Vision Transformer-Conditioned UNet for Domain-Adaptive Semantic Segmentation

Medical image segmentation is dominated by U-Net-style encoder-decoder architectures. Vision Transformers (ViTs) overcome the limited receptive field of convolutional networks through self-attention, enabling modeling of long-range dependencies. Early ViT-based segmentation methods typically retained U-Net-style decoders because pretrained ViT representations were insufficient to support accurate dense prediction. Recent advances in large-scale pretraining have redefined the representation capability of ViTs, reducing the reliance on U-Net-style decoder architectures in modern vision models. This prompts two questions: Is the U-Net paradigm still necessary for medical image segmentation? If not, how should an encoder-only segmentation framework be designed? Motivated by these questions, we explore key architectural choices for encoder-only medical image segmentation based on modern ViT backbones and establish a query-based encoder-only design with multi-level query modeling and learnable block fusion, realized in Encoder-only Segmentation (EoSeg). Extensive experiments across seven benchmark datasets spanning CT, MRI, histopathology, endoscopy, and dermoscopy validate the effectiveness of the proposed design across diverse medical imaging modalities, including mDice scores of 85.50% on Synapse, 91.73% on ACDC, and 93.27% on GlaS. The results demonstrate that a U-Net-style decoder is no longer necessary for medical image segmentation with modern ViT backbones and further show that EoSeg provides an effective encoder-only design. Code is available at: https://github.com/Retinal-Research/EoSeg

Medical image segmentation plays an important role in computer aided diagnosis, treatment planning, and disease monitoring. U-Net has been widely used for biomedical image segmentation because of its encoder decoder structure and skip connections. However, conventional convolution based U-Net models may have limited ability to capture long range dependencies and global contextual information, which can affect performance in complex segmentation tasks. This paper presents a comparative study of five U-Net based architectures: U-Net 3D, Residual U-Net, Attention U-Net, UNETR, and Swin UNETR. The models are evaluated on two benchmark datasets: BraTS 2023 for brain tumor segmentation and DRIVE for retinal vessel segmentation. Experimental results show that Swin UNETR achieves the best overall performance, with Dice scores of 0.8965 on BraTS 2023 and 0.8078 on DRIVE. The results suggest that transformer based U-Net variants are effective for segmentation tasks requiring global contextual modeling, while residual learning remains useful for fine structure segmentation. This study provides practical insights into model selection for medical image segmentation across volumetric MRI and retinal imaging tasks.

Vision Transformers (ViTs) can learn strong image-level representations while their patch representations become less effective for dense prediction during prolonged training. We revisit this dense degradation phenomenon and argue that it is not fully explained by high-norm artifacts alone. Instead, we characterize \emph{semantic diffusion}: an optimization shortcut in which global semantic information spreads through patch tokens beyond what is locally justified. Our analysis shows that dense representation quality is not captured by locality alone: shallow features can remain better aligned with foreground regions yet underperform deeper features, and \texttt{[CLS]} features remain complementary for dense prediction. These observations suggest that the goal should not be to remove global context, but to make token interactions more selective. We therefore study sparse attention as a minimal intervention, replacing softmax attention with entmax-1.5 while preserving global token connectivity. On DINOv1 ViT-S/16 trained for 200 epochs on ImageNet-1K, this change preserves ImageNet linear probing accuracy and substantially improves semantic segmentation performance: VOC mIoU increases from 42.80 to 48.78, ADE20K from 19.85 to 21.97, and Cityscapes from 36.79 to 37.87. These results suggest that selective token mixing is a simple and effective bias for improving dense ViT representations.