Uncertainty-guided transformer for brain tumor segmentation

Med Biol Eng Comput. 2023 Sep 4. doi: 10.1007/s11517-023-02899-8. Online ahead of print.


Multi-model data can enhance brain tumor segmentation for the rich information it provides. However, it also introduces some redundant information that interferes with the segmentation estimation, as some modalities may catch features irrelevant to the tissue of interest. Besides, the ambiguous boundaries and irregulate shapes of different grade tumors lead to a non-confidence estimate of segmentation quality. Given these concerns, we exploit an uncertainty-guided U-shaped transformer with multiple heads to construct drop-out format masks for robust training. Specifically, our drop-out masks are composed of boundary mask, prior probability mask, and conditional probability mask, which can help our approach focus more on uncertainty regions. Extensive experimental results show that our method achieves comparable or higher results than previous state-of-the-art brain tumor segmentation methods, achieving average dice coefficients of [Formula: see text] and Hausdorff distance of 4.91 on the BraTS2021 dataset. Our code is freely available at https://github.com/chaineypung/BTS-UGT.

Keywords: Transformer; Tumor segmentation; Uncertainty mask.