Few-Shot Graph Learning for Molecular Property Prediction

Overview

Few-shot Graph Learning for Molecular Property Prediction

Introduction

This is the source code and dataset for the following paper:

Few-shot Graph Learning for Molecular Property Prediction. In WWW 2021.

Contact Zhichun Guo ([email protected]), if you have any questions.

Datasets

The datasets uploaded can be downloaded to train our model directly.

The original datasets are downloaded from Data. We utilize Original_datasets/splitdata.py to split the datasets according to the molecular properties and save them in different files in the Original_datasets/[DatasetName]/new. Then run main.py, the datasets will be automatically preprocessed by loader.py and the preprocessed results will be saved in the Original_datasets/[DatasetName]/new/[PropertyNumber]/propcessed.

Usage

Installation

We used the following Python packages for the development by python 3.6.

- torch = 1.4.0
- torch-geometric = 1.6.1
- torch-scatter = 2.0.4
- torch-sparse = 0.6.1
- scikit-learn = 0.23.2
- tqdm = 4.50.0
- rdkit

Run code

Datasets and k (for k-shot) can be changed in the last line of main.py.

python main.py

Performance

The performance of meta-learning is not stable for some properties. We report two times results and the number of the iteration where we obtain the best results here for your reference.

Dataset k Iteration Property Results k Iteration Property Results
Sider 1 307/599 Si-T1 75.08/75.74 5 561/585 Si-T1 76.16/76.47
Si-T2 69.44/69.34 Si-T2 68.90/69.77
Si-T3 69.90/71.39 Si-T3 72.23/72.35
Si-T4 71.78/73.60 Si-T4 74.40/74.51
Si-T5 79.40/80.50 Si-T5 81.71/81.87
Si-T6 71.59/72.35 Si-T6 74.90/73.34
Ave. 72.87/73.82 Ave. 74.74/74.70
Tox21 1 1271/1415 SR-HS 73.72/73.90 5 1061/882 SR-HS 74.85/74.74
SR-MMP 78.56/79.62 SR-MMP 80.25/80.27
SR-p53 77.50/77.91 SR-p53 78.86/79.14
Ave. 76.59/77.14 Ave. 77.99/78.05

Acknowledgements

The code is implemented based on Strategies for Pre-training Graph Neural Networks.

Reference

@article{guo2021few,
  title={Few-Shot Graph Learning for Molecular Property Prediction},
  author={Guo, Zhichun and Zhang, Chuxu and Yu, Wenhao and Herr, John and Wiest, Olaf and Jiang, Meng and Chawla, Nitesh V},
  journal={arXiv preprint arXiv:2102.07916},
  year={2021}
}
Owner
Zhichun Guo
Zhichun Guo is a Ph.D. student at University of Notre Dame.
Zhichun Guo
Code accompanying the paper "ProxyFL: Decentralized Federated Learning through Proxy Model Sharing"

ProxyFL Code accompanying the paper "ProxyFL: Decentralized Federated Learning through Proxy Model Sharing" Authors: Shivam Kalra*, Junfeng Wen*, Jess

Layer6 Labs 14 Dec 06, 2022
SporeAgent: Reinforced Scene-level Plausibility for Object Pose Refinement

SporeAgent: Reinforced Scene-level Plausibility for Object Pose Refinement This repository implements the approach described in SporeAgent: Reinforced

Dominik Bauer 5 Jan 02, 2023
RoBERTa Marathi Language model trained from scratch during huggingface 🤗 x flax community week

RoBERTa base model for Marathi Language (मराठी भाषा) Pretrained model on Marathi language using a masked language modeling (MLM) objective. RoBERTa wa

Nipun Sadvilkar 23 Oct 19, 2022
Repo for "Physion: Evaluating Physical Prediction from Vision in Humans and Machines" submission to NeurIPS 2021 (Datasets & Benchmarks track)

Physion: Evaluating Physical Prediction from Vision in Humans and Machines This repo contains code and data to reproduce the results in our paper, Phy

Cognitive Tools Lab 38 Jan 06, 2023
The codes I made while I practiced various TensorFlow examples

TensorFlow_Exercises The codes I made while I practiced various TensorFlow examples About the codes I didn't create these codes by myself, but re-crea

Terry Taewoong Um 614 Dec 08, 2022
Code for CMaskTrack R-CNN (proposed in Occluded Video Instance Segmentation)

CMaskTrack R-CNN for OVIS This repo serves as the official code release of the CMaskTrack R-CNN model on the Occluded Video Instance Segmentation data

Q . J . Y 61 Nov 25, 2022
Code for the prototype tool in our paper "CoProtector: Protect Open-Source Code against Unauthorized Training Usage with Data Poisoning".

CoProtector Code for the prototype tool in our paper "CoProtector: Protect Open-Source Code against Unauthorized Training Usage with Data Poisoning".

Zhensu Sun 1 Oct 26, 2021
quantize aware training package for NCNN on pytorch

ncnnqat ncnnqat is a quantize aware training package for NCNN on pytorch. Table of Contents ncnnqat Table of Contents Installation Usage Code Examples

62 Nov 23, 2022
Bagua is a flexible and performant distributed training algorithm development framework.

Bagua is a flexible and performant distributed training algorithm development framework.

786 Dec 17, 2022
Exploit ILP to learn symmetry breaking constraints of ASP programs.

ILP Symmetry Breaking Overview This project aims to exploit inductive logic programming to lift symmetry breaking constraints of ASP programs. Given a

Research Group Production Systems 1 Apr 13, 2022
Action Recognition for Self-Driving Cars

Action Recognition for Self-Driving Cars This repo contains the codes for the 2021 Fall semester project "Action Recognition for Self-Driving Cars" at

VITA lab at EPFL 3 Apr 07, 2022
Pytorch implementation of the DeepDream computer vision algorithm

deep-dream-in-pytorch Pytorch (https://github.com/pytorch/pytorch) implementation of the deep dream (https://en.wikipedia.org/wiki/DeepDream) computer

102 Dec 05, 2022
Scalable Multi-Agent Reinforcement Learning

Scalable Multi-Agent Reinforcement Learning 1. Featured algorithms: Value Function Factorization with Variable Agent Sub-Teams (VAST) [1] 2. Implement

3 Aug 02, 2022
A package for "Procedural Content Generation via Reinforcement Learning" OpenAI Gym interface.

Readme: Illuminating Diverse Neural Cellular Automata for Level Generation This is the codebase used to generate the results presented in the paper av

Sam Earle 27 Jan 05, 2023
PyTorch implementation of HDN(Homography Decomposition Networks) for planar object tracking

Homography Decomposition Networks for Planar Object Tracking This project is the offical PyTorch implementation of HDN(Homography Decomposition Networ

CaptainHook 48 Dec 15, 2022
Predictive Maintenance LSTM

Predictive-Maintenance-LSTM - Predictive maintenance study for Complex case study, we've obtained failure causes by operational error and more deeply by design mistakes.

Amir M. Sadafi 1 Dec 31, 2021
The code for the NeurIPS 2021 paper "A Unified View of cGANs with and without Classifiers".

Energy-based Conditional Generative Adversarial Network (ECGAN) This is the code for the NeurIPS 2021 paper "A Unified View of cGANs with and without

sianchen 22 May 28, 2022
Weakly Supervised Segmentation by Tensorflow.

Weakly Supervised Segmentation by Tensorflow. Implements semantic segmentation in Simple Does It: Weakly Supervised Instance and Semantic Segmentation, by Khoreva et al. (CVPR 2017).

CHENG-YOU LU 52 Dec 27, 2022
Codes for TS-CAM: Token Semantic Coupled Attention Map for Weakly Supervised Object Localization.

TS-CAM: Token Semantic Coupled Attention Map for Weakly SupervisedObject Localization This is the official implementaion of paper TS-CAM: Token Semant

vasgaowei 112 Jan 02, 2023
A general python framework for visual object tracking and video object segmentation, based on PyTorch

PyTracking A general python framework for visual object tracking and video object segmentation, based on PyTorch. 📣 Two tracking/VOS papers accepted

2.6k Jan 04, 2023