haiku-geometric 0.0.5

No project description provided

Haiku Geometric

Overview | Installation | Quickstart | Examples | Documentation | License

Overview

Haiku Geometric is a collection of graph neural networks (GNNs) implemented using JAX. It tries to provide object-oriented and easy-to-use modules for GNNs.

Haiku Geometric is built on top of Haiku and Jraph. It is deeply inspired by PyTorch Geometric. In most cases, Haiku Geometric tries to replicate the API of PyTorch Geometric to allow code sharing between the two.

Haiku Geometric is still under development and I would advise against using it in production.

Installation

Haiku Geometric can be installed from source:

pip install git+https://github.com/alexOarga/haiku-geometric.git

Alternatively, you can install Haiku Geometric using pip:

pip install haiku-geometric

Quickstart

For instance, we can create a simple graph convolutional network (GCN) of 2 layers as follows:

import jax
import haiku as hk
from haiku_geometric.nn import GCNConv

class GCN(hk.Module):
    def __init__(self, hidden_channels, out_channels):
        super().__init__()
        self.conv1 = GCNConv(hidden_channels)
        self.conv2 = GCNConv(hidden_channels)
        self.linear = hk.Linear(out_channels)

    def __call__(self, nodes,senders, receivers):
        x = self.conv1(nodes, senders, receivers)
        x = jax.nn.relu(x)
        x = self.conv2(x, senders, receivers)
        x = self.linear(nodes)
        return x

def forward(nodes, senders, receivers):
    gcn = GCN(16, 7)
    return gcn(nodes, senders, receivers)

The GNN that we have defined is a Haiku Module. To convert our module in a function that can be used with JAX, we transform it using hk.transform as described in the Haiku documentation.

model = hk.transform(forward)
model = hk.without_apply_rng(model)
rng = jax.random.PRNGKey(42)
params = model.init(rng, nodes=nodes, senders=senders, receivers=receivers)

We can now run a forward pass on the model:

output = model.apply(params=params, nodes=nodes, senders=senders, receivers=receivers)

Documentation

The documentation for Haiku Geometric can be found here.

Examples

Haiku Geometric comes with a few examples that showcase the usage of the library. The following examples are available:

	Link
Quickstart Example
Graph Convolution Networks with Karate Club dataset
Graph Attention Networks with CORA dataset
TopKPooling and GraphConv with PROTEINS dataset

Implemented GNNs modules

Currently, Haiku Geometric includes the following GNN modules:

Model	Description
GCNConv	Graph convolution layer from the Semi-Supervised Classification with Graph Convolutional Networks paper.
GATConv	Graph attention layer from the Graph Attention Networks paper.
SAGEConv	Graph convolution layer from the Inductive Representation Learning on Large Graphs paper.
GINConv	Graph isomorphism network layer from the How Powerful are Graph Neural Networks? paper.
GINEConv	Graph isomorphism network layer from the Strategies for Pre-training Graph Neural Networks paper.
GraphConv	Graph convolution layer from the Weisfeiler and Leman Go Neural: Higher-order Graph Neural Networks paper.
GeneralConv	A general GNN layer adapted from the Design Space for Graph Neural Networks paper.
GatedGraphConv	Graph convolution layer from the Gated Graph Sequence Neural Networks paper.
EdgeConv	Edge convolution layer from the Dynamic Graph CNN for Learning on Point Clouds paper.
PNAConv	Propagation Network layer from the Principal Neighbourhood Aggregation for Graph Nets paper.
MetaLayer	Meta layer from the Relational Inductive Biases, Deep Learning, and Graph Networks paper.
GPSLayer	Graph layer from the Recipe for a General, Powerful, Scalable Graph Transformer paper.

Implemented positional encodings

The following positional encodings are currently available:

Model	Description
LaplacianEncoder	Laplacian positional encoding from the Rethinking Graph Transformers with Spectral Attention paper.
MagLaplacianEncoder	Magnetic Laplacian positional encoding from the Transformers Meet Directed Graphs paper.

Issues

If you encounter any issue, please open an issue.

Running tests

Haiku Geometric can be tested using pytest by running the following command:

python -m pytest test/

License