Multi-Instance Multi-Scale CNN for Medical Image Classification

Abstract

Deep learning for medical image classification faces three major challenges: (1) the number of annotated medical images for training are usually small; (2) regions of interest (ROIs) are relatively small with unclear boundaries in the whole medical images, and may appear in arbitrary positions across the x, y (and also z in 3D images) dimensions. However often only labels of the whole images are annotated, and localized ROIs are unavailable; and (3) ROIs in medical images often appear in varying sizes (scales). We approach these three challenges with a Multi-Instance Multi-Scale (MIMS) CNN: (1) We propose a multi-scale convolutional layer, which extracts patterns of different receptive fields with a shared set of convolutional kernels, so that scale-invariant patterns are captured by this compact set of kernels. As this layer contains only a small number of parameters, training on small datasets becomes feasible; (2) We propose a “top-k pooling” to aggregate the feature maps in varying scales from multiple spatial dimensions, allowing the model to be trained using weak annotations within the multiple instance learning (MIL) framework. Our method is shown to perform well on three classification tasks involving two 3D and two 2D medical image datasets.