Gode

Source code and data for our paper "Enhancing Molecule Representations with Molecule-Centric Knowledge Graphs".

(Old Title: "Bi-level Contrastive Learning for Knowledge-Enhanced Molecule Representations")

Data Preparation:

unzip gode_data.zip

Code

Our code is in the "gode_code" folder.

Here's an overview of the code of corresponding functions:

Molecule-level Pre-training

/m_level_pretrain_and_fine_tune/

KGE training (K-GNN Embedding Initialization)

/kg_emb/

KG-level Pre-training

/k_level_pretrain/

Contrastive Learning

/contrastive_learning/

Fine-tuning

/m_level_pretrain_and_fine_tune/

Data

We detailed the dataset (MolKG) construction and data process in Appendix B of the paper.

After unzipping it, the folder contains

The Entire MolKG Dataset

gode_data/data_process/KG_processed.csv

Processing Scripts

gode_data/dataset_construction/

Thank you for your interests!