AutoML Segmentation for 3D Medical Image Data: Contribution to the MSD Challenge 2018

Abstract: Fueled by recent advances in machine learning, there has been tremendous progress in the field of semantic segmentation for the medical image computing community. However, developed algorithms are often optimized and validated by hand based on one task only. In combination with small datasets, interpreting the generalizability of the results is often difficult. The Medical Segmentation Decathlon challenge addresses this problem, and aims to facilitate development of generalizable 3D semantic segmentation algorithms that require no manual parametrization. Such an algorithm was developed and is presented in this paper. It consists of a 3D convolutional neural network with encoder-decoder architecture employing residual-connections, skip-connections and multi-level generation of predictions. It works on anisotropic voxel-geometries and has anisotropic depth, i.e., the number of downsampling steps is a task-specific parameter. These depths are automatically inferred for each task prior to training. By combining this flexible architecture with on-the-fly data augmentation and little-to-no pre-- or postprocessing, promising results could be achieved. The code developed for this challenge will be available online after the final deadline at: https://github.com/ORippler/MSD_2018