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ioangatop authored Mar 22, 2024
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28 changes: 23 additions & 5 deletions README.md
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Expand Up @@ -24,7 +24,8 @@ _Oncology FM Evaluation Framework by kaiko.ai_

<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.
_`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
Expand Down Expand Up @@ -63,21 +64,37 @@ _eva_ can be used directly from the terminal as a CLI tool as follows:
eva {fit,predict,predict_fit} --config url/or/path/to/the/config.yaml
```

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:
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.zip
```

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.
> 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/).
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

Expand Down Expand Up @@ -117,7 +134,8 @@ _References_:

## 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.
_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).

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2 changes: 1 addition & 1 deletion pyproject.toml
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Expand Up @@ -6,7 +6,7 @@ build-backend = "pdm.backend"

[project]
name = "kaiko-eva"
version = "0.0.0.dev8"
version = "0.0.1"
description = "Evaluation Framework for oncology foundation models."
keywords = [
"machine-learning",
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