Distance-encoding for GNN design
This repository is the official PyTorch implementation of the DEGNN and DEAGN framework reported in the paper:
Distance-Encoding -- Design Provably More PowerfulGNNs for Structural Representation Learning
The project's home page is: http://snap.stanford.edu/distance-encoding/
Authors & Contact
Pan Li, Yanbang Wang, Hongwei Wang, Jure Leskovec
Questions on this repo can be directed to [email protected] (Yanbang Wang)
Installation
Requirements: Python >= 3.5, Anaconda3
- Update conda:
conda update -n base -c defaults conda- Install basic dependencies to virtual environment and activate it:
conda env create -f environment.yml
conda activate degnn-env- Install PyTorch >= 1.4.0 and torch-geometric >= 1.5.0 (please refer to the PyTorch and PyTorch Geometric official websites for more details). Commands examples are:
conda install pytorch=1.4.0 torchvision cudatoolkit=10.1 -c pytorch
pip install torch-scatter==latest+cu101 -f https://pytorch-geometric.com/whl/torch-1.4.0.html
pip install torch-sparse==latest+cu101 -f https://pytorch-geometric.com/whl/torch-1.4.0.html
pip install torch-cluster==latest+cu101 -f https://pytorch-geometric.com/whl/torch-1.4.0.html
pip install torch-spline-conv==latest+cu101 -f https://pytorch-geometric.com/whl/torch-1.4.0.html
pip install torch-geometricThe latest tested combination is: Python 3.8.2 + Pytorch 1.4.0 + torch-geometric 1.5.0.
Quick Start
- To train DEGNN-SPD Task 2 (link prediction) on C.elegans dataset:
python main.py --dataset celegans --feature sp --hidden_features 100 --prop_depth 1 --test_ratio 0.1 --epoch 300This uses 100-dimensional hidden features, 80/10/10 split of train/val/test set, trains for 300 epochs, and perform distance encoding using multiple cpu cores.
- To train DEAGNN-SPD for Task 3 (node-triads prediction) on C.elegans dataset:
python main.py --dataset celegans_tri --hidden_features 100 --prop_depth 2 --epoch 300 --feature sp --max_sp 5 --test_ratio 0.1 --seed 9This enables 2-hop propagation per layer, truncates distance encoding at 5, and uses random seed 9.
- To train DEGNN-LP (i.e. the random walk variant) for Task 1 (node-level prediction) on usa-airports using average accuracy as evaluation metric:
python main.py --dataset usa-airports --metric acc --hidden_features 100 --feature rw --rw_depth 2 --epoch 500 --bs 128 --test_ratio 0.1Note that here the test_ratio consists of validation set and the actual test set.
- To generate Figure2 LEFT of the paper (Simulation to validate Theorem 3.3):
python main.py --dataset simulation --max_sp 10 The result will be plot to ./simulation_results.png.
- All detailed training logs can be found at
<log_dir>/<dataset>/<training-time>.log. A one-line summary will also be appended to<log_dir>/result_summary.logfor each training instance.
Usage Summary
Interface for DE-GNN framework [-h] [--dataset DATASET] [--test_ratio TEST_RATIO]
[--model {DE-GNN,GIN,GCN,GraphSAGE,GAT}] [--layers LAYERS]
[--hidden_features HIDDEN_FEATURES] [--metric {acc,auc}] [--seed SEED] [--gpu GPU]
[--data_usage DATA_USAGE] [--directed DIRECTED] [--parallel] [--prop_depth PROP_DEPTH]
[--use_degree USE_DEGREE] [--use_attributes USE_ATTRIBUTES] [--feature FEATURE]
[--rw_depth RW_DEPTH] [--max_sp MAX_SP] [--epoch EPOCH] [--bs BS] [--lr LR]
[--optimizer OPTIMIZER] [--l2 L2] [--dropout DROPOUT] [--k K] [--n [N [N ...]]]
[--N N] [--T T] [--log_dir LOG_DIR] [--summary_file SUMMARY_FILE] [--debug]
Optinal Arguments
-h, --help show this help message and exit
# general settings
--dataset DATASET dataset name
--test_ratio TEST_RATIO
ratio of the test against whole
--model {DE-GCN,GIN,GAT,GCN,GraphSAGE}
model to use
--layers LAYERS largest number of layers
--hidden_features HIDDEN_FEATURES
hidden dimension
--metric {acc,auc} metric for evaluating performance
--seed SEED seed to initialize all the random modules
--gpu GPU gpu id
--adj_norm {asym,sym,None}
how to normalize adj
--data_usage DATA_USAGE
use partial dataset
--directed DIRECTED (Currently unavailable) whether to treat the graph as directed
--parallel (Currently unavailable) whether to use multi cpu cores to prepare data
# positional encoding settings
--prop_depth PROP_DEPTH
propagation depth (number of hops) for one layer
--use_degree USE_DEGREE
whether to use node degree as the initial feature
--use_attributes USE_ATTRIBUTES
whether to use node attributes as the initial feature
--feature FEATURE distance encoding category: shortest path or random walk (landing probabilities)
--rw_depth RW_DEPTH random walk steps
--max_sp MAX_SP maximum distance to be encoded for shortest path feature
# training settings
--epoch EPOCH number of epochs to train
--bs BS minibatch size
--lr LR learning rate
--optimizer OPTIMIZER
optimizer to use
--l2 L2 l2 regularization weight
--dropout DROPOUT dropout rate
# imulation settings (valid only when dataset == 'simulation')
--k K node degree (k) or synthetic k-regular graph
--n [N [N ...]] a list of number of nodes in each connected k-regular subgraph
--N N total number of nodes in simultation
--T T largest number of layers to be tested
# logging
--log_dir LOG_DIR log directory
--summary_file SUMMARY_FILE
brief summary of training result
--debug whether to use debug mode
Reference
If you make use of the code/experiment of Distance-encoding in your work, please cite our paper:
@misc{li2020distance,
title={Distance Encoding -- Design Provably More Powerful GNNs for Structural Representation Learning},
author={Pan Li and Yanbang Wang and Hongwei Wang and Jure Leskovec},
year={2020},
eprint={2009.00142},
archivePrefix={arXiv},
primaryClass={cs.LG}
}
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