reaction_yield_pretrained_gnn

Source code for the paper: Improving Chemical Reaction Yield Prediction Using Pre-Trained Graph Neural Networks

Data

• The datasets used in the paper
  • Pre-Training Dataset (10M mols collected from Pubchem) - https://arxiv.org/pdf/2010.09885.pdf
  • Chemical Reaction Yield Benchmark Datasets - https://github.com/rxn4chemistry/rxn_yields/

Components

• data/get_pretraining_data.py - pre-training dataset preprocessing functions
• data/get_reaction_yield_data.py - chemical reaction yield benchmark dataset preprocessing functions
• src/dataset.py - data structure & functions
• src/model.py - model architecture & training / inference functions
• src/pretrain.py - pre-training functions
• src/finetune.py - fine-tuning functions
• src/preprocess_util.py - util functions for data preprocessing
• src/util.py - util functions for model training / inference
• main_pretrain.py - script for pre-training
• main_finetune.py - script for fine-tuning
• run.sh - run code example

Dependencies

• Python
• Pytorch
• DGL
• RDKit
• Mordred

Citation

TBU