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Geo2DR: Library to build distributed representations of graphs

Project description

Geo2DR: A library for learning distributed representations of graphs/manifolds.

Project Status: Active – The project has reached a stable, usable state and is being actively developed. PyPI PyPI - License Documentation Status

Documentation | Paper | PyPI Page

This library consists of various graph factorization and embedding algorithms built around a common framework to enable quick construction of systems capable of learning distributed representations of graphs. This library utilises PyTorch to maximise the utilisation of CUDA enabled GPUs for learning, but will also run efficiently on CPUs if a GPU is not available.

Popular sytems such as Deep Graph Kernels (Yanardag and Vishwanathan, 2015), Graph2Vec (Narayanan et al., 2017), and Anonymous Walk Embeddings (AWE) (Ivanov and Burnaev, 2018) are all methods which learn distributed representations of arbitrary sized graphs. Such systems can be characterised by a common pipeline described below.

  1. Decomposition of graphs into descriptive substructures: Each graph in the dataset of graphs is reduced to a set of induced substructure patterns according to some decomposition algorithm. An example is finding all the rooted subgraphs of a graph using the Weisfeiler-Lehman algorithm (Shervashidze et al., 2011) as done in Graph2Vec, or shortest paths as in Deep Graph Kernels to name a few. The union of the sets of substructure patterns induced in each graph across the dataset defines a common "vocabulary" that can describe a graph in relation to another graph based on the induced subgraphs patterns.
  2. Learning distributed vector representations: The distributive hypothesis (Harris, 1954) posits that words which are used and exist within the same context have similar semantic meanings. In a similar way we may define that a graph is contextualized by the substructure patterns producing a new dataset of (graph, induced_subgraph_pattern) pairs. Embedding methods which exploit the distributive hypothesis such as skipgram (Mikolov et al., 2014) can then be used to learn fixed-size distributed vector embeddings of each substructure pattern or graph in an unsupervised manner.

Once the distributed vector representations are learned for each of the graphs in a dataset. The graph embeddings may be used in any downstream application such as graph classification, regression, etc.

Geo2DR implements a variety of graph decomposition algorithms (such as Weisfeiler-Lehman, anonymous walks, graphlets) and learning models which exploits the distributive hypothesis (such as skipgram with noise contrastive sampling, PV-DM). This enables the quick recreation of existing systems such as Graph2Vec or AWE but also the creation of new combinations leading to new(!) systems capable of learning distributed representations. This enables deeper studies into how we can build better representations of graphs and more reliable comparative analyses on the same codebase.

The following substructure induction algorithms are implemented

  • Weisfeiler-Lehman rooted subgraph decomposition
  • Random walks
  • Anonymous walks
  • Graphlets (currently support graphlets of size 2-8)
  • Shortest paths

The following embedding systems are included

  • Skipgram with negative sampling
  • PV-DBOW with negative sampling
  • PV-DM with negative sampling

The following methods are currently implemented in the examples directory

Care was taken so that modules can act independently. This was done so that users can use their own implementations for decompositions/learning algorithms even with different learning frameworks and implementations to allow more freedom and focus on improving what is important to them.


We recommend following the installation procedure within a virtual environment.

Installing dependencies: PyNauty and Pytorch

Geo2DR has two main dependencies that need to be installed prior to installing Geo2DR.

PyNauty dependencies

To build pynauty the following additional components are needed:

  • Python 3.5
  • The most recent version of Nauty.
  • An ANSI C compiler.

In theory, pynauty should work on all platforms where Python is available and Nauty’s source can be complied. The instructions below are for Linux/Unix environment.

Pynauty installation

Download pynauty’s sources as a compressed tar file and unpack it. That should create a directory like pynauty-X.Y.Z/ containing the source files.

Download the most recent sources of nauty from Nauty. That file should be something like nautyXYZ.tar.gz.

Change to the directory pynauty-X.Y.Z/ replacing X.Y.Z with the actual version of pynauty:

cd pynauty-X.Y.Z

Unpack nautyXYZ.tar.gz inside the pynauty-X.Y.Z/ directory. Create a symbolic link named nauty to nauty’s source directory replacing XYZ with the actual version of Nauty:

ln -s nautyXYZ nauty

To build pynauty use the command:

make pynauty

To install pynauty to the virtual environment call the following in the pynauty folder whilst the virtual environment is activated

make virtenv-ins 

Installing PyTorch

Pytorch is installed based on the available hardware of the machine (GPU or CPU) please follow the appropriate pip installation on the official PyTorch website.

Installing Geo2DR

From Pypi

This installation procedure refers to installation from the python package index. This version is stable but may lack the features included currently in this Github repository.

pip install geometric2dr

From source

Geo2DR can be installed into the virtualenvironment from the source folder to get its latest features. If ones wishes to simply use Geo2DR modules one can use the standard pip source install from the project folder containing

pip install .

If you wish to modify some of the source code in geometric2dr for your own task, you can make a developer install. It is slightly slower, but immediately takes on any changes into the source code.

pip install -e .


  1. Why decompose graphs into different substructure patterns?
  • This is because the useful properties of graphs in different datasets may be better captured using specialised decompositions. There is no one-size fits all. There is no free sandwich. The cake is a lie.
  1. How is this different from other libraries for learning representations of graphs, such as PyTorch Geometric or Spektral?
  • The systems produced here learn distributed representations of graphs. These representations are built by taking the perspective that graphs are composed of discrete substructures which characterise the graph in relation to the patterns found in other graphs of a collection under observation. The distributed vector representations are learned by exploiting the distributive hypothesis. Most of representations of graphs learned using systems such as created in PyTorch Geometric rely on a series of spectral/spatial graph convolutions to create node representations which are pooled in various ways to form graph level representations. The foundation of these algorithms can be found in the message-passing+pooling paradigm whereas our foundation is the distributive hypothesis. Hence this library is different and complementary to other existing libraries, and as far as I am aware this is the first.
  1. Hey my model for learning distributed representations is not implemented in the examples!
  • Thanks for telling us. Given the overloaded excitement in machine learning it is impossible to keep up with all the papers. Please open an issue and we will try to get it implemented as soon as possible. Similarly the intention of this library is to enable creation of existing/novel models quickly. Maybe you could make a pull request and contribute!
  1. Do you accept contributions?
  • Yes contributions are always very welcome. A contributions guideline will be made available in due time, the author is also still learning to navigate open source collaboration on GitHub


If this toolkit or any of the examples of pre-existing methods were useful, please cite the original authors and consider citing the library.

    title={Learning distributed representations of graphs with Geo2DR},
    author={Paul Scherer and Pietro Lio},

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