# UNetFormer: A Unified Vision Transformer Model and Pre-Training Framework for 3D Medical Image Segmentation

arXiv: https://arxiv.org/abs/2204.00631 · HTML: https://mlsanity.com/paper/2204.00631/

## Key facts

- Cited by 16 papers in the map (data through 14 Oct 2026).
- Builds on 20 of its 25 references that are in the map.
- First posted on arXiv 1 Apr 2022.

## Builds on (most cited first, 20 of 20)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [Swin Transformer: Hierarchical Vision Transformer using Shifted Windows](https://mlsanity.com/paper/2103.14030/) (2021)
- [Masked Autoencoders Are Scalable Vision Learners](https://mlsanity.com/paper/2111.06377/) (2021)
- [BEiT: BERT Pre-Training of Image Transformers](https://mlsanity.com/paper/2106.08254/) (2021)
- [V-Net: Fully Convolutional Neural Networks for Volumetric Medical Image Segmentation](https://mlsanity.com/paper/1606.04797/) (2016)
- [TransUNet: Transformers Make Strong Encoders for Medical Image Segmentation](https://mlsanity.com/paper/2102.04306/) (2021)
- [Instance Normalization: The Missing Ingredient for Fast Stylization](https://mlsanity.com/paper/1607.08022/) (2016)
- [SimMIM: A Simple Framework for Masked Image Modeling](https://mlsanity.com/paper/2111.09886/) (2021)
- [Per-Pixel Classification is Not All You Need for Semantic Segmentation](https://mlsanity.com/paper/2107.06278/) (2021)
- [UNETR: Transformers for 3D Medical Image Segmentation](https://mlsanity.com/paper/2103.10504/) (2021)
- [Do Vision Transformers See Like Convolutional Neural Networks?](https://mlsanity.com/paper/2108.08810/) (2021)
- [The Medical Segmentation Decathlon](https://mlsanity.com/paper/2106.05735/) (2021)
- [The RSNA-ASNR-MICCAI BraTS 2021 Benchmark on Brain Tumor Segmentation and Radiogenomic Classification](https://mlsanity.com/paper/2107.02314/) (2021)
- [Identifying the Best Machine Learning Algorithms for Brain Tumor Segmentation, Progression Assessment, and Overall Survival Prediction in the BRATS Challenge](https://mlsanity.com/paper/1811.02629/) (2018)
- [3D MRI brain tumor segmentation using autoencoder regularization](https://mlsanity.com/paper/1810.11654/) (2018)
- [TransBTS: Multimodal Brain Tumor Segmentation Using Transformer](https://mlsanity.com/paper/2103.04430/) (2021)
- [Transformers in Medical Imaging: A Survey](https://mlsanity.com/paper/2201.09873/) (2022)
- [nnFormer: Interleaved Transformer for Volumetric Segmentation](https://mlsanity.com/paper/2109.03201/) (2021)
- [Transferable Visual Words: Exploiting the Semantics of Anatomical Patterns for Self-supervised Learning](https://mlsanity.com/paper/2102.10680/) (2021)

## Built on by (most cited first, 16 of 16)

- [Channel Vision Transformers: An Image Is Worth 1 x 16 x 16 Words](https://mlsanity.com/paper/2309.16108/) (2023)
- [CKD-TransBTS: Clinical Knowledge-Driven Hybrid Transformer with Modality-Correlated Cross-Attention for Brain Tumor Segmentation](https://mlsanity.com/paper/2207.07370/) (2022)
- [Disruptive Autoencoders: Leveraging Low-level features for 3D Medical Image Pre-training](https://mlsanity.com/paper/2307.16896/) (2023)
- [A Comprehensive Survey of Transformers for Computer Vision](https://mlsanity.com/paper/2211.06004/) (2022)
- [SegStitch: Multidimensional Transformer for Robust and Efficient Medical Imaging Segmentation](https://mlsanity.com/paper/2408.00496/) (2024)
- [Vision Foundation Models in Medical Image Analysis: Advances and Challenges](https://mlsanity.com/paper/2502.14584/) (2025)
- [Vision Transformers in Medical Imaging: A Review](https://mlsanity.com/paper/2211.10043/) (2022)
- [Robust Wind Turbine Blade Segmentation from RGB Images in the Wild](https://mlsanity.com/paper/2306.14810/) (2023)
- [Keypoint-Augmented Self-Supervised Learning for Medical Image Segmentation with Limited Annotation](https://mlsanity.com/paper/2310.01680/) (2023)
- [Understanding the Tricks of Deep Learning in Medical Image Segmentation: Challenges and Future Directions](https://mlsanity.com/paper/2209.10307/) (2022)
- [TranSOP: Transformer-based Multimodal Classification for Stroke Treatment Outcome Prediction](https://mlsanity.com/paper/2301.10829/) (2023)
- [Multiscale Progressive Text Prompt Network for Medical Image Segmentation](https://mlsanity.com/paper/2307.00174/) (2023)
- [M4Fog: A Global Multi-Regional, Multi-Modal, and Multi-Stage Dataset for Marine Fog Detection and Forecasting to Bridge Ocean and Atmosphere](https://mlsanity.com/paper/2406.13317/) (2024)
- [Learnable Weight Initialization for Volumetric Medical Image Segmentation](https://mlsanity.com/paper/2306.09320/) (2023)
- [MedContext: Learning Contextual Cues for Efficient Volumetric Medical Segmentation](https://mlsanity.com/paper/2402.17725/) (2024)
- [MFogHub: Bridging Multi-Regional and Multi-Satellite Data for Global Marine Fog Detection and Forecasting](https://mlsanity.com/paper/2505.10281/) (2025)

## Abstract (arXiv)

Vision Transformers (ViT)s have recently become popular due to their outstanding modeling capabilities, in particular for capturing long-range information, and scalability to dataset and model sizes which has led to state-of-the-art performance in various computer vision and medical image analysis tasks. In this work, we introduce a unified framework consisting of two architectures, dubbed UNetFormer, with a 3D Swin Transformer-based encoder and Convolutional Neural Network (CNN) and transformer-based decoders. In the proposed model, the encoder is linked to the decoder via skip connections at five different resolutions with deep supervision. The design of proposed architecture allows for meeting a wide range of trade-off requirements between accuracy and computational cost. In addition, we present a methodology for self-supervised pre-training of the encoder backbone via learning to predict randomly masked volumetric tokens using contextual information of visible tokens. We pre-train our framework on a cohort of 5050 CT images, gathered from publicly available CT datasets, and present a systematic investigation of various components such as masking ratio and patch size that affect the representation learning capability and performance of downstream tasks. We validate the effectiveness of our pre-training approach by fine-tuning and testing our model on liver and liver tumor segmentation task using the Medical Segmentation Decathlon (MSD) dataset and achieve state-of-the-art performance in terms of various segmentation metrics. To demonstrate its generalizability, we train and test the model on BraTS 21 dataset for brain tumor segmentation using MRI images and outperform other methods in terms of Dice score. Code: https://github.com/Project-MONAI/research-contributions