Datasets:
File size: 1,393 Bytes
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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) |
|