(k,q)-Compressed Sensing for dMRI with Joint Spatial-Angular Sparsity Prior

Advanced diffusion magnetic resonance imaging (dMRI) techniques, like diffusion spectrum imaging (DSI) and high angular resolution diffusion imaging (HARDI), remain underutilized compared to diffusion tensor imaging because the scan times needed to produce accurate estimations of fiber orientation are significantly longer. To accelerate DSI and HARDI, recent methods from compressed sensing (CS) exploit a sparse underlying representation of the data in the spatial and angular domains to undersample in the respective k- and q-spaces. State-of-the-art frameworks, however, impose sparsity in the spatial and angular domains separately and involve the sum of the corresponding sparse regularizers. In contrast, we propose a unified (k,q)-CS formulation which imposes sparsity jointly in the spatial-angular domain to further increase sparsity of dMRI signals and reduce the required subsampling rate. To efficiently solve this large-scale global reconstruction problem, we introduce a novel adaptation of the FISTA algorithm that exploits dictionary separability. We show on phantom and real HARDI data that our approach achieves significantly more accurate signal reconstructions than the state of the art while sampling only 2-4% of the (k,q)-space, allowing for the potential of new levels of dMRI acceleration.Comment: To be published in the 2017 Computational Diffusion MRI Workshop of MICCA

Distributed multilevel optimization for complex structures

Optimization problems concerning complex structures with many design variables may entail an unacceptable computational cost. This problem can be reduced considerably with a multilevel approach: A structure consisting of several components is optimized as a whole (global) as well as on the component level. In this paper, an optimization method is discussed with applications in the assessment of the impact of new design considerations in the development of a structure. A strategy based on fully stressed design is applied for optimization problems in linear statics. A global model is used to calculate the interactions (e.g., loads) for each of the components. These components are then optimized using the prescribed interactions, followed by a new global calculation to update the interactions. Mixed discrete and continuous design variables as well as different design configurations are possible. An application of this strategy is presented in the form of the full optimization of a vertical tail plane center box of a generic large passenger aircraft. In linear dynamics, the parametrization of the component interactions is problematic due to the frequency dependence. Hence, a modified method is presented in which the speed of component mode synthesis is used to avoid this parametrization. This method is applied to a simple test case that originates from noise control. \u

An optimization method for dynamics of structures with repetitive component patterns

The occurrence of dynamic problems during the operation of machinery may have devastating effects on a product. Therefore, design optimization of these products becomes essential in order to meet safety criteria. In this research, a hybrid design optimization method is proposed where attention is focused on structures having repeating patterns in their geometries. In the proposed method, the analysis is decomposed but the optimization problem itself is treated as a whole. The model of an entire structure is obtained without modeling all the repetitive components using the merits of the Component Mode Synthesis method. Backpropagation Neural Networks are used for surrogate modeling. The optimization is performed using two techniques: Genetic Algorithms (GAs) and Sequential Quadratic Programming (SQP). GAs are utilized to increase the chance of finding the location of the global optimum and since this optimum may not be exact, SQP is employed afterwards to improve the solution. A theoretical test problem is used to demonstrate the method

Environmental boundary conditions for the origin of life converge to an organo-sulfur metabolism

Published in final edited form as: Nat Ecol Evol. 2019 December ; 3(12): 1715–1724. doi:10.1038/s41559-019-1018-8.It has been suggested that a deep memory of early life is hidden in the architecture of metabolic networks, whose reactions could have been catalyzed by small molecules or minerals before genetically encoded enzymes. A major challenge in unravelling these early steps is assessing the plausibility of a connected, thermodynamically consistent proto-metabolism under different geochemical conditions, which are still surrounded by high uncertainty. Here we combine network-based algorithms with physico-chemical constraints on chemical reaction networks to systematically show how different combinations of parameters (temperature, pH, redox potential and availability of molecular precursors) could have affected the evolution of a proto-metabolism. Our analysis of possible trajectories indicates that a subset of boundary conditions converges to an organo-sulfur-based proto-metabolic network fuelled by a thioester- and redox-driven variant of the reductive tricarboxylic acid cycle that is capable of producing lipids and keto acids. Surprisingly, environmental sources of fixed nitrogen and low-potential electron donors are not necessary for the earliest phases of biochemical evolution. We use one of these networks to build a steady-state dynamical metabolic model of a protocell, and find that different combinations of carbon sources and electron donors can support the continuous production of a minimal ancient 'biomass' composed of putative early biopolymers and fatty acids.80NSSC17K0295 - Intramural NASA; 80NSSC17K0296 - Intramural NASA; T32 GM100842 - NIGMS NIH HHSAccepted manuscrip

Population genetics of translational robustness

Recent work has shown that expression level is the main predictor of a gene’s evolutionary rate, and that more highly expressed genes evolve slower. A possible explanation for this observation is selection for proteins which fold properly despite mistranslation, in short selection for translational robustness. Translational robustness leads to the somewhat paradoxical prediction that highly expressed genes are extremely tolerant to missense substitutions but nevertheless evolve very slowly. Here, we study a simple theoretical model of translational robustness that allows us to gain analytic insight into how this paradoxical behavior arises.Comment: 32 pages, 4 figures, Genetics in pres

SWATI: Synthesizing Wordlengths Automatically Using Testing and Induction

In this paper, we present an automated technique SWATI: Synthesizing Wordlengths Automatically Using Testing and Induction, which uses a combination of Nelder-Mead optimization based testing, and induction from examples to automatically synthesize optimal fixedpoint implementation of numerical routines. The design of numerical software is commonly done using floating-point arithmetic in design-environments such as Matlab. However, these designs are often implemented using fixed-point arithmetic for speed and efficiency reasons especially in embedded systems. The fixed-point implementation reduces implementation cost, provides better performance, and reduces power consumption. The conversion from floating-point designs to fixed-point code is subject to two opposing constraints: (i) the word-width of fixed-point types must be minimized, and (ii) the outputs of the fixed-point program must be accurate. In this paper, we propose a new solution to this problem. Our technique takes the floating-point program, specified accuracy and an implementation cost model and provides the fixed-point program with specified accuracy and optimal implementation cost. We demonstrate the effectiveness of our approach on a set of examples from the domain of automated control, robotics and digital signal processing

Templates for Convex Cone Problems with Applications to Sparse Signal Recovery

This paper develops a general framework for solving a variety of convex cone problems that frequently arise in signal processing, machine learning, statistics, and other fields. The approach works as follows: first, determine a conic formulation of the problem; second, determine its dual; third, apply smoothing; and fourth, solve using an optimal first-order method. A merit of this approach is its flexibility: for example, all compressed sensing problems can be solved via this approach. These include models with objective functionals such as the total-variation norm, ||Wx||_1 where W is arbitrary, or a combination thereof. In addition, the paper also introduces a number of technical contributions such as a novel continuation scheme, a novel approach for controlling the step size, and some new results showing that the smooth and unsmoothed problems are sometimes formally equivalent. Combined with our framework, these lead to novel, stable and computationally efficient algorithms. For instance, our general implementation is competitive with state-of-the-art methods for solving intensively studied problems such as the LASSO. Further, numerical experiments show that one can solve the Dantzig selector problem, for which no efficient large-scale solvers exist, in a few hundred iterations. Finally, the paper is accompanied with a software release. This software is not a single, monolithic solver; rather, it is a suite of programs and routines designed to serve as building blocks for constructing complete algorithms.Comment: The TFOCS software is available at http://tfocs.stanford.edu This version has updated reference

Learning Robust Object Recognition Using Composed Scenes from Generative Models

Recurrent feedback connections in the mammalian visual system have been hypothesized to play a role in synthesizing input in the theoretical framework of analysis by synthesis. The comparison of internally synthesized representation with that of the input provides a validation mechanism during perceptual inference and learning. Inspired by these ideas, we proposed that the synthesis machinery can compose new, unobserved images by imagination to train the network itself so as to increase the robustness of the system in novel scenarios. As a proof of concept, we investigated whether images composed by imagination could help an object recognition system to deal with occlusion, which is challenging for the current state-of-the-art deep convolutional neural networks. We fine-tuned a network on images containing objects in various occlusion scenarios, that are imagined or self-generated through a deep generator network. Trained on imagined occluded scenarios under the object persistence constraint, our network discovered more subtle and localized image features that were neglected by the original network for object classification, obtaining better separability of different object classes in the feature space. This leads to significant improvement of object recognition under occlusion for our network relative to the original network trained only on un-occluded images. In addition to providing practical benefits in object recognition under occlusion, this work demonstrates the use of self-generated composition of visual scenes through the synthesis loop, combined with the object persistence constraint, can provide opportunities for neural networks to discover new relevant patterns in the data, and become more flexible in dealing with novel situations.Comment: Accepted by 14th Conference on Computer and Robot Visio