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| # gappa | ||
| # GAPPA: Enhancing Prognosis Prediction in Primary Aldosteronism Post-Adrenalectomy Using Graph-Based Modeling | ||
|
|
||
| ### Pre-requisites: | ||
| - Ubuntu 22.04.2 LTS (GNU/Linux 6.5.0-44-generic x86_64) | ||
| - NVIDIA GPU (Tested on Nvidia GeForce RTX 3090 ) with CUDA Version: 12.0 | ||
| - Python (3.9.13) | ||
| - Anaconda version 22.9.0 | ||
|
|
||
| ### Installation: | ||
| ------------ | ||
| ```bash | ||
| conda env create -f environment.yml | ||
| conda activate gappa_env |
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| name: gappa_env | ||
| channels: | ||
| - defaults | ||
| dependencies: | ||
| - _libgcc_mutex=0.1=main | ||
| - _openmp_mutex=5.1=1_gnu | ||
| - bzip2=1.0.8=h7b6447c_0 | ||
| - ca-certificates=2023.01.10=h06a4308_0 | ||
| - ld_impl_linux-64=2.38=h1181459_1 | ||
| - libffi=3.4.4=h6a678d5_0 | ||
| - libgcc-ng=11.2.0=h1234567_1 | ||
| - libgomp=11.2.0=h1234567_1 | ||
| - libstdcxx-ng=11.2.0=h1234567_1 | ||
| - libuuid=1.41.5=h5eee18b_0 | ||
| - ncurses=6.4=h6a678d5_0 | ||
| - openssl=1.1.1t=h7f8727e_0 | ||
| - pip=24.2=py310h06a4308_0 | ||
| - python=3.10.11=h7a1cb2a_2 | ||
| - readline=8.2=h5eee18b_0 | ||
| - setuptools=66.0.0=py310h06a4308_0 | ||
| - sqlite=3.41.2=h5eee18b_0 | ||
| - tk=8.6.12=h1ccaba5_0 | ||
| - wheel=0.38.4=py310h06a4308_0 | ||
| - xz=5.4.2=h5eee18b_0 | ||
| - zlib=1.2.13=h5eee18b_0 | ||
| - pip: | ||
| - absl-py==2.1.0 | ||
| - acvl-utils==0.2 | ||
| - aenum==3.1.15 | ||
| - aiohappyeyeballs==2.4.0 | ||
| - aiohttp==3.10.5 | ||
| - aiosignal==1.3.1 | ||
| - alembic==1.13.2 | ||
| - aniso8601==9.0.1 | ||
| - annotated-types==0.7.0 | ||
| - antlr4-python3-runtime==4.9.3 | ||
| - argparse==1.4.0 | ||
| - astunparse==1.6.3 | ||
| - async-timeout==4.0.3 | ||
| - attrs==24.2.0 | ||
| - batchgenerators==0.25 | ||
| - beautifulsoup4==4.12.3 | ||
| - blinker==1.8.2 | ||
| - cachetools==5.5.0 | ||
| - certifi==2023.5.7 | ||
| - charset-normalizer==3.1.0 | ||
| - clearml==1.16.3 | ||
| - click==8.1.7 | ||
| - cloudpickle==3.0.0 | ||
| - cmake==3.26.3 | ||
| - connected-components-3d==3.18.0 | ||
| - contextlib2==21.6.0 | ||
| - contourpy==1.0.7 | ||
| - cvxopt==1.3.1 | ||
| - cvxpy==1.3.1 | ||
| - cycler==0.11.0 | ||
| - databricks-sdk==0.30.0 | ||
| - dataclasses==0.6 | ||
| - deprecated==1.2.14 | ||
| - dicom2nifti==2.4.11 | ||
| - dill==0.3.8 | ||
| - docker==7.1.0 | ||
| - docker-pycreds==0.4.0 | ||
| - docopt==0.6.2 | ||
| - dynamic-network-architectures==0.3.1 | ||
| - ecos==2.0.12 | ||
| - einops==0.8.0 | ||
| - entrypoints==0.4 | ||
| - exceptiongroup==1.1.1 | ||
| - execnet==2.1.1 | ||
| - fancyimpute==0.7.0 | ||
| - filelock==3.12.0 | ||
| - flask==3.0.3 | ||
| - flatbuffers==24.3.25 | ||
| - fonttools==4.39.4 | ||
| - frozenlist==1.4.1 | ||
| - fsspec==2024.6.1 | ||
| - furl==2.1.3 | ||
| - future==1.0.0 | ||
| - gast==0.6.0 | ||
| - gdown==4.7.1 | ||
| - gitdb==4.0.11 | ||
| - gitpython==3.1.43 | ||
| - glob2==0.7 | ||
| - google-auth==2.34.0 | ||
| - google-pasta==0.2.0 | ||
| - graphene==3.3 | ||
| - graphql-core==3.2.3 | ||
| - graphql-relay==3.2.0 | ||
| - greenlet==3.0.3 | ||
| - grpcio==1.65.5 | ||
| - gunicorn==22.0.0 | ||
| - h5py==3.11.0 | ||
| - huggingface-hub==0.24.6 | ||
| - hydra-core==1.3.2 | ||
| - idna==3.4 | ||
| - imagecodecs==2024.6.1 | ||
| - imageio==2.35.1 | ||
| - importlib-metadata==7.2.1 | ||
| - iniconfig==2.0.0 | ||
| - itk==5.4.0 | ||
| - itk-core==5.4.0 | ||
| - itk-filtering==5.4.0 | ||
| - itk-io==5.4.0 | ||
| - itk-numerics==5.4.0 | ||
| - itk-registration==5.4.0 | ||
| - itk-segmentation==5.4.0 | ||
| - itsdangerous==2.2.0 | ||
| - jinja2==3.1.2 | ||
| - joblib==1.2.0 | ||
| - jsonschema==4.23.0 | ||
| - jsonschema-specifications==2023.12.1 | ||
| - keras==3.5.0 | ||
| - kiwisolver==1.4.4 | ||
| - knnimpute==0.1.0 | ||
| - lazy-loader==0.4 | ||
| - libclang==18.1.1 | ||
| - libpng-bins==0.0.3 | ||
| - lightly==1.5.12 | ||
| - lightly-utils==0.0.2 | ||
| - lightning-bolts==0.7.0 | ||
| - lightning-utilities==0.11.6 | ||
| - linecache2==1.0.0 | ||
| - lit==16.0.5 | ||
| - lmdb==1.5.1 | ||
| - mako==1.3.5 | ||
| - markdown==3.7 | ||
| - markdown-it-py==3.0.0 | ||
| - markupsafe==2.1.2 | ||
| - matplotlib==3.7.1 | ||
| - mdurl==0.1.2 | ||
| - ml-dtypes==0.4.0 | ||
| - mlflow==2.15.1 | ||
| - mlflow-skinny==2.15.1 | ||
| - mock==5.1.0 | ||
| - monai==1.3.2 | ||
| - mpmath==1.3.0 | ||
| - multidict==6.0.5 | ||
| - multiprocess==0.70.16 | ||
| - namex==0.0.8 | ||
| - networkx==3.1 | ||
| - nibabel==3.2.2 | ||
| - nnunetv2==2.3.1 | ||
| - nose==1.3.7 | ||
| - nptyping==2.5.0 | ||
| - numpy==1.26.0 | ||
| - nvidia-cublas-cu11==11.10.3.66 | ||
| - nvidia-cublas-cu12==12.3.4.1 | ||
| - nvidia-cuda-cupti-cu11==11.7.101 | ||
| - nvidia-cuda-cupti-cu12==12.3.101 | ||
| - nvidia-cuda-nvcc-cu12==12.3.107 | ||
| - nvidia-cuda-nvrtc-cu11==11.7.99 | ||
| - nvidia-cuda-nvrtc-cu12==12.3.107 | ||
| - nvidia-cuda-runtime-cu11==11.7.99 | ||
| - nvidia-cuda-runtime-cu12==12.3.101 | ||
| - nvidia-cudnn-cu11==8.5.0.96 | ||
| - nvidia-cudnn-cu12==8.9.7.29 | ||
| - nvidia-cufft-cu11==10.9.0.58 | ||
| - nvidia-cufft-cu12==11.0.12.1 | ||
| - nvidia-curand-cu11==10.2.10.91 | ||
| - nvidia-curand-cu12==10.3.4.107 | ||
| - nvidia-cusolver-cu11==11.4.0.1 | ||
| - nvidia-cusolver-cu12==11.5.4.101 | ||
| - nvidia-cusparse-cu11==11.7.4.91 | ||
| - nvidia-cusparse-cu12==12.2.0.103 | ||
| - nvidia-nccl-cu11==2.14.3 | ||
| - nvidia-nccl-cu12==2.19.3 | ||
| - nvidia-nvjitlink-cu12==12.3.101 | ||
| - nvidia-nvtx-cu11==11.7.91 | ||
| - omegaconf==2.3.0 | ||
| - opencv-python==4.8.1.78 | ||
| - opentelemetry-api==1.26.0 | ||
| - opentelemetry-sdk==1.26.0 | ||
| - opentelemetry-semantic-conventions==0.47b0 | ||
| - opt-einsum==3.3.0 | ||
| - optree==0.12.1 | ||
| - orderedmultidict==1.0.1 | ||
| - osqp==0.6.3 | ||
| - p-tqdm==1.4.2 | ||
| - packaging==23.1 | ||
| - pandas==2.0.1 | ||
| - path==17.0.0 | ||
| - path-py==12.5.0 | ||
| - pathlib2==2.3.7.post1 | ||
| - pathos==0.3.2 | ||
| - pillow==10.0.1 | ||
| - platformdirs==4.2.2 | ||
| - pluggy==1.0.0 | ||
| - pox==0.3.4 | ||
| - ppft==1.7.6.8 | ||
| - protobuf==4.25.4 | ||
| - psutil==5.9.5 | ||
| - pyarrow==15.0.2 | ||
| - pyasn1==0.6.0 | ||
| - pyasn1-modules==0.4.0 | ||
| - pycad-medic==0.0.10 | ||
| - pydantic==2.8.2 | ||
| - pydantic-core==2.20.1 | ||
| - pydicom==2.4.3 | ||
| - pyg-library==0.2.0 | ||
| - pygments==2.18.0 | ||
| - pyjwt==2.8.0 | ||
| - pykwalify==1.8.0 | ||
| - pylibjpeg-libjpeg==2.2.0 | ||
| - pynrrd==1.0.0 | ||
| - pyparsing==3.0.9 | ||
| - pyqt5==5.15.11 | ||
| - pyqt5-qt5==5.15.14 | ||
| - pyqt5-sip==12.15.0 | ||
| - pyradiomics==3.0.1 | ||
| - pysocks==1.7.1 | ||
| - pytest==7.3.1 | ||
| - pytest-shutil==1.7.0 | ||
| - python-dateutil==2.8.2 | ||
| - python-gdcm==3.0.24.1 | ||
| - python-graphviz==0.20.3 | ||
| - pytorch-ignite==0.5.1 | ||
| - pytorch-lightning==1.9.5 | ||
| - pytorch-lightning-bolts==0.3.2.post1 | ||
| - pytz==2023.3 | ||
| - pywavelets==1.7.0 | ||
| - pyyaml==6.0.2 | ||
| - qdldl==0.1.7 | ||
| - querystring-parser==1.2.4 | ||
| - referencing==0.35.1 | ||
| - regex==2024.7.24 | ||
| - requests==2.31.0 | ||
| - rich==13.7.1 | ||
| - rpds-py==0.20.0 | ||
| - rsa==4.9 | ||
| - rt-utils==1.2.7 | ||
| - ruamel-yaml==0.18.6 | ||
| - ruamel-yaml-clib==0.2.8 | ||
| - safetensors==0.4.4 | ||
| - scikit-image==0.22.0 | ||
| - scikit-learn==1.2.2 | ||
| - scipy==1.10.1 | ||
| - scs==3.2.3 | ||
| - seaborn==0.12.2 | ||
| - sentry-sdk==2.13.0 | ||
| - setproctitle==1.3.3 | ||
| - simpleitk==2.3.0 | ||
| - six==1.16.0 | ||
| - smmap==5.0.1 | ||
| - soupsieve==2.6 | ||
| - sqlalchemy==2.0.32 | ||
| - sqlparse==0.5.1 | ||
| - sympy==1.12 | ||
| - tensorboard==2.17.1 | ||
| - tensorboard-data-server==0.7.2 | ||
| - tensorboardx==2.6.2.2 | ||
| - tensorflow==2.17.0 | ||
| - tensorflow-io-gcs-filesystem==0.37.1 | ||
| - tensorrt==10.3.0 | ||
| - tensorrt-cu12==10.3.0 | ||
| - termcolor==2.4.0 | ||
| - threadpoolctl==3.1.0 | ||
| - tifffile==2024.8.10 | ||
| - tokenizers==0.19.1 | ||
| - tomli==2.0.1 | ||
| - torch==2.0.1 | ||
| - torch-cluster==1.6.3 | ||
| - torch-geometric==2.5.3 | ||
| - torch-scatter==2.1.2 | ||
| - torch-sparse==0.6.18 | ||
| - torchmetrics==1.4.1 | ||
| - torchvision==0.15.2 | ||
| - totalsegmentator==2.4.0 | ||
| - tqdm==4.66.1 | ||
| - traceback2==1.4.0 | ||
| - transformers==4.44.1 | ||
| - triton==2.0.0 | ||
| - typing-extensions==4.12.2 | ||
| - tzdata==2023.3 | ||
| - unittest2==1.1.0 | ||
| - urllib3==2.0.2 | ||
| - vedo==2023.4.6 | ||
| - vtk==9.2.6 | ||
| - wandb==0.17.7 | ||
| - werkzeug==3.0.4 | ||
| - wrapt==1.16.0 | ||
| - xvfbwrapper==0.2.9 | ||
| - yacs==0.1.8 | ||
| - yarl==1.9.4 | ||
| - zipp==3.20.0 | ||
|
|