delphi (aka delphi-2M)
GitHub: https://github.com/gerstung-lab/delphi
ceuadmin/delphi/github
module load ceuadmin/python/3.12.10
python -m venv github
source github/bin/activate
git clone https://github.com/gerstung-lab/delphi src
cd src
pip install -r requirements.txt
pip cache purge
pip list
The last command gives,
Package Version
------------------------ -----------
cloudpickle 3.1.1
contourpy 1.3.3
cycler 0.12.1
filelock 3.19.1
fonttools 4.60.0
fsspec 2025.9.0
Jinja2 3.1.6
joblib 1.5.2
kiwisolver 1.4.9
llvmlite 0.45.0
MarkupSafe 3.0.2
matplotlib 3.10.6
mpmath 1.3.0
networkx 3.5
numba 0.62.0
numpy 1.26.4
nvidia-cublas-cu12 12.1.3.1
nvidia-cuda-cupti-cu12 12.1.105
nvidia-cuda-nvrtc-cu12 12.1.105
nvidia-cuda-runtime-cu12 12.1.105
nvidia-cudnn-cu12 8.9.2.26
nvidia-cufft-cu12 11.0.2.54
nvidia-curand-cu12 10.3.2.106
nvidia-cusolver-cu12 11.4.5.107
nvidia-cusparse-cu12 12.1.0.106
nvidia-nccl-cu12 2.20.5
nvidia-nvjitlink-cu12 12.9.86
nvidia-nvtx-cu12 12.1.105
packaging 25.0
pandas 2.3.2
patsy 1.0.1
pillow 11.3.0
pip 25.0.1
pynndescent 0.5.13
pyparsing 3.2.5
python-dateutil 2.9.0.post0
pytz 2025.2
scikit-learn 1.7.2
scipy 1.16.2
seaborn 0.13.2
shap 0.48.0
six 1.17.0
slicer 0.0.8
statsmodels 0.14.5
sympy 1.14.0
threadpoolctl 3.6.0
torch 2.3.0
tqdm 4.67.1
typing_extensions 4.15.0
tzdata 2025.2
umap-learn 0.5.9.post2
Reference
Shmatko, Artem, Alexander Wolfgang Jung, Kumar Gaurav, Søren Brunak, Laust Hvas Mortensen, Ewan Birney, Tom Fitzgerald, and Moritz Gerstung. 2025. "Learning the Natural History of Human Disease with Generative Transformers." Nature. https://doi.org/10.1038/s41586-025-09529-3.