.
- Complimentary dorm style (double occupancy, shared bath) accommodation at University of Notre Dame for (3) nights. Check-in Friday, June 13th and Check-out Thursday, June 19th (Travel awardees will be responsible for covering registration and housing fees for the conference).
- Group and dining hall meals from Friday dinner to Monday lunch.
Important – 2025 EEID Conference Registration:
All workshop participants are expected to register to attend the 2025 EEID Conference and are responsible for paying the corresponding registration fee. If the conference registration fee is prohibitive to your participation, we will consider limited exceptions and fee waivers on a case-by-case basis. Please contact the workshop planning team at (eeid@nd.edu) for more information.
How to apply: Interested participants must apply using the link below. The organizing committee will select participants based on the quality of their application, the requisite quantitative skills, and with the goal of representing diverse backgrounds and research topics.
Notification: Successful applicants and travel award recipients will be notified via email in mid-April.
**Please note applications closes April 28th
For questions, please contact the workshop organizers via email: eeid@nd.edu.