Efficient pan-cancer whole-slide image classification and outlier detection using convolutional neural networks

Visual analysis of solid tissue mounted on glass slides is currently the primary method used by pathologists for determining the stage, type and subtypes of cancer. Although whole slide images are usually large (10s to 100s thousands pixels wide), an exhaustive though time-consuming assessment is necessary to reduce the risk of misdiagnosis. In an effort to address the many diagnostic challenges faced by trained experts, recent research has been focused on developing automatic prediction systems for this multi-class classification problem. Typically, complex convolutional neural network (CNN) architectures, such as Google’s Inception, are used to tackle this problem. Here, we introduce a greatly simplified CNN architecture, PathCNN, which allows for more efficient use of computational resources and better classification performance. Using this improved architecture, we trained simultaneously on whole-slide images from multiple tumor sites and corresponding non-neoplastic tissue. Dimensionality reduction analysis of the weights of the last layer of the network capture groups of images that faithfully represent the different types of cancer, highlighting at the same time differences in staining and capturing outliers, artifacts and misclassification errors. Our code is available online at: https://github.com/sedab/PathCNN.