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Radiomic representations can quantify properties of regions of interest in medical image data. Classically, they account for pre-defined statistics of shape, texture, and other low-level image features. Alternatively, deep learning-based representations are derived from supervised learning but require expensive annotations from experts and often suffer from overfitting and data imbalance issues. In this work, we address the challenge of learning representations of 3D medical images for an effective quantification under data imbalance. We propose a \emph{self-supervised} representation learning framework to learn high-level features of 3D volumes as a complement to existing radiomics features. Specifically, we demonstrate how to learn image representations in a self-supervised fashion using a 3D Siamese network. More importantly, we deal with data imbalance by exploiting two unsupervised strategies: a) sample re-weighting, and b) balancing the composition of training batches. When combining our learned self-supervised feature with traditional radiomics, we show significant improvement in brain tumor classification and lung cancer staging tasks covering MRI and CT imaging modalities., camera-ready version in MICCAI 2021

Chest radiography is widely used in annual medical screening to check whether lungs are healthy or not. Therefore it would be desirable to develop an intelligent system to help clinicians automatically detect potential abnormalities in chest X-ray images. Here with only healthy X-ray images, we propose a new abnormality detection approach based on an autoencoder which outputs not only the reconstructed normal version of the input image but also a pixel-wise uncertainty prediction. Higher uncertainty often appears at normal region boundaries with relatively larger reconstruction errors, but not at potential abnormal regions in the lung area. Therefore the normalized reconstruction error by the uncertainty provides a natural measurement for abnormality detection in images. Experiments on two chest X-ray datasets show the state-of-the-art performance by the proposed approach.

Convolutional neural networks (CNNs) are vulnerable to adversarial noises, which may result in potentially disastrous consequences in safety or security sensitive systems. This paper proposes a novel mechanism to improve the robustness of medical image classification systems by bringing denoising ability to CNN classifiers with a naturally embedded auto-encoder and high-level feature invariance to general noises. This novel denoising mechanism can be adapted to many model architectures, and therefore can be easily combined with existing models and denoising mechanisms to further improve robustness of CNN classifiers. This proposed method has been confirmed by comprehensive evaluations with two medical image classification tasks.