# HiCMamba: Enhancing Hi-C Resolution and Identifying 3D Genome Structures with State Space Modeling

arXiv: https://arxiv.org/abs/2503.10713 · HTML: https://mlsanity.com/paper/2503.10713/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 11 of its 53 references that are in the map.
- First posted on arXiv 13 Mar 2025.

## Builds on (most cited first, 11 of 11)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [Layer Normalization](https://mlsanity.com/paper/1607.06450/) (2016)
- [Mamba: Linear-Time Sequence Modeling with Selective State Spaces](https://mlsanity.com/paper/2312.00752/) (2023)
- [Gaussian Error Linear Units (GELUs)](https://mlsanity.com/paper/1606.08415/) (2016)
- [VMamba: Visual State Space Model](https://mlsanity.com/paper/2401.10166/) (2024)
- [CvT: Introducing Convolutions to Vision Transformers](https://mlsanity.com/paper/2103.15808/) (2021)
- [Uformer: A General U-Shaped Transformer for Image Restoration](https://mlsanity.com/paper/2106.03106/) (2021)
- [Scaling Up Your Kernels to 31x31: Revisiting Large Kernel Design in CNNs](https://mlsanity.com/paper/2203.06717/) (2022)
- [Facing Off World Model Backbones: RNNs, Transformers, and S4](https://mlsanity.com/paper/2307.02064/) (2023)

## Abstract (arXiv)

Hi-C technology measures genome-wide interaction frequencies, providing a powerful tool for studying the 3D genomic structure within the nucleus. However, high sequencing costs and technical challenges often result in Hi-C data with limited coverage, leading to imprecise estimates of chromatin interaction frequencies. To address this issue, we present a novel deep learning-based method HiCMamba to enhance the resolution of Hi-C contact maps using a state space model. We adopt the UNet-based auto-encoder architecture to stack the proposed holistic scan block, enabling the perception of both global and local receptive fields at multiple scales. Experimental results demonstrate that HiCMamba outperforms state-of-the-art methods while significantly reducing computational resources. Furthermore, the 3D genome structures, including topologically associating domains (TADs) and loops, identified in the contact maps recovered by HiCMamba are validated through associated epigenomic features. Our work demonstrates the potential of a state space model as foundational frameworks in the field of Hi-C resolution enhancement.