A framework for training and evaluating foundation models, using the MEDS ecosystem for data processing and PyTorch Lightning for training.
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EveryQuery
.env
PROJECT_DIR="/home/pac4279/EveryQuery"
DATA_DIR="/n/data1/hms/dbmi/zaklab/payal/mimic"
SAVE_DIR="/n/data1/hms/dbmi/zaklab/payal/EveryQuery/results"
RAW="${DATA_DIR}/raw"
INTERMEDIATE="${DATA_DIR}/intermediate"
PROCESSED="${DATA_DIR}/processed"
run for processing data
MEICAR_process_data input_dir="$RAW" intermediate_dir="$INTERMEDIATE" output_dir="$PROCESSED"
run for training
source .env; set -a; . ./.env; set +a; python source/train.py
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