# Gode

Source Code for our paper: "Gode: Integrating Biochemical Knowledge Graph into Pre-Training Molecule Graph Neural Network through Contrastive Learning"

---


Molecule-centric KG construction
---
```bash
/data_process/
```
Download our processed dataset & more data processing scripts (MolKG): 
[Google Drive](https://drive.google.com/file/d/17lUmWkHURxUWUaKMfWJNGNWmwwze0nUT/view?usp=sharing)


Molecule-level Pre-training
---
```bash
/m_level_pretrain_and_fine_tune/
```
KGE training (K-GNN Embedding Initialization)
---
```bash
/kg_emb/
```

KG-level Pre-training
---
```bash
/k_level_pretrain/
```

Contrastive Learning
---
```bash
/contrastive_learning/
```

Fine-tuning
---
```bash
/m_level_pretrain_and_fine_tune/
```


