-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
0 parents
commit 8634885
Showing
17 changed files
with
23,928 additions
and
0 deletions.
There are no files selected for viewing
Binary file not shown.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,2 @@ | ||
| # Auto detect text files and perform LF normalization | ||
| * text=auto |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,136 @@ | ||
| slurm-* | ||
|
|
||
| # Byte-compiled / optimized / DLL files | ||
| __pycache__/ | ||
| *.py[cod] | ||
| *$py.class | ||
|
|
||
| # C extensions | ||
| *.so | ||
|
|
||
| # Distribution / packaging | ||
| .Python | ||
| build/ | ||
| develop-eggs/ | ||
| dist/ | ||
| downloads/ | ||
| eggs/ | ||
| .eggs/ | ||
| lib/ | ||
| lib64/ | ||
| parts/ | ||
| sdist/ | ||
| var/ | ||
| wheels/ | ||
| pip-wheel-metadata/ | ||
| share/python-wheels/ | ||
| *.egg-info/ | ||
| .installed.cfg | ||
| *.egg | ||
| MANIFEST | ||
|
|
||
| # PyInstaller | ||
| # Usually these files are written by a python script from a template | ||
| # before PyInstaller builds the exe, so as to inject date/other infos into it. | ||
| *.manifest | ||
| *.spec | ||
|
|
||
| # Installer logs | ||
| pip-log.txt | ||
| pip-delete-this-directory.txt | ||
|
|
||
| # Unit test / coverage reports | ||
| htmlcov/ | ||
| .tox/ | ||
| .nox/ | ||
| .coverage | ||
| .coverage.* | ||
| .cache | ||
| nosetests.xml | ||
| coverage.xml | ||
| *.cover | ||
| *.py,cover | ||
| .hypothesis/ | ||
| .pytest_cache/ | ||
|
|
||
| # Translations | ||
| *.mo | ||
| *.pot | ||
|
|
||
| # Django stuff: | ||
| *.log | ||
| local_settings.py | ||
| db.sqlite3 | ||
| db.sqlite3-journal | ||
|
|
||
| # Flask stuff: | ||
| instance/ | ||
| .webassets-cache | ||
|
|
||
| # Scrapy stuff: | ||
| .scrapy | ||
|
|
||
| # Sphinx documentation | ||
| docs/_build/ | ||
|
|
||
| # PyBuilder | ||
| target/ | ||
|
|
||
| # Jupyter Notebook | ||
| .ipynb_checkpoints | ||
|
|
||
| # IPython | ||
| profile_default/ | ||
| ipython_config.py | ||
|
|
||
| # pyenv | ||
| .python-version | ||
|
|
||
| # pipenv | ||
| # According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. | ||
| # However, in case of collaboration, if having platform-specific dependencies or dependencies | ||
| # having no cross-platform support, pipenv may install dependencies that don't work, or not | ||
| # install all needed dependencies. | ||
| #Pipfile.lock | ||
|
|
||
| # PEP 582; used by e.g. github.com/David-OConnor/pyflow | ||
| __pypackages__/ | ||
|
|
||
| # Celery stuff | ||
| celerybeat-schedule | ||
| celerybeat.pid | ||
|
|
||
| # SageMath parsed files | ||
| *.sage.py | ||
|
|
||
| # Environments | ||
| .env | ||
| .venv | ||
| env/ | ||
| venv/ | ||
| ENV/ | ||
| env.bak/ | ||
| venv.bak/ | ||
|
|
||
| # Spyder project settings | ||
| .spyderproject | ||
| .spyproject | ||
|
|
||
| # Rope project settings | ||
| .ropeproject | ||
|
|
||
| # mkdocs documentation | ||
| /site | ||
|
|
||
| # mypy | ||
| .mypy_cache/ | ||
| .dmypy.json | ||
| dmypy.json | ||
|
|
||
| # Pyre type checker | ||
| .pyre/ | ||
|
|
||
| # wandb | ||
| .wandb/ | ||
|
|
||
| MultiviewContrast_ECToy.pth |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,21 @@ | ||
| MIT License | ||
|
|
||
| Copyright (c) 2024 Emma Tysinger | ||
|
|
||
| Permission is hereby granted, free of charge, to any person obtaining a copy | ||
| of this software and associated documentation files (the "Software"), to deal | ||
| in the Software without restriction, including without limitation the rights | ||
| to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | ||
| copies of the Software, and to permit persons to whom the Software is | ||
| furnished to do so, subject to the following conditions: | ||
|
|
||
| The above copyright notice and this permission notice shall be included in all | ||
| copies or substantial portions of the Software. | ||
|
|
||
| THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | ||
| IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | ||
| FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | ||
| AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | ||
| LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | ||
| OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE | ||
| SOFTWARE. |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,40 @@ | ||
| # GearNet-ProtGNN: Protein function prediction model from protein structure and biomedical knowledge | ||
|
|
||
| This repository hosts the official implementation of ProtGNN, a model for predicting protein function. | ||
|
|
||
| ### **Path** | ||
| - Must change line 13 in `os.environ['WAND_EXECUTABLE']` to local path to python in `training_downstream.py` | ||
|
|
||
|
|
||
| ### **Training** | ||
|
|
||
| `training_gearnetprotgnn.py` is the main script to train GearNet-ProtGNN. Parameters to change: | ||
| - `num_epoch`: Number of epochs to train model for | ||
| - `hyperparameter`: True or False (run a hyperparameter sweep or not) | ||
| - `embed_file`: path to pickle file of the protein embeddings from ProtGNN | ||
| The script can be run from the command line or in a bash script like this: | ||
| ``` | ||
| python training_gearnetprotgnn.py | ||
| ``` | ||
|
|
||
| ### **Downstream Prediction Tasks** | ||
|
|
||
| `training_downstream.py` is the main script to run downstream prediction tasks. Parameters to change: | ||
| - `model_path`: Change to path where your model is stored | ||
| - `dataset_type`: 'GO' or 'EC' | ||
| - `branch`: 'MF', 'BP' or 'CC' if dataset_type is 'GO' | ||
| - `freeze`: True or False (freezing GCN layer weights) | ||
|
|
||
| The script can be run from the command line or in a bash script like this: | ||
| ``` | ||
| python training_downstream.py | ||
| ``` | ||
|
|
||
| ### **Embedding Space Visualization** | ||
|
|
||
| There are two notebooks that demonstrate how to visualize the predicted embedding space. | ||
| - `visualize_predicted.ipynb`: Colors predicted embedding space by molecular function and biological process | ||
| - `visualize_by_structure.ipynb`: Colors predicted embedding space by CATH superfamilies | ||
|
|
||
|
|
||
|
|
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,146 @@ | ||
| name: gearnetenv | ||
| channels: | ||
| - conda-forge | ||
| - defaults | ||
| dependencies: | ||
| - _libgcc_mutex=0.1=main | ||
| - _openmp_mutex=5.1=1_gnu | ||
| - asttokens=2.4.1=pyhd8ed1ab_0 | ||
| - backcall=0.2.0=pyh9f0ad1d_0 | ||
| - ca-certificates=2023.11.17=hbcca054_0 | ||
| - comm=0.2.1=pyhd8ed1ab_0 | ||
| - debugpy=1.6.7=py38h6a678d5_0 | ||
| - decorator=5.1.1=pyhd8ed1ab_0 | ||
| - entrypoints=0.4=pyhd8ed1ab_0 | ||
| - executing=2.0.1=pyhd8ed1ab_0 | ||
| - ipykernel=6.28.0=pyhd33586a_0 | ||
| - ipython=8.12.0=pyh41d4057_0 | ||
| - jedi=0.19.1=pyhd8ed1ab_0 | ||
| - jupyter_client=7.3.4=pyhd8ed1ab_0 | ||
| - jupyter_core=5.7.1=py38h578d9bd_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 | ||
| - libsodium=1.0.18=h36c2ea0_1 | ||
| - libstdcxx-ng=11.2.0=h1234567_1 | ||
| - matplotlib-inline=0.1.6=pyhd8ed1ab_0 | ||
| - ncurses=6.4=h6a678d5_0 | ||
| - nest-asyncio=1.5.8=pyhd8ed1ab_0 | ||
| - openssl=3.0.12=h7f8727e_0 | ||
| - packaging=23.2=pyhd8ed1ab_0 | ||
| - parso=0.8.3=pyhd8ed1ab_0 | ||
| - pexpect=4.8.0=pyh1a96a4e_2 | ||
| - pickleshare=0.7.5=py_1003 | ||
| - pip=23.3.1=py38h06a4308_0 | ||
| - platformdirs=4.1.0=pyhd8ed1ab_0 | ||
| - prompt-toolkit=3.0.42=pyha770c72_0 | ||
| - prompt_toolkit=3.0.42=hd8ed1ab_0 | ||
| - ptyprocess=0.7.0=pyhd3deb0d_0 | ||
| - pure_eval=0.2.2=pyhd8ed1ab_0 | ||
| - pygments=2.17.2=pyhd8ed1ab_0 | ||
| - python=3.8.18=h955ad1f_0 | ||
| - python-dateutil=2.8.2=pyhd8ed1ab_0 | ||
| - python_abi=3.8=2_cp38 | ||
| - pyzmq=25.1.0=py38h6a678d5_0 | ||
| - readline=8.2=h5eee18b_0 | ||
| - setuptools=68.2.2=py38h06a4308_0 | ||
| - six=1.16.0=pyh6c4a22f_0 | ||
| - sqlite=3.41.2=h5eee18b_0 | ||
| - stack_data=0.6.2=pyhd8ed1ab_0 | ||
| - tk=8.6.12=h1ccaba5_0 | ||
| - tornado=6.1=py38h0a891b7_3 | ||
| - traitlets=5.14.1=pyhd8ed1ab_0 | ||
| - typing_extensions=4.9.0=pyha770c72_0 | ||
| - wcwidth=0.2.13=pyhd8ed1ab_0 | ||
| - wheel=0.41.2=py38h06a4308_0 | ||
| - xz=5.4.5=h5eee18b_0 | ||
| - zeromq=4.3.4=h2531618_0 | ||
| - zlib=1.2.13=h5eee18b_0 | ||
| - pip: | ||
| - appdirs==1.4.4 | ||
| - attrs==23.2.0 | ||
| - beautifulsoup4==4.12.2 | ||
| - biopython==1.83 | ||
| - bioservices==1.11.2 | ||
| - bs4==0.0.1 | ||
| - cattrs==23.2.3 | ||
| - certifi==2023.11.17 | ||
| - charset-normalizer==3.3.2 | ||
| - click==8.1.7 | ||
| - colorama==0.4.6 | ||
| - colorlog==6.8.0 | ||
| - contourpy==1.1.1 | ||
| - cycler==0.12.1 | ||
| - dataclasses==0.6 | ||
| - dgl==1.1.3 | ||
| - docker-pycreds==0.4.0 | ||
| - easydev==0.12.1 | ||
| - easydict==1.11 | ||
| - exceptiongroup==1.2.0 | ||
| - fair-esm==2.0.0 | ||
| - filelock==3.14.0 | ||
| - fonttools==4.47.0 | ||
| - fsspec==2024.3.1 | ||
| - fuzzywuzzy==0.18.0 | ||
| - gevent==23.9.1 | ||
| - gitdb==4.0.11 | ||
| - gitpython==3.1.42 | ||
| - greenlet==3.0.3 | ||
| - grequests==0.7.0 | ||
| - h5py==3.10.0 | ||
| - huggingface-hub==0.22.2 | ||
| - idna==3.6 | ||
| - importlib-resources==6.1.1 | ||
| - ipywidgets==8.1.2 | ||
| - jinja2==3.1.2 | ||
| - joblib==1.3.2 | ||
| - jupyterlab-widgets==3.0.10 | ||
| - kiwisolver==1.4.5 | ||
| - lmdb==1.4.1 | ||
| - lxml==5.1.0 | ||
| - markupsafe==2.1.3 | ||
| - matplotlib==3.7.5 | ||
| - networkx==3.1 | ||
| - ninja==1.11.1.1 | ||
| - numpy==1.24.4 | ||
| - pandas==2.0.3 | ||
| - pillow==10.2.0 | ||
| - protobuf==4.25.3 | ||
| - psutil==5.9.7 | ||
| - pyparsing==3.1.1 | ||
| - pypdb==2.3 | ||
| - pytdc==0.4.1 | ||
| - pytz==2023.3.post1 | ||
| - pyyaml==6.0.1 | ||
| - rdkit==2023.9.5 | ||
| - rdkit-pypi==2022.9.5 | ||
| - requests==2.31.0 | ||
| - requests-cache==1.1.1 | ||
| - scikit-learn==1.3.2 | ||
| - scipy==1.10.1 | ||
| - seaborn==0.13.2 | ||
| - sentry-sdk==1.40.6 | ||
| - setproctitle==1.3.3 | ||
| - smmap==5.0.1 | ||
| - soupsieve==2.5 | ||
| - suds-community==1.1.2 | ||
| - threadpoolctl==3.2.0 | ||
| - torch==1.12.0+cu116 | ||
| - torch-cluster==1.6.0+pt112cu116 | ||
| - torch-geometric==2.4.0 | ||
| - torch-scatter==2.1.0+pt112cu116 | ||
| - torchaudio==0.12.0+cu116 | ||
| - torchdrug==0.2.1 | ||
| - torchvision==0.13.0+cu116 | ||
| - tqdm==4.66.1 | ||
| - tzdata==2023.4 | ||
| - url-normalize==1.4.3 | ||
| - urllib3==2.1.0 | ||
| - wandb==0.16.3 | ||
| - widgetsnbextension==4.0.10 | ||
| - wrapt==1.16.0 | ||
| - xmltodict==0.13.0 | ||
| - zipp==3.17.0 | ||
| - zope-event==5.0 | ||
| - zope-interface==6.1 |
Oops, something went wrong.