Add model card

README.md

@@ -0,0 +1,45 @@
+---
+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) |