cobel 3.0.0
Closed-loop simulator of complex behavior and learning based on reinforcement learning and deep neural networks.
Requires Python: >=3.11
Keywords: reinforcement learning, neuroscience, simulation

<div align="center">
<img src="https://ruhr-uni-bochum.sciebo.de/s/dajogO0rVC3AOqO/download" alt="CoBeL-RL Logo" width="256"></img>
</div>

# CoBeL-RL: Closed-loop simulator of Complex Behavior and Learning based on Reinforcement Learning and deep neural networks

CoBeL-RL is a closed-loop simulator of complex behavior and learning based on RL and deep neural networks. It provides a neuroscience-oriented framework for efficiently setting up and running simulations. CoBeL-RL offers a set of virtual environments, e.g., T-maze and Morris water maze, which can be simulated at different levels of abstraction, e.g., a simple gridworld or a 3D environment with complex visual stimuli, and set up using intuitive GUI tools. A range of RL algorithms, e.g., Dyna-Q and deep Q-network algorithms, is provided and can be easily extended. CoBeL-RL provides tools for monitoring and analyzing behavior and unit activity, and allows for fine-grained control of the simulation via interfaces to relevant points in its closed-loop. In summary, CoBeL-RL fills an important gap in the software toolbox of computational neuroscience.
(From Diekmann et al. (2023), **https://doi.org/10.3389/fninf.2023.1134405**)

<div align="center">
<img src="https://ruhr-uni-bochum.sciebo.de/s/95Np7R9qDOTRsGT/download" alt="CoBeL-RL Modules" height="256"></img>
</div>

## Installation Guide

You can install CoBeL-RL from PyPI directly via [pip](https://pypi.org/project/pip/):

```
pip install cobel
```

If you wish to build CoBeL-RL from source download or clone the project using git. You can do this by typing the following into your command line : 

```
git clone https://github.com/sencheng/CoBeL-RL.git
```

See [GitHub's documentation](https://docs.github.com/en/repositories/creating-and-managing-repositories/cloning-a-repository) for more details and options for cloning repositories.

Install the `build` package and then create a .wheel file.

```
pip install build
```
```
python -m build .
```

This will create a `dist` folder containing an installable Python .wheel file.


These steps are sufficient to install CoBeL-RL. Get started by running one of the demos below. For new users, we recommend the Dyna-Q demo.

### Optional Dependencies

Per default CoBeL-RL does not install any Deep Learning framework. Instead you can install them as optional dependencies:

 - PyTorch can be installed via the `[torch]` option. PyTorch provides builds for specific platforms and hardware via its own indices. Follow the instructions on the [official website](https://pytorch.org/) to instead install the build which best fits your system.
 - Tensorflow can be installed via the `[tensorflow-cpu]` or `[tensorflow-cuda]` option.
 - Flax can installed via the `[flax-cpu]`, `[flax-cuda]` or `[flax-tpu]` option.

## Dyna-Q Demo

To run the Dyna-Q demo:

```
python demo/gridworld/demo_dyna_q.py
```

This should run the demo and visualize a 5 x 5 gridworld without obstacles.

## DQN Demo

Install PyTorch using the `[torch]` optional dependency. Alternatively, install PyTorch by following the instructions on the [official website](https://pytorch.org/).

To run the DQN demo:

```
python demo/topology/demo_dqn.py
```

This should run the demo and visualize a 10 x 2 linear track topology environment.
The pose, i.e., position and rotation, of each node serve as input to the DQN.

## 3D Simulators

CoBeL-RL allows for topological and continuous environments to be combined
with simulators which render complex visual observations.
Choose one of the 3D simulators below and follow the listed instructions.
Either will run the DQN demo and combine it with the simulator in question.

<details>

<summary>
Unity
</summary>

Follow the installation instructions on the [Unity Simulator repository](https://github.com/sencheng/Unity-Simulator).

You will need to set up an environment variable for the Unity path to run the demos.

```bash
export UNITY_EXECUTABLE="/path/to/unity/"
```

Alternatively, you can provide the path to the executable directly
in the demo script as a parameter to the simulator during initialization

```py
UnitySimulator('room', '/path/to/unity/', resize=(30, 1))
```

or as a command line argument.

```bash
python demo/unity/demo_dqn.py --executable /path/to/unity/
```

 </details> 
 
 <details>

<summary>
Godot
</summary>


Follow the installation instructions on the [Godot Simulator repository](https://github.com/sencheng/Godot-Simulator).

You will need to set up an environment variable for the Godot path to run the demos.

```bash
export GODOT_EXECUTABLE="/path/to/godot/"
```

Alternatively, you can provide the path to the executable directly
in the demo script as a parameter to the simulator during initialization

```py
GodotSimulator('room.tscn', '/path/to/godot/', resize=(30, 1))
```

or as a command line argument.

```bash
python demo/godot/demo_dqn.py --executable /path/to/godot/
```
  
 </details>

## Supported Deep Learning Frameworks

CoBeL-RL uses interface classes so that its Deep RL agents can be combined with different Deep Learning frameworks.
Currently, three frameworks are supported: PyTorch, Tensorflow and Flax.
Below you can find example code snippets which show how the same network can be set up with each of these in CoBeL-RL.

<details>
<summary>
PyTorch
</summary>

```py
from torch import Tensor
from torch.nn import Linear
from torch.nn.functional import relu
from cobel.network import TorchNetwork

class Model(nn.Module):

    def __init__(self) -> None:
        super().__init__()
        self.hidden_1 = Linear(in_features=6, out_features=64)
        self.hidden_2 = Linear(in_features=64, out_features=64)
        self.output = Linear(in_features=64, out_features=4)
        self.double()

    def forward(self, layer_input: Tensor) -> Tensor:
        x = self.hidden_1(layer_input)
        x = relu(x)
        x = self.hidden_2(x)
        x = relu(x)
        x = self.output(x)

        return x

network = Model()
model = TorchNetwork(network)
```

</details>

<details>
<summary>
Tensorflow
</summary>

```py
from tensorflow.keras.models import Sequential
from tensorflow.keras.layers import Input, Dense
from cobel.network import KerasNetwork

network = Sequential([
    Input((6, )),
    Dense(64, activation='relu', name='hidden_1'),
    Dense(64, activation='relu', name='hidden_2'),
    Dense(4, name='output'),
])
network.compile(optimizer='adam', loss='mse')
model = KerasNetwork(network)
```

</details>

<details>
<summary>
Flax (experimental)
</summary>

```py
from flax.nnx import Module, Linear, Rngs, relu
from cobel.network import FlaxNetwork

class Model(Module):

    def __init__(self) -> None:
        rngs = Rngs(0)
        self.hidden_1 = Linear(6, 64, rngs=rngs)
        self.hidden_2 = Linear(64, 64, rngs=rngs)
        self.output = Linear(64, 4, rngs=rngs)

    def __call__(self, layer_input):
        x = self.hidden_1(layer_input)
        x = relu(x)
        x = self.hidden_2(x)
        x = relu(x)
        x = self.output(x)

        return x

network = Model()
model = FlaxNetwork(network)
```

</details>
 
## List of publications

* Kappel, D., & Cheng, S. (2025). Global remapping emerges as the mechanism for renewal of context-dependent behavior in a reinforcement learning model. In Frontiers in Computational Neuroscience (Vol. 18). Frontiers Media SA. [[DOI]](https://doi.org/10.3389/fncom.2024.1462110) 
* Zeng X, Diekmann N, Wiskott L and Cheng S (2023) Modeling the function of episodic memory in spatial learning. Front. Psychol. 14:1160648. [[DOI]]( https://doi.org/10.3389/fpsyg.2023.1160648)
* Diekmann, N., Vijayabaskaran, S., Zeng, X., Kappel, D., Menezes, M. C., & Cheng, S. (2023). CoBeL-RL: A neuroscience-oriented simulation framework for complex behavior and learning. In Frontiers in Neuroinformatics (Vol. 17). Frontiers Media SA. [[DOI]](https://doi.org/10.3389/fninf.2023.1134405)
* Diekmann, N., & Cheng, S. (2023). A model of hippocampal replay driven by experience and environmental structure facilitates spatial learning. In eLife (Vol. 12). eLife Sciences Publications, Ltd. [[DOI]](https://doi.org/10.7554/elife.82301) 
* Vijayabaskaran, S., & Cheng, S. (2022). Navigation task and action space drive the emergence of egocentric and allocentric spatial representations. In D. Bush (Ed.), PLOS Computational Biology (Vol. 18, Issue 10, p. e1010320). Public Library of Science (PLoS). [[DOI]](https://doi.org/10.1371/journal.pcbi.1010320) 
* Walther, T., Diekmann, N., Vijayabaskaran, S. et al. Context-dependent extinction learning emerging from raw sensory inputs: a reinforcement learning approach. Sci Rep 11, 2713 (2021). [[DOI]](https://doi.org/10.1038/s41598-021-81157-z) 

## Citing CoBeL-RL

Please cite our methods paper:

```
@article{DiekmannEtAl2023,
    author = {Diekmann, Nicolas and Vijayabaskaran, Sandhiya and Zeng, Xiangshuai and Kappel, David and Menezes, Matheus Chaves and Cheng, Sen},
    title = {CoBeL-RL: A neuroscience-oriented simulation framework for complex behavior and learning},
    journal = {Frontiers in Neuroinformatics},
    volume = {17},
    month = {March},
    year = {2023},
    doi = {10.3389/fninf.2023.1134405},
}
```

## Notes

CoBeL-RL is developed by the Computational Neuroscience group of the Institute for Neural Computation at the Ruhr University Bochum.
Check out our [homepage](https://www.ini.rub.de/research/groups/computational_neuroscience/) for more information on us and our research.

For a similar framework built around spiking neural networks check out our sister framework [CoBeL-spike](https://www.github.com/sencheng/CoBeL-spike).

## Code Contributors

Thomas Walther, Nicolas Diekmann, Sandhiya Vijayabaskaran, Filippos Panagiotou, Xiangshuai Zeng, Matheus Chaves Menezes, David Kappel, Jon Recalde, Alexander Jungeilges, Shipra Prasad, Maria Camila Sanchez Lopez, William Forchap, Kilian Kandt, Marius Tenhumberg, Athithan Konoswaran, Henriette Knopp, Tim Nyul, Denis Meral, Brandon Finnenthal, Zenon Zacouris, Florian Becker, Pascal Kosak, Jasper Angl, Chuan Jin, Umut Yilmaz, Maximilian Frese, Frederik Hüttemann, Christopher Thomas, Gerrit Simon Fischer, Duc Cuong Tommy Tran, Maximilian Wojak, Oleksandr Chaban, Sebastian Benedict Schäfer, David Jarne Nörtemann, Philip Woltersdorf, Aya Altamimi, Nick Kellermann, Gianluca De Stefano, Patrick Del Fedele, Yorick Sen, Jan Tekautschitz