Convolutional Sparse Coding (CSC) is an increasingly popular model in the signal and image processing communities, tackling some of the limitations of traditional patchbased sparse representations. Although several works have addressed the dictionary learning problem under this model, these relied on an ADMM formulation in the Fourier domain, losing the sense of locality and the relation to the traditional patch-based sparse pursuit. A recent work suggested a novel theoretical analysis of this global model, providing guarantees that rely on a localized sparsity measure. Herein, we extend this local-global relation by showing how one can efficiently solve the convolutional sparse pursuit problem and train the filters involved, while operating locally on image patches. Our approach provides an intuitive algorithm that can leverage standard techniques from the sparse representations field. The proposed method is fast to train, simple to implement, and flexible enough that it can be easily deployed in a variety of applications. We demonstrate the proposed training scheme for image inpainting and image separation, while achieving state-of-the-art results.

Highlights d DeepAb, a deep learning method for antibody structure, is presented d Structures from DeepAb are more accurate than alternatives d Outputs of DeepAb provide interpretable insights into structure predictions d DeepAb predictions should facilitate design of novel antibody therapeutics

Summary Deep learning is catalyzing a scientific revolution fueled by big data, accessible toolkits, and powerful computational resources, impacting many fields, including protein structural modeling. Protein structural modeling, such as predicting structure from amino acid sequence and evolutionary information, designing proteins toward desirable functionality, or predicting properties or behavior of a protein, is critical to understand and engineer biological systems at the molecular level. In this review, we summarize the recent advances in applying deep learning techniques to tackle problems in protein structural modeling and design. We dissect the emerging approaches using deep learning techniques for protein structural modeling and discuss advances and challenges that must be addressed. We argue for the central importance of structure, following the “sequence structure function” paradigm. This review is directed to help both computational biologists to gain familiarity with the deep learning methods applied in protein modeling, and computer scientists to gain perspective on the biologically meaningful problems that may benefit from deep learning techniques.

The recently proposed Multi-Layer Convolutional Sparse Coding (ML-CSC) model, consisting of a cascade of convolutional sparse layers, provides a new interpretation of Convolutional Neural Networks (CNNs). Under this framework, the forward pass in a CNN is equivalent to a pursuit algorithm aiming to estimate the nested sparse representation vectors from a given input signal. Despite having served as a pivotal connection between CNNs and sparse modeling, a deeper understanding of the ML-CSC is still lacking. In this work, we propose a sound pursuit algorithm for the ML-CSC model by adopting a projection approach. We provide new and improved bounds on the stability of the solution of such pursuit and we analyze different practical alternatives to implement this in practice. We show that the training of the filters is essential to allow for non-trivial signals in the model, and we derive an online algorithm to learn the dictionaries from real data, effectively resulting in cascaded sparse convolutional layers. Last, but not least, we demonstrate the applicability of the ML-CSC model for several applications in an unsupervised setting, providing competitive results. Our work represents a bridge between matrix factorization, sparse dictionary learning and sparse autoencoders, and we analyze these connections in detail.

Abstract-The celebrated sparse representation model has led to remarkable results in various signal processing tasks in the last decade. However, despite its initial purpose of serving as a global prior for entire signals, it has been commonly used for modeling low dimensional patches due to the computational constraints it entails when deployed with learned dictionaries. A way around this problem has been recently proposed, adopting a convolutional sparse representation model. This approach assumes that the global dictionary is a concatenation of banded Circulant matrices. While several works have presented algorithmic solutions to the global pursuit problem under this new model, very few truly-effective guarantees are known for the success of such methods. In this work, we address the theoretical aspects of the convolutional sparse model providing the first meaningful answers to questions of uniqueness of solutions and success of pursuit algorithms, both greedy and convex relaxations, in ideal and noisy regimes. To this end, we generalize mathematical quantities, such as the 0 norm, mutual coherence, Spark and RIP to their counterparts in the convolutional setting, intrinsically capturing local measures of the global model. On the algorithmic side, we demonstrate how to solve the global pursuit problem by using simple local processing, thus offering a first of its kind bridge between global modeling of signals and their patch-based local treatment.