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Improve documentation for evaluate package (#543)
* Changed documentation theme to sphinx-book-theme * Added details about Pandoc requirment * Added initial document for accuracy.py * Fix pre-commit hook errors * Added confusion matrix doc * Add auroc doc and fix titles * Add average precision docs * Added more documents for metrics * Add index for user guide in side bar * Minor patches (#542) * Fix capitalization of Python * Change ValueError to TypeError and update docstrings * Add Precision-Recall Curve to experimental metrics (#544) * Add ROC curve (#545) * Add ROC metrics to experimental module * fix typo * Fix docstrings * Add AUROC (#546) * Add AUROC metric to experimental module * Refactor binary and multiclass ROC functions * Refactor tests to use a common thresholds list * Fix mypy error * Add regression metrics (#547) * Add regression support * update docstrings * Ignore `no-any-return` errors * Integrate experimental metrics with other modules (#549) * integrate experimental metrics with other modules * add average precision metric to experimental metrics package * fix tutorials * Add type hints and keyword arguments to metrics classes * Update nbsphinx version to 0.9.3 * Update nbconvert version to 7.14.2 * Fix type annotations and formatting issues * Update kernel display name in mortality_prediction.ipynb * Add guard clause to prevent module execution on import * Update `torch_distributed.py` with type hints * Add multiclass and multilabel average precision metrics * Change jupyter kernel * Fix type annotations for metric values in ClassificationPlotter --------- Co-authored-by: Amrit K <amritk@vectorinstitute.ai> * Changed documentation theme to sphinx-book-theme * Don't update deps * Pre-commit fixes * Add doc for ROC Curve * Fix footer in docs * Bump to 0.2.3 Signed-off-by: Amrit Krishnan <amrit110@gmail.com> * Add logo and css fixes * Fix formatting of conf.py file * Small fix * Move evaluation metrics docs under API reference * Fix poetry build * Improve documentation structure * Formatting fixes --------- Signed-off-by: Amrit Krishnan <amrit110@gmail.com> Co-authored-by: Franklin <41602287+fcogidi@users.noreply.github.com> Co-authored-by: Amrit K <amritk@vectorinstitute.ai> Co-authored-by: Amrit Krishnan <amrit110@gmail.com>
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footer a.logo { | ||
/* Using flex here (to vertically align the child img) causes aspect-ratio issues */ | ||
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{% block extrafooter %} | ||
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<div class="footer-container" style="text-align: center;"> | ||
<div class="footer-small-text"> | ||
<br> All <a href="https://github.com/VectorInstitute/cyclops">source code for cyclops</a> is freely available under the terms of an <a href="https://opensource.org/licenses/Apache-2.0">Apache-2.0</a> license. | ||
</div> | ||
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<div class="footer-small-text"> | ||
This work is made possible due to the data obtained from the <a href="https://www.geminimedicine.ca/">GEMINI study</a>. | ||
</div> | ||
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<hr/> | ||
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<div class="logo"> | ||
<a class="logo" href="https://vectorinstitute.ai/"> | ||
<span class="logo"></span> | ||
<img alt="Logo of the Vector Institute" style="width:90px; max-width:90px;" src="{{ pathto('_static/logos/vector_logo.png', 1) }}" /> | ||
</a> | ||
<a class="logo" href="https://www.geminimedicine.ca/"> | ||
<span class="logo"></span> | ||
<img alt="Logo of GEMINI" style="width:90px; max-width:90px;" src="{{ pathto('_static/logos/gemini_logo.png', 1) }}" /> | ||
</a> | ||
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{% endblock %} |
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🧑🏿💻 Developing | ||
======================= | ||
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Using poetry | ||
------------ | ||
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The development environment can be set up using `poetry <https://python-poetry.org/docs/#installation>`__. Hence, make sure it is installed and then run: | ||
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.. code:: bash | ||
python3 -m poetry install | ||
source $(poetry env info --path)/bin/activate | ||
In order to install dependencies for testing (codestyle, unit tests, integration tests), run: | ||
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.. code:: bash | ||
python3 -m poetry install --with test | ||
API documentation is built using `Sphinx <https://www.sphinx-doc.org/en/master/>`__ and can be locally built by: | ||
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.. code:: bash | ||
python3 -m poetry install --with docs | ||
cd docs | ||
make html SPHINXOPTS="-D nbsphinx_allow_errors=True" | ||
If you need to build the documentations locally, make sure to install ``Pandoc`` in addition to ``docs`` poetry group. | ||
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Contributing | ||
------------ | ||
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Contributing to cyclops is welcomed. See `Contributing <https://vectorinstitute.github.io/cyclops/api/contributing.html>`__ for guidelines. |
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Evaluation | ||
========== |
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Installation | ||
============ | ||
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Using pip | ||
--------- | ||
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.. code:: bash | ||
python3 -m pip install pycyclops | ||
``cyclops`` has many optional dependencies that are used for specific functionality. For example, the `monai <https://github.com/Project-MONAI/MONAI>`__ library is used for loading DICOM images to create datasets. All optional dependencies can be installed with ``pycyclops[all]``, and specific sets of dependencies are listed in the sections below. | ||
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+-----------------------------+--------------------------+---------------------------------------------------------------------------------------------------------------+ | ||
| Dependency | pip extra | Notes | | ||
+=============================+==========================+===============================================================================================================+ | ||
| xgboost | xgboost | Allows use of `XGBoost <https://xgboost.readthedocs.io/en/stable/>`__ model | | ||
+-----------------------------+--------------------------+---------------------------------------------------------------------------------------------------------------+ | ||
| torch | torch | Allows use of `PyTorch <https://pytorch.org/>`__ models | | ||
+-----------------------------+--------------------------+---------------------------------------------------------------------------------------------------------------+ | ||
| torchvision | torchvision | Allows use of `Torchvision <https://pytorch.org/vision/stable/index.html>`__ library | | ||
+-----------------------------+--------------------------+---------------------------------------------------------------------------------------------------------------+ | ||
| torchxrayvision | torchxrayvision | Uses `TorchXRayVision <https://mlmed.org/torchxrayvision/>`__ library | | ||
+-----------------------------+--------------------------+---------------------------------------------------------------------------------------------------------------+ | ||
| monai | monai | Uses `MONAI <https://github.com/Project-MONAI/MONAI>`__ to load and transform images | | ||
+-----------------------------+--------------------------+---------------------------------------------------------------------------------------------------------------+ | ||
| alibi | alibi | Uses `Alibi <https://docs.seldon.io/projects/alibi/en/stable/>`__ for additional explainability functionality | | ||
+-----------------------------+--------------------------+---------------------------------------------------------------------------------------------------------------+ | ||
| alibi-detect | alibi-detect | Uses `Alibi Detect <https://docs.seldon.io/projects/alibi-detect/en/stable/>`__ for dataset shift detection | | ||
+-----------------------------+--------------------------+---------------------------------------------------------------------------------------------------------------+ |
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Model Report | ||
============ |
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Monitoring | ||
========== |
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