The 2025 Short Course on the Application of Machine Learning for Automated Quantification of Behavior

The Jackson Laboratory

Oct 12-17, 2025

7:45 am - 8:30 pm EST

Instructors: to be announced.

General Information

Over the past few years, behavior quantification and modeling has experienced an explosion of innovation and discovery largely enabled by application of new machine learning methods. These methods have enabled the quantification of behavior at high temporal and spatial resolution, and in concordance with simultaneous measurement and manipulation of neural and genetic function. However, access to this revolutionary technology is limited primarily due to a lack of adequate resources and training. Democratization of this technology through training of the next generation of scientists is necessary to elevate the field of quantitative behavior. The Short Course on the Application of Machine Learning for Automated Quantification of Behavior will disseminate the theoretical and technical knowledge of this field, and train researchers to apply machine learning methods to behavior quantitation and modeling. Our goal is to build an educational program that fosters productive and interactive dialogue, teaches proper methodology, and provides support structure to nurture and lower the barrier of entry into this nascent field. The course will:

Who: This course is appropriate for early career researchers from the fields of neuroscience, genetics, and biomedical research.

Prerequisites: Scripting and programming knowledge is required. If you can write and execute a for loop you are ready for this course.

Where: 600 Main Street, Bar Harbor, Maine. Get directions with OpenStreetMap or Google Maps.

When: Oct 12-17, 2025. Add to your Google Calendar.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.).



Schedule

Sunday, Oct 12

AFTERNOONArrival and registration
6:00 Dinner
7:00 Poster session
8:30 End

Monday, Oct 13

8:00 Welcome and Announcements
08:05 Google Colab, Jupyter Notebooks and Python (beginner) OR
Advanced Research Software Engineering (advanced)
10:00 Coffee/tea
10:15 Google Colab, Jupyter Notebooks and Python (continued)
Advanced Research Software Engineering (continued)
12:15 Lunch
1:00 Special activities
3:00 Introduction to Machine Learning with Python (beginner) OR
Advanced Research Software Engineering (continued) part 1 and part 2
6:00 Dinner
7:15 Evening discussion
8:30 End

Tuesday, Oct 14

07:45 Announcements
08:00 Worm tracking in 96-well plates: what can you do with 10k behaviour assays per day? André Brown, Ph.D., MRC Laboratory of Medical Sciences
09:00 Quantifying and modeling behavior using deep learning Talmo Pereira, Ph.D., The Salk Institute for Biological Studies
10:00 Coffee/tea
10:15 Measuring animal behavior in three dimensions Lili Karashchuk, Ph.D., Allen Institute for Neural Dynamics
11:15 Towards a Transformative Framework for Neural and Behavioral Analysis in Naturalistic Contexts Anqi Wu, Ph.D., Georgia Institute of Technology
12:15 Lunch
1:00 Special activities
3:00 Workshop: Pose estimation fundamentals with MMPose Ann Kennedy, Ph.D., The Scripps Research Institute
4:30 Workshop: Quantifying behaviors in your SLEAP Talmo Pereira, Ph.D., The Salk Institute for Biological Studies
6:00 Dinner
7:15 Evening discussion
8:30 End

Wednesday, Oct 15

07:45 Announcements
08:00 Using Motion Sequencing to reveal the neural basis of natural behavior Bob Datta, M.D., Ph.D., Harvard University
09:00 New methods for analyzing videos of behaving animals Josh Shaevitz, Ph.D., Princeton University
10:00 Coffee/tea
10:15 Themes and Variations in Animal Behavior Gordon Berman, Ph.D., Emory University
11:15 Mapping the landscape of social behavior Ugne Klibaite, Ph.D., Harvard University
12:15 Lunch
1:00 Special activities
3:00 Workshop: Automated Behavior Classification Ann Kennedy, Ph.D., The Scripps Research Institute
4:30 Workshop: Quantifying behaviors in your SLEAP Simon Nilsson, Ph.D., Platea Biosciences
6:00 Lobster Dinner
7:15 Evening discussion
8:30 End

Thursday, Oct 16

07:45 Announcements
08:00 Training and interpreting Generative-AI models of animal behavior Kristin Branson, Ph.D., Janelia Research Campus
09:00 Tool Development Bridging Behavior, Body and Brain Sam Golden, Ph.D., Washington University
10:00 Coffee/tea
10:15 Automated Behavior Classification Ann Kennedy, Ph.D., The Scripps Research Institute
11:15 AI-Powered Biomechanical Analysis James Cotton, M.D., Ph.D., Northwestern University
12:15 Lunch
1:15 Special activities
3:30 Workshop: Motion Mapping Gordon Berman, Ph.D., Emory University
4:30 Workshop: Introductory Moseq John Jacoby, B.S., M.S., Harvard University
6:00 Dinner
7:15 Evening discussion
8:30 End

Friday, Oct 17

07:45 Announcements
08:00 Dynamical signatures of social digging Ben de Bivort, Ph.D., Harvard University
09:00 Nanoparticle-enabled Motion Capture in Small Laboratory Animals Jeff Markowitz, Ph.D., Georgia Tech and Emory University
10:00 Coffee/tea
10:15 Genetic and preclinical studies utilizing advanced behavioral phenotyping in the laboratory mouse Vivek Kumar, Ph.D., The Jackson Laboratory
11:15 DeepSqueak: Using Machine Learning to Accelerate Bioacoustics Research Kevin Coffey, Ph.D., University of Washington
12:15 Lunch
1:00 Workshop: Statistical tests for behavioral annotations Ben de Bivort, Ph.D., Harvard University
2:30 Special activities
6:00 Dinner
8:00 End