# RefineFormer3D: Efficient 3D Medical Image Segmentation via Adaptive Multi-Scale Transformer with Cross Attention Fusion

arXiv: https://arxiv.org/abs/2602.16320 · HTML: https://mlsanity.com/paper/2602.16320/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 32 of its 44 references that are in the map.
- First posted on arXiv 18 Feb 2026.

## Builds on (most cited first, 30 of 32)

- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [Swin Transformer: Hierarchical Vision Transformer using Shifted Windows](https://mlsanity.com/paper/2103.14030/) (2021)
- [Squeeze-and-Excitation Networks](https://mlsanity.com/paper/1709.01507/) (2017)
- [SegFormer: Simple and Efficient Design for Semantic Segmentation with Transformers](https://mlsanity.com/paper/2105.15203/) (2021)
- [V-Net: Fully Convolutional Neural Networks for Volumetric Medical Image Segmentation](https://mlsanity.com/paper/1606.04797/) (2016)
- [Decoupled Weight Decay Regularization](https://mlsanity.com/paper/1711.05101/) (2017)
- [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)
- [3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation](https://mlsanity.com/paper/1606.06650/) (2016)
- [Rethinking Semantic Segmentation from a Sequence-to-Sequence Perspective with Transformers](https://mlsanity.com/paper/2012.15840/) (2020)
- [Swin-Unet: Unet-like Pure Transformer for Medical Image Segmentation](https://mlsanity.com/paper/2105.05537/) (2021)
- [Deep Networks with Stochastic Depth](https://mlsanity.com/paper/1603.09382/) (2016)
- [UNETR: Transformers for 3D Medical Image Segmentation](https://mlsanity.com/paper/2103.10504/) (2021)
- [Swin UNETR: Swin Transformers for Semantic Segmentation of Brain Tumors in MRI Images](https://mlsanity.com/paper/2201.01266/) (2022)
- [GhostNet: More Features from Cheap Operations](https://mlsanity.com/paper/1911.11907/) (2019)
- [Vision Transformer with Deformable Attention](https://mlsanity.com/paper/2201.00520/) (2022)
- [nnU-Net: Self-adapting Framework for U-Net-Based Medical Image Segmentation](https://mlsanity.com/paper/1809.10486/) (2018)
- [TransBTS: Multimodal Brain Tumor Segmentation Using Transformer](https://mlsanity.com/paper/2103.04430/) (2021)
- [TransFuse: Fusing Transformers and CNNs for Medical Image Segmentation](https://mlsanity.com/paper/2102.08005/) (2021)
- [CoTr: Efficiently Bridging CNN and Transformer for 3D Medical Image Segmentation](https://mlsanity.com/paper/2103.03024/) (2021)
- [nnFormer: Interleaved Transformer for Volumetric Segmentation](https://mlsanity.com/paper/2109.03201/) (2021)
- [Global Self-Attention as a Replacement for Graph Convolution](https://mlsanity.com/paper/2108.03348/) (2021)
- [Non-local Attention Optimized Deep Image Compression](https://mlsanity.com/paper/1904.09757/) (2019)
- [LeViT-UNet: Make Faster Encoders with Transformer for Medical Image Segmentation](https://mlsanity.com/paper/2107.08623/) (2021)
- [P2T: Pyramid Pooling Transformer for Scene Understanding](https://mlsanity.com/paper/2106.12011/) (2021)
- [On the Role of Attention Masks and LayerNorm in Transformers](https://mlsanity.com/paper/2405.18781/) (2024)
- [Frequency-Adaptive Dilated Convolution for Semantic Segmentation](https://mlsanity.com/paper/2403.05369/) (2024)
- [SegFormer3D: an Efficient Transformer for 3D Medical Image Segmentation](https://mlsanity.com/paper/2404.10156/) (2024)
- [Deeply-Supervised CNN for Prostate Segmentation](https://mlsanity.com/paper/1703.07523/) (2017)
- [Beyond BatchNorm: Towards a Unified Understanding of Normalization in Deep Learning](https://mlsanity.com/paper/2106.05956/) (2021)

## Abstract (arXiv)

Accurate and computationally efficient 3D medical image segmentation remains a critical challenge in clinical workflows. Transformer-based architectures often demonstrate superior global contextual modeling but at the expense of excessive parameter counts and memory demands, restricting their clinical deployment. We propose RefineFormer3D, a lightweight hierarchical transformer architecture that balances segmentation accuracy and computational efficiency for volumetric medical imaging. The architecture integrates three key components: (i) GhostConv3D-based patch embedding for efficient feature extraction with minimal redundancy, (ii) MixFFN3D module with low-rank projections and depthwise convolutions for parameter-efficient feature extraction, and (iii) a cross-attention fusion decoder enabling adaptive multi-scale skip connection integration. RefineFormer3D contains only 2.94M parameters, substantially fewer than contemporary transformer-based methods. Extensive experiments on ACDC and BraTS benchmarks demonstrate that RefineFormer3D achieves 93.44% and 85.9% average Dice scores respectively, outperforming or matching state-of-the-art methods while requiring significantly fewer parameters. Furthermore, the model achieves fast inference (8.35 ms per volume on GPU) with low memory requirements, supporting deployment in resource-constrained clinical environments. These results establish RefineFormer3D as an effective and scalable solution for practical 3D medical image segmentation.