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Curvilinear structures frequently appear in microscopy imaging as the object of interest. Crystallographic defects, i.edislocations, are one of the curvilinear structures that have been repeatedly investigated under transmission electronmicroscopy (TEM) and their 3D structural information is of great importance for understanding the properties ofmaterials. 3D information of dislocations is often obtained by tomography which is a cumbersome process since itis required to acquire many images with different tilt angles and similar imaging conditions. Although, alternativestereoscopy methods lower the number of required images to two, they still require human intervention and shape priorsfor accurate 3D estimation. We propose a fully automated pipeline for both detection and matching of curvilinearstructures in stereo pairs by utilizing deep convolutional neural networks (CNNs) without making any prior assumptionon 3D shapes. In this work, we mainly focus on 3D reconstruction of dislocations from stereo pairs of TEM images.

We present a novel method to reconstruct a spectral central view and its aligned disparity map from spatio-spectrally coded light fields. Since we do not reconstruct an intermediate full light field from the coded measurement, we refer to this as principal reconstruction. The coded light fields correspond to those captured by a light field camera in the unfocused design with a spectrally coded microlens array. In this application, the spectrally coded light field camera can be interpreted as a single-shot spectral depth camera. We investigate several multi-task deep learning methods and propose a new auxiliary loss-based training strategy to enhance the reconstruction performance. The results are evaluated using a synthetic as well as a new real-world spectral light field dataset that we captured using a custom-built camera. The results are compared to state-of-the art compressed sensing reconstruction and disparity estimation. We achieve a high reconstruction quality for both synthetic and real-world coded light fields. The disparity estimation quality is on par with or even outperforms state-of-the-art disparity estimation from uncoded RGB light fields.

With the advances of data-driven machine learning research, a wide variety of prediction problems have been tackled. It has become critical to explore how machine learning and specifically deep learning methods can be exploited to analyse healthcare data. A major limitation of existing methods has been the focus on grid-like data; however, the structure of physiological recordings are often irregular and unordered which makes it difficult to conceptualise them as a matrix. As such, graph neural networks have attracted significant attention by exploiting implicit information that resides in a biological system, with interactive nodes connected by edges whose weights can be either temporal associations or anatomical junctions. In this survey, we thoroughly review the different types of graph architectures and their applications in healthcare. We provide an overview of these methods in a systematic manner, organized by their domain of application including functional connectivity, anatomical structure and electrical-based analysis. We also outline the limitations of existing techniques and discuss potential directions for future research.

We present a learning-based approach for removing unwanted obstructions, such as window reflections, fence occlusions or raindrops, from a short sequence of images captured by a moving camera. Our method leverages the motion differences between the background and the obstructing elements to recover both layers. Specifically, we alternate between estimating dense optical flow fields of the two layers and reconstructing each layer from the flow-warped images via a deep convolutional neural network. The learning-based layer reconstruction allows us to accommodate potential errors in the flow estimation and brittle assumptions such as brightness consistency. We show that training on synthetically generated data transfers well to real images. Our results on numerous challenging scenarios of reflection and fence removal demonstrate the effectiveness of the proposed method.

With the advent of deep neural networks, learning-based approaches for 3D reconstruction have gained popularity. However, unlike for images, in 3D there is no canonical representation which is both computationally and memory efficient yet allows for representing high-resolution geometry of arbitrary topology. Many of the state-of-the-art learning-based 3D reconstruction approaches can hence only represent very coarse 3D geometry or are limited to a restricted domain. In this paper, we propose occupancy networks, a new representation for learning-based 3D reconstruction methods. Occupancy networks implicitly represent the 3D surface as the continuous decision boundary of a deep neural network classifier. In contrast to existing approaches, our representation encodes a description of the 3D output at infinite resolution without excessive memory footprint. We validate that our representation can efficiently encode 3D structure and can be inferred from various kinds of input. Our experiments demonstrate competitive results, both qualitatively and quantitatively, for the challenging tasks of 3D reconstruction from single images, noisy point clouds and coarse discrete voxel grids. We believe that occupancy networks will become a useful tool in a wide variety of learning-based 3D tasks.

Methods proposed in the literature towards continual deep learning typically operate in a task-based sequential learning setup. A sequence of tasks is learned, one at a time, with all data of current task available but not of previous or future tasks. Task boundaries and identities are known at all times. This setup, however, is rarely encountered in practical applications. Therefore we investigate how to transform continual learning to an online setup. We develop a system that keeps on learning over time in a streaming fashion, with data distributions gradually changing and without the notion of separate tasks. To this end, we build on the work on Memory Aware Synapses, and show how this method can be made online by providing a protocol to decide i) when to update the importance weights, ii) which data to use to update them, and iii) how to accumulate the importance weights at each update step. Experimental results show the validity of the approach in the context of two applications: (self-)supervised learning of a face recognition model by watching soap series and learning a robot to avoid collisions.

Matter evolved under influence of gravity from minuscule density fluctuations. Non-perturbative structure formed hierarchically over all scales, and developed non-Gaussian features in the Universe, known as the Cosmic Web. To fully understand the structure formation of the Universe is one of the holy grails of modern astrophysics. Astrophysicists survey large volumes of the Universe and employ a large ensemble of computer simulations to compare with the observed data in order to extract the full information of our own Universe. However, to evolve trillions of galaxies over billions of years even with the simplest physics is a daunting task. We build a deep neural network, the Deep Density Displacement Model (hereafter D$^3$M), to predict the non-linear structure formation of the Universe from simple linear perturbation theory. Our extensive analysis, demonstrates that D$^3$M outperforms the second order perturbation theory (hereafter 2LPT), the commonly used fast approximate simulation method, in point-wise comparison, 2-point correlation, and 3-point correlation. We also show that D$^3$M is able to accurately extrapolate far beyond its training data, and predict structure formation for significantly different cosmological parameters. Our study proves, for the first time, that deep learning is a practical and accurate alternative to approximate simulations of the gravitational structure formation of the Universe.

Deep learning (DL) is a high dimensional data reduction technique for constructing high-dimensional predictors in input-output models. DL is a form of machine learning that uses hierarchical layers of latent features. In this article, we review the state-of-the-art of deep learning from a modeling and algorithmic perspective. We provide a list of successful areas of applications in Artificial Intelligence (AI), Image Processing, Robotics and Automation. Deep learning is predictive in its nature rather then inferential and can be viewed as a black-box methodology for high-dimensional function estimation.

Purpose: MR image reconstruction exploits regularization to compensate for missing k-space data. In this work, we propose to learn the probability distribution of MR image patches with neural networks and use this distribution as prior information constraining images during reconstruction, effectively employing it as regularization. Methods: We use variational autoencoders (VAE) to learn the distribution of MR image patches, which models the high-dimensional distribution by a latent parameter model of lower dimensions in a non-linear fashion. The proposed algorithm uses the learned prior in a Maximum-A-Posteriori estimation formulation. We evaluate the proposed reconstruction method with T1 weighted images and also apply our method on images with white matter lesions. Results: Visual evaluation of the samples showed that the VAE algorithm can approximate the distribution of MR patches well. The proposed reconstruction algorithm using the VAE prior produced high quality reconstructions. The algorithm achieved normalized RMSE, CNR and CN values of 2.77\%, 0.43, 0.11; 4.29\%, 0.43, 0.11, 6.36\%, 0.47, 0.11 and 10.00\%, 0.42, 0.10 for undersampling ratios of 2, 3, 4 and 5, respectively, where it outperformed most of the alternative methods. In the experiments on images with white matter lesions, the method faithfully reconstructed the lesions. Conclusion: We introduced a novel method for MR reconstruction, which takes a new perspective on regularization by using priors learned by neural networks. Results suggest the method compares favorably against the other evaluated methods and can reconstruct lesions as well. Keywords: Reconstruction, MRI, prior probability, MAP estimation, machine learning, variational inference, deep learning

Recent works have shown that exploiting multi-scale representations deeply learned via convolutional neural networks (CNN) is of tremendous importance for accurate contour detection. This paper presents a novel approach for predicting contours which advances the state of the art in two fundamental aspects, i.e. multi-scale feature generation and fusion. Different from previous works directly consider- ing multi-scale feature maps obtained from the inner layers of a primary CNN architecture, we introduce a hierarchical deep model which produces more rich and complementary representations. Furthermore, to refine and robustly fuse the representations learned at different scales, the novel Attention-Gated Conditional Random Fields (AG-CRFs) are proposed. The experiments ran on two publicly available datasets (BSDS500 and NYUDv2) demonstrate the effectiveness of the latent AG-CRF model and of the overall hierarchical framework.