Top 10 BraTS 2020 challenge solution: Brain tumor segmentation with self-ensembled, deeply-supervised 3D-Unet like neural networks

Brain tumor segmentation is a critical task for patient's disease management. To this end, we trained multiple U-net like neural networks, mainly with deep supervision and stochastic weight averaging, on the Multimodal Brain Tumor Segmentation Challenge (BraTS) 2020 training dataset, in a cross-validated fashion. Final brain tumor segmentations were produced by first averaging independently two sets of models, and then custom merging the labelmaps to account for individual performance of each set. Our performance on the online validation dataset with test time augmentation were as follows: Dice of 0.81, 0.91 and 0.85; Hausdorff (95%) of 20.6, 4,3, 5.7 mm for the enhancing tumor, whole tumor and tumor core, respectively. Similarly, our ensemble achieved a Dice of 0.79, 0.89 and 0.84, as well as Hausdorff (95%) of 20.4, 6.7 and 19.5mm on the final test dataset. More complicated training schemes and neural network architectures were investigated, without significant performance gain, at the cost of greatly increased training time. While relatively straightforward, our approach yielded good and balanced performance for each tumor subregions. Our solution is open sourced at https://github.com/lescientifik/xxxxx.