eccDNAMamba/real_vs_pseudo_eccdna_gallus_gallus

Real vs. Pseudo-eccDNA Discrimination (Gallus gallus)

This dataset supports the Real vs. Pseudo-eccDNA Discrimination task for gallus gallus eccDNA.
The goal is to train models that can distinguish true eccDNA sequences from pseudo-eccDNAs
randomly extracted from linear genomic regions with matched length distributions.

Each entry contains:

• sequence: raw eccDNA sequence (A/T/C/G)
• label:
  • 1 → Real eccDNA
  • 0 → Pseudo-eccDNA (negative control)

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📁 Folder Structure

real_vs_pseudo_eccdna_discrimination_gallus_gallus/
├── data/
│   └── real_vs_pseudo_eccdna_discrimination_gallus_gallus.csv
└── README.md

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🚀 Quick Usage

from datasets import load_dataset, load_from_disk

# Load from Hugging Face Hub (after upload)
dataset = load_dataset("your-username/real_vs_pseudo_eccdna_discrimination_gallus_gallus")

# Example: view label distribution
df = dataset["train"].to_pandas()
print(df['label'].value_counts())

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Task Description

True eccDNAs are experimentally verified circular DNA molecules,
whereas pseudo-eccDNAs are generated by randomly extracting linear genomic segments
to match the true eccDNA length distribution.
This task assesses a model’s ability to capture circular topology and regulatory context
beyond simple sequence composition.

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Citation

If you use this dataset, please cite:

@inproceedings{liu2025eccdnamamba,
  title={eccDNAMamba: A Pre-Trained Model for Ultra-Long eccDNA Sequence Analysis},
  author={Zhenke Liu and Jien Li and Ziqi Zhang},
  booktitle={ICML 2025 GenBio Workshop},
  year={2025},
  url={https://openreview.net/forum?id=56xKN7KJjy}
}