PyRCN 0.0.18
A scikit-learn-compatible framework for Reservoir Computing in Python
Requires Python: >=3.9

# PyRCN
**A Python 3 framework for Reservoir Computing with a [scikit-learn](https://scikit-learn.org/stable/)-compatible API.**

[![PyPI version](https://badge.fury.io/py/PyRCN.svg)](https://badge.fury.io/py/PyRCN)
[![Documentation Status](https://readthedocs.org/projects/pyrcn/badge/?version=latest)](https://pyrcn.readthedocs.io/en/latest/?badge=latest)

PyRCN ("Python Reservoir Computing Networks") is a light-weight and transparent Python 3 framework for Reservoir Computing and is based on widely used scientific Python packages, such as numpy or scipy. 
The API is fully scikit-learn-compatible, so that users of scikit-learn do not need to refactor their code in order to use the estimators implemented by this framework. 
Scikit-learn's built-in parameter optimization methods and example datasets can also be used in the usual way.

PyRCN is used by the [Chair of Speech Technology and Cognitive Systems, Institute for Acoustics and Speech Communications, Technische Universität Dresden, Dresden, Germany](https://tu-dresden.de/ing/elektrotechnik/ias/stks?set_language=en) 
and [IDLab (Internet and Data Lab), Ghent University, Ghent, Belgium](https://www.ugent.be/ea/idlab/en). 

Currently, it implements Echo State Networks (ESNs) by Herbert Jaeger and Extreme Learning Machines (ELMs) by Guang-Bin Huang in different flavors, e.g. Classifier and Regressor. It is actively developed to be extended into several directions:

- Interaction with [sktime](http://sktime.org/)
- Interaction with [hmmlearn](https://hmmlearn.readthedocs.io/en/stable/)
- More towards future work: Related architectures, such as Liquid State Machines (LSMs) and Perturbative Neural Networks (PNNs)

PyRCN has successfully been used for several tasks:

- Music Information Retrieval (MIR)
    - Multipitch tracking
    - Onset detection
    - $f_{0}$ analysis of spoken language
    - GCI detection in raw audio signals
- Time Series Prediction
    - Mackey-Glass benchmark test
    - Stock price prediction
- Ongoing research tasks:
    - Beat tracking in music signals
    - Pattern recognition in sensor data
    - Phoneme recognition
    - Unsupervised pre-training of RCNs and optimization of ESNs

Please see the [References section](#references) for more information. For code examples, see [Getting started](#getting-started).

## Installation

### Prerequisites

PyRCN is developed using Python 3.9 or newer. It depends on the following packages:

- [numpy>=1.18.1](https://numpy.org/)
- [scikit-learn>=1.4](https://scikit-learn.org/stable/)
- [joblib>=0.13.2](https://joblib.readthedocs.io)
- [pandas>=1.0.0](https://pandas.pydata.org/)
- [matplotlib](https://matplotlib.org/)
- [seaborn](https://seaborn.pydata.org/)

### Installation from PyPI

The easiest and recommended way to install ``PyRCN`` is to use ``pip`` from [PyPI](https://pypi.org) :

```
pip install pyrcn
```

### Installation from source

If you plan to contribute to ``PyRCN``, you can also install the package from source.

Clone the Git repository:

```
git clone https://github.com/TUD-STKS/PyRCN.git
```

Install the package using ``setup.py``:
```
python setup.py install --user
```

## Offcial documentation

See [the official PyRCN documentation](https://pyrcn.readthedocs.io/en/latest/?badge=latest)
to learn more about the main features of PyRCN, its API and the installation process.

## Package structure
The package is structured in the following way: 

- `doc`
    - This folder includes the package documentation.
- `examples`
    - This folder includes example code as Jupyter Notebooks and python scripts.
- `images`
    - This folder includes the logos used in ´README.md´.
- `pyrcn`
    - This folder includes the actual Python package.


## Getting Started

PyRCN includes currently variants of Echo State Networks (ESNs) and Extreme Learning Machines (ELMs): Regressors and Classifiers.

Basic example for the ESNClassifier:

```python
from sklearn.model_selection import train_test_split
from pyrcn.datasets import load_digits
from pyrcn.echo_state_network import ESNClassifier

X, y = load_digits(return_X_y=True, as_sequence=True)
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.2, random_state=42)

clf = ESNClassifier()
clf.fit(X=X_train, y=y_train)

y_pred_classes = clf.predict(X=X_test)  # output is the class for each input example
y_pred_proba = clf.predict_proba(X=X_test)  #  output are the class probabilities for each input example
```

Basic example for the ESNRegressor:

```python
from pyrcn.datasets import mackey_glass
from pyrcn.echo_state_network import ESNRegressor

X, y = mackey_glass(n_timesteps=20000)

reg = ESNRegressor()
reg.fit(X=X[:8000], y=y[:8000])

y_pred = reg.predict(X[8000:])  # output is the prediction for each input example
```

An extensive introduction to getting started with PyRCN is included in the [examples](https://github.com/TUD-STKS/PyRCN/blob/main/examples) directory. 
The notebook [digits](https://github.com/TUD-STKS/PyRCN/blob/main/examples/digits.ipynb) or its corresponding [Python script](https://github.com/TUD-STKS/PyRCN/blob/main/examples/digits.py) show how to set up an ESN for a small hand-written digit recognition experiment. 
Launch the digits notebook on Binder: 

[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/TUD-STKS/PyRCN/main?filepath=examples%2Fdigits.ipynb)

The notebook [PyRCN_Intro](https://github.com/TUD-STKS/PyRCN/blob/main/examples/PyRCN_Intro.ipynb) or its corresponding [Python script](https://github.com/TUD-STKS/PyRCN/blob/main/examples/PyRCN_Intro.py) show how to construct different RCNs with building blocks. 

[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/TUD-STKS/PyRCN/main?filepath=examples%2FPyRCN_Intro.ipynb)

The notebook [Impulse responses](https://github.com/TUD-STKS/PyRCN/blob/main/examples/esn_impulse_responses.ipynb) is an interactive tool to demonstrate the impact of different hyper-parameters on the impulse responses of an ESN. 

[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/TUD-STKS/PyRCN/main?filepath=examples%2Fesn_impulse_responses.ipynb)

Fore more advanced examples, please have a look at our [Automatic Music Transcription Repository](https://github.com/TUD-STKS/Automatic-Music-Transcription), in which we provide an entire feature extraction, training and test pipeline for multipitch tracking and for note onset detection using PyRCN. This is currently transferred to this repository.

## Citation

If you use PyRCN, please cite the following publication:

```latex
@misc{steiner2021pyrcn,
      title={PyRCN: A Toolbox for Exploration and Application of Reservoir Computing Networks}, 
      author={Peter Steiner and Azarakhsh Jalalvand and Simon Stone and Peter Birkholz},
      year={2021},
      eprint={2103.04807},
      archivePrefix={arXiv},
      primaryClass={cs.LG}
}
```

## References

[Unsupervised Pretraining of Echo State Networks for Onset Detection](https://link.springer.com/chapter/10.1007/978-3-030-85099-9_12)

```
@InProceedings{src:Steiner-21e,
   author="Peter Steiner and Azarakhsh Jalalvand and Peter Birkholz",
   editor="Igor Farka{\v{s}} and Paolo Masulli and Sebastian Otte and Stefan Wermter",
   title="{U}nsupervised {P}retraining of {E}cho {S}tate {N}etworks for {O}nset {D}etection",
   booktitle="Artificial Neural Networks and Machine Learning -- ICANN 2021",
   year="2021",
   publisher="Springer International Publishing",
   address="Cham",
   pages="59--70",
   isbn="978-3-030-86383-8"
}


```

[Improved Acoustic Modeling for Automatic Piano Music Transcription Using Echo State Networks](https://link.springer.com/chapter/10.1007/978-3-030-85099-9_12)

```
@InProceedings{src:Steiner-21d,
	author="Peter Steiner and Azarakhsh Jalalvand and Peter Birkholz",
	editor="Ignacio Rojas and Gonzalo Joya and Andreu Catala",
	title="{I}mproved {A}coustic {M}odeling for {A}utomatic {P}iano {M}usic {T}ranscription {U}sing {E}cho {S}tate {N}etworks",
	booktitle="Advances in Computational Intelligence",
	year="2021",
	publisher="Springer International Publishing",
	address="Cham",
	pages="143--154",
	isbn="978-3-030-85099-9"
}
```

Glottal Closure Instant Detection using Echo State Networks
- [Paper](http://www.essv.de/pdf/2021_161_168.pdf)
- [Repository](https://github.com/TUD-STKS/gci_estimation)
- Reference
```latex
@InProceedings{src:Steiner-21c,
	title = {Glottal Closure Instant Detection using Echo State Networks},
	author = {Peter Steiner and Ian S. Howard and Peter Birkholz},
	year = {2021},
	pages = {161--168},
	keywords = {Oral},
	booktitle = {Studientexte zur Sprachkommunikation: Elektronische Sprachsignalverarbeitung 2021},
	editor = {Stefan Hillmann and Benjamin Weiss and Thilo Michael and Sebastian Möller},
	publisher = {TUDpress, Dresden},
	isbn = {978-3-95908-227-3}
}
```

Cluster-based Input Weight Initialization for Echo State Networks

```latex
@article{Steiner2022cluster,
	author = {Steiner, Peter and Jalalvand, Azarakhsh and Birkholz, Peter},
	doi = {10.1109/TNNLS.2022.3145565},
	issn = {2162-2388},
	journal = {IEEE Transactions on Neural Networks and Learning Systems},
	keywords = {},
	month = {},
	number = {},
	pages = {1--12},
	title = {Cluster-based Input Weight Initialization for Echo State Networks},
	volume = {},
	year = {2022},
}
```

PyRCN: A Toolbox for Exploration and Application of Reservoir Computing Networks

```latex
@article{Steiner2022pyrcn,
	title = {PyRCN: A Toolbox for Exploration and Application of Reservoir Computing Networks},
	journal = {Engineering Applications of Artificial Intelligence},
	volume = {113},
	pages = {104964},
	year = {2022},
	issn = {0952-1976},
	doi = {10.1016/j.engappai.2022.104964},
	url = {https://www.sciencedirect.com/science/article/pii/S0952197622001713},
	author = {Peter Steiner and Azarakhsh Jalalvand and Simon Stone and Peter Birkholz},
}
```

[Feature Engineering and Stacked ESNs for Musical Onset Detection](https://ieeexplore.ieee.org/abstract/document/9413205)

```latex
@INPROCEEDINGS{src:Steiner-21b,
    author={Peter Steiner and Azarakhsh Jalalvand and Simon Stone and Peter Birkholz},
    booktitle={2020 25th International Conference on Pattern Recognition (ICPR)},
    title={{F}eature {E}ngineering and {S}tacked {E}cho {S}tate {N}etworks for {M}usical {O}nset {D}etection},
    year={2021},
    volume={},
    number={},
    pages={9537--9544},
    doi={10.1109/ICPR48806.2021.9413205}
}
```

[Multipitch tracking in music signals using Echo State Networks](https://ieeexplore.ieee.org/abstract/document/9287638)

```latex
@INPROCEEDINGS{src:Steiner-21a,
    author={Peter Steiner and Simon Stone and Peter Birkholz and Azarakhsh Jalalvand},
    booktitle={2020 28th European Signal Processing Conference (EUSIPCO)},
    title={{M}ultipitch tracking in music signals using {E}cho {S}tate {N}etworks},
    year={2021},
    volume={},
    number={},
    pages={126--130},
    keywords={},
    doi={10.23919/Eusipco47968.2020.9287638},
    ISSN={2076-1465},
    month={Jan},
```

[Note Onset Detection using Echo State Networks](http://www.essv.de/pdf/2020_157_164.pdf)

```latex
@InProceedings{src:Steiner-20,
	title = {Note Onset Detection using Echo State Networks},
	author = {Peter Steiner and Simon Stone and Peter Birkholz},
	year = {2020},
	pages = {157--164},
	keywords = {Poster},
	booktitle = {Studientexte zur Sprachkommunikation: Elektronische Sprachsignalverarbeitung 2020},
	editor = {Ronald Böck and Ingo Siegert and Andreas Wendemuth},
	publisher = {TUDpress, Dresden},
	isbn = {978-3-959081-93-1}
} 
```

[Multiple-F0 Estimation using Echo State Networks](https://www.music-ir.org/mirex/abstracts/2019/SBJ1.pdf)

```latex
@inproceedings{src:Steiner-19,
  title={{M}ultiple-{F}0 {E}stimation using {E}cho {S}tate {N}etworks},
  booktitle={{MIREX}},
  author={Peter Steiner and Azarakhsh Jalalvand and Peter Birkholz},
  year={2019},
  url = {https://www.music-ir.org/mirex/abstracts/2019/SBJ1.pdf}
}
```


## Acknowledgments
This research was funded by the European Social Fund (Application number: 100327771) and co-financed by tax funds based on the budget approved by the members of the Saxon State Parliament, and by Ghent University.