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license: apache-2.0
tags:
- biology
- protein
- molecule
- dna
- rna
- graph-neural-network
---
# Cuttlefish-Encoder
Graph encoder component of [Cuttlefish](https://huggingface.co/zihaojing/Cuttlefish), pretrained with masked reconstruction on all-atom structures (proteins, molecules, DNA, RNA).
## Usage
```python
from huggingface_hub import snapshot_download
encoder_dir = snapshot_download("zihaojing/Cuttlefish-Encoder")
# Load via the Cuttlefish codebase
# See https://github.com/your-repo/cuttlefish for full usage
```
## Pretraining data
Pretrained on **[Cuttlefish-Encoder-Data](https://huggingface.co/datasets/zihaojing/Cuttlefish-Encoder-Data)**, covering:
- Molecules (SMILES → 3D graph)
- Proteins (PDB/CIF → all-atom graph)
- DNA and RNA sequences
## Model details
- Architecture: All-atom graph encoder with masked reconstruction pretraining
- Encoder hidden dim: 256
- Modalities: molecule, protein, dna, rna
## Related resources
| Resource | Link |
|---|---|
| Full Cuttlefish LLM | [zihaojing/Cuttlefish](https://huggingface.co/zihaojing/Cuttlefish) |
| SFT instruction data | [zihaojing/Cuttlefish-SFT-Data](https://huggingface.co/datasets/zihaojing/Cuttlefish-SFT-Data) |
| Encoder pretraining data | [zihaojing/Cuttlefish-Encoder-Data](https://huggingface.co/datasets/zihaojing/Cuttlefish-Encoder-Data) |
|