Distance Encoding for GNN Design

Overview

Distance-encoding for GNN design

This repository is the official PyTorch implementation of the DEGNN and DEAGNN framework reported in the paper:
Distance-Encoding -- Design Provably More PowerfulGNNs for Structural Representation Learning, to appear in NeurIPS 2020.

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 emailed 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-geometric

The latest tested combination is: Python 3.8.2 + Pytorch 1.4.0 + torch-geometric 1.5.0.

Quick Start

python main.py --dataset celegans --feature sp --hidden_features 100 --prop_depth 1 --test_ratio 0.1 --epoch 300

    This uses 100-dimensional hidden features, 80/10/10 split of train/val/test set, and trains for 300 epochs.

  • 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 --l2 1e-3 --test_ratio 0.1 --seed 9

    This 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 0.1

Note that here the test_ratio currently contains both validation set and the actual test set, and will be changed to contain only 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.log for 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:

@article{li2020distance,
  title={Distance Encoding: Design Provably More Powerful Neural Networks for Graph Representation Learning},
  author={Li, Pan and Wang, Yanbang and Wang, Hongwei and Leskovec, Jure},
  journal={Advances in Neural Information Processing Systems},
  volume={33},
  year={2020}
}
OCTIS: Comparing Topic Models is Simple! A python package to optimize and evaluate topic models (accepted at EACL2021 demo track)

OCTIS : Optimizing and Comparing Topic Models is Simple! OCTIS (Optimizing and Comparing Topic models Is Simple) aims at training, analyzing and compa

MIND 478 Jan 01, 2023
RETRO-pytorch - Implementation of RETRO, Deepmind's Retrieval based Attention net, in Pytorch

RETRO - Pytorch (wip) Implementation of RETRO, Deepmind's Retrieval based Attent

Phil Wang 556 Jan 04, 2023
The open-source and free to use Python package miseval was developed to establish a standardized medical image segmentation evaluation procedure

miseval: a metric library for Medical Image Segmentation EVALuation The open-source and free to use Python package miseval was developed to establish

59 Dec 10, 2022
A module that used for encrypt code which includes RSA and AES

软件加密模块 requirement: Crypto,pycryptodome,pyqt5 本地加密信息为随机字符串 使用说明 命令行参数 -h 帮助 -checkWorking 检查是否能正常工作,后接1确认指令 -checkEndDate 检查截至日期,后接1确认指令 -activateCode

2 Sep 27, 2022
Streaming over lightweight data transformations

Description Data augmentation libarary for Deep Learning, which supports images, segmentation masks, labels and keypoints. Furthermore, SOLT is fast a

Research Unit of Medical Imaging, Physics and Technology 256 Jan 08, 2023
FusionNet: A deep fully residual convolutional neural network for image segmentation in connectomics

FusionNet_Pytorch FusionNet: A deep fully residual convolutional neural network for image segmentation in connectomics Requirements Pytorch 0.1.11 Pyt

Choi Gunho 102 Dec 13, 2022
An Efficient Training Approach for Very Large Scale Face Recognition or F²C for simplicity.

Fast Face Classification (F²C) This is the code of our paper An Efficient Training Approach for Very Large Scale Face Recognition or F²C for simplicit

33 Jun 27, 2021
The official repository for paper ''Domain Generalization for Vision-based Driving Trajectory Generation'' submitted to ICRA 2022

DG-TrajGen The official repository for paper ''Domain Generalization for Vision-based Driving Trajectory Generation'' submitted to ICRA 2022. Our Meth

Wang 25 Sep 26, 2022
Learning to Estimate Hidden Motions with Global Motion Aggregation

Learning to Estimate Hidden Motions with Global Motion Aggregation (GMA) This repository contains the source code for our paper: Learning to Estimate

Shihao Jiang (Zac) 221 Dec 18, 2022
《K-Adapter: Infusing Knowledge into Pre-Trained Models with Adapters》(2020)

K-Adapter: Infusing Knowledge into Pre-Trained Models with Adapters This repository is the implementation of the paper "K-Adapter: Infusing Knowledge

Microsoft 118 Dec 13, 2022
Open-source Monocular Python HawkEye for Tennis

Tennis Tracking 🎾 Objectives Track the ball Detect court lines Detect the players To track the ball we used TrackNet - deep learning network for trac

ArtLabs 188 Jan 08, 2023
Custom IMDB Dataset is extracted between 2020-2021 and custom distilBERT model is trained for movie success probability prediction

IMDB Success Predictor Project involves Web Scraping custom IMDB data between 2020 and 2021 of 10000 movies and shows sorted by number of votes ,fine

Gautam Diwan 1 Jan 18, 2022
Code for technical report "An Improved Baseline for Sentence-level Relation Extraction".

RE_improved_baseline Code for technical report "An Improved Baseline for Sentence-level Relation Extraction". Requirements torch = 1.8.1 transformers

Wenxuan Zhou 74 Nov 29, 2022
Revisiting Contrastive Methods for Unsupervised Learning of Visual Representations. [2021]

Revisiting Contrastive Methods for Unsupervised Learning of Visual Representations This repo contains the Pytorch implementation of our paper: Revisit

Wouter Van Gansbeke 80 Nov 20, 2022
git《USD-Seg:Learning Universal Shape Dictionary for Realtime Instance Segmentation》(2020) GitHub: [fig2]

USD-Seg This project is an implement of paper USD-Seg:Learning Universal Shape Dictionary for Realtime Instance Segmentation, based on FCOS detector f

Ruolin Ye 80 Nov 28, 2022
A medical imaging framework for Pytorch

Welcome to MedicalTorch MedicalTorch is an open-source framework for PyTorch, implementing an extensive set of loaders, pre-processors and datasets fo

Christian S. Perone 799 Jan 03, 2023
A supplementary code for Editable Neural Networks, an ICLR 2020 submission.

Editable neural networks A supplementary code for Editable Neural Networks, an ICLR 2020 submission by Anton Sinitsin, Vsevolod Plokhotnyuk, Dmitry Py

Anton Sinitsin 32 Nov 29, 2022
Implementation of 🦩 Flamingo, state-of-the-art few-shot visual question answering attention net out of Deepmind, in Pytorch

🦩 Flamingo - Pytorch Implementation of Flamingo, state-of-the-art few-shot visual question answering attention net, in Pytorch. It will include the p

Phil Wang 630 Dec 28, 2022
Distributed Asynchronous Hyperparameter Optimization better than HyperOpt.

UltraOpt : Distributed Asynchronous Hyperparameter Optimization better than HyperOpt. UltraOpt is a simple and efficient library to minimize expensive

98 Aug 16, 2022