Datasets:
File size: 2,231 Bytes
ca54bc7 5c50a59 ca54bc7 5c50a59 ca54bc7 5c50a59 ca54bc7 5c50a59 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 | ---
license: apache-2.0
task_categories:
- graph-ml
tags:
- biology
- protein
- molecule
- dna
- rna
- pretraining
---
# Cuttlefish-Encoder-Data
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.
- **Paper:** [Scaling-Aware Adapter for Structure-Grounded LLM Reasoning](https://huggingface.co/papers/2602.02780)
- **GitHub Repository:** [zihao-jing/Cuttlefish](https://github.com/zihao-jing/Cuttlefish)
- **Encoder Model:** [zihaojing/Cuttlefish-Encoder](https://huggingface.co/zihaojing/Cuttlefish-Encoder)
## Dataset structure
```
molecules/ # molecule encoder training data
nacid/ # DNA and RNA encoder training data
protein/ # protein encoder training data (PDB structures)
test/ # held-out test samples
```
## Schema
| Field | Description |
|---|---|
| `modality` | `"molecule"`, `"protein"`, `"dna"`, or `"rna"` |
| `node_feat` | Atom/node features (N × d) |
| `pos` | 3D coordinates in Å (N × 3) |
| `edge_index` | Spatial graph edges in COO (2 × E) |
| `edge_feat_dist` | Edge distances (E × 1, optional) |
## Usage
```python
from datasets import load_dataset
ds = load_dataset("zihaojing/Cuttlefish-Encoder-Data")
```
## Related resources
| Resource | Link |
|---|---|
| Cuttlefish LLM | [zihaojing/Cuttlefish](https://huggingface.co/zihaojing/Cuttlefish) |
| Cuttlefish-Encoder | [zihaojing/Cuttlefish-Encoder](https://huggingface.co/zihaojing/Cuttlefish-Encoder) |
| SFT instruction data | [zihaojing/Cuttlefish-SFT-Data](https://huggingface.co/datasets/zihaojing/Cuttlefish-SFT-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 and Wang, Boyu and Hu, Pingzhao},
booktitle = {Proceedings of the 43rd International Conference on Machine Learning (ICML)},
year = {2026},
url = {https://arxiv.org/abs/2602.02780}
}
``` |