Factorised spatial representation learning: application in semi-supervised myocardial segmentation

The success and generalisation of deep learning algorithms heavily depend on learning good feature representations. In medical imaging this entails representing anatomical information, as well as properties related to the specific imaging setting. Anatomical information is required to perform further analysis, whereas imaging information is key to disentangle scanner variability and potential artefacts. The ability to factorise these would allow for training algorithms only on the relevant information according to the task. To date, such factorisation has not been attempted. In this paper, we propose a methodology of latent space factorisation relying on the cycle-consistency principle. As an example application, we consider cardiac MR segmentation, where we separate information related to the myocardium from other features related to imaging and surrounding substructures. We demonstrate the proposed method's utility in a semi-supervised setting: we use very few labelled images together with many unlabelled images to train a myocardium segmentation neural network. Specifically, we achieve comparable performance to fully supervised networks using a fraction of labelled images in experiments on ACDC and a dataset from Edinburgh Imaging Facility QMRI. Code will be made available at https://github.com/agis85/spatial_factorisation.Comment: Accepted in MICCAI 201

Challenges in Disentangling Independent Factors of Variation

We study the problem of building models that disentangle independent factors of variation. Such models could be used to encode features that can efficiently be used for classification and to transfer attributes between different images in image synthesis. As data we use a weakly labeled training set. Our weak labels indicate what single factor has changed between two data samples, although the relative value of the change is unknown. This labeling is of particular interest as it may be readily available without annotation costs. To make use of weak labels we introduce an autoencoder model and train it through constraints on image pairs and triplets. We formally prove that without additional knowledge there is no guarantee that two images with the same factor of variation will be mapped to the same feature. We call this issue the reference ambiguity. Moreover, we show the role of the feature dimensionality and adversarial training. We demonstrate experimentally that the proposed model can successfully transfer attributes on several datasets, but show also cases when the reference ambiguity occurs.Comment: Submitted to ICLR 201