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
Point detection through multi-instance deep heatmap regression for sutures in endoscopy

Suture detection PyTorch This repo contains the reference implementation of suture detection model in PyTorch for the paper Point detection through mu

artificial intelligence in the area of cardiovascular healthcare 3 Jul 16, 2022
GemNet model in PyTorch, as proposed in "GemNet: Universal Directional Graph Neural Networks for Molecules" (NeurIPS 2021)

GemNet: Universal Directional Graph Neural Networks for Molecules Reference implementation in PyTorch of the geometric message passing neural network

Data Analytics and Machine Learning Group 124 Dec 30, 2022
This repository contains the code to replicate the analysis from the paper "Moving On - Investigating Inventors' Ethnic Origins Using Supervised Learning"

Replication Code for 'Moving On' - Investigating Inventors' Ethnic Origins Using Supervised Learning This repository contains the code to replicate th

Matthias Niggli 0 Jan 04, 2022
Contains a bunch of different python programm tasks

py_tasks Contains a bunch of different python programm tasks Armstrong.py - calculate Armsrong numbers in range from 0 to n with / without cache and c

Dmitry Chmerenko 1 Dec 17, 2021
LowRankModels.jl is a julia package for modeling and fitting generalized low rank models.

LowRankModels.jl LowRankModels.jl is a Julia package for modeling and fitting generalized low rank models (GLRMs). GLRMs model a data array by a low r

Madeleine Udell 183 Dec 17, 2022
This repository contains the segmentation user interface from the OpenSurfaces project, extracted as a lightweight tool

OpenSurfaces Segmentation UI This repository contains the segmentation user interface from the OpenSurfaces project, extracted as a lightweight tool.

Sean Bell 66 Jul 11, 2022
NitroFE is a Python feature engineering engine which provides a variety of modules designed to internally save past dependent values for providing continuous calculation.

NitroFE is a Python feature engineering engine which provides a variety of modules designed to internally save past dependent values for providing continuous calculation.

100 Sep 28, 2022
Privacy-Preserving Machine Learning (PPML) Tutorial Presented at PyConDE 2022

PPML: Machine Learning on Data you cannot see Repository for the tutorial on Privacy-Preserving Machine Learning (PPML) presented at PyConDE 2022 Abst

Valerio Maggio 10 Aug 16, 2022
Paper: Cross-View Kernel Similarity Metric Learning Using Pairwise Constraints for Person Re-identification

Cross-View Kernel Similarity Metric Learning Using Pairwise Constraints for Person Re-identification T M Feroz Ali, Subhasis Chaudhuri, ICVGIP-20-21

T M Feroz Ali 3 Jun 17, 2022
*ObjDetApp* deploys a pytorch model for object detection

*ObjDetApp* deploys a pytorch model for object detection

Will Chao 1 Dec 26, 2021
PyTorch version repo for CSRNet: Dilated Convolutional Neural Networks for Understanding the Highly Congested Scenes

Study-CSRNet-pytorch This is the PyTorch version repo for CSRNet: Dilated Convolutional Neural Networks for Understanding the Highly Congested Scenes

0 Mar 01, 2022
Putting NeRF on a Diet: Semantically Consistent Few-Shot View Synthesis

Putting NeRF on a Diet: Semantically Consistent Few-Shot View Synthesis Website | ICCV paper | arXiv | Twitter This repository contains the official i

Ajay Jain 73 Dec 27, 2022
Mememoji - A facial expression classification system that recognizes 6 basic emotions: happy, sad, surprise, fear, anger and neutral.

a project built with deep convolutional neural network and ❤️ Table of Contents Motivation The Database The Model 3.1 Input Layer 3.2 Convolutional La

Jostine Ho 761 Dec 05, 2022
Modeling Category-Selective Cortical Regions with Topographic Variational Autoencoders

Modeling Category-Selective Cortical Regions with Topographic Variational Autoencoders

1 Oct 11, 2021
[NeurIPS'21] "AugMax: Adversarial Composition of Random Augmentations for Robust Training" by Haotao Wang, Chaowei Xiao, Jean Kossaifi, Zhiding Yu, Animashree Anandkumar, and Zhangyang Wang.

AugMax: Adversarial Composition of Random Augmentations for Robust Training Haotao Wang, Chaowei Xiao, Jean Kossaifi, Zhiding Yu, Anima Anandkumar, an

VITA 112 Nov 07, 2022
DAN: Unfolding the Alternating Optimization for Blind Super Resolution

DAN-Basd-on-Openmmlab DAN: Unfolding the Alternating Optimization for Blind Super Resolution We reproduce DAN via mmediting based on open-sourced code

AlexZou 72 Dec 13, 2022
Vision Transformer and MLP-Mixer Architectures

Vision Transformer and MLP-Mixer Architectures Update (2.7.2021): Added the "When Vision Transformers Outperform ResNets..." paper, and SAM (Sharpness

Google Research 6.4k Jan 04, 2023
Official Matlab Implementation for "Tiny Obstacle Discovery by Occlusion-aware Multilayer Regression", TIP 2020

Tiny Obstacle Discovery by Occlusion-aware Multilayer Regression Official Matlab Implementation for "Tiny Obstacle Discovery by Occlusion-aware Multil

Xuefeng 5 Jan 15, 2022
DPT: Deformable Patch-based Transformer for Visual Recognition (ACM MM2021)

DPT This repo is the official implementation of DPT: Deformable Patch-based Transformer for Visual Recognition (ACM MM2021). We provide code and model

CASIA-IVA-Lab 111 Dec 21, 2022
Supplemental Code for "ImpressionNet :A Multi view Approach to Predict Socio Facial Impressions"

Supplemental Code for "ImpressionNet :A Multi view Approach to Predict Socio Facial Impressions" Environment requirement This code is based on Python

Rohan Kumar Gupta 1 Dec 19, 2021