Deep Learning with Importance Sampling for Brain Tumor MR Segmentation

Abstract: Segmentation of magnetic resonance images is an important part of planning radiotherapy treat-ments for patients with brain tumours but due to the number of images contained within a scan and the level of detail required, manual segmentation is a time consuming task. Convolutional neural networks have been proposed as tools for automated segmentation and shown promising results. However, the data sets used for training these deep learning models are often imbalanced and contain data that does not contribute to the performance of the model. By carefully selecting which data to train on, there is potential to both speed up the training and increase the network’s ability to detect tumours. This thesis implements the method of importance sampling for training a convolutional neural network for patch-based segmentation of three dimensional multimodal magnetic resonance images of the brain and compares it with the standard way of sampling in terms of network performance and training time. Training is done for two different patch sizes. Features of the most frequently sampled volumes are also analysed. Importance sampling is found to speed up training in terms of number of epochs and also yield models with improved performance. Analysis of the sampling trends indicate that when patches are large, small tumours are somewhat frequently trained on, however more investigation is needed to confirm what features may influence the sampling frequency of a patch.