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DOE OSTI2021

An uncertainty-focused database approach to extract spatiotemporal trends from qualitative and discontinuous lake-status histories

Changes in lake status are often interpreted as palaeoclimate indicators due to their dependence on precipitation and evaporation. The Global Lake Status Database (GLSDB) has since long provided a standardised synopsis of qualitative lake status over the last 30,000 14C years. Potential sources of uncertainty however are not recorded in the GLSDB. Here we present an updated and improved relational-database framework that incorporates uncertainty in both chronology and the interpretation of palaeoenvironmental data. The database uses peer-reviewed palaeolimnological studies to produce a consensus on qualitative lake-status histories, whose chronologies are revised and standardized through the recalibration of radiocarbon dates and the application of Bayesian age-depth modelling for stratigraphic archives. Quantitative information on absolute water-level elevation is preserved if available from geomorphological sources. We also propose a new probabilistic analytical framework that accounts for these uncertainties to reconstruct synoptic, integrated environmental signals. The process is based on a Monte Carlo algorithm that iteratively samples individual lake-status histories within the limits of their uncertainties to produce many possible scenarios. We then use Recursively-Subtracted Empirical Orthogonal Function analysis to extract dominant patterns of lake-status variability from these scenarios. As a proof of concept, we apply this framework to 67 sites in eastern and southern Africa whose lake-status histories cover part of the late Pleistocene and/or Holocene. We show that, despite the sometimes large temporal and interpretation uncertainties, and the inclusion of highly discontinuous lake-status time series, identifying the major known millennial-scale climatic phases during the last 20,000 years is possible. Our framework was also able to identify an antiphased response between the lake basins in eastern and interior southern Africa to these changes. Here, we propose that our new database and methodology framework serves as a template for efficient lake-status data synthesis, encourages the incorporation of lake-status data in palaeoclimate syntheses, and expands the possibilities for the use of such data in the evaluation of climate models.

58 GEOSCIENCES↗

DOE OSTI2021

Space to Air High-Altitude Region Adjoint Neutron Transport

Neutrons from an atmospheric nuclear explosion can be detected by sensors in orbit. Current tools for characterizing the neutron energy spectrum assume a known source and use forward transport to recreate the detector response. In realistic scenarios the true source is unknown, making this an inefficient, iterative approach. In contrast, the adjoint approach directly solves for the source spectrum, enabling source reconstruction. The time–energy fluence at the satellite and adjoint transport equation allow a Monte Carlo method to characterize the neutron source’s energy spectrum directly in a new model: the Space to High-Altitude Region Adjoint (SAHARA) model. A new adjoint source event estimator was developed in SAHARA to find feasible solutions to the neutron transport problem given the constraints of the adjoint environment. This work explores SAHARA’s development and performance for mono-energetic and continuous neutron energy sources. In general, the identified spectra were shifted towards energies approximately 5% lower than the true source spectra, but SAHARA was able to capture the correct spectral shapes. Continuous energy sources, including real-world sources Fat Man and Little Boy, resulted in identifiable spectra that could have been produced by the same distribution as the true sources as demonstrated by two-dimensional (2D) Kolmogorov–Smirnov tests.

LaMere, Zachary W.↗

NASA NTRS1988

Interferometric tomography of continuous fields with incomplete projections

Interferometric tomography in the presence of an opaque object is investigated. The developed iterative algorithm does not need to augment the missing information. It is based on the successive reconstruction of the difference field, the difference between the object field to be reconstructed and its estimate, only in the difined region. The application of the algorithm results in stable convergence.

Cha, Soyoung S.↗

NASA NTRS1989

Interferometric tomography of continuous fields with incomplete projections

Interferometric tomography in the presence of an opaque object has been investigated. In principle the developed iterative algorithm does not need to augment the missing information. It is based on the successive reconstruction of the difference field, the difference between the object field to be reconstructed and its estimate, in the defined region only. The application of the algorithm results in stable convergence.

Cha, Soyoung S.↗

DOE OSTI2022

Knowledge-matching based computational framework for genome-scale metabolic model refinement

Genome-scale metabolic models (GEMs) are mathematically structured knowledge base reconstructed from annotated genome of different organisms. With the advancement of next-generation sequencing technology, many organisms have had their genomes sequenced. However, obtaining a high-quality GEM is highly time-consuming, even with the introduction of several genome-scale reconstruction tools that offer automated draft network generation and gap filling. It has been recognized that the iterative process of manual curation and refinement is the limiting step of GEM development, and how to expedite the GEM refinement is still an open question. As cellular metabolism is a complex system with very high degree of freedom and redundancy, the principles and techniques developed in process systems engineering can be adapted to expedite GEM refinement. In this paper we present a knowledge-matching based computation framework for GEM refinement, and demonstrate the effectiveness of the proposed solution using the refinement of a GEM for Clostridium tyrobutyricum.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1992

Interferometric reconstruction of three-dimensional high-speed aerodynamic flows

Holographic interferometry can be a very useful diagnostic tool in high-speed aerodynamic testing. During this summer research period, various possible approaches for accurately reconstructing three-dimensional flows from limited data were examined. The approach based on the combination of the following three techniques appears to be promising: (1) Continuous Local Basis Function Method - this computational tomographic method has a power to accurately reconstruct continuous regions and is appropriate from well-conditioned to moderately limited data; (2) Variable Basis Method - this computational tomographic method provides accuracy near discontinuities, i.e., shock regions, and is appropriate from moderately-limited to severely-limited data; and (3) Complementary Field Method - this is a general iterative reconstructor that can be coupled with any computational tomographic techniques. Mathematically, it can be shown that this method can provide better accuracy than the direct reconstruction as in a conventional approach. Our numerical simulation of experiments demonstrated improved reconstruction results even when these techniques were individually tested.

Cha, Soyoung Stephen↗

DOE OSTI2026

Reconstructing Quasar Spectra and Measuring the Lyα Forest with SpenderQ

Quasar spectra carry the imprint of foreground intergalactic medium (IGM) through absorption features. In particular, absorption caused by neutral hydrogen gas, the "Lyα forest," is a key spectroscopic tracer for cosmological analyses used to measure cosmic expansion and test physics beyond the standard model. Despite their importance, current methods for measuring Lyα absorption cannot directly derive the intrinsic quasar continuum and make strong assumptions on its shape, thus distorting the measured Lyα clustering. We present SpenderQ , a ML-based approach for directly reconstructing the intrinsic quasar spectra and measuring the Lyα forest from observations. SpenderQ uses the Spender spectrum autoencoder to learn a compact and redshift-invariant latent encoding of quasar spectra, combined with an iterative procedure to identify and mask absorption regions. To demonstrate its performance, we apply SpenderQ to 400,000 synthetic quasar spectra created to validate the Dark Energy Spectroscopic Instrument Year 1 Lyα cosmological analyses. SpenderQ accurately reconstructs the true intrinsic quasar spectra, including the broad Lyβ, Lyα, SiIV, CIV, and CIII emission lines. Redward of Lyα, SpenderQ provides percent-level reconstructions of the true quasar spectra. Blueward of Lyα, SpenderQ reconstructs the true spectra to < 5%. SpenderQ reproduces the shapes of individual quasar spectra more robustly than the current state-of-the-art. We, thus, expect it will significantly reduce biases in Lyα clustering measurements and enable studies of quasars and their physical properties. SpenderQ also provides informative latent variable encodings that can be used to, e.g., classify quasars with Broad Absorption Lines. Overall, SpenderQ provides a new data-driven approach for unbiased Lyα forest measurements in cosmological, quasar, and IGM studies.

Hahn, ChangHoon [Arizona U., Astron. Dept. - Stewa↗

DOE OSTI2021

Beyond Taylor’s hypothesis: a novel volumetric reconstruction of velocity and density fields for variable‑density and shear flows

Abstract This work presents a novel numerical procedure for reconstructing volumetric density and velocity fields from planar laser-induced fluorescence (PLIF) and stereoscopic particle image velocimetry (SPIV) data. This new method is theoretically and practically demonstrated to provide more accurate 3D vortical structures and density fields in high shear flows than reconstruction methods based on the mean convective velocity. While Taylor’s hypothesis of frozen turbulence is commonly applied by using the local mean streamwise velocity, the proposed algorithm uses the measured local instantaneous velocity for data convection. It consists of a step-by-step reconstruction based on a mixed Lagrangian–Eulerian solver that includes the 3D interpolation of scattered flow data and that relaxes the Taylor’s hypothesis by iterative enforcement of the incompressibility constraint on the velocity field. This methodology provides 3D fields with temporal resolution, spatial resolution, and accuracy comparable to that of real 3D snapshots, thus providing a practical alternative to tomographic measurements. The procedure is validated using numerical data of the constant-density channel flow available on the Johns Hopkins University Turbulence Database (JHTDB), showing the accurate reconstruction of the 3D velocity field. The algorithm is applied to an experimental dataset of PLIF and SPIV measurements of a variable-density jet flow, demonstrating its capability to provide 3D velocity and density fields that are more consistent with the Navier–Stokes equations compared to the mean flow convective method. Graphic abstract

42 ENGINEERING↗

DOE OSTI2020

Filtered Backprojection in Compton Imaging using a Spherical Harmonic Wiener Filter with Pixelated CdZnTe

Filtered backprojection is an image reconstruction technique for Compton imaging that provides reasonably high resolution at much lower computational costs when compared to iterative methods. Here, this work applies a Wiener filter that has been derived for spherical harmonics on Compton imaging using the OrionUM pixelated CdZnTe imaging-spectrometer. To regularize the filter, an investigation is made into the power spectral density of the signal and noise to develop an appropriate spectral signal-to-noise ratio model for the restoration process. Experimental measurements were conducted with two 228Th sources placed 30° apart. The resulting filtered image of the two sources have an average full-width-at-half-maximum (FWHM) of 9.8° or 7.5° when using a mean squared error and structural similarity optimization approach respectively; an improvement from the 29.0° FWHM image when using simple backprojection.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2020

GNET2: an R package for constructing gene regulatory networks from transcriptomic data

Abstract Motivation The Gene Network Estimation Tool (GNET) is designed to build gene regulatory networks (GRNs) from transcriptomic gene expression data with a probabilistic graphical model. The data preprocessing, model construction and visualization modules of the original GNET software were developed on different programming platforms, which were inconvenient for users to deploy and use. Results Here, we present GNET2, an improved implementation of GNET as an integrated R package. GNET2 provides more flexibility for parameter initialization and regulatory module construction based on the core iterative modeling process of the original algorithm. The data exchange interface of GNET2 is handled within an R session automatically. Given the growing demand for regulatory network reconstruction from transcriptomic data, GNET2 offers a convenient option for GRN inference on large datasets. Availability and implementation The source code of GNET2 is available at https://github.com/jianlin-cheng/GNET2. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

3D imaging of magnetic domains in Nd 2 Fe 14 B using scanning hard X-ray nanotomography

Nanoscale structural and electronic heterogeneities are prevalent in condensed matter physics. Investigating these heterogeneities in 3D has become an important task for understanding material properties. To provide a tool to unravel the connection between nanoscale heterogeneity and macroscopic emergent properties in magnetic materials, scanning transmission X-ray microscopy (STXM) is combined with X-ray magnetic circular dichroism. A vector tomography algorithm has been developed to reconstruct the full 3D magnetic vector field without any prior noise assumptions or knowledge about the sample. Two tomographic scans around the vertical axis are acquired on single-crystalline Nd 2 Fe 14 B pillars tilted at two different angles, with 2D STXM projections recorded using a focused 120 nm X-ray beam with left and right circular polarization. Image alignment and iterative registration have been implemented based on the 2D STXM projections for the two tilts. Dichroic projections obtained from difference images are used for the tomographic reconstruction to obtain the 3D magnetization distribution at the nanoscale.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2024

The motional Stark effect diagnostic for ITER

An overview of the plans for the motional Stark effect (MSE) diagnostic installation on the International Thermonuclear Experimental Reactor (ITER) is presented. The MSE diagnostic uniquely provides spatially localized magnetic field measurements inside the plasma. These are used to constrain equilibrium reconstructions to determine q(r), the safety factor as a function of minor radius. Meeting the system requirements to deliver q-profiles and related quantities with the specified radial resolution of 20 points over the minor radius, 10 ms time resolution, and better than 10% accuracy is challenging. MSE systems observe the D/H-α emission near 656.3 nm from neutral beams. As the beam atoms traverse the magnetic field, B⃗, at high velocity, v⃗, they experience a Lorentz electric field, v⃗×B⃗, which causes the spectral emission to be split and polarized due to the Stark effect. Traditional MSE-LP (line polarization) measurements determine the direction of the magnetic field in the observation volume using polarimetric analysis of the detected light. The harsh conditions of ITER are expected to deposit thin films of contaminants on the first mirror, which would alter the polarization state of reflected light significantly. On ITER, the combination of high magnetic field strength and high energy beams makes the Stark spectrum resolution suitable for the determination of the magnetic field magnitude from the line shift, so this approach has been selected. Every aspect of the measurement system must be planned for the burning plasma environment and carefully analyzed ahead of time. Current status and plans for the system are presented.

Instruments & Instrumentation↗

NASA NTRS2016

High Resolution Image Reconstruction from Projection of Low Resolution Images DIffering in Subpixel Shifts

In this paper, we demonstrate a simple algorithm that projects low resolution (LR) images differing in subpixel shifts on a high resolution (HR) also called super resolution (SR) grid. The algorithm is very effective in accuracy as well as time efficiency. A number of spatial interpolation techniques using nearest neighbor, inverse-distance weighted averages, Radial Basis Functions (RBF) etc. used in projection yield comparable results. For best accuracy of reconstructing SR image by a factor of two requires four LR images differing in four independent subpixel shifts. The algorithm has two steps: i) registration of low resolution images and (ii) shifting the low resolution images to align with reference image and projecting them on high resolution grid based on the shifts of each low resolution image using different interpolation techniques. Experiments are conducted by simulating low resolution images by subpixel shifts and subsampling of original high resolution image and the reconstructing the high resolution images from the simulated low resolution images. The results of accuracy of reconstruction are compared by using mean squared error measure between original high resolution image and reconstructed image. The algorithm was tested on remote sensing images and found to outperform previously proposed techniques such as Iterative Back Projection algorithm (IBP), Maximum Likelihood (ML), and Maximum a posterior (MAP) algorithms. The algorithm is robust and is not overly sensitive to the registration inaccuracies.

0↗

DOE OSTI2023

Control optimization for parametric Hamiltonians by pulse reconstruction

Optimal control techniques provide a means to tailor the control pulses required to generate customized quantum gates, which helps to improve the resilience of quantum simulations to gate errors and device noise. However, the significant amount of (classical) computation required to generate customized gates can quickly undermine the effectiveness of this approach, especially when pulse optimization needs to be iterated. We propose a method to reduce the computational time required to generate the control pulse for a Hamiltonian that is parametrically dependent on a time-varying quantity. We use simple interpolation schemes to accurately reconstruct the control pulses from a set of pulses obtained in advance for a discrete set of predetermined parameter values. We obtain a reconstruction with very high fidelity and a significant reduction in computational effort. We report the results of the application of the proposed method to device-level quantum simulations of the unitary (real) time evolution of two interacting neutrons based on superconducting qubits.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

NASA NTRS2011

Ares I-X Best Estimated Trajectory and Comparison with Pre-Flight Predictions

The Ares I-X trajectory reconstruction produced best estimated trajectories of the flight test vehicle ascent through stage separation, and of the first and upper stage entries after separation. The trajectory reconstruction process combines on-board, ground-based, and atmospheric measurements to produce the trajectory estimates. The Ares I-X vehicle had a number of on-board and ground based sensors that were available, including inertial measurement units, radar, air- data, and weather balloons. However, due to problems with calibrations and/or data, not all of the sensor data were used. The trajectory estimate was generated using an Iterative Extended Kalman Filter algorithm, which is an industry standard processing algorithm for filtering and estimation applications. This paper describes the methodology and results of the trajectory reconstruction process, including flight data preprocessing and input uncertainties, trajectory estimation algorithms, output transformations, and comparisons with preflight predictions.

Karlgaard, Christopher D.↗

NASA NTRS2011

Ares I-X Best Estimated Trajectory Analysis and Results

The Ares I-X trajectory reconstruction produced best estimated trajectories of the flight test vehicle ascent through stage separation, and of the first and upper stage entries after separation. The trajectory reconstruction process combines on-board, ground-based, and atmospheric measurements to produce the trajectory estimates. The Ares I-X vehicle had a number of on-board and ground based sensors that were available, including inertial measurement units, radar, air-data, and weather balloons. However, due to problems with calibrations and/or data, not all of the sensor data were used. The trajectory estimate was generated using an Iterative Extended Kalman Filter algorithm, which is an industry standard processing algorithm for filtering and estimation applications. This paper describes the methodology and results of the trajectory reconstruction process, including flight data preprocessing and input uncertainties, trajectory estimation algorithms, output transformations, and comparisons with preflight predictions.

Karlgaard, Christopher D.↗

DOE OSTI2022

Accelerating error correction in tomographic reconstruction

Abstract Spurred by recent advances in detector technology and X-ray optics, upgrades to scanning-probe-based tomographic imaging have led to an exponential growth in the amount and complexity of experimental data and have created a clear opportunity for tomographic imaging to approach single-atom sensitivity. The improved spatial resolution, however, is highly susceptible to systematic and random experimental errors, such as center of rotation drifts, which may lead to imaging artifacts and prevent reliable data extraction. Here, we present a model-based approach that simultaneously optimizes the reconstructed specimen and sinogram alignment as a single optimization problem for tomographic reconstruction with center of rotation error correction. Our algorithm utilizes an adaptive regularizer that is dynamically adjusted at each alternating iteration step. Furthermore, we describe its implementation in a software package targeting high-throughput workflows for execution on distributed-memory clusters. We demonstrate the performance of our solver on large-scale synthetic problems and show that it is robust to a wide range of noise and experimental drifts with near-ideal throughput.

Ali, Sajid (ORCID:0000000321864636)↗

NASA NTRS1987

Use of maximum entropy method with parallel processing machine

The maximum entropy method (MEM) and balanced correlation method were used to reconstruct the images of low-intensity X-ray objects obtained experimentally by means of a uniformly redundant array coded aperture system. The reconstructed images from MEM are clearly superior. However, the MEM algorithm is computationally more time-consuming because of its iterative nature. On the other hand, both the inherently two-dimensional character of images and the iterative computations of MEM suggest the use of parallel processing machines. Accordingly, computations were carried out on the massively parallel processor at Goddard Space Flight Center as well as on the serial processing machine VAX 8600, and the results are compared.

Yin, Lo I.↗