probinet 1.1
Python package for probabilistic network analysis.
Requires Python: <3.13,>=3.10

# ProbINet

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Welcome to the documentation for the **Prob**abilistic **I**nference on **Net**works (``ProbINet``) Python
package. This project is a collaborative effort to consolidate state-of-the-art probabilistic generative modeling implementations from various
scientific publications. Our focus lies in advancing network analysis techniques with an emphasis on recent modeling
approaches that relax the restrictive conditional independence assumption, enabling the modeling of joint
distributions of network data.

The ``ProbINet`` package is designed to be a comprehensive and user-friendly toolset for
researchers and practitioners interested in modeling network data through probabilistic 
generative approaches. Our goal is to provide a unified resource that brings together different advances scattered across many code repositories.
By doing so, we aim not only to enhance the usability of existing models, but also to facilitate the comparison
of different approaches. Moreover, through a range of tutorials, we aim at simplifying the use of these methods
to perform inferential tasks, including the prediction of missing network edges, node clustering (community detection),
anomaly identification, and the generation of synthetic data from latent variables.

## Models Overview

The package integrates a wide range of probabilistic  generative models tailored for various network data types and analytical goals. The following 
  table summarizes the models currently implemented in ``ProbINet``:

| **Name**         | **Description**                                                                                       | **Network Properties**                   |
|-----------------|----------------------------------------------------------------------------------------------------|----------------------------------------|
| **CRep**        | Models directed networks with communities and reciprocity [CSDB22].                                                       | Directed, Weighted, Communities, Reciprocity                 |
| **JointCRep**   | Captures community structure and reciprocity with a joint edge distribution [SCDB21].                   | Directed, Communities, Reciprocity       |
| **DynCRep**     | Extends CRep for dynamic networks [SCDB22].                                                             | Directed, Weighted, Dynamic, Communities, Reciprocity           |
| **ACD**         | Identifies anomalous edges and node community memberships in weighted networks [SDB22]. | Directed, Weighted, Communities, Anomalies       |
| **MTCOV**       | Extracts overlapping communities in multilayer networks using topology and node attributes [CPDB20].       | Weighted, Multilayer, Attributes, Communities      |

For more details on each model, please refer to the [documentation](https://mpi-is.github.io/probinet/). References to the original papers can be found [here](https://mpi-is.github.io/probinet/references.html).


## Installation


This package requires Python 3.10 or higher. Please ensure you have one of these versions before proceeding with the installation.
To get started, follow these steps:

1. Clone the repository and navigate to the `probinet` directory:

```bash
   git clone https://github.com/MPI-IS/probinet.git
   cd probinet
````

2. Create a virtual environment. For example, using ``venv``:

```bash
   python3 -m venv --copies venv
   . venv/bin/activate
   (venv) pip install -U pip # optional but always advised!
```

3. Install the ``ProbINet`` package by running:

```bash
   (venv) pip install probinet
```

## Usage

Run the ``ProbINet`` package as a whole with the `run_probinet` command. This command can be run 
from any directory after the package is installed.

A list of the parameters that can be passed as arguments is available by running:

```bash
    run_probinet --help
```

To run a specific model, pass the model name as an argument. The available models are: `CRep`, `JointCRep`, `MTCOV`, `DynCRep`, and `ACD`. For example, to run the `CRep` model, use:

```bash
    run_probinet CRep
```

To see the specific options for a model, use the `-h` flag. For example, to see the options for the `CRep` model, use:

```bash
    run_probinet CRep -h
```

The `run_probinet` command can be run at different logging levels. To run the command with the `DEBUG` level, use:

```bash
    run_probinet CRep -d
```

To set arguments with double dashes (e.g., `--convergence_tol`), include them in the command line 
as follows:

```bash
    run_probinet CRep --convergence_tol 0.1
```

Some commands can also be executed using shorter versions of the arguments. For example, the 
`--convergence_tol` argument can be shortened to `-tol`:

```bash
    run_probinet CRep -tol 0.1
```
These shorter versions can be found in the help message of each model.

## Tests

To run the tests:

```bash
    python -m unittest
```

## Documentation

The documentation can be built locally. First, install the `dev` extra:

```bash
    pip install ".[dev]"
```

To build the documentation, run:

```bash
    cd docs
    make html
```

The documentation will be available in the `docs/build/html` directory.

## Tutorials

The tutorials are available in the [tutorials](https://github.com/MPI-IS/probinet/tree/develop/docs/source/tutorials) 
directory.
Each tutorial is a Jupyter 
notebook that can be run in a Jupyter environment. 

## Where to start

If you are new to this type of modeling, we suggest checking out the [Inputs and Outputs](https://mpi-is.github.io/probinet/start.html) section. 
This section provides an overview of the input and output data structures used in the package.

## Authors

- [Diego Baptista Theuerkauf](https://github.com/diegoabt)
- [Jean-Claude Passy](https://is.mpg.de/person/jpassy)

The authors of the original implementations integrated to this package are:

- [Caterina De Bacco](https://cdebacco.com/) 
- [Martina Contisciani](https://github.com/mcontisc) 
- [Hadiseh Safdari](https://github.com/hds-safdari)

See the references in the documentation for more details.

Special thanks to [Alejandro Posada](https://is.mpg.de/~posada) for his contributions to the 
logo design. A sincere thank you to [Valkyrie Felso](https://github.com/vmfelso) and [Kathy Su](https://github.com/ksu00) for their invaluable feedback. 
We also deeply appreciate [Kibidi Neocosmos](https://github.com/kibidi) for serving as a beta user and helping refine the 
package.

## Contributing

Would you like to contribute to the development of **ProbINet**? Contributions are welcome and 
appreciated! You can find detailed information on how to get started here: [Contributing Guide](https://mpi-is.github.io/probinet/contributing.html).


## License

This project is licensed under the GNU GPL version 3 - see the [LICENSE](https://github.com/MPI-IS/probinet/blob/develop/LICENSE.md) file for
details.


## Copyright

© 2024, Max Planck Society / Software Workshop - Max Planck Institute for Intelligent Systems