HGP-SL

Hierarchical Graph Pooling with Structure Learning (Preprint version is available on arXiv).

This is a PyTorch implementation of the HGP-SL algorithm, which learns a low-dimensional representation for the entire graph. Specifically, the graph pooling operation utilizes node features and graph structure information to perform down-sampling on graphs. Then, a structure learning layer is stacked on the pooling operation, which aims to learn a refined graph structure that can best preserve the essential topological information.

Requirements

• python3.6
• pytorch==1.3.0
• torch-scatter==1.4.0
• torch-sparse==0.4.3
• torch-cluster==1.4.5
• torch-geometric==1.3.2

Note: An older version of torch-sparse is needed, lower than 0.4.4. This code repository is heavily built on pytorch_geometric, which is a Geometric Deep Learning Extension Library for PyTorch. Please refer here for how to install and utilize the library.

Datasets

Graph classification benchmarks are publicly available at here.

This folder contains the following comma separated text files (replace DS by the name of the dataset):

n = total number of nodes

m = total number of edges

N = number of graphs

(1) DS_A.txt (m lines)

sparse (block diagonal) adjacency matrix for all graphs, each line corresponds to (row, col) resp. (node_id, node_id)

(2) DS_graph_indicator.txt (n lines)

column vector of graph identifiers for all nodes of all graphs, the value in the i-th line is the graph_id of the node with node_id i

(3) DS_graph_labels.txt (N lines)

class labels for all graphs in the dataset, the value in the i-th line is the class label of the graph with graph_id i

(4) DS_node_labels.txt (n lines)

column vector of node labels, the value in the i-th line corresponds to the node with node_id i

There are OPTIONAL files if the respective information is available:

(5) DS_edge_labels.txt (m lines; same size as DS_A_sparse.txt)

labels for the edges in DS_A_sparse.txt

(6) DS_edge_attributes.txt (m lines; same size as DS_A.txt)

attributes for the edges in DS_A.txt

(7) DS_node_attributes.txt (n lines)

matrix of node attributes, the comma seperated values in the i-th line is the attribute vector of the node with node_id i

(8) DS_graph_attributes.txt (N lines)

regression values for all graphs in the dataset, the value in the i-th line is the attribute of the graph with graph_id i

Run

To run HGP-SL, just execute the following command for graph classification task:

python main.py

Parameter Settings

Datasets	lr	weight_decay	batch_size	pool_ratio	dropout	net_layers
PROTEINS	0.001	0.001	512	0.5	0.0	3
Mutagenicity	0.001	0.001	512	0.8	0.0	3
NCI109	0.001	0.001	512	0.8	0.0	3
NCI1	0.001	0.001	512	0.8	0.0	3
DD	0.0001	0.001	64	0.3	0.5	2
ENZYMES	0.001	0.001	128	0.8	0.0	2

Citing

If you find HGP-SL useful for your research, please consider citing the following paper:

@article{zhang2019hierarchical,
  title={Hierarchical Graph Pooling with Structure Learning},
  author={Zhang, Zhen and Bu, Jiajun and Ester, Martin and Zhang, Jianfeng and Yao, Chengwei and Yu, Zhi and Wang, Can},
  journal={arXiv preprint arXiv:1911.05954},
  year={2019}
}