Improve model card: add metadata, paper, and code links

README.md

@@ -1,26 +1,34 @@
 ---
 license: apache-2.0
+pipeline_tag: graph-ml
 tags:
-  - biology
-  - protein
-  - molecule
-  - dna
-  - rna
-  - graph-neural-network
+- 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).
+Graph encoder component of **Cuttlefish**, a unified all-atom LLM that grounds language reasoning in geometric cues while scaling modality tokens with structural complexity.
+
+This model was presented in the paper [Scaling-Aware Adapter for Structure-Grounded LLM Reasoning](https://arxiv.org/abs/2602.02780).
+
+- **Code:** [GitHub - zihao-jing/Cuttlefish](https://github.com/zihao-jing/Cuttlefish)
+- **Pretrained with:** Masked reconstruction on all-atom structures.
 
 ## Usage
 
+You can download the encoder using the `huggingface_hub` library:
+
 ```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
+# See https://github.com/zihao-jing/Cuttlefish for full usage
 ```
 
 ## Pretraining data
@@ -32,9 +40,9 @@ Pretrained on **[Cuttlefish-Encoder-Data](https://huggingface.co/datasets/zihaoj
 
 ## Model details
 
-- Architecture: All-atom graph encoder with masked reconstruction pretraining
-- Encoder hidden dim: 256
-- Modalities: molecule, protein, dna, rna
+- **Architecture**: All-atom graph encoder with Scaling-Aware Patching.
+- **Encoder hidden dim**: 256
+- **Modalities**: molecule, protein, dna, rna
 
 ## Related resources
 
@@ -43,3 +51,15 @@ Pretrained on **[Cuttlefish-Encoder-Data](https://huggingface.co/datasets/zihaoj
 | 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) |
+
+## Citation
+
+```bibtex
+@article{jing2026cuttlefish,
+  title     = {Cuttlefish: Scaling-Aware Adapter for Structure-Grounded LLM Reasoning},
+  author    = {Jing, Zihao and Zeng, Qiuhao and Fang, Ruiyi and Li, Yan Yi and Sun, Yan Table, Boyu and Hu, Pingzhao},
+  booktitle = {Proceedings of the 43rd International Conference on Machine Learning (ICML)},
+  year      = {2026},
+  url       = {https://arxiv.org/abs/2602.02780}
+}
+```