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