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
The implementation of DeBERTa

DeBERTa: Decoding-enhanced BERT with Disentangled Attention This repository is the official implementation of DeBERTa: Decoding-enhanced BERT with Dis

Microsoft 1.2k Jan 06, 2023
This repository contains the code for the paper ``Identifiable VAEs via Sparse Decoding''.

Sparse VAE This repository contains the code for the paper ``Identifiable VAEs via Sparse Decoding''. Data Sources The datasets used in this paper wer

Gemma Moran 17 Dec 12, 2022
Super Pix Adv - Offical implemention of Robust Superpixel-Guided Attentional Adversarial Attack (CVPR2020)

Super_Pix_Adv Offical implemention of Robust Superpixel-Guided Attentional Adver

DLight 8 Oct 26, 2022
Implementation of the Swin Transformer in PyTorch.

Swin Transformer - PyTorch Implementation of the Swin Transformer architecture. This paper presents a new vision Transformer, called Swin Transformer,

597 Jan 03, 2023
免费获取http代理并生成proxifier配置文件

freeproxy 免费获取http代理并生成proxifier配置文件 公众号:台下言书 工具说明:https://mp.weixin.qq.com/s?__biz=MzIyNDkwNjQ5Ng==&mid=2247484425&idx=1&sn=56ccbe130822aa35038095317

说书人 32 Mar 25, 2022
A general 3D Object Detection codebase in PyTorch.

Det3D is the first 3D Object Detection toolbox which provides off the box implementations of many 3D object detection algorithms such as PointPillars, SECOND, PIXOR, etc, as well as state-of-the-art

Benjin Zhu 1.4k Jan 05, 2023
IDA file loader for UF2, created for the DEFCON 29 hardware badge

UF2 Loader for IDA The DEFCON 29 badge uses the UF2 bootloader, which conveniently allows you to dump and flash the firmware over USB as a mass storag

Kevin Colley 6 Feb 08, 2022
Neural Turing Machine (NTM) & Differentiable Neural Computer (DNC) with pytorch & visdom

Neural Turing Machine (NTM) & Differentiable Neural Computer (DNC) with pytorch & visdom Sample on-line plotting while training(avg loss)/testing(writ

Jingwei Zhang 269 Nov 15, 2022
A repository for the paper "Improved Adversarial Systems for 3D Object Generation and Reconstruction".

Improved Adversarial Systems for 3D Object Generation and Reconstruction: This is a repository for the paper "Improved Adversarial Systems for 3D Obje

Edward Smith 188 Dec 25, 2022
FCA: Learning a 3D Full-coverage Vehicle Camouflage for Multi-view Physical Adversarial Attack

FCA: Learning a 3D Full-coverage Vehicle Camouflage for Multi-view Physical Adversarial Attack Case study of the FCA. The code can be find in FCA. Cas

IDRL 21 Dec 15, 2022
PyTorch implementation of SCAFFOLD (Stochastic Controlled Averaging for Federated Learning, ICML 2020).

Scaffold-Federated-Learning PyTorch implementation of SCAFFOLD (Stochastic Controlled Averaging for Federated Learning, ICML 2020). Environment numpy=

KI 30 Dec 29, 2022
Implementation of 'X-Linear Attention Networks for Image Captioning' [CVPR 2020]

Introduction This repository is for X-Linear Attention Networks for Image Captioning (CVPR 2020). The original paper can be found here. Please cite wi

JDAI-CV 240 Dec 17, 2022
Tweesent-back - Tweesent backend uses fastAPI as the web framework

TweeSent Backend Tweesent backend. This repo uses fastAPI as the web framework.

0 Mar 26, 2022
Torch-based tool for quantizing high-dimensional vectors using additive codebooks

Trainable multi-codebook quantization This repository implements a utility for use with PyTorch, and ideally GPUs, for training an efficient quantizer

Daniel Povey 41 Jan 07, 2023
AdaNet is a lightweight TensorFlow-based framework for automatically learning high-quality models with minimal expert intervention

AdaNet is a lightweight TensorFlow-based framework for automatically learning high-quality models with minimal expert intervention. AdaNet buil

3.4k Jan 07, 2023
Deep learning library for solving differential equations and more

DeepXDE Voting on whether we should have a Slack channel for discussion. DeepXDE is a library for scientific machine learning. Use DeepXDE if you need

Lu Lu 1.4k Dec 29, 2022
VarCLR: Variable Semantic Representation Pre-training via Contrastive Learning

    VarCLR: Variable Representation Pre-training via Contrastive Learning New: Paper accepted by ICSE 2022. Preprint at arXiv! This repository contain

squaresLab 32 Oct 24, 2022
A Light in the Dark: Deep Learning Practices for Industrial Computer Vision

A Light in the Dark: Deep Learning Practices for Industrial Computer Vision This is the repository for our Paper/Contribution to the WI2022 in Nürnber

Maximilian Harl 6 Jan 17, 2022
An Open-Source Package for Information Retrieval.

OpenMatch An Open-Source Package for Information Retrieval. 😃 What's New Top Spot on TREC-COVID Challenge (May 2020, Round2) The twin goals of the ch

THUNLP 439 Dec 27, 2022
A high-performance anchor-free YOLO. Exceeding yolov3~v5 with ONNX, TensorRT, NCNN, and Openvino supported.

YOLOX is an anchor-free version of YOLO, with a simpler design but better performance! It aims to bridge the gap between research and industrial communities. For more details, please refer to our rep

7.7k Jan 06, 2023