Datasets:
Link paper and GitHub repository to dataset card
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by nielsr HF Staff - opened
README.md
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license: apache-2.0
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# Cuttlefish-Encoder-Data
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## Dataset structure
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| Cuttlefish LLM | [zihaojing/Cuttlefish](https://huggingface.co/zihaojing/Cuttlefish) |
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| Cuttlefish-Encoder | [zihaojing/Cuttlefish-Encoder](https://huggingface.co/zihaojing/Cuttlefish-Encoder) |
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| SFT instruction data | [zihaojing/Cuttlefish-SFT-Data](https://huggingface.co/datasets/zihaojing/Cuttlefish-SFT-Data) |
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---
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license: apache-2.0
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task_categories:
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- graph-ml
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tags:
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- biology
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- protein
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- molecule
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- dna
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- rna
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- pretraining
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# Cuttlefish-Encoder-Data
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This repository contains the encoder pretraining dataset for **Cuttlefish**, a unified all-atom LLM designed for structure-grounded reasoning. It consists of all-atom structural graphs for molecules, proteins, DNA, and RNA in a unified parquet format, used for masked-reconstruction pretraining of the graph encoder.
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- **Paper:** [Scaling-Aware Adapter for Structure-Grounded LLM Reasoning](https://huggingface.co/papers/2602.02780)
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- **GitHub Repository:** [zihao-jing/Cuttlefish](https://github.com/zihao-jing/Cuttlefish)
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- **Encoder Model:** [zihaojing/Cuttlefish-Encoder](https://huggingface.co/zihaojing/Cuttlefish-Encoder)
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## Dataset structure
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| Cuttlefish LLM | [zihaojing/Cuttlefish](https://huggingface.co/zihaojing/Cuttlefish) |
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| Cuttlefish-Encoder | [zihaojing/Cuttlefish-Encoder](https://huggingface.co/zihaojing/Cuttlefish-Encoder) |
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| SFT instruction data | [zihaojing/Cuttlefish-SFT-Data](https://huggingface.co/datasets/zihaojing/Cuttlefish-SFT-Data) |
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## Citation
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```bibtex
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@article{jing2026cuttlefish,
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title = {Cuttlefish: Scaling-Aware Adapter for Structure-Grounded LLM Reasoning},
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author = {Jing, Zihao and Zeng, Qiuhao and Fang, Ruiyi and Li, Yan Yi and Sun, Yan and Wang, Boyu and Hu, Pingzhao},
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booktitle = {Proceedings of the 43rd International Conference on Machine Learning (ICML)},
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year = {2026},
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url = {https://arxiv.org/abs/2602.02780}
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}
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```
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