eccDNAMamba/real_vs_pseudo_eccdna_homo_sapiens

Real vs. Pseudo-eccDNA Discrimination (Homo sapiens)

This dataset supports the Real vs. Pseudo-eccDNA Discrimination task for human 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)

📁 Folder Structure

<pre> realvspseudoeccdnadiscriminationhuman/ ├── data/ │ └── realvspseudoeccdnadiscriminationhuman.csv └── README.md </pre>

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.

Citation

If you use this dataset, please cite: <pre><code class="language-python">

@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} } </code></pre>