| --- |
| 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) | |
|
|
