The 2024 Short Course on the Application of Machine Learning for Automated Quantification of Behavior

The Jackson Laboratory

Oct 13-18, 2024

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 13-18, 2024. 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 13

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

Monday, Oct 14

09:15 Google Colab, Jupyter Notebooks and Python (beginner) OR
Scientific Software Engineering (advanced)
10:30 Coffee/tea
10:45 Google Colab, Jupyter Notebooks and Python (continued)
Scientific Software Engineering (continued)
12:30 Lunch
1:15 Introduction to Machine Learning with Python (beginner) OR
1:15 Scientific Software Engineering (continued)
3:30 Special activities
6:00 Dinner
7:00 Evening discussion
8:30 End

Tuesday, Oct 15

07:45 Announcements
08:00 Training and interpreting Generative-AI models of animal behavior Kristin Branson, Ph.D., Janelia Research Campus
09:00 Quantifying behavior using deep learning Talmo Pereira, Ph.D., The Salk Institute for Biological Studies
10:00 Coffee/tea
10:15 New approaches to 3D motion capture in freely moving mice Jeff Markowitz, Ph.D., Georgia Tech and Emory University
11:15 Tracking and modeling movement in Hydra Adrienne Fairhall, Ph.D., University of Washington
12:15 Lunch
1:00 Special activities
3:00 Workshop: Training a convolutional network for pose recognition from scratch Kristin Branson, Ph.D., Janelia Research Campus
6:00 Dinner
7:00 Evening discussion: Identity Matters Moses Davis, Ph.D., The Jackson Laboratory
8:30 End

Wednesday, Oct 16

07:45 Announcements
08:00 A universal translator behavior across species Oren Forkosh, Ph.D., The Hebrew University of Jerusalem
09:00 Supervised behavior analysis Ann Kennedy, Ph.D., The Scripps Research Institute
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 Machine learning tools for analyzing pose, identity and behavior across scales Alexander Mathis, Ph.D., Ecole Polytechnique Federale de Lausanne
12:15 Lunch
1:00 Special activities
3:00 Workshop: Supervised behavior analysis Ann Kennedy, Ph.D., The Scripps Research Institute
6:00 Lobster Dinner
7:00 Evening discussion / Student Projects
8:30 End

Thursday, Oct 17

07:45 Announcements
08:00 The structure of behavioral spaces Greg Stephens, Ph.D., Vrije Universiteit Amsterdam
09:00 Measuring behavior across scales Gordon Berman, Ph.D., Emory University
10:00 Coffee/tea
10:15 Mapping the landscape of social behavior Ugne Klibaite, Ph.D., Harvard University
10:15 Measuring animal behavior in three dimensions Lili Karashchuk, Ph.D., Allen Institute for Neural Dynamics
12:15 Lunch and shuttle to town pier
1:15 Bay cruise
3:30 Workshop: Motion Mapping Gordon Berman, Ph.D., Emory University
5:00 Workshop: Moseq Caleb Weinreb, Ph.D., Harvard University
6:30 Dinner
7:30 Evening discussion: Ethical considerations in brain and behavioral quantification Karen Rommelfanger, Ph.D., Institute of Neuroethics
8:30 End

Friday, Oct 18

07:45 Announcements
08:00 From the lab to the wild: how do we study mice hunting for prey? Emily Dennis, Ph.D., Janelia Research Campus
09:00 TBD TBD
10:00 Coffee/tea
10:15 Behavioral drift as an evolutionary strategy Ben de Bivort, Ph.D., Harvard University
11:15 Latent States of Brains and Behavior Scott Linderman, Ph.D., Stanford University
12:15 Lunch
1:00 Special activities
3:30 Workshop: Statistical tests for behavioral annotations Ben de Bivort, Ph.D., Harvard University
5:00 Workshop: Physics of behavior: posture, trajectories and embedding, models Greg Stephens, Ph.D., Vrije Universiteit Amsterdam
6:00 Dinner
7:00 Evening discussion
8:00 End