kaiko-eva 0.0.2__py3-none-any.whl → 0.1.0__py3-none-any.whl

kaiko_eva-0.0.2.dist-info/METADATA

@@ -1,431 +0,0 @@
-Metadata-Version: 2.1
-Name: kaiko-eva
-Version: 0.0.2
-Summary: Evaluation Framework for oncology foundation models.
-Keywords: machine-learning,evaluation-framework,oncology,foundation-models
-Author-Email: Ioannis Gatopoulos <ioannis@kaiko.ai>, =?utf-8?q?Nicolas_K=C3=A4nzig?= <nicolas@kaiko.ai>, Roman Moser <roman@kaiko.ai>
-Maintainer-Email: Ioannis Gatopoulos <ioannis@kaiko.ai>, =?utf-8?q?Nicolas_K=C3=A4nzig?= <nicolas@kaiko.ai>, Roman Moser <roman@kaiko.ai>
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-Classifier: Topic :: Software Development :: Build Tools
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Project-URL: Homepage, https://kaiko-ai.github.io/eva/dev/
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-Requires-Python: >=3.10
-Requires-Dist: torch==2.3.0
-Requires-Dist: lightning>=2.2.2
-Requires-Dist: jsonargparse[omegaconf]==4.28
-Requires-Dist: tensorboard>=2.16.2
-Requires-Dist: loguru>=0.7.2
-Requires-Dist: pandas>=2.2.0
-Requires-Dist: transformers>=4.38.2
-Requires-Dist: onnxruntime>=1.17.1
-Requires-Dist: onnx>=1.16.0
-Requires-Dist: toolz>=0.12.1
-Requires-Dist: rich>=13.7.1
-Requires-Dist: h5py>=3.10.0; extra == "vision"
-Requires-Dist: nibabel>=5.2.0; extra == "vision"
-Requires-Dist: opencv-python-headless>=4.9.0.80; extra == "vision"
-Requires-Dist: timm>=0.9.12; extra == "vision"
-Requires-Dist: torchvision>=0.17.0; extra == "vision"
-Requires-Dist: h5py>=3.10.0; extra == "all"
-Requires-Dist: nibabel>=5.2.0; extra == "all"
-Requires-Dist: opencv-python-headless>=4.9.0.80; extra == "all"
-Requires-Dist: timm>=0.9.12; extra == "all"
-Requires-Dist: torchvision>=0.17.0; extra == "all"
-Provides-Extra: vision
-Provides-Extra: all
-Description-Content-Type: text/markdown
-
-<div align="center">
-
-<br />
-
-<img src="https://github.com/kaiko-ai/eva/blob/main/docs/images/eva-logo.png?raw=true" width="340">
-
-<br />
-<br />
-
-_Oncology FM Evaluation Framework by kaiko.ai_
-
-[![PyPI](https://img.shields.io/pypi/v/kaiko-eva.svg?logo=python)](https://pypi.python.org/pypi/kaiko-eva)
-[![docs](https://img.shields.io/badge/📚_docs-latest-green)](https://kaiko-ai.github.io/eva/latest)
-[![license](https://img.shields.io/badge/⚖️_License-Apache%202.0-blue.svg?labelColor=gray)](https://github.com/kaiko-ai/eva#license)<br>
-[![paper](http://img.shields.io/badge/OpenReview-MIDL_2024-B31B1B.svg)](https://openreview.net/forum?id=FNBQOPj18N&noteId=FNBQOPj18N)
-
-<p align="center">
-  <a href="https://github.com/kaiko-ai/eva#installation">Installation</a> •
-  <a href="https://github.com/kaiko-ai/eva#how-to-use">How To Use</a> •
-  <a href="https://kaiko-ai.github.io/eva/">Documentation</a> •
-  <a href="https://kaiko-ai.github.io/eva/dev/datasets/">Datasets</a> •
-  <a href="https://github.com/kaiko-ai/eva#benchmarks">Benchmarks</a> <br>
-  <a href="https://github.com/kaiko-ai/eva#contributing">Contribute</a> •
-  <a href="https://github.com/kaiko-ai/eva#acknowledgements">Acknowledgements</a>
-</p>
-
-</div>
-
-<br />
-
-_`eva`_ is an evaluation framework for oncology foundation models (FMs) by [kaiko.ai](https://kaiko.ai/).
-Check out the [documentation](https://kaiko-ai.github.io/eva/) for more information.
-
-### Highlights:
-- Easy and reliable benchmark of Oncology FMs
-- Automatic embedding inference and evaluation of a downstream task
-- Native support of popular medical [datasets](https://kaiko-ai.github.io/eva/dev/datasets/) and models
-- Produce statistics over multiple evaluation fits and multiple metrics
-
-## Installation
-
-Simple installation from PyPI:
-```sh
-# to install the core version only
-pip install kaiko-eva
-
-# to install the expanded `vision` version
-pip install 'kaiko-eva[vision]'
-
-# to install everything
-pip install 'kaiko-eva[all]'
-```
-
-To install the latest version of the `main` branch:
-```sh
-pip install "kaiko-eva[all] @ git+https://github.com/kaiko-ai/eva.git"
-```
-
-You can verify that the installation was successful by executing:
-```sh
-eva --version
-```
-
-## How To Use
-
-_`eva`_ can be used directly from the terminal as a CLI tool as follows:
-```sh
-eva {fit,predict,predict_fit} --config url/or/path/to/the/config.yaml 
-```
-
-When used as a CLI tool, _`eva`_ supports configuration files (`.yaml`) as an argument to define its functionality.
-Native supported configs can be found at the [configs](https://github.com/kaiko-ai/eva/tree/main/configs) directory
-of the repo. Apart from cloning the repo, you can download the latest config folder as `.zip` from your browser from
-[here](https://download-directory.github.io/?url=https://github.com/kaiko-ai/eva/tree/main/configs). Alternatively,
-from a specific release the configs can be downloaded from the terminal as follows:
-```sh
-curl -LO https://github.com/kaiko-ai/eva/releases/download/0.0.1/configs.zip | unzip configs
-```
-
-For example, to perform a downstream evaluation of DINO ViT-S/16 on the BACH dataset with
-linear probing by first inferring the embeddings and performing 5 sequential fits, execute:
-```sh
-# from a locally stored config file
-eva predict_fit --config ./configs/vision/dino_vit/offline/bach.yaml
-
-# from a remote stored config file
-eva predict_fit --config https://raw.githubusercontent.com/kaiko-ai/eva/main/configs/vision/dino_vit/offline/bach.yaml
-```
-
-> [!NOTE] 
-> All the datasets that support automatic download in the repo have by default the option to automatically download set to false.
-> For automatic download you have to manually set download=true.
-
-
-To view all the possibles, execute:
-```sh
-eva --help
-```
-
-For more information, please refer to the [documentation](https://kaiko-ai.github.io/eva/dev/user-guide/tutorials/offline_vs_online/)
-and [tutorials](https://kaiko-ai.github.io/eva/dev/user-guide/advanced/replicate_evaluations/).
-
-## Benchmarks
-
-In this section you will find model benchmarks which were generated with _`eva`_.
-
-### Table I: WSI patch-level benchmark
-
-<br />
-
-<div align="center">
-
-| Model                                            | BACH  | CRC   | MHIST | PCam/val | PCam/test |
-|--------------------------------------------------|-------|-------|-------|----------|-----------|
-| ViT-S/16 _(random)_	<sup>[1]</sup>               | 0.410 | 0.617 | 0.501 | 0.753    | 0.728     |
-| ViT-S/16 _(ImageNet)_ <sup>[1]</sup>             | 0.695 | 0.935 | 0.831 | 0.864    | 0.849     |
-| ViT-B/8 _(ImageNet)_ <sup>[1]</sup>              | 0.710 | 0.939 | 0.814 | 0.870    | 0.856     |
-| ViT-L/14 _(ImageNet)_ <sup>[1]</sup>             | 0.707 | 0.916 | 0.832 | 0.873    | 0.888     |
-| DINO<sub>(p=16)</sub> <sup>[2]</sup>             | 0.801 | 0.934 | 0.768 | 0.889    | 0.895     |
-| Phikon <sup>[3]</sup>                            | 0.725 | 0.935 | 0.777 | 0.912    | 0.915     |
-| UNI <sup>[4]</sup>                               | 0.814 | 0.950 | 0.837 | 0.936    | 0.938     |
-| ViT-S/16 _(kaiko.ai)_ <sup>[5]</sup>             | 0.797 | 0.943 | 0.828 | 0.903    | 0.893     |
-| ViT-S/8 _(kaiko.ai)_ <sup>[5]</sup>              | 0.834 | 0.946 | 0.832 | 0.897    | 0.887     |
-| ViT-B/16 _(kaiko.ai)_	<sup>[5]</sup>             | 0.810 | 0.960 | 0.826 | 0.900    | 0.898     |
-| ViT-B/8 _(kaiko.ai)_ <sup>[5]</sup>              | 0.865 | 0.956 | 0.809 | 0.913    | 0.921     |
-| ViT-L/14 _(kaiko.ai)_ <sup>[5]</sup>             | 0.870 | 0.930 | 0.809 | 0.908    | 0.898     |
-
-_Table I: Linear probing evaluation of FMs on patch-level downstream datasets.<br> We report averaged balanced accuracy
-over 5 runs, with an average standard deviation of ±0.003._
-
-</div>
-
-<br />
-
-_References_:
-1. _"Emerging properties in self-supervised vision transformers”_, [arXiv](https://arxiv.org/abs/2104.14294)
-2. _"Benchmarking self-supervised learning on diverse pathology datasets”_, [arXiv](https://arxiv.org/abs/2212.04690)
-3. _"Scaling self-supervised learning for histopathology with masked image modeling”_, [medRxiv](https://www.medrxiv.org/content/10.1101/2023.07.21.23292757v1)
-4. _"A General-Purpose Self-Supervised Model for Computational Pathology”_, [arXiv](https://arxiv.org/abs/2308.15474)
-5. _"Towards Training Large-Scale Pathology Foundation Models: from TCGA to Hospital Scale”_, [arXiv](https://arxiv.org/pdf/2404.15217)
-
-## Contributing
-
-_`eva`_ is an open source project and welcomes contributions of all kinds. Please checkout the [developer](./docs/DEVELOPER_GUIDE.md)
-and [contributing guide](./docs/CONTRIBUTING.md) for help on how to do so.
-
-All contributors must follow the [code of conduct](./docs/CODE_OF_CONDUCT.md).
-
-
-## Acknowledgements
-
-Our codebase is built using multiple opensource contributions
-
-<div align="center">
-
-[![python](https://img.shields.io/badge/-Python-blue?logo=python&logoColor=white)](https://github.com/pre-commit/pre-commit)
-[![pytorch](https://img.shields.io/badge/PyTorch-ee4c2c?logo=pytorch&logoColor=white)](https://pytorch.org/get-started/locally/)
-[![lightning](https://img.shields.io/badge/-⚡️_Lightning-792ee5?logo=pytorchlightning&logoColor=white)](https://pytorchlightning.ai/)<br>
-[![black](https://img.shields.io/badge/Code%20Style-Black-black.svg?labelColor=gray)](https://black.readthedocs.io/en/stable/)
-[![isort](https://img.shields.io/badge/%20imports-isort-%231674b1?style=flat&labelColor=ef8336)](https://pycqa.github.io/isort/)
-[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
-[![Checked with pyright](https://microsoft.github.io/pyright/img/pyright_badge.svg)](https://microsoft.github.io/pyright/)<br>
-[![pdm-managed](https://img.shields.io/badge/pdm-managed-blueviolet)](https://pdm-project.org)
-[![Nox](https://img.shields.io/badge/%F0%9F%A6%8A-Nox-D85E00.svg)](https://github.com/wntrblm/nox)
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-
-</div>
-
-
-## Citation
-
-If you find this repository useful, please consider giving a star ⭐ and adding the following citation:
-
-```
-@inproceedings{
-kaiko.ai2024eva,
-title={eva: Evaluation framework for pathology foundation models},
-author={kaiko.ai and Ioannis Gatopoulos and Nicolas K{\"a}nzig and Roman Moser and Sebastian Ot{\'a}lora},
-booktitle={Medical Imaging with Deep Learning},
-year={2024},
-url={https://openreview.net/forum?id=FNBQOPj18N}
-}
-```
-
-<br />
-
-<div align="center">
-  <img src="https://github.com/kaiko-ai/eva/blob/main/docs/images/kaiko-logo.png?raw=true" width="200">
-</div>

kaiko_eva-0.0.2.dist-info/RECORD

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