Official implementation of "Motif-based Graph Self-Supervised Learning forMolecular Property Prediction"

Related tags

Deep LearningMGSSL
Overview

Motif-based Graph Self-Supervised Learning for Molecular Property Prediction

Official Pytorch implementation of NeurIPS'21 paper "Motif-based Graph Self-Supervised Learning for Molecular Property Prediction" (https://arxiv.org/abs/2110.00987).

Requirements

pytorch                   1.7.0             
torch-geometric           1.6.3
rdkit                     2021.03.1
tqdm                      4.31.1
tensorboardx              1.6

To install RDKit, please follow the instructions here http://www.rdkit.org/docs/Install.html

  • motif_based_pretrain/ contains codes for motif-based graph self-supervised pretraining.
  • finetune/ contains codes for finetuning on MoleculeNet benchmarks for evaluation.

Training

You can pretrain the model by

cd motif_based_pretrain
python pretrain_motif.py

Evaluation

You can evaluate the pretrained model by finetuning on downstream tasks

cd finetune
python finetune.py

Cite

If you find this repo to be useful, please cite our paper. Thank you.

@article{zhang2021motif,
  title={Motif-based Graph Self-Supervised Learning for Molecular Property Prediction},
  author={Zhang, Zaixi and Liu, Qi and Wang, Hao and Lu, Chengqiang and Lee, Chee-Kong},
  journal={arXiv preprint arXiv:2110.00987},
  year={2021}
}
Owner
zaixi
I am Zaixi Zhang from USTC
zaixi
A Python implementation of global optimization with gaussian processes.

Bayesian Optimization Pure Python implementation of bayesian global optimization with gaussian processes. PyPI (pip): $ pip install bayesian-optimizat

fernando 6.5k Jan 02, 2023
FinGAT: A Financial Graph Attention Networkto Recommend Top-K Profitable Stocks

FinGAT: A Financial Graph Attention Networkto Recommend Top-K Profitable Stocks This is our implementation for the paper: FinGAT: A Financial Graph At

Yu-Che Tsai 64 Dec 13, 2022
RepVGG: Making VGG-style ConvNets Great Again

RepVGG: Making VGG-style ConvNets Great Again (PyTorch) This is a super simple ConvNet architecture that achieves over 80% top-1 accuracy on ImageNet

2.8k Jan 04, 2023
ICLR 2021 i-Mix: A Domain-Agnostic Strategy for Contrastive Representation Learning

Introduction PyTorch code for the ICLR 2021 paper [i-Mix: A Domain-Agnostic Strategy for Contrastive Representation Learning]. @inproceedings{lee2021i

Kibok Lee 68 Nov 27, 2022
OpenDILab RL Kubernetes Custom Resource and Operator Lib

DI Orchestrator DI Orchestrator is designed to manage DI (Decision Intelligence) jobs using Kubernetes Custom Resource and Operator. Prerequisites A w

OpenDILab 205 Dec 29, 2022
TextBPN Adaptive Boundary Proposal Network for Arbitrary Shape Text Detection

TextBPN Adaptive Boundary Proposal Network for Arbitrary Shape Text Detection; Accepted by ICCV2021. Note: The complete code (including training and t

S.X.Zhang 84 Dec 13, 2022
DPC: Unsupervised Deep Point Correspondence via Cross and Self Construction (3DV 2021)

DPC: Unsupervised Deep Point Correspondence via Cross and Self Construction (3DV 2021) This repo is the implementation of DPC. Tested environment Pyth

Dvir Ginzburg 30 Nov 30, 2022
An evaluation toolkit for voice conversion models.

Voice-conversion-evaluation An evaluation toolkit for voice conversion models. Sample test pair Generate the metadata for evaluating models. The direc

30 Aug 29, 2022
One line to host them all. Bootstrap your image search case in minutes.

One line to host them all. Bootstrap your image search case in minutes. Survey NOW gives the world access to customized neural image search in just on

Jina AI 403 Dec 30, 2022
Self-Correcting Quantum Many-Body Control using Reinforcement Learning with Tensor Networks

Self-Correcting Quantum Many-Body Control using Reinforcement Learning with Tensor Networks This repository contains the code and data for the corresp

Friederike Metz 7 Apr 23, 2022
DeepStruc is a Conditional Variational Autoencoder which can predict the mono-metallic nanoparticle from a Pair Distribution Function.

ChemRxiv | [Paper] XXX DeepStruc Welcome to DeepStruc, a Deep Generative Model (DGM) that learns the relation between PDF and atomic structure and the

Emil Thyge Skaaning Kjær 13 Aug 01, 2022
Doge-Prediction - Coding Club prediction ig

Doge-Prediction Coding Club prediction ig Basically: Create an application that

1 Jan 10, 2022
ML powered analytics engine for outlier detection and root cause analysis.

Website • Docs • Blog • LinkedIn • Community Slack ML powered analytics engine for outlier detection and root cause analysis ✨ What is Chaos Genius? C

Chaos Genius 523 Jan 04, 2023
A Simulated Optimal Intrusion Response Game

Optimal Intrusion Response An OpenAI Gym interface to a MDP/Markov Game model for optimal intrusion response of a realistic infrastructure simulated u

Kim Hammar 10 Dec 09, 2022
TensorFlow, PyTorch and Numpy layers for generating Orthogonal Polynomials

OrthNet TensorFlow, PyTorch and Numpy layers for generating multi-dimensional Orthogonal Polynomials 1. Installation 2. Usage 3. Polynomials 4. Base C

Chuan 29 May 25, 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
Extracting knowledge graphs from language models as a diagnostic benchmark of model performance.

Interpreting Language Models Through Knowledge Graph Extraction Idea: How do we interpret what a language model learns at various stages of training?

EPFL Machine Learning and Optimization Laboratory 9 Oct 25, 2022
The backbone CSPDarkNet of YOLOX.

YOLOX-Backbone The backbone CSPDarkNet of YOLOX. In this project, you can enjoy: CSPDarkNet-S CSPDarkNet-M CSPDarkNet-L CSPDarkNet-X CSPDarkNet-Tiny C

Jianhua Yang 9 Aug 22, 2022
The pure and clear PyTorch Distributed Training Framework.

The pure and clear PyTorch Distributed Training Framework. Introduction Requirements and Usage Dependency Dataset Basic Usage Slurm Cluster Usage Base

WILL LEE 208 Dec 20, 2022
Model that predicts the probability of a Twitter user being anti-vaccination.

stylebody {text-align: justify}/style AVAXTAR: Anti-VAXx Tweet AnalyzeR AVAXTAR is a python package to identify anti-vaccine users on twitter. The

10 Sep 27, 2022