Repository for 'Probabilistic Graph Transformers Are Universal Feature Maps Capable of Representing any Finite Dataset' (paper)

These codes were used to generate illustrations of the paper.

The problem of representing a finite dataset equipped with a dissimilarity metric using a trainable feature map is one of the basic questions in machine learning. A hallmark of deep learning models is the capacity of a model’s hidden layers to efficiently encode discrete Euclidean data into low- dimensional Euclidean feature spaces, from which their last layer can readout predictions. How- ever, when the finite dataset is not Euclidean, it has been empirically confirmed that representations in non-Euclidean spaces systematically outperform traditional Euclidean feature representations. In this paper, we prove that given any n-point metric space X there exists a probabilistic graph transformer (PGT) which can bi-α-Hölder embed X into univariate Gaussian mixtures MG(R) of Delon and Desolneux (2020) with small distortion to X ’s metric for any α ∈ (1/2, 1). Moreover, this PGT’s depth and width are approximately linear in n. We then show that, for any “distortion level” D > 2, there is a PGT which can represent X in MG(R) such that any uniformly sam- pled pair of points in X are bi-Lipschitz embedded with distortion at-most D2, with probability O(n^{−4e/D} ). We show that if X has a suitable geometric prior (e.g. X is a combinatorial tree or a finite subspace of a suitable Riemann manifold), then the PGT architecture can deterministically bi-Lipschitz embed X into MG(R) with low metric distortion. As applications, we consider PGT embeddings of 2-Hop combinatorial graphs (such as friendship graphs, cocktail graphs, complete bipartite, etc...), trees, and n-point subsets of Riemannian manifolds.

All experiments have been conducted using Python 3 using mainly Pytorch and Numpy librairies. We also requieres an optimal transport library. To that end, we use the fast implementation provided in geomloss.

Finally, one need the following libraries:

• numpy
• torch
• geomloss
• time

For the experiment about the n-dimensional sphere, we also use:

• faiss
• cupy

For visualization:

• plotly (3D plots)
• networkx (graph plots)
• matplotlib
• icosphere

Reproduce the illustartions of paragraph 4.1, "Embedding of metric tree". We first need to train the three different embeddings.

To train the neural network to embed into Euclidean space, run the following script:

python Tree_Euclidean.py

To train the neural network to embed into Hyperbolic space (single Gaussian measure), run the following script:

python Tree_Hyperbolic.py

To train the neural network to embed into the space of Gaussian mixtures, run the following script:

python Tree_MG.py

Finally, to combine all the results and generates the figures, use the folloying commad:

python Tree_compare.py

Reproduce the illustartions of paragraph 4.2, "Embedding a random graph: what parameters matter?".

Run the following bash script to train the Probabilistic Graph Transformers with the different number of mixtures. The same network is trained for 8 different seed parameters, on at most 4 GPUS.

bash batch_RandomTree_mixtures.sh

Run the following command to generate the figures based on the previously trained networks. The figure is obtained by averaging the results of 8 different trainning with different seed parameters.

python RandomTree_mixtures.py

Run the following bash script to train the Probabilistic Graph Transformers with the different parameters. The same network is trained for 8 different seed parameters, on at most 4 GPUS.

bash batch_RandomTree_anchors.sh

Run the following command to generate the figures based on the previously trained networks. The figure is obtained by averaging the results of 8 different trainning with different seed parameters.

python RandomTree_anchors.py

We first train a neural network to embed points from the n-dimensional sphere to the Euclidean space. The same network is trained for 8 different seed parameters, on at most 4 GPUS.

bash batch_Sphere_Euclidean.sh

We also train our Probabilistic Graph Transformer to embed the n-dimensional sphere into the space of Gaussian mixtures. This is done on several GPUS (if several available) using the commad:

bash batch_Sphere_MG.sh

Finally, we display and compare results by calling the following python script:

python Sphere_dimension_compare.py