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skada

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Domain adaptation toolbox compatible with scikit-learn and pytorch

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# SKADA - Domain Adaptation with scikit-learn and PyTorch

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SKADA is a library for domain adaptation (DA) with a scikit-learn and PyTorch/skorch
compatible API with the following features:

- DA estimators and transformers with a scikit-learn compatible API (fit, transform, predict).
- PyTorch/skorch API for deep learning DA algorithms.
- Classifier/Regressor and data Adapter DA algorithms compatible with scikit-learn pipelines.
- Compatible with scikit-learn validation loops (cross_val_score, GridSearchCV, etc).

**Citation**: If you use this library in your research, please cite the following reference:

```
Gnassounou T., Kachaiev O., Flamary R., Collas A., Lalou Y., de Mathelin A., Gramfort A., Bueno R., Michel F., Mellot A.,  Loison V., Odonnat A., Moreau T. (2024). SKADA : Scikit Adaptation (version 0.3.0). URL: https://scikit-adaptation.github.io/
```

or in Bibtex format :

```bibtex
@misc{gnassounou2024skada,
author = {Gnassounou, Théo and Kachaiev, Oleksii and Flamary, Rémi and Collas, Antoine and Lalou, Yanis and de Mathelin, Antoine and Gramfort, Alexandre and Bueno, Ruben and Michel, Florent and Mellot, Apolline and  Loison, Virginie and Odonnat, Ambroise and Moreau, Thomas},
month = {7},
title = {SKADA : Scikit Adaptation},
url = {https://scikit-adaptation.github.io/},
year = {2024}
}
```

## Implemented algorithms

The following algorithms are currently implemented.

### Domain adaptation algorithms

- Sample reweighting methods (Gaussian [1], Discriminant [2], KLIEPReweight [3],
  DensityRatio [4], TarS [21], KMMReweight [23])
- Sample mapping methods (CORAL [5], Optimal Transport DA OTDA [6], LinearMonge [7], LS-ConS [21])
- Subspace methods (SubspaceAlignment [8], TCA [9], Transfer Subspace Learning [27])
- Other methods (JDOT [10], DASVM [11], OT Label Propagation [28])

Any methods that can be cast as an adaptation of the input data can be used in one of two ways:
- a scikit-learn transformer (Adapter) which provides both a full Classifier/Regressor estimator
 - or an `Adapter` that can be used in a DA pipeline with `make_da_pipeline`.
 Refer to the examples below and visit [the gallery](https://scikit-adaptation.github.io/auto_examples/index.html)for more details.

### Deep learning domain adaptation algorithms

- Deep Correlation alignment (DeepCORAL [12])
- Deep joint distribution optimal (DeepJDOT [13])
- Divergence minimization (MMD/DAN [14])
- Adversarial/discriminator based DA (DANN [15], CDAN [16])

### DA metrics

- Importance Weighted [17]
- Prediction entropy [18]
- Soft neighborhood density [19]
- Deep Embedded Validation (DEV) [20]
- Circular Validation [11]

## Installation

The library is not yet available on PyPI. You can install it from the source code.
```python
pip install git+https://github.com/scikit-adaptation/skada
```

## Short examples

We provide here a few examples to illustrate the use of the library. For more
details, please refer to this [example](https://scikit-adaptation.github.io/auto_examples/plot_how_to_use_skada.html), the [quick start guide](https://scikit-adaptation.github.io/quickstart.html) and the [gallery](https://scikit-adaptation.github.io/auto_examples/index.html).

First, the DA data in the SKADA API is stored in the following format:

```python
X, y, sample_domain
```

Where `X` is the input data, `y` is the target labels and `sample_domain` is the
domain labels (positive for source and negative for target domains). We provide
below an example ho how to fit a DA estimator:

```python
from skada import CORAL

da = CORAL()
da.fit(X, y, sample_domain=sample_domain) # sample_domain passed by name

ypred = da.predict(Xt) # predict on test data
```

One can also use `Adapter` classes to create a full pipeline with DA:

```python
from skada import CORALAdapter, make_da_pipeline
from sklearn.preprocessing import StandardScaler
from sklearn.linear_model import LogisticRegression

pipe = make_da_pipeline(StandardScaler(), CORALAdapter(), LogisticRegression())

pipe.fit(X, y, sample_domain=sample_domain) # sample_domain passed by name
```

Please note that for `Adapter` classes that implement sample reweighting, the
subsequent classifier/regressor must require sample_weights as input. This is
done with the `set_fit_requires` method. For instance, with `LogisticRegression`, you
would use `LogisticRegression().set_fit_requires('sample_weight')`:

```python
from skada import GaussianReweightAdapter, make_da_pipeline
pipe = make_da_pipeline(GaussianReweightAdapter(),
                        LogisticRegression().set_fit_request(sample_weight=True))
```

Finally SKADA can be used for cross validation scores estimation and hyperparameter
selection :

```python
from sklearn.model_selection import cross_val_score, GridSearchCV
from sklearn.preprocessing import StandardScaler
from sklearn.linear_model import LogisticRegression

from skada import CORALAdapter, make_da_pipeline
from skada.model_selection import SourceTargetShuffleSplit
from skada.metrics import PredictionEntropyScorer

# make pipeline
pipe = make_da_pipeline(StandardScaler(), CORALAdapter(), LogisticRegression())

# split and score
cv = SourceTargetShuffleSplit()
scorer = PredictionEntropyScorer()

# cross val score
scores = cross_val_score(pipe, X, y, params={'sample_domain': sample_domain},
                         cv=cv, scoring=scorer)

# grid search
param_grid = {'coraladapter__reg': [0.1, 0.5, 0.9]}
grid_search = GridSearchCV(estimator=pipe,
                           param_grid=param_grid,
                           cv=cv, scoring=scorer)

grid_search.fit(X, y, sample_domain=sample_domain)
```

## Acknowledgements

This toolbox has been created and is maintained by the SKADA team that includes the following members:

* [Théo Gnassounou](https://tgnassou.github.io/)
* [Oleksii Kachaiev](https://kachayev.github.io/talks/)
* [Rémi Flamary](https://remi.flamary.com/)
* [Antoine Collas](https://www.antoinecollas.fr/)
* [Yanis Lalou](https://github.com/YanisLalou)
* [Antoine de Mathelin](https://scholar.google.com/citations?user=h79bffAAAAAJ&hl=fr)
* [Ruben Bueno]()

SKADA has benefited from the financing or manpower from the following partners:

## License

The library is distributed under the 3-Clause BSD license.

## References

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