TensorFlow 2 implementation of Deep Graph Convolutional Neural Networks.
Project description
DGCNN [TensorFlow]
TensorFlow 2 implementation of An endtoend deep learning architecture for graph classification based on work by M. Zhang et al., 2018.
Moreover, we offer an attention based modification of the above by utilising graph attention (Veličković et al., 2017) to learn edge weights.
Installation
Simply run pip install dgcnn
. The only dependency is tensorflow>=2.0.0
.
Usage
The core data structure is the graph signal. If we have N nodes in a graph each having C observed features then the graph signal is the tensor with shape (batch, N, C) corresponding to the data produced by all nodes. Often we have sequences of graph signals in a time series. We will call them temporal graph signals and assume a shape of (batch, time steps, N, C). For each graph signal we also need to have the corresponding adjacency matrices of shape (batch, N, N) or (batch, timesteps, N, N) for temporal and nontemporal data, respectively. While DGCNNs can operate on graphs with different nodecounts, C should always be the same and each batch should only contain graphs with the same number of nodes.
The DeepGraphConvolution
Layer
This adaptable layer contains the whole DGCNN architecture and operates on both temporal and nontemporal data. It takes the graph signals and their corresponding adjacency matrices and performs the following steps (as described in the paper):
We initialize the layer by providing . The layer has many optional parameters that are described in the table below.

It iteratively applies
GraphConvolution
layers h times with variable hidden feature dimensions . 
After that, it concatenates all the outputs of the graph convolutions into one tensor which has the shape (..., N, ).

Finally it applies
SortPooling
as described in the paper to obtain the output tensor of shape (..., k, ).
Import this layer with from gdcnn.components import DeepGraphConvolution
.
Initiated it with the following parameters:
Parameter  Function 

hidden_conv_units (required) 
List of the hidden feature dimensions used in the graph convolutions. in the paper. 
k (required) 
Number of nodes to be kept after SortPooling. 
flatten_signals (default: False) 
If True , flattens the last 2 dimensions of the output tensor into 1 
attention_heads (default: None) 
If given, then instead of using as the transition matrix inside the graph convolutions, we will use an attention based transition matrix. Utilizing dgcnn.attention.AttentionMechanism as the internal attention mechanism. This sets the number of attention heads used. 
attention_units (default: None) 
Also needs to be provided if attention_heads is set. This is the size of the internal embedding used by the attention mechanism. 
use_sortpooling (default: True) 
Whether or not to apply sortpooling at the end of the procedure. If False, we will simply return the concatinated graph convolution outputs. 
Thus, if we have nontemporal graph signals with 10 nodes and 5 features each and we would like to apply a DGCNN containing 3 graph convolutions with hidden feature dimensions of 10, 5 and 2 and SortPooling that keeps the 5 most relevant nodes. Then we would run
from dgcnn.components import DeepGraphConvolution from tensorflow.keras.layers import Input from tensorflow.keras import Model # generating random graph signals as test data graph_signal = np.random.normal(size=(100, 10, 5) # corresponding fully connected adjacency matrices adjacency = np.ones((100, 10, 10)) # inputs to the DGCNN X = Input(shape=(10, 5), name="graph_signal") E = Input(shape=(10, 10), name="adjacency") # DGCNN # Note that we pass the signals and adjacencies as a tuple. # The graph signal always goes first! output = DeepGraphConvolution([10, 5, 2], k=5 )((X, E)) # defining model model = Model(inputs=[X, E], outputs=output)
Further layers and features
The documentation contains information on how to use the internal SortPooling
, GraphConvolution
and AttentionMechanism
layers and also describes more optional parameters like regularisers, initialisers and constrains that can be used.
Contribute
Bug reports, fixes and additional features are always welcome! Make sure to run the tests with python setup.py test
and write your own for new features. Thanks.
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