PyTorch-Geometric Implementation of MarkovGNN: Graph Neural Networks on Markov Diffusion

Overview

MarkovGNN

This is the official PyTorch-Geometric implementation of MarkovGNN paper under the title "MarkovGNN: Graph Neural Networks on Markov Diffusion". This method uses different markov graphs in different layers of the GNN.

PDF is available in arXiv

System requirements

Users will need to install the following tools (CPU version).

PyTorch: 1.7.0
PyTorch-Geometric: 1.6.1
PyTorchSparse: 0.6.8
PyTorch Scatter: 2.0.5
PyTorch Cluster: 1.5.8
PyTorch Spline Conv: 1.2.0
NetworkX: 2.2
scikit-learn: 0.23.2
Matplotlib: 3.0.3

How to run

To use random seed disable the seed-fixing portion in the main.py file. A list of sample commands to run the MarkovGCN models.

python main.py --edgelist datasets/input2f/email.edgelist --label datasets/input2f/email.nodes.labels --eps 0.26 --epoch 200 --alpha 0.1 --nlayers 3 --lrate 0.01 --droprate 0.3 --markov_agg

python main.py --edgelist datasets/input2f/usaairports.edgelist --label datasets/input2f/usaairports.nodes.labels --oneindexed 1 --epoch 200 --alpha 1.0 --eps 0.09 --lrate 0.01 --nlayers 4 --normrow 0 --inflate 1.5 --markov_agg

python main.py --edgelist datasets/input2f/yeast.edgelist --label datasets/input2f/yeast.nodes.labels --oneindexed 1 --onelabeled 1 --eps 0.75 --epoch 200 --inflate 1.7 --lrate 0.01 --alpha 0.8 --droprate 0.1 --nlayers 3 

python main.py --edgelist datasets/input3f/squirrel_edges.txt --label datasets/input3f/squirrel_labels.txt --feature datasets/input3f/squirrel_features.txt --epoch 200 --eps 0.05 --droprate 0.25 --markov_agg --nlayers 6 --markov_agg

python main.py --edgelist datasets/input3f/chameleon_edges.txt --label datasets/input3f/chameleon_labels.txt --feature datasets/input3f/chameleon_features.txt --epoch 200 --alpha 0.8 --nlayers 3 --eps 0.2 --inflate 1.5 --droprate 0.5 --markov_agg

python main.py --edgelist datasets/input3f/chameleon_edges.txt --label datasets/input3f/chameleon_labels.txt --feature datasets/input3f/chameleon_features.txt --epoch 200 --alpha 0.2 --nlayers 2 --eps 0.06 --inflate 1.8 --droprate 0.7 --markov_agg

python main.py --eps 0.03 --droprate 0.85 --epoch 300 --alpha 0.05 --nlayers 2 --lrate 0.005 --inflate 1.8 --markov_agg

python main.py --eps 0.03 --droprate 0.85 --epoch 300 --alpha 0.05 --nlayers 2 --lrate 0.001 --inflate 3.5 --markov_agg --dataset Citeseer

python main.py --edgelist datasets/input3f/actor_edges.txt --label datasets/input3f/actor_labels.txt --feature datasets/input3f/actor_features.txt --epoch 200  --alpha 0.4 --markov_agg --nlayers 4

python main.py --edgelist datasets/input3f/actor_edges.txt --label datasets/input3f/actor_labels.txt --feature datasets/input3f/actor_features.txt --epoch 200  --alpha 0.2 --markov_agg --nlayers 3 --eps 0.3

To compare the results with respect to vanilla GCN, use the argument --use_gcn in the command line.

Parameters

There are several options to run the method which are outlined in the main.py file.

--markov_dense -> markov process uses dense matrix multiplication (sparse matrix multiplicaiton is the default option)
--markov_agg -> i-th layer uses a markov matrix from i-th iteration, this option with higher threshold will produce better runtime
--use_gcn -> run the vanilla GCN model.
  e.g., $ python main.py --edgelist datasets/input3f/actor_edges.txt --label datasets/input3f/actor_labels.txt --feature datasets/input3f/actor_features.txt --epoch 200  --use_gcn

Citation

If you find this repository helpful, please cite the following paper:

@article{rahman2022markovgnn,
  title={{MarkovGNN: Graph} Neural Networks on Markov Diffusion},
  author={Rahman, Md. Khaledur and Agrawal, Abhigya and Azad, Ariful},
  booktitle={arXiv preprint arXiv:2202.02470},
  year={2022}
}

Contact

Please create an issue if you face any problem to run this method. Don't hesitate to contact the following person if you have any questions: Md. Khaledur Rahman ([email protected]).

Owner
HipGraph: High-Performance Graph Analytics and Learning
HipGraph: High-Performance Graph Analytics and Learning
Official implementation of "Membership Inference Attacks Against Self-supervised Speech Models"

Introduction Official implementation of "Membership Inference Attacks Against Self-supervised Speech Models". In this work, we demonstrate that existi

Wei-Cheng Tseng 7 Nov 01, 2022
An end-to-end machine learning library to directly optimize AUC loss

LibAUC An end-to-end machine learning library for AUC optimization. Why LibAUC? Deep AUC Maximization (DAM) is a paradigm for learning a deep neural n

Andrew 75 Dec 12, 2022
Informer: Beyond Efficient Transformer for Long Sequence Time-Series Forecasting

Informer: Beyond Efficient Transformer for Long Sequence Time-Series Forecasting This is the origin Pytorch implementation of Informer in the followin

Haoyi 3.1k Dec 29, 2022
Model Quantization Benchmark

Introduction MQBench is an open-source model quantization toolkit based on PyTorch fx. The envision of MQBench is to provide: SOTA Algorithms. With MQ

500 Jan 06, 2023
Pose estimation with MoveNet Lightning

Pose Estimation With MoveNet Lightning MoveNet is the TensorFlow pre-trained model that identifies 17 different key points of the human body. It is th

Yash Vora 2 Jan 04, 2022
ChineseBERT: Chinese Pretraining Enhanced by Glyph and Pinyin Information

ChineseBERT: Chinese Pretraining Enhanced by Glyph and Pinyin Information This repository contains code, model, dataset for ChineseBERT at ACL2021. Ch

413 Dec 01, 2022
Kindle is an easy model build package for PyTorch.

Kindle is an easy model build package for PyTorch. Building a deep learning model became so simple that almost all model can be made by copy and paste from other existing model codes. So why code? wh

Jongkuk Lim 77 Nov 11, 2022
Code for the SIGGRAPH 2021 paper "Consistent Depth of Moving Objects in Video".

Consistent Depth of Moving Objects in Video This repository contains training code for the SIGGRAPH 2021 paper "Consistent Depth of Moving Objects in

Google 203 Jan 05, 2023
Learning-Augmented Dynamic Power Management

Learning-Augmented Dynamic Power Management This repository contains source code accompanying paper Learning-Augmented Dynamic Power Management with M

Adam 0 Feb 22, 2022
TensorFlow implementation of "A Simple Baseline for Bayesian Uncertainty in Deep Learning"

TensorFlow implementation of "A Simple Baseline for Bayesian Uncertainty in Deep Learning"

YeongHyeon Park 7 Aug 28, 2022
A benchmark for the task of translation suggestion

WeTS: A Benchmark for Translation Suggestion Translation Suggestion (TS), which provides alternatives for specific words or phrases given the entire d

zhyang 55 Dec 24, 2022
An open-source Deep Learning Engine for Healthcare that aims to treat & prevent major diseases

AlphaCare Background AlphaCare is a work-in-progress, open-source Deep Learning Engine for Healthcare that aims to treat and prevent major diseases. T

Siraj Raval 44 Nov 05, 2022
Official code for the publication "HyFactor: Hydrogen-count labelled graph-based defactorization Autoencoder".

HyFactor Graph-based architectures are becoming increasingly popular as a tool for structure generation. Here, we introduce a novel open-source archit

Laboratoire-de-Chemoinformatique 11 Oct 10, 2022
Semi-supervised Stance Detection of Tweets Via Distant Network Supervision

SANDS This is an annonymous repository containing code and data necessary to reproduce the results published in "Semi-supervised Stance Detection of T

2 Sep 22, 2022
Official implementation of the paper Chunked Autoregressive GAN for Conditional Waveform Synthesis

PyEmits, a python package for easy manipulation in time-series data. Time-series data is very common in real life. Engineering FSI industry (Financial

Descript 150 Dec 06, 2022
Codes for "CSDI: Conditional Score-based Diffusion Models for Probabilistic Time Series Imputation"

CSDI This is the github repository for the NeurIPS 2021 paper "CSDI: Conditional Score-based Diffusion Models for Probabilistic Time Series Imputation

106 Jan 04, 2023
Vertical Federated Principal Component Analysis and Its Kernel Extension on Feature-wise Distributed Data based on Pytorch Framework

VFedPCA+VFedAKPCA This is the official source code for the Paper: Vertical Federated Principal Component Analysis and Its Kernel Extension on Feature-

John 9 Sep 18, 2022
Human annotated noisy labels for CIFAR-10 and CIFAR-100.

Dataloader for CIFAR-N CIFAR-10N noise_label = torch.load('./data/CIFAR-10_human.pt') clean_label = noise_label['clean_label'] worst_label = noise_lab

<a href=[email protected]"> 117 Nov 30, 2022
Gas detection for Raspberry Pi using ADS1x15 and MQ-2 sensors

Gas detection Gas detection for Raspberry Pi using ADS1x15 and MQ-2 sensors. Description The MQ-2 sensor can detect multiple gases (CO, H2, CH4, LPG,

Filip Š 15 Sep 30, 2022
[ICCV 2021] Released code for Causal Attention for Unbiased Visual Recognition

CaaM This repo contains the codes of training our CaaM on NICO/ImageNet9 dataset. Due to my recent limited bandwidth, this codebase is still messy, wh

Wang Tan 66 Dec 31, 2022