# VIViT: Variable-Input Vision Transformer Framework for 3D MR Image Segmentation

arXiv: https://arxiv.org/abs/2505.08693 · HTML: https://mlsanity.com/paper/2505.08693/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 25 of its 30 references that are in the map.
- First posted on arXiv 13 May 2025.

## Builds on (most cited first, 25 of 25)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [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)
- [DINOv2: Learning Robust Visual Features without Supervision](https://mlsanity.com/paper/2304.07193/) (2023)
- [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)
- [DINO: DETR with Improved DeNoising Anchor Boxes for End-to-End Object Detection](https://mlsanity.com/paper/2203.03605/) (2022)
- [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)
- [The RSNA-ASNR-MICCAI BraTS 2021 Benchmark on Brain Tumor Segmentation and Radiogenomic Classification](https://mlsanity.com/paper/2107.02314/) (2021)
- [MONAI: An open-source framework for deep learning in healthcare](https://mlsanity.com/paper/2211.02701/) (2022)
- [Self-Supervised Pre-Training of Swin Transformers for 3D Medical Image Analysis](https://mlsanity.com/paper/2111.14791/) (2021)
- [3D MRI brain tumor segmentation using autoencoder regularization](https://mlsanity.com/paper/1810.11654/) (2018)
- [3D UX-Net: A Large Kernel Volumetric ConvNet Modernizing Hierarchical Transformer for Medical Image Segmentation](https://mlsanity.com/paper/2209.15076/) (2022)
- [MedViT: A Robust Vision Transformer for Generalized Medical Image Classification](https://mlsanity.com/paper/2302.09462/) (2023)
- [TransMed: Transformers Advance Multi-modal Medical Image Classification](https://mlsanity.com/paper/2103.05940/) (2021)
- [Self Pre-training with Masked Autoencoders for Medical Image Classification and Segmentation](https://mlsanity.com/paper/2203.05573/) (2022)
- [Domain and Content Adaptive Convolution based Multi-Source Domain Generalization for Medical Image Segmentation](https://mlsanity.com/paper/2109.05676/) (2021)
- [ModDrop++: A Dynamic Filter Network with Intra-subject Co-training for Multiple Sclerosis Lesion Segmentation with Missing Modalities](https://mlsanity.com/paper/2203.04959/) (2022)
- [Medical Image Segmentation on MRI Images with Missing Modalities: A Review](https://mlsanity.com/paper/2203.06217/) (2022)
- [A Unified Hyper-GAN Model for Unpaired Multi-contrast MR Image Translation](https://mlsanity.com/paper/2107.11945/) (2021)
- [Deep learning and its application to medical image segmentation](https://mlsanity.com/paper/1803.08691/) (2018)
- [LKD-Net: Large Kernel Convolution Network for Single Image Dehazing](https://mlsanity.com/paper/2209.01788/) (2022)
- [Self Pre-training with Adaptive Mask Autoencoders for Variable-Contrast 3D Medical Imaging](https://mlsanity.com/paper/2501.09096/) (2025)

## Abstract (arXiv)

Self-supervised pretrain techniques have been widely used to improve the downstream tasks' performance. However, real-world magnetic resonance (MR) studies usually consist of different sets of contrasts due to different acquisition protocols, which poses challenges for the current deep learning methods on large-scale pretrain and different downstream tasks with different input requirements, since these methods typically require a fixed set of input modalities or, contrasts. To address this challenge, we propose variable-input ViT (VIViT), a transformer-based framework designed for self-supervised pretraining and segmentation finetuning for variable contrasts in each study. With this ability, our approach can maximize the data availability in pretrain, and can transfer the learned knowledge from pretrain to downstream tasks despite variations in input requirements. We validate our method on brain infarct and brain tumor segmentation, where our method outperforms current CNN and ViT-based models with a mean Dice score of 0.624 and 0.883 respectively. These results highlight the efficacy of our design for better adaptability and performance on tasks with real-world heterogeneous MR data.