# eccDNAMamba: A Pre-Trained Model for Ultra-Long eccDNA Sequence Analysis

arXiv: https://arxiv.org/abs/2506.18940 · HTML: https://mlsanity.com/paper/2506.18940/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 8 of its 28 references that are in the map.
- First posted on arXiv 22 Jun 2025.

## Builds on (most cited first, 8 of 8)

- [Mamba: Linear-Time Sequence Modeling with Selective State Spaces](https://mlsanity.com/paper/2312.00752/) (2023)
- [Neural Machine Translation of Rare Words with Subword Units](https://mlsanity.com/paper/1508.07909/) (2015)
- [Transformers are SSMs: Generalized Models and Efficient Algorithms Through Structured State Space Duality](https://mlsanity.com/paper/2405.21060/) (2024)
- [SpanBERT: Improving Pre-training by Representing and Predicting Spans](https://mlsanity.com/paper/1907.10529/) (2019)
- [Bidirectional LSTM-CRF Models for Sequence Tagging](https://mlsanity.com/paper/1508.01991/) (2015)
- [HyenaDNA: Long-Range Genomic Sequence Modeling at Single Nucleotide Resolution](https://mlsanity.com/paper/2306.15794/) (2023)
- [DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome](https://mlsanity.com/paper/2306.15006/) (2023)
- [Caduceus: Bi-Directional Equivariant Long-Range DNA Sequence Modeling](https://mlsanity.com/paper/2403.03234/) (2024)

## Built on by (most cited first, 1 of 1)

- [GENEB: Why Genomic Models Are Hard to Compare](https://mlsanity.com/paper/2606.04525/) (2026)

## Abstract (arXiv)

Extrachromosomal circular DNA (eccDNA) plays key regulatory roles and contributes to oncogene overexpression in cancer through high-copy amplification and long-range interactions. Despite advances in modeling, no pre-trained models currently support full-length circular eccDNA for downstream analysis. Existing genomic models are either limited to single-nucleotide resolution or hindered by the inefficiency of the quadratic attention mechanism. Here, we introduce eccDNAMamba, the first bidirectional state-space encoder tailored for circular DNA sequences. It combines forward and reverse passes for full-context representation learning with linear-time complexity, and preserves circular structure through a novel augmentation strategy. Tested on two real-world datasets, eccDNAMamba achieves strong classification performance and scales to sequences up to 200 Kbp, offering a robust and efficient framework for modeling circular genomes. Our codes are available at https://github.com/zzq1zh/GenAI-Lab.