English

Look Ma, no code: fine tuning nnU-Net for the AutoPET II challenge by only adjusting its JSON plans

Image and Video Processing 2023-12-13 v2 Computer Vision and Pattern Recognition

Abstract

We participate in the AutoPET II challenge by modifying nnU-Net only through its easy to understand and modify 'nnUNetPlans.json' file. By switching to a UNet with residual encoder, increasing the batch size and increasing the patch size we obtain a configuration that substantially outperforms the automatically configured nnU-Net baseline (5-fold cross-validation Dice score of 65.14 vs 33.28) at the expense of increased compute requirements for model training. Our final submission ensembles the two most promising configurations.

Keywords

Cite

@article{arxiv.2309.13747,
  title  = {Look Ma, no code: fine tuning nnU-Net for the AutoPET II challenge by only adjusting its JSON plans},
  author = {Fabian Isensee and Klaus H. Maier-Hein},
  journal= {arXiv preprint arXiv:2309.13747},
  year   = {2023}
}