Deeply supervised UNet for semantic segmentation to assist dermatopathological assessment of Basal Cell Carcinoma (BCC)

Accurate and fast assessment of resection margins is an essential part of a dermatopathologist's clinical routine. In this work, we successfully develop a deep learning method to assist the pathologists by marking critical regions that have a high probability of exhibiting pathological features in Whole Slide Images (WSI). We focus on detecting Basal Cell Carcinoma (BCC) through semantic segmentation using several models based on the UNet architecture. The study includes 650 WSI with 3443 tissue sections in total. Two clinical dermatopathologists annotated the data, marking tumor tissues' exact location on 100 WSI. The rest of the data, with ground-truth section-wise labels, is used to further validate and test the models. We analyze two different encoders for the first part of the UNet network and two additional training strategies: a) deep supervision, b) linear combination of decoder outputs, and obtain some interpretations about what the network's decoder does in each case. The best model achieves over 96%, accuracy, sensitivity, and specificity on the test set.

Deep Relevance Regularization: Interpretable and Robust Tumor Typing of Imaging Mass Spectrometry Data

Neural networks have recently been established as a viable classification method for imaging mass spectrometry data for tumor typing. For multi-laboratory scenarios however, certain confounding factors may strongly impede their performance. In this work, we introduce Deep Relevance Regularization, a method of restricting what the neural network can focus on during classification, in order to improve the classification performance. We demonstrate how Deep Relevance Regularization robustifies neural networks against confounding factors on a challenging inter-lab dataset consisting of breast and ovarian carcinoma. We further show that this makes the relevance map -- a way of visualizing the discriminative parts of the mass spectrum -- sparser, thereby making the classifier easier to interpret