metadata
license: apache-2.0
tags:
- biology
- protein
- molecule
- dna
- rna
- graph-neural-network
Cuttlefish-Encoder
Graph encoder component of Cuttlefish, pretrained with masked reconstruction on all-atom structures (proteins, molecules, DNA, RNA).
Usage
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, 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 |
| SFT instruction data | zihaojing/Cuttlefish-SFT-Data |
| Encoder pretraining data | zihaojing/Cuttlefish-Encoder-Data |