README.md

---
license: apache-2.0
task_categories:
  - graph-ml
tags:
  - biology
  - protein
  - molecule
  - dna
  - rna
  - pretraining
---

# Cuttlefish-Encoder-Data

Encoder pretraining dataset for [Cuttlefish-Encoder](https://huggingface.co/zihaojing/Cuttlefish-Encoder). Contains all-atom structural graphs for molecules, proteins, DNA, and RNA in a unified parquet format.

## 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) |