# HER-Seg: Holistically Efficient Segmentation for High-Resolution Medical Images

arXiv: https://arxiv.org/abs/2504.06205 · HTML: https://mlsanity.com/paper/2504.06205/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 28 of its 46 references that are in the map.
- First posted on arXiv 8 Apr 2025.

## Builds on (most cited first, 28 of 28)

- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [Segment Anything](https://mlsanity.com/paper/2304.02643/) (2023)
- [Mamba: Linear-Time Sequence Modeling with Selective State Spaces](https://mlsanity.com/paper/2312.00752/) (2023)
- [RoFormer: Enhanced Transformer with Rotary Position Embedding](https://mlsanity.com/paper/2104.09864/) (2021)
- [SAM 2: Segment Anything in Images and Videos](https://mlsanity.com/paper/2408.00714/) (2024)
- [Transformers are RNNs: Fast Autoregressive Transformers with Linear Attention](https://mlsanity.com/paper/2006.16236/) (2020)
- [Swin-Unet: Unet-like Pure Transformer for Medical Image Segmentation](https://mlsanity.com/paper/2105.05537/) (2021)
- [Skin Lesion Analysis Toward Melanoma Detection 2018: A Challenge Hosted by the International Skin Imaging Collaboration (ISIC)](https://mlsanity.com/paper/1902.03368/) (2019)
- [UNet++: Redesigning Skip Connections to Exploit Multiscale Features in Image Segmentation](https://mlsanity.com/paper/1912.05074/) (2019)
- [MetaFormer Is Actually What You Need for Vision](https://mlsanity.com/paper/2111.11418/) (2021)
- [Faster Segment Anything: Towards Lightweight SAM for Mobile Applications](https://mlsanity.com/paper/2306.14289/) (2023)
- [Attention Gated Networks: Learning to Leverage Salient Regions in Medical Images](https://mlsanity.com/paper/1808.08114/) (2018)
- [SegMamba: Long-range Sequential Modeling Mamba For 3D Medical Image Segmentation](https://mlsanity.com/paper/2401.13560/) (2024)
- [REFUGE Challenge: A Unified Framework for Evaluating Automated Methods for Glaucoma Assessment from Fundus Photographs](https://mlsanity.com/paper/1910.03667/) (2019)
- [A Benchmark for Endoluminal Scene Segmentation of Colonoscopy Images](https://mlsanity.com/paper/1612.00799/) (2016)
- [EfficientSAM: Leveraged Masked Image Pretraining for Efficient Segment Anything](https://mlsanity.com/paper/2312.00863/) (2023)
- [UNeXt: MLP-based Rapid Medical Image Segmentation Network](https://mlsanity.com/paper/2203.04967/) (2022)
- [Swin-UMamba: Mamba-based UNet with ImageNet-based pretraining](https://mlsanity.com/paper/2402.03302/) (2024)
- [U-KAN Makes Strong Backbone for Medical Image Segmentation and Generation](https://mlsanity.com/paper/2406.02918/) (2024)
- [EfficientViT: Memory Efficient Vision Transformer with Cascaded Group Attention](https://mlsanity.com/paper/2305.07027/) (2023)
- [RepViT: Revisiting Mobile CNN From ViT Perspective](https://mlsanity.com/paper/2307.09283/) (2023)
- [EMCAD: Efficient Multi-scale Convolutional Attention Decoding for Medical Image Segmentation](https://mlsanity.com/paper/2405.06880/) (2024)
- [TinySAM: Pushing the Envelope for Efficient Segment Anything Model](https://mlsanity.com/paper/2312.13789/) (2023)
- [ACC-UNet: A Completely Convolutional UNet model for the 2020s](https://mlsanity.com/paper/2308.13680/) (2023)
- [Modality-agnostic Domain Generalizable Medical Image Segmentation by Multi-Frequency in Multi-Scale Attention](https://mlsanity.com/paper/2405.06284/) (2024)
- [Serp-Mamba: Advancing High-Resolution Retinal Vessel Segmentation with Selective State-Space Model](https://mlsanity.com/paper/2409.04356/) (2024)
- [SelfReg-UNet: Self-Regularized UNet for Medical Image Segmentation](https://mlsanity.com/paper/2406.14896/) (2024)

## Abstract (arXiv)

High-resolution segmentation is critical for precise disease diagnosis by extracting fine-grained morphological details. Existing hierarchical encoder-decoder frameworks have demonstrated remarkable adaptability across diverse medical segmentation tasks. While beneficial, they usually require the huge computation and memory cost when handling large-size segmentation, which limits their applications in foundation model building and real-world clinical scenarios. To address this limitation, we propose a holistically efficient framework for high-resolution medical image segmentation, called HER-Seg. Specifically, we first devise a computation-efficient image encoder (CE-Encoder) to model long-range dependencies with linear complexity while maintaining sufficient representations. In particular, we introduce the dual-gated linear attention (DLA) mechanism to perform cascaded token filtering, selectively retaining important tokens while ignoring irrelevant ones to enhance attention computation efficiency. Then, we introduce a memory-efficient mask decoder (ME-Decoder) to eliminate the demand for the hierarchical structure by leveraging cross-scale segmentation decoding. Extensive experiments reveal that HER-Seg outperforms state-of-the-arts in high-resolution medical 2D, 3D and video segmentation tasks. In particular, our HER-Seg requires only 0.59GB training GPU memory and 9.39G inference FLOPs per 1024×1024 image, demonstrating superior memory and computation efficiency. The code is available at https://github.com/xq141839/HER-Seg.