Deep semi-supervised segmentation with weight-averaged consistency targets

Recently proposed techniques for semi-supervised learning such as Temporal Ensembling and Mean Teacher have achieved state-of-the-art results in many important classification benchmarks. In this work, we expand the Mean Teacher approach to segmentation tasks and show that it can bring important improvements in a realistic small data regime using a publicly available multi-center dataset from the Magnetic Resonance Imaging (MRI) domain. We also devise a method to solve the problems that arise when using traditional data augmentation strategies for segmentation tasks on our new training scheme.Comment: 8 pages, 1 figure, accepted for DLMIA/MICCA

Advances in low-memory subgradient optimization

One of the main goals in the development of non-smooth optimization is to cope with high dimensional problems by decomposition, duality or Lagrangian relaxation which greatly reduces the number of variables at the cost of worsening differentiability of objective or constraints. Small or medium dimensionality of resulting non-smooth problems allows to use bundle-type algorithms to achieve higher rates of convergence and obtain higher accuracy, which of course came at the cost of additional memory requirements, typically of the order of n2, where n is the number of variables of non-smooth problem. However with the rapid development of more and more sophisticated models in industry, economy, finance, et all such memory requirements are becoming too hard to satisfy. It raised the interest in subgradient-based low-memory algorithms and later developments in this area significantly improved over their early variants still preserving O(n) memory requirements. To review these developments this chapter is devoted to the black-box subgradient algorithms with the minimal requirements for the storage of auxiliary results, which are necessary to execute these algorithms. To provide historical perspective this survey starts with the original result of N.Z. Shor which opened this field with the application to the classical transportation problem. The theoretical complexity bounds for smooth and non-smooth convex and quasi-convex optimization problems are briefly exposed in what follows to introduce to the relevant fundamentals of non-smooth optimization. Special attention in this section is given to the adaptive step-size policy which aims to attain lowest complexity bounds. Unfortunately the non-differentiability of objective function in convex optimization essentially slows down the theoretical low bounds for the rate of convergence in subgradient optimization compared to the smooth case but there are different modern techniques that allow to solve non-smooth convex optimization problems faster then dictate lower complexity bounds. In this work the particular attention is given to Nesterov smoothing technique, Nesterov Universal approach, and Legendre (saddle point) representation approach. The new results on Universal Mirror Prox algorithms represent the original parts of the survey. To demonstrate application of non-smooth convex optimization algorithms for solution of huge-scale extremal problems we consider convex optimization problems with non-smooth functional constraints and propose two adaptive Mirror Descent methods. The first method is of primal-dual variety and proved to be optimal in terms of lower oracle bounds for the class of Lipschitz-continuous convex objective and constraints. The advantages of application of this method to sparse Truss Topology Design problem are discussed in certain details. The second method can be applied for solution of convex and quasi-convex optimization problems and is optimal in a sense of complexity bounds. The conclusion part of the survey contains the important references that characterize recent developments of non-smooth convex optimization

Projection methods in conic optimization

There exist efficient algorithms to project a point onto the intersection of a convex cone and an affine subspace. Those conic projections are in turn the work-horse of a range of algorithms in conic optimization, having a variety of applications in science, finance and engineering. This chapter reviews some of these algorithms, emphasizing the so-called regularization algorithms for linear conic optimization, and applications in polynomial optimization. This is a presentation of the material of several recent research articles; we aim here at clarifying the ideas, presenting them in a general framework, and pointing out important techniques

Proteomic Analysis of S-Acylated Proteins in Human B Cells Reveals Palmitoylation of the Immune Regulators CD20 and CD23

S-palmitoylation is a reversible post-translational modification important for controlling the membrane targeting and function of numerous membrane proteins with diverse roles in signalling, scaffolding, and trafficking. We sought to identify novel palmitoylated proteins in B lymphocytes using acyl-biotin exchange chemistry, coupled with differential analysis by liquid-chromatography tandem mass spectrometry. In total, we identified 57 novel palmitoylated protein candidates from human EBV-transformed lymphoid cells. Two of them, namely CD20 and CD23 (low affinity immunoglobulin epsilon Fc receptor), are immune regulators that are effective/potential therapeutic targets for haematological malignancies, autoimmune diseases and allergic disorders. Palmitoylation of CD20 and CD23 was confirmed by heterologous expression of alanine mutants coupled with bioorthogonal metabolic labeling. This study demonstrates a new subset of palmitoylated proteins in B cells, illustrating the ubiquitous role of protein palmitoylation in immune regulation

Structural hierarchies define toughness and defect-tolerance despite simple and mechanically inferior brittle building blocks

Mineralized biological materials such as bone, sea sponges or diatoms provide load-bearing and armor functions and universally feature structural hierarchies from nano to macro. Here we report a systematic investigation of the effect of hierarchical structures on toughness and defect-tolerance based on a single and mechanically inferior brittle base material, silica, using a bottom-up approach rooted in atomistic modeling. Our analysis reveals drastic changes in the material crack-propagation resistance (R-curve) solely due to the introduction of hierarchical structures that also result in a vastly increased toughness and defect-tolerance, enabling stable crack propagation over an extensive range of crack sizes. Over a range of up to four hierarchy levels, we find an exponential increase in the defect-tolerance approaching hundred micrometers without introducing additional mechanisms or materials. This presents a significant departure from the defect-tolerance of the base material, silica, which is brittle and highly sensitive even to extremely small nanometer-scale defects