# FSS-UBrain: Multi-region Few-Shot Brain Tumor MRI Segmentation

arXiv: https://arxiv.org/abs/2609.32273 · HTML: https://mlsanity.com/paper/2609.32273/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 32 of its 53 references that are in the map.
- First posted on arXiv 26 Sep 2026.

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

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [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)
- [Segment Anything](https://mlsanity.com/paper/2304.02643/) (2023)
- [FiLM: Visual Reasoning with a General Conditioning Layer](https://mlsanity.com/paper/1709.07871/) (2017)
- [V-Net: Fully Convolutional Neural Networks for Volumetric Medical Image Segmentation](https://mlsanity.com/paper/1606.04797/) (2016)
- [Rethinking Atrous Convolution for Semantic Image Segmentation](https://mlsanity.com/paper/1706.05587/) (2017)
- [TransUNet: Transformers Make Strong Encoders for Medical Image Segmentation](https://mlsanity.com/paper/2102.04306/) (2021)
- [Group Normalization](https://mlsanity.com/paper/1803.08494/) (2018)
- [3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation](https://mlsanity.com/paper/1606.06650/) (2016)
- [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)
- [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)
- [A Survey on Visual Transformer](https://mlsanity.com/paper/2012.12556/) (2020)
- [UNet++: Redesigning Skip Connections to Exploit Multiscale Features in Image Segmentation](https://mlsanity.com/paper/1912.05074/) (2019)
- [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)
- [PANet: Few-Shot Image Semantic Segmentation with Prototype Alignment](https://mlsanity.com/paper/1908.06391/) (2019)
- [Deeply-Supervised Nets](https://mlsanity.com/paper/1409.5185/) (2014)
- [One-Shot Learning for Semantic Segmentation](https://mlsanity.com/paper/1709.03410/) (2017)
- [VM-UNet: Vision Mamba UNet for Medical Image Segmentation](https://mlsanity.com/paper/2402.02491/) (2024)
- [Prior Guided Feature Enrichment Network for Few-Shot Segmentation](https://mlsanity.com/paper/2008.01449/) (2020)
- [CoTr: Efficiently Bridging CNN and Transformer for 3D Medical Image Segmentation](https://mlsanity.com/paper/2103.03024/) (2021)
- [Hypercorrelation Squeeze for Few-Shot Segmentation](https://mlsanity.com/paper/2104.01538/) (2021)
- [Self-Supervision with Superpixels: Training Few-shot Medical Image Segmentation without Annotation](https://mlsanity.com/paper/2007.09886/) (2020)
- [The 2024 Brain Tumor Segmentation (BraTS) Challenge: Glioma Segmentation on Post-treatment MRI](https://mlsanity.com/paper/2405.18368/) (2024)
- [CKD-TransBTS: Clinical Knowledge-Driven Hybrid Transformer with Modality-Correlated Cross-Attention for Brain Tumor Segmentation](https://mlsanity.com/paper/2207.07370/) (2022)
- [Q-Net: Query-Informed Few-Shot Medical Image Segmentation](https://mlsanity.com/paper/2208.11451/) (2022)
- [Few Shot Medical Image Segmentation with Cross Attention Transformer](https://mlsanity.com/paper/2303.13867/) (2023)

## Abstract (arXiv)

Accurate delineation of whole tumor (WT), tumor core (TC), and enhancing tumor (ET) from multimodal magnetic resonance imaging remains challenging under limited annotation, cross-cohort variation, and severe target sparsity. We propose FSS-UBrain, a region-wise one-shot segmentation framework that uses a labeled positive support slice to condition binary query segmentation separately for WT, TC, and ET. Support-derived foreground and background descriptors guide query-feature adaptation, bottleneck interaction, decoder-side reconstruction, and boundary refinement. Episodic training additionally incorporates hard-negative and fully negative queries with empty-query regularization to suppress spurious foreground activation when the selected region is absent. Although inference operates on two-dimensional support--query slice pairs, checkpoint selection, threshold calibration, and final evaluation are performed after volumetric reconstruction. FSS-UBrain is evaluated on a held-out BraTS 2020 split and under target-supported cross-cohort protocols on BraTS 2023 and BraTS-Africa. Cases used as target support are excluded from the query cohorts, and no target-domain fine-tuning or test-time parameter updates are performed. On BraTS 2020, FSS-UBrain achieves volumetric Dice scores of 89.82%, 82.14%, and 77.42% for WT, TC, and ET, respectively, with corresponding 95th-percentile Hausdorff distance (HD95) values of 11.12, 9.01, and 4.46 mm. It also achieves the highest mean Dice and lowest finite-pair mean HD95 point estimates on BraTS 2023 and BraTS-Africa among the compared few-shot methods. These findings support target-conditioned few-shot segmentation while highlighting sensitivity to support selection and cohort-specific variation.