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GRAPE_ (Graph Representation leArning, Predictions and Evaluation) is a fast graph processing and embedding library, designed to scale with big graphs and to run on both off-the-shelf laptop and desktop computers and High-Performance Computing clusters of workstations.
The library is written in Rust and Python programming languages, and has been developed by AnacletoLAB <https://anacletolab.di.unimi.it/> (Dept. of Computer Science of the University of Milan), in collaboration with the Robinson Lab - Jackson Laboratory for Genomic Medicine <https://www.jax.org/research-and-faculty/research-labs/the-robinson-lab> and with the BBOP - Lawrence Berkeley National Laboratory <http://www.berkeleybop.org/index.html>_.
The library is composed of two main modules, Ensmallen <https://github.com/AnacletoLAB/ensmallen>, which is the Rust/Python high-performance graph processing submodule, and Embiggen <https://github.com/monarch-initiative/embiggen>, which is the Python Graph Representation learning, Prediction and Evaluation submodule.
GRAPE_As usual, just install it from PyPi by running:
.. code:: shell
pip install grapeGenerally, the installation does not take longer than a minute.
It is possible to manually compile Ensmallen <https://github.com/AnacletoLAB/ensmallen/blob/master/CONTRIBUTING.md>_ for any OS, libc version, and CPU architecture (such as Arm, AArch64, RiscV, Mips) which are supported by Rust and LLVM. Just open an issue if you need some help.
|features|
80K+ graphs <https://github.com/AnacletoLAB/grape/blob/main/tutorials/Ensmallen_Automatic_graph_retrieval_utilities.ipynb>_Support for multiple graph formats <https://github.com/AnacletoLAB/grape/blob/main/tutorials/Loading_a_Graph_in_Ensmallen.ipynb>_human readable reports of graph characteristics <https://github.com/AnacletoLAB/grape/blob/main/tutorials/Create%20extensive%20knowledge%20graph%20reports%20using%20GRAPE.ipynb>_also with degree normalization! <https://github.com/AnacletoLAB/grape/blob/main/tutorials/Using%20degree-normalization%20in%20random-walk-based%20embedding%20models.ipynb>_First <https://github.com/AnacletoLAB/grape/blob/main/tutorials/Using_First-order_LINE_to_embed_Cora.ipynb>_ and second order LINE <https://github.com/AnacletoLAB/grape/blob/main/tutorials/Using_Second-order_LINE_to_embed_Cora.ipynb>_Karate Club <https://github.com/benedekrozemberczki/karateclub> and PyKEEN <https://github.com/pykeen/pykeen>edge prediction <https://github.com/AnacletoLAB/grape/blob/main/tutorials/Multi-modal%20GCN%20for%20edge%20prediction.ipynb>_, edge-label prediction and node-label predictionBaseline Perceptron for edge prediction <https://github.com/AnacletoLAB/grape/blob/main/tutorials/Edge%20Predictions%20on%20STRING%20Homo%20Sapiens%20using%20a%20Perceptron.ipynb>_Integrated support to parallelize holdouts across a SLURM cluster <https://github.com/AnacletoLAB/grape/blob/main/tutorials/Using%20HPC%20SLURM%20in%20the%20GRAPE%20evaluation%20pipelines.ipynb>_Diameter <https://github.com/AnacletoLAB/grape/blob/main/tutorials/Exact%20billion-scale%20graph%20diameter%20with%20GRAPE.ipynb>, Vertex cover <https://github.com/AnacletoLAB/grape/blob/main/tutorials/Billion-scale%202-approximated%20vertex%20cover%20with%20GRAPE.ipynb>, connected components <https://github.com/AnacletoLAB/grape/blob/main/tutorials/Billion-scale%20connected%20components%20with%20GRAPE.ipynb>, Triangles <https://github.com/AnacletoLAB/grape/blob/main/tutorials/Billion-scale%20triangles%20on%20multigraphs%20with%20GRAPE.ipynb>, Squares <https://github.com/AnacletoLAB/grape/blob/main/tutorials/Billion-scale%20squares%20on%20multigraphs%20with%20GRAPE.ipynb>, Betweenness Centrality <https://github.com/AnacletoLAB/grape/blob/main/tutorials/Efficient%20Betweenness%20Centrality%20with%20GRAPE.ipynb>, HyperBall-based approximated Closeness and Harmonic centralities <https://github.com/AnacletoLAB/grape/blob/main/tutorials/HyperBall-based%20approximated%20Harmonic%20and%20Closeness%20with%20GRAPE.ipynb>, Exact Closeness centrality <https://github.com/AnacletoLAB/grape/blob/main/tutorials/Efficient%20Weighted%20and%20Unweighted%20Closeness%20Centrality%20with%20GRAPE.ipynb> and Exact Harmonic centrality <https://github.com/AnacletoLAB/grape/blob/main/tutorials/HyperBall-based%20approximated%20Harmonic%20and%20Closeness%20with%20GRAPE.ipynb>__set operations on graph edges <https://github.com/AnacletoLAB/grape/blob/main/tutorials/Graph%20set%20algebra.ipynb>_You can find tutorials covering various aspects of the GRAPE library here <https://github.com/AnacletoLAB/grape/tree/main/tutorials>_.
All tutorials are as self-contained as possible and can be immediately executed on COLAB.
If you believe that any example may be of help, do feel free to open a GitHub issue describing what we are missing in this tutorial <https://github.com/AnacletoLAB/grape/issues/new>_.
On line documentation (currently being updated)
The on line documentation of the library is available `here <https://anacletolab.github.io/grape/index.html>`__.
Since Ensmallen is written in Rust, and PyO3 (the crate we use for the Python bindings), `doesn't support typing <https://github.com/PyO3/pyo3/issues/510>`_, the documentation is obtained generating an empty skeleton package. This allows to have a proper documentation but you won't be able to see the source-code in it.
Using the automatic method suggestions utilityTo aid working with the library, GRAPE provides an integrated recommender system meant to help you either to find a method or, if a method has been renamed for any reason, find its new name.
As an example, after having loaded the STRING Homo Sapiens graph <https://string-db.org/cgi/organisms>_, the function for computing the connected components can be retrieved by simply typing components as follows:
.. code:: python
from grape.datasets.string import HomoSapiens
graph = HomoSapiens()
graph.componentsThe code above will raise the following error, and will suggest methods with a similar or related name:
.. code-block:: python
AttributeError Traceback (most recent call last)
<ipython-input-3-52fac30ac7f6> in <module>()
----> 2 graph.components
AttributeError: The method 'components' does not exists, did you mean one of the following?
* 'remove_components'
* 'connected_components'
* 'strongly_connected_components'
* 'get_connected_components_number'
* 'get_total_edge_weights'
* 'get_mininum_edge_weight'
* 'get_maximum_edge_weight'
* 'get_unchecked_maximum_node_degree'
* 'get_unchecked_minimum_node_degree'
* 'get_weighted_maximum_node_degree'In our example the method we need for computing the graph components would be connected_components.
Now the easiest way to get the method documentation is to use Python's help <https://docs.python.org/3/library/functions.html#help>_
as follows:
.. code:: python
help(graph.connected_components)And the above will return you:
.. code-block:: rst
connected_components(verbose) method of builtins.Graph instance
Compute the connected components building in parallel a spanning tree using [bader's algorithm](https://www.sciencedirect.com/science/article/abs/pii/S0743731505000882).
**This works only for undirected graphs.**
The returned quadruple contains:
- Vector of the connected component for each node.
- Number of connected components.
- Minimum connected component size.
- Maximum connected component size.
Parameters
----------
verbose: Optional[bool]
Whether to show a loading bar or not.
Raises
-------
ValueError
If the given graph is directed.
ValueError
If the system configuration does not allow for the creation of the thread pool.Please cite the following paper if it was useful for your research:
.. code:: bib
@article{cappelletti2023grape,
title={GRAPE for Fast and Scalable Graph Processing and random walk-based Embedding},
author={Cappelletti, L. and Fontana, T. and Casiraghi, E. and Ravanmehr, V. and Callahan, T.J. and Cano, C. and Joachimiak, M.P. and Mungall, C.J. and Robinson, P.N. and Reese, J. and Valentini, G.},
year={2023},
doi={10.1038/s43588-023-00465-8},
journal={Nature Computational Science}}.. |pip| image:: https://badge.fury.io/py/grape.svg :target: https://badge.fury.io/py/grape :alt: Pypi project
.. |features| image:: https://github.com/AnacletoLAB/grape/blob/main/images/sequence_diagram.png?raw=true :target: https://github.com/AnacletoLAB/grape :alt: Features
.. |downloads| image:: https://static.pepy.tech/badge/grape :target: https://pepy.tech/project/grape :alt: Pypi total project downloads
.. _Grape: https://github.com/AnacletoLAB/grape .. _Ensmallen: https://github.com/AnacletoLAB/ensmallen
.. _Embiggen: https://github.com/monarch-initiative/embiggen
.. _AnacletoLAB: https://anacletolab.di.unimi.it/ .. _RobinsonLab: https://www.jax.org/research-and-faculty/research-labs/the-robinson-lab/ .. _BPOP: http://www.berkeleybop.org/index.html
.. |license| image:: https://img.shields.io/badge/License-MIT-blue.svg :target: https://opensource.org/licenses/MIT :alt: License
.. |tutorials| image:: https://img.shields.io/badge/Tutorials-Jupyter%20Notebooks-blue.svg :target: https://github.com/AnacletoLAB/grape/tree/main/tutorials :alt: Tutorials
.. |documentation| image:: https://img.shields.io/badge/Documentation-Available%20here-blue.svg :target: https://anacletolab.github.io/grape/index.html :alt: Documentation
.. |python_version| image:: https://img.shields.io/badge/Python-3.7+-blue.svg :target: https://pypi.org/project/embiggen/#history :alt: Supported Python versions
.. |twitter| image:: https://badges.aleen42.com/src/twitter.svg :target: https://twitter.com/grapelib :alt: Twitter
.. |telegram| image:: https://badges.aleen42.com/src/telegram.svg :target: https://t.me/grape_lib :alt: Telegram Group
.. |discord| image:: https://badges.aleen42.com/src/discord.svg :target: https://discord.gg/Nda2cqYvTN :alt: Discord Server
.. |logo| image:: images/grape_logo.png :target: https://github.com/AnacletoLAB/grape :width: 80