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README.md

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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) |