DatathonsDatathon 2025
Session Commands
Necessary commands for summer school sessions during the 2025 datathon
Necessary commands for the 2025 Datathon Summer School sessions will be posted here.
Day 1
EMBED
Rohan Isaac: Intro to EMBEDv2
Environment: pandas-env
cp -r /mnt/efs/data/notebooks/day1/EMBEDv2/ ~/Jacob Jeon: ROI Detection Models in EMBED
Environment: roi-detection
Copy the files to your home directory
cp -r /mnt/efs/data/notebooks/day1/embed_detection ~/Create a symlink between the source data and your home directory
ln -s /mnt/efs/data/datasets/EMBED_detection ~/embed_detection/dataIntro to MRKR
Environment: pandas-env
cp -r /mnt/efs/data/notebooks/day1/mrkr ~/Day 2
Updates to Emory CXR
Environment: linear_probing
cp -r /mnt/efs/data/notebooks/day1/emory-cxr ~/Foundation Models for Classification, Regression, and Survival Prediction
Environment: linear_probing
cp -r /mnt/efs/data/notebooks/day2/linear-probing/ ~/Foundation Models
BiomedParse
https://github.com/f10409/BiomedParse_demo
MedSigLIP
https://github.com/f10409/MedSigLIP_demo
MedGemma
https://github.com/f10409/MedGemma_demo
Day 3
Time Series Modelling
Create a symlink between the source data and your home directory
ln -s /mnt/efs/data/datasets/mimiciv ~/mimicivCopy the notebooks to your home directory
cp -r /mnt/efs/data/notebooks/day3/MIMIC_ARIMA_TFT_day3.ipynb ~/
cp -r /mnt/efs/data/notebooks/day3/B2AI_voice_analysis.ipynb ~/