Multi-task deep learning for image segmentation using recursive approximation tasks

Fully supervised deep neural networks for segmentation usually require a massive amount of pixel-level labels which are manually expensive to create. In this work, we develop a multi-task learning method to relax this constraint. We regard the segmentation problem as a sequence of approximation subproblems that are recursively defined and in increasing levels of approximation accuracy. The subproblems are handled by a framework that consists of 1) a segmentation task that learns from pixel-level ground truth segmentation masks of a small fraction of the images, 2) a recursive approximation task that conducts partial object regions learning and data-driven mask evolution starting from partial masks of each object instance, and 3) other problem oriented auxiliary tasks that are trained with sparse annotations and promote the learning of dedicated features. Most training images are only labeled by (rough) partial masks, which do not contain exact object boundaries, rather than by their full segmentation masks. During the training phase, the approximation task learns the statistics of these partial masks, and the partial regions are recursively increased towards object boundaries aided by the learned information from the segmentation task in a fully data-driven fashion. The network is trained on an extremely small amount of precisely segmented images and a large set of coarse labels. Annotations can thus be obtained in a cheap way. We demonstrate the efficiency of our approach in three applications with microscopy images and ultrasound images.

3D deformable registration of longitudinal abdominopelvic CT images using unsupervised deep learning

This study investigates the use of the unsupervised deep learning framework VoxelMorph for deformable registration of longitudinal abdominopelvic CT images acquired in patients with bone metastases from breast cancer. The CT images were refined prior to registration by automatically removing the CT table and all other extra-corporeal components. To improve the learning capabilities of VoxelMorph when only a limited amount of training data is available, a novel incremental training strategy is proposed based on simulated deformations of consecutive CT images. In a 4-fold cross-validation scheme, the incremental training strategy achieved significantly better registration performance compared to training on a single volume. Although our deformable image registration method did not outperform iterative registration using NiftyReg (considered as a benchmark) in terms of registration quality, the registrations were approximately 300 times faster. This study showed the feasibility of deep learning based deformable registration of longitudinal abdominopelvic CT images via a novel incremental training strategy based on simulated deformations.

On Learned Operator Correction

We discuss the possibility to learn a data-driven explicit model correction for inverse problems and whether such a model correction can be used within a variational framework to obtain regularised reconstructions. This paper discusses the conceptual difficulty to learn such a forward model correction and proceeds to present a possible solution as forward-backward correction that explicitly corrects in both data and solution spaces. We then derive conditions under which solutions to the variational problem with a learned correction converge to solutions obtained with the correct operator. The proposed approach is evaluated on an application to limited view photoacoustic tomography and compared to the established framework of Bayesian approximation error method.

iUNets: Fully invertible U-Nets with Learnable Up- and Downsampling

U-Nets have been established as a standard neural network design architecture for image-to-image learning problems such as segmentation and inverse problems in imaging. For high-dimensional applications, as they for example appear in 3D medical imaging, U-Nets however have prohibitive memory requirements. Here, we present a new fully-invertible U-Net-based architecture called the \emph{iUNet}, which allows for the application of highly memory-efficient backpropagation procedures. For this, we introduce learnable and invertible up- and downsampling operations. An open source library in Pytorch for 1D, 2D and 3D data is made available.

Rethinking Medical Image Reconstruction via Shape Prior, Going Deeper and Faster: Deep Joint Indirect Registration and Reconstruction

Indirect image registration is a promising technique to improve image reconstruction quality by providing a shape prior for the reconstruction task. In this paper, we propose a novel hybrid method that seeks to reconstruct high quality images from few measurements whilst requiring low computational cost. With this purpose, our framework intertwines indirect registration and reconstruction tasks is a single functional. It is based on two major novelties. Firstly, we introduce a model based on deep nets to solve the indirect registration problem, in which the inversion and registration mappings are recurrently connected through a fixed-point interaction based sparse optimisation. Secondly, we introduce specific inversion blocks, that use the explicit physical forward operator, to map the acquired measurements to the image reconstruction. We also introduce registration blocks based deep nets to predict the registration parameters and warp transformation accurately and efficiently. We demonstrate, through extensive numerical and visual experiments, that our framework outperforms significantly classic reconstruction schemes and other bi-task method; this in terms of both image quality and computational time. Finally, we show generalisation capabilities of our approach by demonstrating their performance on fast Magnetic Resonance Imaging (MRI), sparse view computed tomography (CT) and low dose CT with measurements much below the Nyquist limit.

Dynamic Spectral Residual Superpixels

We consider the problem of segmenting an image into superpixels in the context of $k$-means clustering, in which we wish to decompose an image into local, homogeneous regions corresponding to the underlying objects. Our novel approach builds upon the widely used Simple Linear Iterative Clustering (SLIC), and incorporate a measure of objects' structure based on the spectral residual of an image. Based on this combination, we propose a modified initialisation scheme and search metric, which helps keeps fine-details. This combination leads to better adherence to object boundaries, while preventing unnecessary segmentation of large, uniform areas, while remaining computationally tractable in comparison to other methods. We demonstrate through numerical and visual experiments that our approach outperforms the state-of-the-art techniques.

Variational Osmosis for Non-linear Image Fusion

We propose a new variational model for nonlinear image fusion. Our approach incorporates the osmosis model proposed in Vogel et al. (2013) and Weickert et al. (2013) as an energy term in a variational model. The osmosis energy is known to realize visually plausible image data fusion. As a consequence, our method is invariant to multiplicative brightness changes. On the practical side, it requires minimal supervision and parameter tuning and can encode prior information on the structure of the images to be fused. We develop a primal-dual algorithm for solving this new image fusion model and we apply the resulting minimisation scheme to multi-modal image fusion for face fusion, colour transfer and some cultural heritage conservation challenges. Visual comparison to state-of-the-art proves the quality and flexibility of our method.

PDE-Inspired Algorithms for Semi-Supervised Learning on Point Clouds

Given a data set and a subset of labels the problem of semi-supervised learning on point clouds is to extend the labels to the entire data set. In this paper we extend the labels by minimising the constrained discrete $p$-Dirichlet energy. Under suitable conditions the discrete problem can be connected, in the large data limit, with the minimiser of a weighted continuum $p$-Dirichlet energy with the same constraints. We take advantage of this connection by designing numerical schemes that first estimate the density of the data and then apply PDE methods, such as pseudo-spectral methods, to solve the corresponding Euler-Lagrange equation. We prove that our scheme is consistent in the large data limit for two methods of density estimation: kernel density estimation and spline kernel density estimation.

GraphX$^{NET}-$ Chest X-Ray Classification Under Extreme Minimal Supervision

The task of classifying X-ray data is a problem of both theoretical and clinical interest. Whilst supervised deep learning methods rely upon huge amounts of labelled data, the critical problem of achieving a good classification accuracy when an extremely small amount of labelled data is available has yet to be tackled. In this work, we introduce a novel semi-supervised framework for X-ray classification which is based on a graph-based optimisation model. To the best of our knowledge, this is the first method that exploits graph-based semi-supervised learning for X-ray data classification. Furthermore, we introduce a new multi-class classification functional with carefully selected class priors which allows for a smooth solution that strengthens the synergy between the limited number of labels and the huge amount of unlabelled data. We demonstrate, through a set of numerical and visual experiments, that our method produces highly competitive results on the ChestX-ray14 data set whilst drastically reducing the need for annotated data.

A multi-task U-net for segmentation with lazy labels

The need for labour intensive pixel-wise annotation is a major limitation of many fully supervised learning methods for image segmentation. In this paper, we propose a deep convolutional neural network for multi-class segmentation that circumvents this problem by being trainable on coarse data labels combined with only a very small number of images with pixel-wise annotations. We call this new labelling strategy 'lazy' labels. Image segmentation is then stratified into three connected tasks: rough detection of class instances, separation of wrongly connected objects without a clear boundary, and pixel-wise segmentation to find the accurate boundaries of each object. These problems are integrated into a multitask learning framework and the model is trained end-to-end in a semi-supervised fashion. The method is applied on a dataset of food microscopy images. We show that the model gives accurate segmentation results even if exact boundary labels are missing for a majority of the annotated data. This allows more flexibility and efficiency for training deep neural networks that are data hungry in a practical setting where manual annotation is expensive, by collecting more lazy (rough) annotations than precisely segmented images.