The 2022 Short Course on the Application of Machine Learning for Automated Quantification of Behavior
The Jackson Laboratory
Oct 10-13, 2022
7:45 am - 8:30 pm EST
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:
teach the theoretical basis of machine learning and its applications to
quantitative animal behavior analyses
offer hands-on training in experimental workflow, analysis tools and
algorithms
showcase key biological applications
foster organic collaborations across disparate fields
Who:
This course is appropriate for early career researchers from the fields of neuroscience,
genetics, and biomedical research.
Prerequisites:
Basic scripting or programming knowledge is suggested but not required.
Requirements:
Participants must bring a laptop with a
Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.).
They should have a few specific software packages installed (listed below).
Accessibility:
We are committed to making this workshop
accessible to everybody. For workshops at a physical location, the workshop organizers have checked that:
The room is wheelchair / scooter accessible.
Accessible restrooms are available.
Materials will be provided in advance of the workshop and
large-print handouts are available if needed by notifying the
organizers in advance. If we can help making learning easier for
you (e.g. sign-language interpreters, lactation facilities) please
get in touch (using contact details below) and we will
attempt to provide them.
Contact:
Please email
to-be-announced
for more information.
Python is a popular language for
research computing, and great for general-purpose programming as
well. Installing all of its research packages individually can be
a bit difficult, so we recommend
Anaconda,
an all-in-one installer.
Regardless of how you choose to install it,
please make sure you install Python version 3.x
(e.g., 3.6 is fine).
We will teach Python using the Jupyter Notebook,
a programming environment that runs in a web browser (Jupyter Notebook will be installed by Anaconda). For this to work you will need a reasonably
up-to-date browser. The current versions of the Chrome, Safari and
Firefox browsers are all
supported
(some older browsers, including Internet Explorer version 9
and below, are not).
Download the Anaconda for Windows installer with Python 3. (If you are not sure which version to choose, you probably want the 64-bit Graphical Installer Anaconda3-...-Windows-x86_64.exe)
Install Python 3 by running the Anaconda Installer, using all of the defaults for installation except make sure to check Add Anaconda to my PATH environment variable.
Download the Anaconda Installer with Python 3 for Linux.
(The installation requires using the shell. If you aren't
comfortable doing the installation yourself
stop here and request help at the workshop.)
Open a terminal window and navigate to the directory where
the executable is downloaded (e.g., `cd ~/Downloads`).
Type
bash Anaconda3-
and then press
Tab to autocomplete the full file name. The name of
file you just downloaded should appear.
Press Enter
(or Return depending on your keyboard).
You will follow the text-only prompts.
To move through the text, press Spacebar.
Type yes and press enter to approve the license.
Press Enter (or Return)
to approve the default location
for the files.
Type yes and press
Enter (or Return)
to prepend Anaconda to your PATH
(this makes the Anaconda distribution the default Python).