Quick start

Choose a project folder

Data, cache, results and model weights go into sub-folders of it:

neuroatlas config init ~/neuroatlas

To keep one of them elsewhere, add for example --data-root /path/to/datasets. Configuration explains the four folders.

Run sleep staging

Download Sleep-EDF and the BIOT weights, then run sleep staging:

neuroatlas data download sleep_edf_expanded --mirror aws
neuroatlas models download biot_pretrained

neuroatlas check sleep_stage -m biot_pretrained          # quick test on one batch
neuroatlas run sleep_stage -m biot_pretrained --debug    # fold 0 only
neuroatlas run sleep_stage -m biot_pretrained            # all folds
neuroatlas results sleep_stage

The walkthrough is a full example with the expected output.

Run any benchmark

Every benchmark runs the same way:

neuroatlas show epilepsy                          # description, datasets and commands
neuroatlas run epilepsy -m cbramod_pretrained     # its default dataset (Siena)
neuroatlas run epilepsy -m all_fm --dataset full  # all EEG FMs on all datasets you have
neuroatlas results epilepsy

neuroatlas list benchmarks lists all twelve, and neuroatlas show <benchmark> describes one. Benchmarks describes them by domain.

To run many jobs on a cluster, neuroatlas submit writes one HTCondor or SLURM job per dataset and model (Running on a cluster). run/default_runs.sh lists every experiment in the paper.