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At least 145 records · Page 8

AutoAtlas: Neural Network for 3D Unsupervised Partitioning and Representation Learning

Here we present a novel neural network architecture called AutoAtlas for fully unsupervised partitioning and representation learning of 3D brain Magnetic Resonance Imaging (MRI) volumes. AutoAtlas consists of two neural network components: one neural network to perform multi-label partitioning based on local texture in the volume, and a second neural network to compress the information contained within each partition. We train both of these components simultaneously by optimizing a loss function that is designed to promote accurate reconstruction of each partition, while encouraging spatially smooth and contiguous partitioning, and discouraging relatively small partitions. We show that the partitions adapt to the subject specific structural variations of brain tissue while consistently appearing at similar spatial locations across subjects. AutoAtlas also produces very low dimensional features that represent local texture of each partition. We demonstrate prediction of metadata associated with each subject using the derived feature representations and compare the results to prediction using features derived from FreeSurfer anatomical parcellation. Since our features are intrinsically linked to distinct partitions, we can then map values of interest, such as partition-specific feature importance scores onto the brain for visualization.

42 ENGINEERING↗

HBMax: Optimizing Memory Efficiency for Parallel Influence Maximization on Multicore Architectures

The goal of influence maximization is to select k most-influential vertices or seeds in a network, where influence is defined by a given diffusion process. The problem has a number of important applications such as viral marketing, information spread, and epidemic control. Although computing optimal seed set is NP-Hard, due to the submodular nature of the problem efficient approximation algorithms exist. However, even state-of-the-art parallel implementations are limited by a sampling step that incurs large memory footprints. This in turn limits the problem size reach and approximation quality. In this work, we study the memory footprint of the sampling process collecting reverse reachability information in the IMM algorithm over large real-world social networks. We present an adaptive and memory-efficient optimization approach for a state-of-the-art multi-threaded parallel influence maximization algorithm. Our approach,HuffMax, uses a portion of the reverse reachable (RR) sets collected by the algorithm to learn the characteristics of the graph. Then, it compresses the intermediate reverse reachability information with Huffman coding, and queries directly on the compressed data to preserve the memory savings obtained through compression. We also propose an efficient sampling strategy based on the distribution of RR sets, which can further reduce the computation time for typical social networks with long-tail distributions. Considering a NUMA architecture, we scale up our solution on 128-core CPUs and reduce the memory footprint by up to 45.7% with negligible time overhead (or even faster) and without perceivable loss of accuracy.

Chen, Xinyu↗

Sylvester-preconditioned adaptive-rank implicit time integrators for advection-diffusion equations with variable coefficients

Here, we consider the adaptive-rank integration of multi-dimensional time-dependent advection-diffusion partial differential equations (PDEs) with variable coefficients. We employ a standard finite-difference method for spatial discretization coupled with high-order diagonally implicit Runge-Kutta temporal schemes. The discrete equation is a generalized Sylvester equation (GSE), which we solve with a projection-based adaptive-rank algorithm structured around two key strategies: (i) constructing dimension-wise subspaces using a novel atypical extended Krylov strategy, and (ii) efficiently solving the basis coefficient matrix with a preconditioned GMRES solver. The low-rank decomposition is performed in 2D using SVD and with high-order SVD (HOSVD) in 3D to represent the tensor in a compressed Tucker format. For d-dimensional problems (here, d = 2 or 3), the computational complexity and memory storage of the approach are found numerically to scale as and $\mathscr{O}(Nr^2) + \mathscr{O} (r^{d+1})$ and $\mathscr{O}(Nr) + \mathscr{O} (r^{d})$, respectively, with the one-dimensional resolution and the maximal rank during the Krylov iteration (which we find to be largely independent of on our numerical examples). We present numerical examples that illustrate the advertised properties of the algorithm.

97 MATHEMATICS AND COMPUTING↗

Viscoelastic analysis of mussel threads reveals energy dissipative mechanisms

Mussels use byssal threads to secure themselves to rocks and as shock absorbers during cyclic loading from wave motion. Byssal threads combine high strength and toughness with extensibility of nearly 200%. Researchers attribute tensile properties of byssal threads to their elaborate multi-domain collagenous protein cores. Because the elastic properties have been previously scrutinized, we instead examined byssal thread viscoelastic behaviour, which is crucial for withstanding cyclic loading. By targeting protein domains in the collagenous core via chemical treatments, stress relaxation experiments provided insights on domain contributions and were coupled with in situ small-angle X-ray scattering to investigate relaxation-specific molecular reorganizations. Results show that when silk-like domains in the core were disrupted, the stress relaxation of the threads decreased by nearly 50% and lateral molecular spacing also decreased, suggesting that these domains are essential for energy dissipation and assume a compressed molecular rearrangement when disrupted. A generalized Maxwell model was developed to describe the stress relaxation response. The model predicts that maximal damping (energy dissipation) occurs at around 0.1 Hz which closely resembles the wave frequency along the California coast and implies that these materials may be well adapted to the cyclic loading of the ambient conditions.

36 MATERIALS SCIENCE↗

Accelerating matrix-centric graph processing on GPUs through bit-level optimizations

Even though it is well known that binary values are common in graph applications (e.g., adjacency matrix), how to leverage the phenomenon for efficiency has not yet been adequately explored. This paper presents a systematic study on how to unlock the potential of the bit-level optimizations of graph computations that involve binary values. It proposes a two-level representation named Bit-Block Compressed Sparse Row (B2SR) and presents a series of optimizations to the graph operations on B2SR by the intrinsics of modern GPUs. It additionally introduces Deep Reinforcement Learning (DRL) as an efficient way to best configure the bit-level optimizations on the fly. Additionally, the DQN-based adaptive tile size selector with dedicated model training can reach 68% prediction accuracy. Evaluations on NVIDIA Pascal and Volta GPUs show that the optimizations bring up to 40× and 6555× for essential GraphBLAS kernels SpMV and SpGEMM, respectively, making GraphBLAS-based BFS accelerate up to 433×, SSSP, PR, and CC up to 35×, and TC up to 52×.

79 ASTRONOMY AND ASTROPHYSICS↗

Direct numerical simulations of turbulent reacting flows with shock waves and stiff chemistry using many-core/GPU acceleration

Compressible reacting flows may display sharp spatial variation related to shocks, contact discontinuities or reactive zones embedded within relatively smooth regions. The presence of such phenomena emphasizes the relevance of shock-capturing schemes such as the weighted essentially non-oscillatory (WENO) scheme as an essential ingredient of the numerical solver. However, these schemes are complex and have more computational cost than the simple high-order compact or non-compact schemes. In this paper, we present the implementation of a seventh-order, minimally-dissipative mapped WENO (WENO7M) scheme in a newly developed direct numerical simulation (DNS) code called KAUST Adaptive Reactive Flows Solver (KARFS). In order to make efficient use of the computer resources and reduce the solution time, without compromising the resolution requirement, the WENO routines are accelerated via graphics processing unit (GPU) computation. The performance characteristics and scalability of the code are studied using different grid sizes and block decomposition. Furthermore, the performance portability of KARFS is demonstrated on a variety of architectures including NVIDIA Tesla P100 GPUs and NVIDIA Kepler K20X GPUs. In addition, the capability and potential of the newly implemented WENO7M scheme in KARFS to perform DNS of compressible flows is also demonstrated with model problems involving shocks, isotropic turbulence, detonations and flame propagation into a stratified mixture with complex chemical kinetics.

97 MATHEMATICS AND COMPUTING↗

PeleLMeX: an AMR Low Mach Number Reactive Flow Simulation Code without level sub-cycling

PeleLMeX simulates chemically reacting low Mach number flows with block-structured adaptive mesh refinement (AMR). The code is built upon the AMReX library, which provides the underlying data structures and tools to manage and operate on them across massively parallel computing architectures. PeleLMeX algorithmic features are inherited from its predecessor PeleLM but key improvements allow representation of more complex physical processes. Together with its compressible flow counterpart PeleC, the thermo-chemistry library PelePhysics and the multi-physics library PeleMP, it forms the Pele suite of open-source reactive flow simulation codes.

97 MATHEMATICS AND COMPUTING↗

Stretchable form of single crystal silicon for high performance electronics on rubber substrates

The present invention provides stretchable, and optionally printable, semiconductors and electronic circuits capable of providing good performance when stretched, compressed, flexed or otherwise deformed. Stretchable semiconductors and electronic circuits of the present invention preferred for some applications are flexible, in addition to being stretchable, and thus are capable of significant elongation, flexing, bending or other deformation along one or more axes. Further, stretchable semiconductors and electronic circuits of the present invention may be adapted to a wide range of device configurations to provide fully flexible electronic and optoelectronic devices.

Rogers, John A.↗

Predicting concrete compressive strength using hybrid ensembling of surrogate machine learning models

This study aims to implement a hybrid ensemble surrogate machine learning technique in predicting the compressive strength (CS) of concrete, an important parameter used for durability design and service life prediction of concrete structures in civil engineering projects. For this purpose, an experimental database consisting of 1030 records has been compiled from the machine learning repository of the University of California, Irvine. The database was used to train and validate four conventional machine learning (CML) models, namely Artificial Neural Network (ANN), Linear and Non-Linear Multivariate Adaptive Regression Splines (MARS-L and MARS-C), Gaussian Process Regression (GPR), and Minimax Probability Machine Regression (MPMR). Subsequently, the predicted outputs of CML models were combined and trained using ANN to construct the Hybrid Ensemble Model (HENSM). It is observed that the proposed HENSM produces higher predictive accuracy compared to the CML models used in the present study. The predictive performance of all models for CS prediction was compared using the testing dataset and it is found that the HENSM model attained the highest predictive accuracy in both phases. Based on the experimental results, the newly constructed HENSM model is very potential to be a new alternative in handling the overfitting issues of CML models and hence, can be used to predict the concrete CS, including the design of less polluting and more sustainable concrete constructions.

36 MATERIALS SCIENCE↗

Automated pipeline processing X-ray diffraction data from dynamic compression experiments on the Extreme Conditions Beamline of PETRA III

Presented and discussed here is the implementation of a software solution that provides prompt X-ray diffraction data analysis during fast dynamic compression experiments conducted within the dynamic diamond anvil cell technique. It includes efficient data collection, streaming of data and metadata to a high-performance cluster (HPC), fast azimuthal data integration on the cluster, and tools for controlling the data processing steps and visualizing the data using the DIOPTAS software package. This data processing pipeline is invaluable for a great number of studies. The potential of the pipeline is illustrated with two examples of data collected on ammonia–water mixtures and multiphase mineral assemblies under high pressure. The pipeline is designed to be generic in nature and could be readily adapted to provide rapid feedback for many other X-ray diffraction techniques, e.g. large-volume press studies, in situ stress/strain studies, phase transformation studies, chemical reactions studied with high-resolution diffraction etc.

97 MATHEMATICS AND COMPUTING↗

Lion Cub: Minimizing Communication Overhead in Distributed Lion

Communication overhead is a key challenge in distributed deep learning, especially on slower Ethernet intercon nects, and given current hardware trends, communication is likely to become a major bottleneck. While gradient compression techniques have been explored for SGD and Adam, the Lion optimizer has the distinct advantage that its update vectors are the output of a sign operation, enabling straightforward quantization. However, simply compressing updates for communication and using techniques like majority voting fails to lead to end-to-end speedups due to inefficient communication algorithms and reduced convergence. We analyze three factors critical to distributed learning with Lion: optimizing communication methods, identifying effective quantization methods, and assessing the necessity of momentum synchronization. Our findings show that quantization techniques adapted to Lion and selective momentum synchronization can significantly reduce communication costs while maintaining convergence. We combine these into Lion Cub, which enables up to 5x speedups in end-to-end training compared to Lion. This highlights Lion’s potential as a communication-efficient solution for distributed training.

97 MATHEMATICS AND COMPUTING↗

Randomized Sketching Algorithms for Low-Memory Dynamic Optimization

This paper develops a novel limited-memory method to solve dynamic optimization problems. The memory requirements for such problems often present a major obstacle, particularly for problems with PDE constraints such as optimal flow control, full waveform inversion, and optical tomography. In these problems, PDE constraints uniquely determine the state of a physical system for a given control; the goal is to find the value of the control that minimizes an objective. While the control is often low dimensional, the state is typically more expensive to store. This paper suggests using randomized matrix approximation to compress the state as it is generated and shows how to use the compressed state to reliably solve the original dynamic optimization problem. Concretely, the compressed state is used to compute approximate gradients and to apply the Hessian to vectors. The approximation error in these quantities is controlled by the target rank of the sketch. This approximate first- and second-order information can readily be used in any optimization algorithm. As an example, we develop a sketched trust-region method that adaptively chooses the target rank using a posteriori error information and provably converges to a stationary point of the original problem. Numerical experiments with the sketched trust-region method show promising performance on challenging problems such as the optimal control of an advection-reaction-diffusion equation and the optimal control of fluid flow past a cylinder.

97 MATHEMATICS AND COMPUTING↗

More chemical detection through less sampling: amplifying chemical signals in hyperspectral data cubes through compressive sensing

Compressive sensing (CS) is a method of sampling which permits some classes of signals to be reconstructed with high accuracy even when they were sampled at sub-Nyquist rates. In this paper we explore a phenomenon in which bandwise CS sampling of a hyperspectral data cube followed by reconstruction can actually result in amplification of chemical signals contained in the cube. Perhaps most surprisingly, chemical signal amplification generally seems to increase as the level of sampling decreases. In some examples, the chemical signal is significantly stronger in a data cube reconstructed from 10% CS sampling than it is in the raw, 100% sampled data cube. We explore this phenomenon in two real-world datasets including the Physical Sciences Inc. Fabry-Perot interferometer sensor multispectral dataset and the Johns Hopkins Applied Physics Lab FTIR-based longwave infrared sensor hyperspectral dataset. Each of these datasets contains the release of a chemical simulant, such as glacial acetic acid, triethyl phospate, and sulfur hexafluoride, and in all cases we use the adaptive coherence estimator (ACE) to detect a target signal in the hyperspectral data cube. We end the paper by suggesting some theoretical justifications for why chemical signals would be amplified in CS sampled and reconstructed hyperspectral data cubes and discuss some practical implications.

Hyperspectral imagery, Compressive Sensing, single↗

Reverse scaling of a bonded-sphere DEM model: Formulation and application to lignocellulosic biomass microstructures

We explore scaling laws for adapting a bonded-sphere discrete element method (BS-DEM) model developed for woody structural mechanics at the millimeter scale to model the mechanics of realistic lignocellulosic biomass microstructures. Two scaling approaches, i.e., the reverse coarse graining (RCG) and equivalent bulk behavior (EBB), are proposed based on the classical mechanics principles and assessed in the single-particle compression and rectangular cuboid block tension tests. The EBB approach is recommended for BS-DEM models with general 3D geometries and is applied to simulate the microindentation test on a realistic microscale pinewood specimen. Simulations are performed to elucidate the impact of specimen thickness and loading position on the specimen’s force–deformation behavior. Furthermore, the range of Young’s modulus obtained from the calibrated BS-DEM simulations can match the experimental measurements. This is the first-of-its-kind study that has explored scale-bridging modeling approaches in biomass micromechanics and has proposed solutions based on BS-DEM models in the microscale.

59 BASIC BIOLOGICAL SCIENCES↗

Circular Reprocessing of Thermoset Polyurethane Foams

Thermoset polyurethane (PU) foams are widely used in industrial applications, but they cannot be recycled by conventional melt reprocessing because of their cross-linked structures. The introduction of carbamate exchange catalysts converts thermoset PU into covalent adaptable networks (CANs), which are amenable to reprocessing at elevated temperatures. However, this approach has produced solid PU films, which have fewer uses and lower commercial demand. In this work, simultaneous reprocessing and refoaming of thermoset PU foams is demonstrated by leveraging the melt-processability of PU CANs and allowing cell growth by gas generation in a twin-screw extruder. The optimal operating temperature of the refoaming process is determined through chemical, thermal, and structural analysis of PU foam extrudates. The foam-to-foam extrusion process produces controllable, continuous, and uniform foam structures, as characterized by cell diameter and cell number density. Low-density PU foams are obtained through a process simulating injection molding. The compression properties of reprocessed PU foam are compared with as-synthesized PU foam to demonstrate efficacy of the refoaming processes. These results demonstrate that PU foams can be prepared through recycling while maintaining microstructural and chemical integrity. In the future, this strategy may be applied to thermoset PU foams of various chemical compositions and shows promise for scalability.

36 MATERIALS SCIENCE↗

Single-shot in-line x-ray phase-contrast imaging of void-shockwave interactions in fusion energy materials

Recent breakthroughs in nuclear fusion, specifically the report of reactions exceeding scientific breakeven at the National Ignition Facility (NIF), highlight the potential of inertial fusion energy (IFE) as a sustainable and virtually limitless energy source. However, further progress in IFE requires characterization of defects in ablator materials and how they affect fuel capsule compression. Voids within the ablator can degrade energy yield, but their impact on the density distribution has primarily been studied through simulations, with limited high-resolution experimental validation. To address this, we used the x-ray free-electron laser (XFEL) at the matter in extreme conditions (MECs) instrument at the Linac coherent light source (LCLS) to capture 2D x-ray phase-contrast (XPC) images of a void-bearing sample with a composition similar to inertial confinement fusion (ICF) ablators. By driving a compressive shockwave through the sample using MEC's long-pulse laser system, we analyzed how voids influence shockwave propagation and density distribution during compression. To quantify this impact, we extracted phase information using two phase retrieval algorithms. First, we applied the contrast transfer function (CTF) method, paired with Tikhonov regularization and a fast optimization approach to generate an initial phase estimate. We then refined the result using a projected gradient descent (PGD) method that works directly with the sample's refractive index. Comparing these results with radiation adaptive grid Eulerian (xRAGE) radiation hydrodynamic simulations enables identification of model validation needs or improvements. By calculating phase maps in situ, it becomes possible to reconstruct areal density maps, improving understanding of laser-capsule interactions and advancing IFE research.

Hodge, D. S. [Colorado State Univ., Fort Collins, ↗

Lagrangian particle model for 3D simulation of pellets and SPI fragments in tokamaks

A 3D numerical model for the ablation of pellets and shattered pellet injection (SPI) fragments in tokamaks in the plasma disruption mitigation and fueling parameter space has been developed based on the Lagrangian particle code [R. Samulyak, X. Wang, H.-S. Chen, Lagrangian Particle Method for Compressible Fluid Dynamics, J. Comput. Phys., 362 (2018), 1-19]. The pellet code implements the low magnetic Reynolds number MHD equations, kinetic models for the electronic heating, a pellet surface ablation model, an equation of state that supports multiple ionization states, radiation, and a model for grad-B drift of the ablated material across the magnetic field. The Lagrangian particle algorithm is highly adaptive, capable of simulating a large number of fragments in 3D while eliminating numerical difficulties of dealing with the tokamak background plasma. The code has achieved good agreement with theory for spherically symmetric ablation flows. Axisymmetric simulations of neon and deuterium pellets in magnetic fields ranging from 1 to 6 Tesla have been compared with previous simulations using the FronTier code, and very good agreement has also been obtained. Furthermore, the main physics contribution of the paper is a detailed study of the influence of 3D effects, in particular grad-B drift, on pellet ablation rates and properties of ablation clouds. Smaller reductions of ablation rates in magnetic fields compared to axially symmetric simulations have been demonstrated because the ablated material is not confined to narrowing channels in the presence of grad-B drift. Contribution of various factors in the grad-B drift model has also been quantified.

97 MATHEMATICS AND COMPUTING↗

Electronic Configurational Transformation of Network Modifiers in Aluminate Glass above Megabar Pressures

Electronic responses of glasses under extreme pressures differ from those of crystalline analogs. Their distinct electronic environments are found in network formers with well-defined, covalent-bonded coordination environments (e.g., [4] Si and [4] Al) and in network modifiers with more disordered, ionic-bonded configurations (e.g., [5,6,7] Ca). Deciphering the evolution of the bonding environment of network modifier cations upon compression provides atomic insights into the pressure-driven hardening and transport properties of glasses. Despite the importance, in contrast to extensive efforts to uncover how network formers behave under pressure, considerable structural disorder around network modifiers makes it challenging to probe their electronic bonding environments under compression. Our understanding of the evolution of network modifiers above megabars is currently absent. Here, we report a discovery of highly densified electronic configurations of network modifier Ca in aluminate glass under extreme compression via the first inelastic X-ray scattering at the Ca L-edge up to 140 GPa. As evidenced by the prominent pressure-driven increases in electronic dispersion and delocalization, densified calcium environments are characterized by a decreased average Ca–O distance, the formation of highly coordinated calcium, a broader distribution of topological variables, and a greater distortion of Ca polyhedra above megabars. The spectral features for the Ca environments reveal significant electronic and bonding modifications, including pressure-driven increases in the ligand field interaction, the covalence characteristic of the Ca–O bond, and the electron–hole Coulomb interaction. These densification paths identify the electronic adaptation of network modifiers above megabars, shedding light on the origins of enhanced electron transport and the electron-storing capacity of glasses under pressure.

amorphous materials↗