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At least 1,603 records · Page 89

All sources NASA NTRS DOE OSTI

DOE OSTI2022

Comparison of multiobjective optimization methods for the $\mathrm{LCLS-II}$ photoinjector

Particle accelerators are among some of the largest science experiments in the world and can consist of thousands of components with a wide variety of input ranges. These systems can easily become unwieldy optimization problems during design and operations studies. Starting in the early 2000s, searching for better beam dynamics configurations became synonymous with heuristic optimization methods in the accelerator physics community. Genetic algorithms and particle swarm optimization are currently the most widely used. These algorithms can take thousands of simulation evaluations to find optimal solutions for one machine prototype. For large facilities such as the Linac Coherent Light Source (LCLS) and others, this equates to a limited exploration of many possible design configurations. In this paper, the LCLS-II photoinjector is optimized with three optimization algorithms. All optimizations were started from both a uniform random and Latin hypercube sample. In all cases, the optimizations started from Latin hypercube samples outperformed optimizations started from uniform samples. All three algorithms were able to optimize the photoinjector, with the model-based methods approximating the Pareto front in fewer simulation evaluations. This work, in combination with previous optimization observations, indicates objective penalties have a strong impact on the efficiency of such methods. In general, we recommend heuristic methods for initial optimizations and model-based methods when information about the objective space is available.

43 PARTICLE ACCELERATORS↗

NASA NTRS2011

Time delay and distance measurement

A method for measuring time delay and distance may include providing an electromagnetic radiation carrier frequency and modulating one or more of amplitude, phase, frequency, polarization, and pointing angle of the carrier frequency with a return to zero (RZ) pseudo random noise (PN) code. The RZ PN code may have a constant bit period and a pulse duration that is less than the bit period. A receiver may detect the electromagnetic radiation and calculate the scattering profile versus time (or range) by computing a cross correlation function between the recorded received signal and a three-state RZ PN code kernel in the receiver. The method also may be used for pulse delay time (i.e., PPM) communications.

Abshire, James B.↗

DOE OSTI2022

Persistent memory as an effective alternative to random access memory in metagenome assembly

Abstract Background The assembly of metagenomes decomposes members of complex microbe communities and allows the characterization of these genomes without laborious cultivation or single-cell metagenomics. Metagenome assembly is a process that is memory intensive and time consuming. Multi-terabyte sequences can become too large to be assembled on a single computer node, and there is no reliable method to predict the memory requirement due to data-specific memory consumption pattern. Currently, out-of-memory (OOM) is one of the most prevalent factors that causes metagenome assembly failures. Results In this study, we explored the possibility of using Persistent Memory (PMem) as a less expensive substitute for dynamic random access memory (DRAM) to reduce OOM and increase the scalability of metagenome assemblers. We evaluated the execution time and memory usage of three popular metagenome assemblers (MetaSPAdes, MEGAHIT, and MetaHipMer2) in datasets up to one terabase. We found that PMem can enable metagenome assemblers on terabyte-sized datasets by partially or fully substituting DRAM. Depending on the configured DRAM/PMEM ratio, running metagenome assemblies with PMem can achieve a similar speed as DRAM, while in the worst case it showed a roughly two-fold slowdown. In addition, different assemblers displayed distinct memory/speed trade-offs in the same hardware/software environment. Conclusions We demonstrated that PMem is capable of expanding the capacity of DRAM to allow larger metagenome assembly with a potential tradeoff in speed. Because PMem can be used directly without any application-specific code modification, these findings are likely to be generalized to other memory-intensive bioinformatics applications.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Method and apparatus for constructing informative outcomes to guide multi-policy decision making

In Multi-Policy Decision-Making (MPDM), many computationally-expensive forward simulations are performed in order to predict the performance of a set of candidate policies. In risk-aware formulations of MPDM, only the worst outcomes affect the decision making process, and efficiently finding these influential outcomes becomes the core challenge. Recently, stochastic gradient optimization algorithms, using a heuristic function, were shown to be significantly superior to random sampling. In this disclosure, it was shown that accurate gradients can be computed-even through a complex forward simulation—using approaches similar to those in dep networks. The proposed approach finds influential outcomes more reliably, and is faster than earlier methods, allowing one to evaluate more policies while simultaneously eliminating the need to design an easily-differentiable heuristic function.

Olson, Edwin↗

DOE OSTI2021

A learning-augmented approach for AC optimal power flow

Because of the high nonlinearity of AC optimal power flow (OPF), numerous efforts have been made in recent decades to find efficient methods. Machine learning (ML) has proven to significantly reduce the computational costs in many real-world problems. Thus, this paper develops a learning-augmented method for solving AC OPF, which integrates both power network equations and ML to yield near-optimal solutions. More specifically, ML models are developed to first predict bus voltage magnitudes and angles. Then, physics-based network equations are employed to calculate the power injection at different buses. Three ML algorithms, i.e., random forest, multi-target decision tree, and extreme learning machine, are explored and compared. To evaluate the efficiency of the proposed learning-augmented AC OPF solver, the MATPOWER Interior Point Solver is adopted as a baseline. Case studies on both 500-bus and 4918-bus test networks show that the proposed learning-augmented method has reduced the computational time by 15–100 times depending on the network size with a minimal loss in optimality.

42 ENGINEERING↗

NASA NTRS2012

Implementation of a Smeared Crack Band Model in a Micromechanics Framework

The smeared crack band theory is implemented within the generalized method of cells and high-fidelity generalized method of cells micromechanics models to capture progressive failure within the constituents of a composite material while retaining objectivity with respect to the size of the discretization elements used in the model. An repeating unit cell containing 13 randomly arranged fibers is modeled and subjected to a combination of transverse tension/compression and transverse shear loading. The implementation is verified against experimental data (where available), and an equivalent finite element model utilizing the same implementation of the crack band theory. To evaluate the performance of the crack band theory within a repeating unit cell that is more amenable to a multiscale implementation, a single fiber is modeled with generalized method of cells and high-fidelity generalized method of cells using a relatively coarse subcell mesh which is subjected to the same loading scenarios as the multiple fiber repeating unit cell. The generalized method of cells and high-fidelity generalized method of cells models are validated against a very refined finite element model.

Pineda, Evan J.↗

NASA NTRS2012

Progressive Failure of a Unidirectional Fiber-Reinforced Composite Using the Method of Cells: Discretization Objective Computational Results

Pineda, Evan J.↗

DOE OSTI2020

Conditional Karhunen-Loève expansion for uncertainty quantification and active learning in partial differential equation models

We use a conditional Karhunen-Lo` eve (KL) model to quantify and reduce uncertainty in a stochastic partial differential equation (SPDE) problem with partially-known space-dependent coefficient, Y (x). We assume that a small number of Y (x) measurements are available and model Y (x) with a KL expansion. We achieve reduction in uncertainty by conditioning the KL expansion coefficients on measurements. We consider two approaches for conditioning the KL expansion: In Approach 1, we condition the KL model first and then truncate it. In Approach 2, we first truncate the KL expansion and then condition it. We employ the conditional KL expansion together with Monte Carlo and sparse grid collocation methods to compute the moments of the solution of the SPDE problem. Uncertainty of the problem is further reduced by adaptively selecting additional observation locations using two active learning methods. Method 1 minimizes the variance of the PDE coefficient, while Method 2 minimizes the variance of the solution of the PDE. We demonstrate that conditioning leads to dimension reduction of the KL representation of Y (x). For a linear diffusion SPDE with uncertain log-normal coefficient, we show that Approach 1 provides a more accurate approximation of the conditional log-normal coefficient and solution of the SPDE than Approach 2 for the same number of random dimensions in a conditional KL expansion. Furthermore, Approach 2 provides a good estimate for the number of terms of the truncated KL expansion of the conditional field of Approach 1. Finally, we demonstrate that active learning based on Method 2 is more efficient for uncertainty reduction in the SPDE’s states (i.e., it leads to a larger reduction of the variance) than active learning using Method 2.

Conditioned Karhunen-Lo` eve expanion, machine lea↗

DOE OSTI2022

Model-Form Epistemic Uncertainty Quantification for Modeling with Differential Equations: Application to Epidemiology

Modeling real-world phenomena to any degree of accuracy is a challenge that the scientific research community has navigated since its foundation. Lack of information and limited computational and observational resources necessitate modeling assumptions which, when invalid, lead to model-form error (MFE). The work reported herein explored a novel method to represent model-form uncertainty (MFU) that combines Bayesian statistics with the emerging field of universal differential equations (UDEs). The fundamental principle behind UDEs is simple: use known equational forms that govern a dynamical system when you have them; then incorporate data-driven approaches – in this case neural networks (NNs) – embedded within the governing equations to learn the interacting terms that were underrepresented. Utilizing epidemiology as our motivating exemplar, this report will highlight the challenges of modeling novel infectious diseases while introducing ways to incorporate NN approximations to MFE. Prior to embarking on a Bayesian calibration, we first explored methods to augment the standard (non-Bayesian) UDE training procedure to account for uncertainty and increase robustness of training. In addition, it is often the case that uncertainty in observations is significant; this may be due to randomness or lack of precision in the measurement process. This uncertainty typically manifests as “noisy” observations which deviate from a true underlying signal. To account for such variability, the NN approximation to MFE is endowed with a probabilistic representation and is updated using available observational data in a Bayesian framework. By representing the MFU explicitly and deploying an embedded, data-driven model, this approach enables an agile, expressive, and interpretable method for representing MFU. In this report we will provide evidence that Bayesian UDEs show promise as a novel framework for any science-based, data-driven MFU representation; while emphasizing that significant advances must be made in the calibration of Bayesian NNs to ensure a robust calibration procedure.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Effectiveness of fat grafting in scar reduction: A systematic review and meta‐analysis

Abstract Background Scar brings great physical and mental pain to patients. Fat grafting may be a new and simple way to treat scar. This review aimed to systematically evaluate the correlation between fat grafting and scar reduction. Methods The author searched Chinese and English literature databases such as CNKI, Wanfang Data, Cqvip, Pubmed, Web of Science, Embase, CBM, etc. for articles published in the period from 2011 to 2021 about the randomized controlled trials (RCTs) to assess the effect of fat grating on scar reduction, and then performed meta‐analysis with Review Manager 5.4. Results A total of nine articles were included in the assessment of the effect of fat grafting on scar reduction, with meta‐analysis suggesting statistical significance (OR = 5.63, 95% CI: 3.01–10.53, p < 0.01). There was statistical significance in the difference observed between the simple fat grating group ( p = 0.004) and the group of existing therapies combined with fat grafting ( p < 0.0001). Conclusion Fat grafting may be a good method for scar treatment, especially when it's combined with other therapies. Still, due to the limitations of included RCTs, more large‐scale high‐quality RCTs must be carried out before solid conclusions can be drawn.

Zhang, Xiaoyuan↗

DOE OSTI2022

A dictionary learning algorithm for compression and reconstruction of streaming data in preset order

There has been an emerging interest in developing and applying dictionary learning (DL) to process massive datasets in the last decade. Many of these efforts, however, focus on employing DL to compress and extract a set of important features from data, while considering restoring the original data from this set a secondary goal. On the other hand, although several methods are able to process streaming data by updating the dictionary incrementally as new snapshots pass by, most of those algorithms are designed for the setting where the snapshots are randomly drawn from a probability distribution. In this paper, we present a new DL approach to compress and denoise massive dataset in real time, in which the data are streamed through in a preset order (instances are videos and temporal experimental data), so at any time, we can only observe a biased sample set of the whole data. Here, our approach incrementally builds up the dictionary in a relatively simple manner: if the new snapshot is adequately explained by the current dictionary, we perform a sparse coding to find its sparse representation; otherwise, we add the new snapshot to the dictionary, with a Gram-Schmidt process to maintain the orthogonality. To compress and denoise noisy datasets, we apply the denoising to the snapshot directly before sparse coding, which deviates from traditional dictionary learning approach that achieves denoising via sparse coding. Compared to full-batch matrix decomposition methods, where the whole data is kept in memory, and other mini-batch approaches, where unbiased sampling is often assumed, our approach has minimal requirement in data sampling and storage: i) each snapshot is only seen once then discarded, and ii) the snapshots are drawn in a preset order, so can be highly biased. Through experiments on climate simulations and scanning transmission electron microscopy (STEM) data, we demonstrate that the proposed approach performs competitively to those methods in data reconstruction and denoising.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

A Prospective Randomized Trial of the Influence of Music on Anxiety in Patients Starting Radiation Therapy for Cancer

One of the most downloaded articles in 2017 from the International Journal of Radiation Oncology, Biology, and Physics was a study suggesting that music therapy during radiation therapy (RT) simulation substantially reduces anxiety. To further evaluate the potential of music's clinical efficacy in the context of radiation therapy, we conducted a randomized trial evaluating the influence of genre-based music chosen by the study participant on anxiety during the first RT treatment session with a method that is applicable to routine clinical practice.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2023

Effects of head modeling errors on the spatial frequency representation of MEG

Abstract Objectives. We aim to investigate the effects of head model inaccuracies on signal and source reconstruction accuracies for various sensor array distances to the head. This allows for the assessment of the importance of head modeling for next-generation magnetoencephalography (MEG) sensors, optically-pumped magnetometers (OPM). Approach. A 1-shell boundary element method (BEM) spherical head model with 642 vertices of radius 9 cm and conductivity of 0.33 S m −1 was defined. The vertices were then randomly perturbed radially up to 2%, 4%, 6%, 8% and 10% of the radius. For each head perturbation case, the forward signal was calculated for dipolar sources located at 2 cm, 4 cm, 6 cm and 8 cm from the origin (center of the sphere), and for a 324 sensor array located at 10 cm to 15 cm from the origin. Equivalent current dipole (ECD) source localization was performed for each of these forward signals. The signal for each perturbed spherical head case was then analyzed in the spatial frequency domain, and the signal and ECD errors were quantified relative to the unperturbed case. Main results. In the noiseless and high signal-to-noise ratio (SNR) case of approximately ≥6 dB, inaccuracies in our spherical BEM head conductor models lead to increased signal and ECD inaccuracies when sensor arrays are placed closer to the head. This is true especially in the case of deep and superficial sources. In the noisy case however, the higher SNR for closer sensor arrays allows for an improved ECD fit and outweighs the effects of head geometry inaccuracies. Significance. OPMs may be placed directly on the head, as opposed to the more commonly used superconducting quantum interference device sensors which must be placed a few centimeters away from the head. OPMs thus allow for signals of higher spatial resolution to be captured, resulting in potentially more accurate source localizations. Our results suggest that an increased emphasis on accurate head modeling for OPMs may be necessary to fully realize its improved source localization potential.

Yeo, Wan-Jin (ORCID:0000000241417123)↗

DOE OSTI2020

Co-locality to co-functionality: Eukaryotic gene neighborhoods as a resource for function

Diverging from the classic paradigm of random gene order in eukaryotes, gene proximity can be leveraged to systematically identify functionally related gene neighborhoods in eukaryotes, utilizing techniques pioneered in bacteria. Current methods of identifying gene neighborhoods typically rely on sequence similarity to characterized gene products. However, this approach is not robust for non model organisms like algae, which are evolutionarily distant from well-characterized model organisms. Here, we utilize a comparative genomic approach to identify evolutionarily conserved Proximal Orthologous Gene (POG) pairs conserved across at least two taxonomic classes of green algae. A total of 317 gene neighborhoods were identified. In some cases, gene proximity appears to have been conserved since before the streptophyte-chlorophyte split, 1,000 million years ago. Using functional inferences derived from reconstructed evolutionary relationships, we identified several novel functional clusters. A putative mycosporine-like amino acid (MAA), "sunscreen", neighborhood contains genes similar to either vertebrate or cyanobacterial pathways, suggesting a novel mosaic biosynthetic pathway in green algae. One of two putative arsenic-detoxification neighborhoods includes an organoarsenical transporter (ArsJ), a glyceraldehyde 3-phosphate dehydrogenase-like gene, homologs of which are involved in arsenic detoxification in bacteria, and a novel algal-specific phosphoglycerate kinase-like gene (PGK). Mutants of the ArsJ-like transporter and PGK-like genes in Chlamydomonas reinhardtii were found to be sensitive to arsenate, providing experimental support for the role of these identified neighbors in resistance to arsenate. Potential evolutionary origins of neighborhoods are discussed, and updated annotations for formerly poorly annotated genes are presented, highlighting the potential of this strategy for functional annotation.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Exploring Sensitivity of ICF Outputs to Design Parameters in Experiments Using Machine Learning

We report building a sustainable burn platform in inertial confinement fusion (ICF) requires an understanding of the complex coupling of physical processes and the effects that key experimental design changes have on implosion performance. While simulation codes are used to model ICF implosions, incomplete physics and the need for approximations deteriorate their predictive capability. Identification of relationships between controllable design inputs and measurable outcomes can help guide the future design of experiments and development of simulation codes, which can potentially improve the accuracy of the computational models used to simulate ICF implosions. In this article, we leverage developments in machine learning (ML) and methods for ML feature importance/sensitivity analysis to identify complex relationships in ways that are difficult to process using expert judgment alone. We present work using random forest (RF) regression for prediction of yield, velocity, and other experimental outcomes given a suite of design parameters, along with an assessment of important relationships and uncertainties in the prediction model. We show that RF models are capable of learning and predicting on ICF experimental data with high accuracy, and we extract feature importance metrics that provide insight into the physical significance of different controllable design inputs for various ICF design configurations. These results can be used to augment expert intuition and simulation results for optimal design of future ICF experiments.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

NASA NTRS1974

A theory of wave scatter from an inhomogeneous medium with a slightly rough boundary and its application to sea ice

An analytical theory of electromagnetic wave scattering from an inhomogeneous medium with a slightly rough boundary surface is formulated. The inhomogeneity in the medium is assumed to vary continuously in the vertical direction and to have a small random variation in the horizontal direction. The medium is assumed to consist of two layers. Maxwell's equations are solved by using the small perturbation method together with Fourier transform technique. The resulting differential equations are solved by using WKB and variation of parameter methods. Field amplitudes in each medium are determined by taking boundary conditions into account. The expressions for first order polarized radar backscatter cross-section are obtained. An attempt is made to apply the developed theory to compute sea ice scatter. Numerical calculations are performed for polarized radar backscatter cross-section at two frequencies, 13.3 GHz and 400 MHz. It is shown that WKB method is applicable at both of these frequencies. Theoretical results are compared with the experimental results obtained from NASA Earth Resources Program mission 126. Theoretical results and experimental results are in good agreement.

Parashar, S. K.↗

NASA NTRS1978

Review of industry interest in space processing

The interest on the part of selected U.S. corporation in using the research facilities and capabilities for materials processing in space utilizing the Space Shuttle was assessed. The effectiveness of the interview techniques as a method for gaining insight into the complex array of issues related to materials processing in space was evaluated. The survey, conducted was intended as a random sample of individuals, representing industry, who were currently involved in materials processing in space.

Mcdowell, J. R.↗

NASA NTRS1979

A perturbative treatment of aerosol scattering of infrared radiation

Calculations of long-wave atmospheric heating and cooling rates using the rate equations of Rodgers and Walshaw (1966) with the Malkmus (1967) random band model are presented. A perturbation scheme is developed for the inclusion of aerosol scattering effects in the numerical calculation. Unlike the flux differencing method for calculating long-wave heating and cooling rates, this scheme allows aerosol effects to be included in a simple manner with only a small additional use of computer time. The calculations indicate good agreement with those of previous investigators and demonstrate the expected equivalence of the flux-differencing method and the flux-divergence equation of Rodgers and Walshaw (1966), even at stratospheric altitudes. It is found that aerosols lead to a net heating in the lower troposphere due to infrared scattering and absorption.

Yueh, W. R.↗