# Rethinking Decoder Design: Improving Biomarker Segmentation Using Depth-to-Space Restoration and Residual Linear Attention

arXiv: https://arxiv.org/abs/2506.18335 · HTML: https://mlsanity.com/paper/2506.18335/

## Key facts

- Cited by 4 papers in the map (data through 14 Oct 2026).
- Builds on 43 of its 65 references that are in the map.
- First posted on arXiv 23 Jun 2025.

## Builds on (most cited first, 30 of 43)

- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [Segment Anything](https://mlsanity.com/paper/2304.02643/) (2023)
- [Fully Convolutional Networks for Semantic Segmentation](https://mlsanity.com/paper/1411.4038/) (2014)
- [Squeeze-and-Excitation Networks](https://mlsanity.com/paper/1709.01507/) (2017)
- [DeepLab: Semantic Image Segmentation with Deep Convolutional Nets, Atrous Convolution, and Fully Connected CRFs](https://mlsanity.com/paper/1606.00915/) (2016)
- [SegFormer: Simple and Efficient Design for Semantic Segmentation with Transformers](https://mlsanity.com/paper/2105.15203/) (2021)
- [CBAM: Convolutional Block Attention Module](https://mlsanity.com/paper/1807.06521/) (2018)
- [TransUNet: Transformers Make Strong Encoders for Medical Image Segmentation](https://mlsanity.com/paper/2102.04306/) (2021)
- [UNet++: A Nested U-Net Architecture for Medical Image Segmentation](https://mlsanity.com/paper/1807.10165/) (2018)
- [Attention U-Net: Learning Where to Look for the Pancreas](https://mlsanity.com/paper/1804.03999/) (2018)
- [Swin-Unet: Unet-like Pure Transformer for Medical Image Segmentation](https://mlsanity.com/paper/2105.05537/) (2021)
- [Real-Time Single Image and Video Super-Resolution Using an Efficient Sub-Pixel Convolutional Neural Network](https://mlsanity.com/paper/1609.05158/) (2016)
- [Uformer: A General U-Shaped Transformer for Image Restoration](https://mlsanity.com/paper/2106.03106/) (2021)
- [Albumentations: fast and flexible image augmentations](https://mlsanity.com/paper/1809.06839/) (2018)
- [Deep Layer Aggregation](https://mlsanity.com/paper/1707.06484/) (2017)
- [U2-Net: Going Deeper with Nested U-Structure for Salient Object Detection](https://mlsanity.com/paper/2005.09007/) (2020)
- [Conditional Positional Encodings for Vision Transformers](https://mlsanity.com/paper/2102.10882/) (2021)
- [HoVer-Net: Simultaneous Segmentation and Classification of Nuclei in Multi-Tissue Histology Images](https://mlsanity.com/paper/1812.06499/) (2018)
- [UNet 3+: A Full-Scale Connected UNet for Medical Image Segmentation](https://mlsanity.com/paper/2004.08790/) (2020)
- [3D MRI brain tumor segmentation using autoencoder regularization](https://mlsanity.com/paper/1810.11654/) (2018)
- [A survey of loss functions for semantic segmentation](https://mlsanity.com/paper/2006.14822/) (2020)
- [UCTransNet: Rethinking the Skip Connections in U-Net from a Channel-wise Perspective with Transformer](https://mlsanity.com/paper/2109.04335/) (2021)
- [Recurrent Residual Convolutional Neural Network based on U-Net (R2U-Net) for Medical Image Segmentation](https://mlsanity.com/paper/1802.06955/) (2018)
- [How Much Position Information Do Convolutional Neural Networks Encode?](https://mlsanity.com/paper/2001.08248/) (2020)
- [Polyp-PVT: Polyp Segmentation with Pyramid Vision Transformers](https://mlsanity.com/paper/2108.06932/) (2021)
- [Amulet: Aggregating Multi-level Convolutional Features for Salient Object Detection](https://mlsanity.com/paper/1708.02001/) (2017)
- [EMCAD: Efficient Multi-scale Convolutional Attention Decoding for Medical Image Segmentation](https://mlsanity.com/paper/2405.06880/) (2024)
- [All-in-SAM: from Weak Annotation to Pixel-wise Nuclei Segmentation with Prompt-based Finetuning](https://mlsanity.com/paper/2307.00290/) (2023)
- [DDANet: Dual Decoder Attention Network for Automatic Polyp Segmentation](https://mlsanity.com/paper/2012.15245/) (2020)
- [RAUNet: Residual Attention U-Net for Semantic Segmentation of Cataract Surgical Instruments](https://mlsanity.com/paper/1909.10360/) (2019)

## Built on by (most cited first, 4 of 4)

- [Revisiting the Ordering of Channel and Spatial Attention: A Comprehensive Study on Sequential and Parallel Designs](https://mlsanity.com/paper/2601.07310/) (2026)
- [DTC: A Deformable Transposed Convolution Module for Medical Image Segmentation](https://mlsanity.com/paper/2601.17939/) (2026)
- [FSS-Net: Frequency-Spatial Synergy Network with Wavelet Attention for Carotid Artery Ultrasound Segmentation](https://mlsanity.com/paper/2606.10378/) (2026)
- [MedCAGD: Context-Aware Gated Decoder for Efficient Medical Image Segmentation](https://mlsanity.com/paper/2607.00409/) (2026)

## Abstract (arXiv)

Segmenting biomarkers in medical images is crucial for various biotech applications. Despite advances, Transformer and CNN based methods often struggle with variations in staining and morphology, limiting feature extraction. In medical image segmentation, where datasets often have limited sample availability, recent state-of-the-art (SOTA) methods achieve higher accuracy by leveraging pre-trained encoders, whereas end-to-end methods tend to underperform. This is due to challenges in effectively transferring rich multiscale features from encoders to decoders, as well as limitations in decoder efficiency. To address these issues, we propose an architecture that captures multi-scale local and global contextual information and a novel decoder design, which effectively integrates features from the encoder, emphasizes important channels and regions, and reconstructs spatial dimensions to enhance segmentation accuracy. Our method, compatible with various encoders, outperforms SOTA methods, as demonstrated by experiments on four datasets and ablation studies. Specifically, our method achieves absolute performance gains of 2.76% on MoNuSeg, 3.12% on DSB, 2.87% on Electron Microscopy, and 4.03% on TNBC datasets compared to existing SOTA methods. Code: https://github.com/saadwazir/MCADS-Decoder