README.md

metadata

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

Cuttlefish-Encoder-Data

Encoder pretraining dataset for 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

from datasets import load_dataset
ds = load_dataset("zihaojing/Cuttlefish-Encoder-Data")

Related resources

Resource	Link
Cuttlefish LLM	zihaojing/Cuttlefish
Cuttlefish-Encoder	zihaojing/Cuttlefish-Encoder
SFT instruction data	zihaojing/Cuttlefish-SFT-Data