PrenventAD benchmark

Using BrainLM (and perhaps more) to explore phenotype prediction in PreventAD.

Run this project

Please use uv to install this project for the smoothest experience.

git clone git@github.com:SIMEXP/prevent-ad-benchmark.git

The brainLM submodule is for record keeping. However, if you wish to pull it, run:

git submodule update --init --recursive

Create virtual environment

On Rorqual, remember to add module:

module add cudacore/.12.6.2
module load httpproxy

With uv

uv venv
uv sync --extra build
uv sync --extra build --extra compile

You can either activate the environment with source .venv/bin/activate and use this environment in the conventional python way, or prepend any command you want to run with uv run to activate the environment.

Download models and example data

With uv, example:

uv run invoke prepare.models
uv run invoke prepare.data

Or with your virtual environment

source .venv/bin/activate
invoke prepare.models
invoke prepare.atlas
invoke prepare.data
invoke prepare.brainlm-workflow-timeseries
invoke prepare.prepare.gigaconnectome-workflow-timeseries

Check out uv run invoke --list for the commands and documentations.

Other unrelated notes

uv

Quick tutorial with pip->uv table