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Scalable Asynchronous Domain Decomposition Solvers

We discuss how parallel implementations of linear iterative solvers generally alternate between phases of data exchange and phases of local computation. Increasingly large problem sizes and more heterogeneous compute architectures make load balancing and the design of low latency network interconnects that are able to satisfy the communication requirements of linear solvers very challenging tasks. In particular, global communication patterns such as inner products become increasingly limiting at scale. We explore the use of asynchronous communication based on one-sided Message Passing Interface primitives in the context of domain decomposition solvers. In particular, a scalable asynchronous two-level Schwarz method is presented. We discuss practical issues encountered in the development of a scalable solver and show experimental results obtained on a state-of-the-art supercomputer system that illustrate the benefits of asynchronous solvers in load balanced as well as load imbalanced scenarios. Using the novel method, we can observe speedups of up to four times over its classical synchronous equivalent.

97 MATHEMATICS AND COMPUTING↗

DEEP NEURAL NETWORKS FOR NON-LINEAR MODEL-BASED ULTRASOUND RECONSTRUCTION

Ultrasound reflection tomography is widely used to image large complex specimens that are only accessible from a single side, such as well systems and nuclear power plant containment walls. Typical methods for inverting the measurement rely on delay-and-sum algorithms that rapidly produce reconstructions but with significant artifacts. Recently, model-based reconstruction approaches using a linear forward model have been shown to significantly improve image quality compared to the conventional approach. Nonetheless, even these techniques result in artifacts for complex objects because of the inherent non-linearity of the ultrasound forward model.In this paper, we propose a non-iterative model-based reconstruction method for inverting measurements that are based on non-linear forward models for ultrasound imaging. Our approach involves obtaining an approximate estimate of the reconstruction using a simple linear back-projection and training a deep neural network to refine this to the actual reconstruction. As a result, we apply our method to simulated and experimental ultrasound data to demonstrate dramatic improvements in image quality compared to the delay-and-sum approach and the linear model-based reconstruction approach.

97 MATHEMATICS AND COMPUTING↗

Target tracking via recursive Bayesian state estimation in cognitive radar networks

To cope with complicated environments and stealthier targets, incorporating intelligence and cognition cycles into target tracking is of great importance in modern sensor network management. With remarkable advances in sensor techniques and deployable platforms, a sensing system has freedom to select a subset of available radars, plan their trajectories, and transmit designed waveforms. In this paper, we propose a general framework for single target tracking in cognitive networks of radars, including consideration of waveform design, path planning, and radar selection, which are separately but not jointly taken into account in existing work. The tracking procedure, built on the theories of dynamic graphical models (DGM) and recursive Bayesian state estimation (RBSE), is formulated as two iterative steps: (i) solving a combinatorial optimization problem to select the optimal subset of radars, waveforms, and locations for the next tracking instant, and (ii) acquiring the recursive Bayesian state estimation to accurately track the target. Further, an illustrative example introduces a specific scenario in 2-D space. Simulation results based on the scenario demonstrate that the proposed framework can accurately track the target under the management of the network of radars.

47 OTHER INSTRUMENTATION↗

Analytical Modeling of a Double-Sided Flux Concentrating E-Core Transverse Flux Machine with Pole Windings

In this paper, a nonlinear analytical model based on the Magnetic Equivalent Circuit (MEC) method is developed for a double-sided E-Core Transverse Flux Machine (TFM). The proposed TFM has a cylindrical rotor, sandwiched between E-core stators on both sides. Ferrite magnets are used in the rotor with flux concentrating design to attain high airgap flux density, better magnet utilization, and higher torque density. The MEC model was developed using a series-parallel combination of flux tubes to estimate the reluctance network for different parts of the machine including air gaps, permanent magnets, and the stator and rotor ferromagnetic materials, in a two-dimensional (2-D) frame. An iterative Gauss-Siedel method is integrated with the MEC model to capture the effects of magnetic saturation. A single phase, 1 kW, 400 rpm E-Core TFM is analytically modeled and its results for flux linkage, no-load EMF, and generated torque, are verified with Finite Element Analysis (FEA). The analytical model significantly reduces the computation time while estimating results with less than 10 percent error.

30 DIRECT ENERGY CONVERSION↗

Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome

INTRODUCTION Although much effort has been devoted to studying yeast in the past few decades, our understanding of this model organism is still limited. Rapidly developing DNA synthesis techniques have made a “build-to-understand” approach feasible to reengineer on the genome scale. Here, we report on the completion of a 770-kilobase synthetic yeast chromosome II (synII). SynII was characterized using extensive Trans-Omics tests. Despite considerable sequence alterations, synII is virtually indistinguishable from wild type. However, an up-regulation of translational machinery was observed and can be reversed by restoring the transfer RNA (tRNA) gene copy number. RATIONALE Following the “design-build-test-debug” working loop, synII was successfully designed and constructed in vivo. Extensive Trans-Omics tests were conducted, including phenomics, transcriptomics, proteomics, metabolomics, chromosome segregation, and replication analyses. By both complementation assays and SCRaMbLE (synthetic chromosome rearrangement and modification by loxP -mediated evolution), we targeted and debugged the origin of a growth defect at 37°C in glycerol medium. RESULTS To efficiently construct megabase-long chromosomes, we developed an I- Sce I–mediated strategy, which enables parallel integration of synthetic chromosome arms and reduced the overall integration time by 50% for synII. An I- Sce I site is introduced for generating a double-strand break to promote targeted homologous recombination during mitotic growth. Despite hundreds of modifications introduced, there are still regions sharing substantial sequence similarity that might lead to undesirable meiotic recombinations when intercrossing the two semisynthetic chromosome arm strains. Induction of the I- Sce I–mediated double-strand break is otherwise lethal and thus introduced a strong selective pressure for targeted homologous recombination. Since our strategy is designed to generate a markerless synII and leave the URA3 marker on the wild-type chromosome, we observed a tenfold increase in URA3 -deficient colonies upon I- Sce I induction, meaning that our strategy can greatly bias the crossover events toward the designated regions. By incorporating comprehensive phenotyping approaches at multiple levels, we demonstrated that synII was capable of powering the growth of yeast indistinguishably from wild-type cells (see the figure), showing highly consistent biological processes comparable to the native strain. Meanwhile, we also noticed modest but potentially significant up-regulation of the translational machinery. The main alteration underlying this change in expression is the deletion of 13 tRNA genes. A growth defect was observed in one very specific condition—high temperature (37°C) in medium with glycerol as a carbon source—where colony size was reduced significantly. We targeted and debugged this defect by two distinct approaches. The first approach involved phenotype screening of all intermediate strains followed by a complementation assay with wild-type sequences in the synthetic strain. By doing so, we identified a modification resulting from PCRTag recoding in TSC10 , which is involved in regulation of the yeast high-osmolarity glycerol (HOG) response pathway. After replacement with wild-type TSC10 , the defect was greatly mitigated. The other approach, debugging by SCRaMbLE, showed rearrangements in regions containing HOG regulation genes. Both approaches indicated that the defect is related to HOG response dysregulation. Thus, the phenotypic defect can be pinpointed and debugged through multiple alternative routes in the complex cellular interactome network. CONCLUSION We have demonstrated that synII segregates, replicates, and functions in a highly similar fashion compared with its wild-type counterpart. Furthermore, we believe that the iterative “design-build-test-debug” cycle methodology, established here, will facilitate progression of the Sc2.0 project in the face of the increasing synthetic genome complexity. SynII characterization. ( A ) Cell cycle comparison between synII and BY4741 revealed by the percentage of cells with separated CEN2-GFP dots, metaphase spindles, and anaphase spindles. ( B ) Replication profiling of synII (red) and BY4741 (black) expressed as relative copy number by deep sequencing. ( C ) RNA sequencing analysis revealed that the significant up-regulation of translational machinery in synII is induced by the deletion of tRNA genes in synII.

Shen, Yue↗

A Novel Atmospheric Correction Algorithm to Exploit the Diurnal Variability in Hypertemporal Geostationary Observations

This study developed a new atmospheric correction algorithm, GeoNEX-AC, that is independent from the traditional use of spectral band ratios but dedicated to exploiting information from the diurnal variability in the hypertemporal geostationary observations. The algorithm starts by evaluating smooth segments of the diurnal time series of the top-of-atmosphere (TOA) reflectance to identify clear-sky and snow-free observations. It then attempts to retrieve the Ross-Thick–Li-Sparse (RTLS) surface bi-directional reflectance distribution function (BRDF) parameters and the daily mean atmospheric optical depth (AOD) with an atmospheric radiative transfer model (RTM) to optimally simulate the observed diurnal variability in the clear-sky TOA reflectance. Once the initial RTLS parameters are retrieved after the algorithm’s burn-in period, they serve as the prior information to estimate the AOD levels for the following days and update the surface BRDF information with the new clear-sky observations. This process is iterated through the full time span of the observations, skipping only totally cloudy days or when surface snow is detected. We tested the algorithm over various Aerosol Robotic Network (AERONET) sites and the retrieved results well agree with the ground-based measurements. This study demonstrates that the high-frequency diurnal geostationary observations contain unique information that can help to address the atmospheric correction problem from new directions.

atmospheric correction↗

A Framework for International Collaboration on ITER Using Large-Scale Data Transfer to Enable Near-Real-Time Analysis

The global nature of the ITER project along with its projected ~ petabyte per day data generation presents a unique challenge, but also an opportunity for the fusion community to rethink, optimize, and enhance our scientific discovery process. Recognizing this, collaborative research with computational scientists was undertaken over the past several years to create a framework for large-scale data movement across wide-area networks (WANs), to enable global near-real time analysis of fusion data. This would broaden the available computational resources for analysis/simulation, and increase the number of researchers actively participating in experiments. An official demonstration of this framework for fast, large data transfer and real-time analysis was carried out between the KSTAR tokamak in Daejeon, Korea and PPPL in Princeton, USA. Streaming large data transfer, with near real-time movie creation and analysis of the KSTAR Electron Cyclotron Emission imaging (ECEI) data, was performed using the I/O framework ADIOS, and comparisons made at PPPL with simulation results from the XGC1 code. These demonstrations were made possible utilizing an optimized network configuration at PPPL, which achieved over 8.8 Gbps (88% utilization) in throughput tests from NFRI to PPPL. This demonstration showed the feasibility for large-scale data analysis of KSTAR data, and provides a nascent framework to enable use of globally distributed computational and personnel resources in pursuit of scientific knowledge from the ITER experiment.

43 PARTICLE ACCELERATORS↗

Iterative multi-task learning and inference from seismic images

Seismic interpretation aims to extract quantitative and interpretable attributes from a seismic image produced using some migration method to inform characteristics of a subsurface reservoir or target of interest. Current paradigms for computing seismic attributes mostly rely on single-task algorithms. We develop an iterative, multi-task machine learning method to learn and infer multiple attributes from a seismic image. This method is composed of two stages: a multi-task inference stage and a multi-modal, multi-task refinement stage. The basic mechanism of this method is that we train a multi-task inference neural network (NN) to estimate a set of attributes, including a relative geological time (RGT), a denoised higher-resolution (DHR) seismic image, and multiple fault attributes (including probability, dip, and strike), from a low-resolution, noisy seismic image; then we input the inferred attributes to a multi-task refinement NN to enhance the raw inference results iteratively. The two multi-task NNs are trained separately based on synthetic seismic images and associated attributes generated by a geological modeling algorithm. The software we intend to release is a PyTorch implementation of this multi-task learning method for both 2D and 3D cases along with scripts to run the training/validation. The algorithm and software can be a useful tool for automatic seismic interpretation.

Gao, Kai↗

High-pressure and temperature neural network reactive force field for energetic materials

Reactive force fields for molecular dynamics have enabled a wide range of studies in numerous material classes. These force fields are computationally inexpensive compared with electronic structure calculations and allow for simulations of millions of atoms. However, the accuracy of traditional force fields is limited by their functional forms, preventing continual refinement and improvement. Therefore, we develop a neural network-based reactive interatomic potential for the prediction of the mechanical, thermal, and chemical responses of energetic materials at extreme conditions. The training set is expanded in an automatic iterative approach and consists of various CHNO materials and their reactions under ambient and shock-loading conditions. Further, this new potential shows improved accuracy over the current state-of-the-art force fields for a wide range of properties such as detonation performance, decomposition product formation, and vibrational spectra under ambient and shock-loading conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Binary operations on neuromorphic hardware with application to linear algebraic operations and stochastic equations

Abstract Non-von Neumann computational hardware, based on neuron-inspired, non-linear elements connected via linear, weighted synapses—so-called neuromorphic systems—is a viable computational substrate. Since neuromorphic systems have been shown to use less power than CPUs for many applications, they are of potential use in autonomous systems such as robots, drones, and satellites, for which power resources are at a premium. The power used by neuromorphic systems is approximately proportional to the number of spiking events produced by neurons on-chip. However, typical information encoding on these chips is in the form of firing rates that unarily encode information. That is, the number of spikes generated by a neuron is meant to be proportional to an encoded value used in a computation or algorithm. Unary encoding is less efficient (produces more spikes) than binary encoding. For this reason, here we present neuromorphic computational mechanisms for implementing binary two’s complement operations. We use the mechanisms to construct a neuromorphic, binary matrix multiplication algorithm that may be used as a primitive for linear differential equation integration, deep networks, and other standard calculations. We also construct a random walk circuit and apply it in Brownian motion simulations. We study how both algorithms scale in circuit size and iteration time.

97 MATHEMATICS AND COMPUTING↗

Learning Symbolic Expressions: Mixed-Integer Formulations, Cuts, and Heuristics

Here, in this paper, we consider the problem of learning a regression function without assuming its functional form. This problem is referred to as symbolic regression. An expression tree is typically used to represent a solution function, which is determined by assigning operators and operands to the nodes. Cozad and Sahinidis propose a nonconvex mixed-integer nonlinear program (MINLP), in which binary variables are used to assign operators and nonlinear expressions are used to propagate data values through nonlinear operators, such as square, square root, and exponential. We extend this formulation by adding new cuts that improve the solution of this challenging MINLP. We also propose a heuristic that iteratively builds an expression tree by solving a restricted MINLP. We perform computational experiments and compare our approach with a mixed-integer program–based method and a neural network–based method from the literature.

97 MATHEMATICS AND COMPUTING↗

An optimization model for the US Air-Traffic System

A systematic approach for monitoring U.S. air traffic was developed in the context of system-wide planning and control. Towards this end, a network optimization model with nonlinear objectives was chosen as the central element in the planning/control system. The network representation was selected because: (1) it provides a comprehensive structure for depicting essential aspects of the air traffic system, (2) it can be solved efficiently for large scale problems, and (3) the design can be easily communicated to non-technical users through computer graphics. Briefly, the network planning models consider the flow of traffic through a graph as the basic structure. Nodes depict locations and time periods for either individual planes or for aggregated groups of airplanes. Arcs define variables as actual airplanes flying through space or as delays across time periods. As such, a special case of the network can be used to model the so called flow control problem. Due to the large number of interacting variables and the difficulty in subdividing the problem into relatively independent subproblems, an integrated model was designed which will depict the entire high level (above 29000 feet) jet route system for the 48 contiguous states in the U.S. As a first step in demonstrating the concept's feasibility a nonlinear risk/cost model was developed for the Indianapolis Airspace. The nonlinear network program --NLPNETG-- was employed in solving the resulting test cases. This optimization program uses the Truncated-Newton method (quadratic approximation) for determining the search direction at each iteration in the nonlinear algorithm. It was shown that aircraft could be re-routed in an optimal fashion whenever traffic congestion increased beyond an acceptable level, as measured by the nonlinear risk function.

Mulvey, J. M.↗

On the structure of parallelism in a highly concurrent PDE solver

A parallel multigrid algorithm for solving elliptic partial differential equations is developed and evaluated. A V-cycle multigrid method is altered to increase the degree of parallelism. A numerical analysis of the resulting concurrent-iteration multigrid algorithm is performed; its architectural implications are considered; highly parallel systems without shared memory are examined (including mesh-connected arrays, mesh-shuffle-connected systems, permutation networks, and direct VLSI embeddings); and the results of numerical experiments are presented in tables and graphs.

Gannon, D.↗

Deep Neural Network for Precision Multi-band Infrared Image Segmentation

Image segmentation is one of the fundamental steps in computer vision. Separating targets from background clutter with high precision is a challenging operation for both humans and computers. Currently, segmenting objects from IR images is done by tedious manual work. The implementation of a Deep Neural Network (DNN) to perform precision segmentation of multi-band IR video images is presented. A customized pix2pix DNN with multiple layers of generative encoder/decoder and discriminator architecture is used in the IR image segmentation process. Real and synthetic images and ground truths are employed to train the DNN. Iterative training is performed to achieve optimum accuracy of segmentation using a minimal number of training data. Special training images are created to enhance the missing features and to increase the segmentation accuracy of the objects. Retraining strategies are developed to minimize the DNN training time. Single pixel accuracy has been achieved in IR target boundary segmentation using DNNs. The segmentation accuracy between the customized pix2pix DNN and simple thresholding, GraphCut, simple neural network and ResNet models are compared.

Torres, Gil↗

Subsonic Aircraft With Regression and Neural-Network Approximators Designed

At the NASA Glenn Research Center, NASA Langley Research Center's Flight Optimization System (FLOPS) and the design optimization testbed COMETBOARDS with regression and neural-network-analysis approximators have been coupled to obtain a preliminary aircraft design methodology. For a subsonic aircraft, the optimal design, that is the airframe-engine combination, is obtained by the simulation. The aircraft is powered by two high-bypass-ratio engines with a nominal thrust of about 35,000 lbf. It is to carry 150 passengers at a cruise speed of Mach 0.8 over a range of 3000 n mi and to operate on a 6000-ft runway. The aircraft design utilized a neural network and a regression-approximations-based analysis tool, along with a multioptimizer cascade algorithm that uses sequential linear programming, sequential quadratic programming, the method of feasible directions, and then sequential quadratic programming again. Optimal aircraft weight versus the number of design iterations is shown. The central processing unit (CPU) time to solution is given. It is shown that the regression-method-based analyzer exhibited a smoother convergence pattern than the FLOPS code. The optimum weight obtained by the approximation technique and the FLOPS code differed by 1.3 percent. Prediction by the approximation technique exhibited no error for the aircraft wing area and turbine entry temperature, whereas it was within 2 percent for most other parameters. Cascade strategy was required by FLOPS as well as the approximators. The regression method had a tendency to hug the data points, whereas the neural network exhibited a propensity to follow a mean path. The performance of the neural network and regression methods was considered adequate. It was at about the same level for small, standard, and large models with redundancy ratios (defined as the number of input-output pairs to the number of unknown coefficients) of 14, 28, and 57, respectively. In an SGI octane workstation (Silicon Graphics, Inc., Mountainview, CA), the regression training required a fraction of a CPU second, whereas neural network training was between 1 and 9 min, as given. For a single analysis cycle, the 3-sec CPU time required by the FLOPS code was reduced to milliseconds by the approximators. For design calculations, the time with the FLOPS code was 34 min. It was reduced to 2 sec with the regression method and to 4 min by the neural network technique. The performance of the regression and neural network methods was found to be satisfactory for the analysis and design optimization of the subsonic aircraft.

Patnaik, Surya N.↗

TRANSENSOR: Transformer Real-time Assessment INtelligent System with Embedded Network of Sensors and Optical Readout. Final Report

Utilities across the world are wrestling with evolving market dynamics, population growth and climate change. Distributed Energy Resources (DERs) such as solar photovoltaics, distributed generators and energy storage systems are becoming important parts of the U.S. energy mix. These factors are driving an increasing need for low-cost grid asset monitoring. Aside from being costly, traditional utility monitoring systems are not sufficiently robust and do not provide real-time visibility into the condition of grid assets such as transformers. Lack of accurate real-time measurements on performance has resulted in the use of lagging indicators, such as oil sample analysis. To address this need, an innovative embedded optical sensing technology, Transformer Real-time Assessment Intelligent System (TRANSENSOR) was developed, validated and demonstrated in this project. To date, TRANSENSOR has focused on transformers but is extendable to other grid assets. In addition to the technology being embedded into new transformers during manufacturing, a retrofit configuration that can be installed on existing transformers in the field was also developed. It is anticipated that the ability to retrofit existing transformers will help accelerate adoption of the underlying TRANSENSOR technology. Phase 1 of the project focused on laboratory development and qualification of the technology. Following iterations and exploration of relevant optical sensing modalities and multiplexed configurations of interest for the transformer environment, an effective candidate configuration was agreed upon, down-selected and custom-designed for embedding into General Electric (GE) network transformers. Two new GE 500 kilovolt ampere (kVA), 27 kilovolt (kV) distribution network transformers were built with embedded fiber-optic (FO) sensors and successfully qualified per industry standards at GE’s Shreveport, Louisiana facility during Phase 1 of the project. Following the successful completion of Phase 1, the team proceeded to Phase 2, which focused on a field demonstration of the technology. Over Phase 2, the first new GE transformer built with embedded fiber-optic sensors was installed in an above-ground cage and connected to the grid at Con Edison’s Astoria facility. A second transformer equipped with TRANSENSOR was installed in an underground vault. Additionally, an older (1982 year model) GE transformer in an above-ground cage was retrofitted with fiber- optic sensors and reconnected to the grid at ConEd’s facility. Analysis of data acquired from the sensors showed interesting correlations with transformer loading. Additionally, key events such as transformer low-voltage network connection, primary-side energizing, and a pressure loss event from an oil sampling were detected by the TRANSENSOR system. Online data processing/feature extraction algorithms for the second transformer in the underground vault detected key features and event alerts that were transmitted through a wireless 4G connection. The remote deployment concept showed promising results with data collection running for a total of 8 months across the three (3) GE transformers instrumented for the Phase 2 field demonstration. This sets the stage well for further development and commercialization.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Sequential computation of elementary modes and minimal cut sets in genome-scale metabolic networks using alternate integer linear programming

Elementary (flux) modes (EMs) have served as a valuable tool for investigating structural and functional properties of metabolic networks. Identification of the full set of EMs in genome-scale networks remains challenging due to combinatorial explosion of EMs in complex networks. It is often, however, that only a small subset of relevant EMs needs to be known, for which optimization-based sequential computation is a useful alternative. Most of the currently available methods along this line are based on the iterative use of mixed integer linear programming (MILP), the effectiveness of which significantly deteriorates as the number of iterations builds up. To alleviate the computational burden associated with the MILP implementation, we here present a novel optimization algorithm termed alternate integer linear programming (AILP). Results: Our algorithm was designed to iteratively solve a pair of integer programming (IP) and linear programming (LP) to compute EMs in a sequential manner. In each step, the IP identifies a minimal subset of reactions, the deletion of which disables all previously identified EMs. Thus, a subsequent LP solution subject to this reaction deletion constraint becomes a distinct EM. In cases where no feasible LP solution is available, IP-derived reaction deletion sets represent minimal cut sets (MCSs). Despite the additional computation of MCSs, AILP achieved significant time reduction in computing EMs by orders of magnitude. The proposed AILP algorithm not only offers a computational advantage in the EM analysis of genome-scale networks, but also improves the understanding of the linkage between EMs and MCSs.

59 BASIC BIOLOGICAL SCIENCES↗

Deep learning for exploring ultra-thin ferroelectrics with highly improved sensitivity of piezoresponse force microscopy

Hafnium oxide-based ferroelectrics have been extensively studied because of their existing ferroelectricity, even in ultra-thin film form. However, studying the weak response from ultra-thin film requires improved measurement sensitivity. In general, resonance-enhanced piezoresponse force microscopy (PFM) has been used to characterize ferroelectricity by fitting a simple harmonic oscillation model with the resonance spectrum. However, an iterative approach, such as traditional least squares (LS) fitting, is sensitive to noise and can result in the misunderstanding of weak responses. In this study, we developed the deep neural network (DNN) hybrid with deep denoising autoencoder (DDA) and principal component analysis (PCA) to extract resonance information. The DDA/PCA-DNN improves the PFM sensitivity down to 0.3 pm, allowing measurement of weak piezoresponse with low excitation voltage in 10-nm-thick Hf 0.5 Zr 0.5 O 2 thin films. Our hybrid approaches could provide more chances to explore the low piezoresponse of the ultra-thin ferroelectrics and could be applied to other microscopic techniques.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗