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DOE OSTI2022

DeepAdversaries: examining the robustness of deep learning models for galaxy morphology classification

With increased adoption of supervised deep learning methods for work with cosmological survey data, the assessment of data perturbation effects (that can naturally occur in the data processing and analysis pipelines) and the development of methods that increase model robustness are increasingly important. In the context of morphological classification of galaxies, we study the effects of perturbations in imaging data. In particular, we examine the consequences of using neural networks when training on baseline data and testing on perturbed data. We consider perturbations associated with two primary sources: (a) increased observational noise as represented by higher levels of Poisson noise and (b) data processing noise incurred by steps such as image compression or telescope errors as represented by one-pixel adversarial attacks. We also test the efficacy of domain adaptation techniques in mitigating the perturbation-driven errors. We use classification accuracy, latent space visualizations, and latent space distance to assess model robustness in the face of these perturbations. For deep learning models without domain adaptation, we find that processing pixel-level errors easily flip the classification into an incorrect class and that higher observational noise makes the model trained on low-noise data unable to classify galaxy morphologies. On the other hand, we show that training with domain adaptation improves model robustness and mitigates the effects of these perturbations, improving the classification accuracy up to 23% on data with higher observational noise. Domain adaptation also increases up to a factor of ${\approx}2.3$ the latent space distance between the baseline and the incorrectly classified one-pixel perturbed image, making the model more robust to inadvertent perturbations. Successful development and implementation of methods that increase model robustness in astronomical survey pipelines will help pave the way for many more uses of deep learning for astronomy.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

Stabilizing and Improving Qubit Coherence by Engineering the Noise Spectrum of Two-Level Systems

Superconducting circuits are a leading platform for quantum computing. However, their coherence times are still limited and exhibit temporal fluctuations. Those phenomena are often attributed to the coupling between qubits and material defects that can be well described as an ensemble of two-level systems (TLSs). Among them, charge fluctuators inside amorphous oxide layers contribute to both low-frequency 1 / f charge noise and high-frequency dielectric loss, causing fast qubit dephasing and relaxation. Moreover, spectral diffusion from mutual TLS interactions varies the noise amplitude over time, fluctuating the qubit lifetime. Here, we propose to mitigate those harmful effects by engineering the relevant TLS noise spectral densities. Specifically, our protocols smooth the high-frequency noise spectrum and suppress the low-frequency noise amplitude via depolarizing and dephasing the TLSs, respectively. As a result, we predict a drastic stabilization in qubit lifetime and an increase in qubit pure dephasing time. Our detailed analysis of feasible experimental implementations shows that the improvement is not compromised by spurious coupling from the applied noise to the qubit.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2021

New, improved analysis of correlation ECE data to accurately determine turbulent electron temperature spectra and magnitudes (invited)

Turbulent electron temperature fluctuation measurement using a correlation electron cyclotron emission (CECE) radiometer has become an important diagnostic for studying energy transport in fusion plasmas, and its use is widespread in tokamaks (DIII-D, ASDEX Upgrade, Alcator C-Mod, Tore Supra, EAST, TCV, HL-2A, etc.). The CECE diagnostic typically performs correlation analysis between two closely spaced (within the turbulent correlation length) ECE channels that are dominated by uncorrelated thermal noise emission. This allows electron temperature fluctuations embedded in the thermal noise to be revealed and fluctuation level and spectra determined. We have demonstrated a new, improved CECE coherency-based analysis for calculating the temperature fluctuation frequency spectrum and level, which has been verified both numerically through the simulation of synthetic ECE radiometer data and through analysis of experimental data from the CECE system on DIII-D. The new formulation places coherency-based analysis on a firm foundational footing and corrects some currently published methodologies. This new method accurately accounts for bias error in the coherence function and correctly calculates noise levels for a fixed data record length. It provides excellent accuracy in determining temperature fluctuation level (e.g., <10% error) even for a small realization number in the ensemble average. The method also has a smaller uncertainty (i.e., error bar) in the power spectrum when compared to the more standard cross-power method when evaluated at low coherency. Direct calculation of system noise level using correlation between randomized intermediate frequency signals is recommended.

Wang, G. (ORCID:0000000225739827)↗

DOE OSTI2022

EIC Transverse emittance growth due to crab cavity RF noise: Estimates and mitigation

The Electron-Ion Collider (EIC) requires crab cavities to compensate for a 25 mrad crossing angle and achieve maximum luminosity. The crab cavity Radio Frequency (RF) system will inject low levels of noise to the crabbing field, generating transverse emittance growth and potentially limiting luminosity lifetime. In this work, we estimate the transverse emittance growth rate as a function of the Crab Cavity RF noise and quantify RF noise specifications for reasonable performance. Finally, we evaluate the possible mitigation of the RF noise induced emittance growth via a dedicated feedback system.

43 PARTICLE ACCELERATORS↗

DOE OSTI2023

Semi-supervised graph neural networks for pileup noise removal

Abstract The high instantaneous luminosity of the CERN Large Hadron Collider leads to multiple proton–proton interactions in the same or nearby bunch crossings (pileup). Advanced pileup mitigation algorithms are designed to remove this noise from pileup particles and improve the performance of crucial physics observables. This study implements a semi-supervised graph neural network for particle-level pileup noise removal, by identifying individual particles produced from pileup. The graph neural network is firstly trained on charged particles with known labels, which can be obtained from detector measurements on data or simulation, and then inferred on neutral particles for which such labels are missing. This semi-supervised approach does not depend on the neutral particle pileup label information from simulation, and thus allows us to perform training directly on experimental data. The performance of this approach is found to be consistently better than widely-used domain algorithms and comparable to the fully-supervised training using simulation truth information. The study serves as the first attempt at applying semi-supervised learning techniques to pileup mitigation, and opens up a new direction of fully data-driven machine learning pileup mitigation studies.

43 PARTICLE ACCELERATORS↗

DOE OSTI2022

TEAMER: DAISY Flow-noise Testing (Abstract)

Evaluating impacts of marine energy devices is generally difficult given the dynamic environment where these devices need to be placed. The University of Washington’s (UW) DAISY (The Drifting Acoustic Instrumentation SYstem) is designed to measure radiated noise around marine energy converters operating in energetic waves and currents. In currents, a primary limitation for measurement fidelity at low frequencies (< 100 Hz) is the potential for non-propagating “flow-noise” to mask propagating sound and inflate estimates of the radiated noise from marine energy converters at frequencies that overlap with hearing sensitivities of fish and some marine mammals. While free-drifting measurements help to minimize the relative velocity that produces flow-noise, significant levels were still observed during initial DAISY tests. This motivated the development of a fabric “flow shield” around the hydrophone that disrupts both flow-noise generation mechanisms proposed by the initial tests. First, the flow shield is a source of substantial drag which keeps the hydrophone package moving with the approximate velocity of the surrounding water, compensating for differential wind or current forcing on the surface expression. By minimizing relative velocity around the hydrophone, turbulence shed by the hydrophone is also minimized. Second, the flow shield creates a largely quiescent pocket around the hydrophone, minimizing advection of free stream turbulence over the hydrophone element. Field data collected in these experiments will test effectiveness of these flow shields and provide quantitative data use and deployment.

16 TIDAL AND WAVE POWER↗

DOE OSTI2025

Pickup Specifications for Crab Cavity Noise Feedback Pickup

The Electron-Ion Collider will employ crab cavities to compensate for the significant 25 mrad crossing angle, leading to an order of magnitude increase in luminosity. The crab cavity Radio Frequency system will inject low levels of noise to the crabbing field, generating transverse emittance growth and potentially limiting luminosity lifetime. A novel dedicated feedback system acting through the crab cavities has been proposed to mitigate emittance growth. The perfor mance of the noise feedback will largely depend on its pickup precision. In this note we present pickup specifications to achieve the required performance.

43 PARTICLE ACCELERATORS↗

DOE OSTI2024

On forced RF generation of CW magnetrons for accelerators

CW magnetrons, initially developed for industrial RF heaters, were suggested to power RF cavities of superconducting accelerators due to their higher efficiency and lower cost than traditionally used klystrons, IOTs or solid-state amplifiers. RF amplifiers driven by a master oscillator serve as coherent RF sources. CW magnetrons are regenerative RF generators with a huge regenerative gain. This causes regenerative instability with a quite large noise when a magnetron operates with the anode voltage above the threshold of self-excitation. Traditionally, an injection locking by a small signal is used for stabilization of magnetrons. In this case CW magnetrons with the injection-locked oscillations generate a high level of noise. This may preclude use of standard CW magnetrons in this operating mode in the Superconducting RF (SRF) accelerators. In this article we described a method developed for forced RF generation of CW magnetrons when the magnetron startup is provided by the injected forcing signal and the regenerative noise is suppressed. The method is most suitable for powering high Q-factor cavities.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2024

CovTransformer: A transformer model for SARS-CoV-2 lineage frequency forecasting

With hundreds of SARS-CoV-2 lineages circulating in the global population, there is an ongoing need for predicting and forecasting lineage frequencies and thus identifying rapidly expanding lineages. Accurate prediction would allow for more focused experimental efforts to understand pathogenicity of future dominating lineages and characterize the extent of their immune escape. Here, we first show that the inherent noise and biases in lineage frequency data make a commonly-used regression-based approach unreliable. To address this weakness, we constructed a machine learning model for SARS-CoV-2 lineage frequency forecasting, called CovTransformer, based on the transformer architecture. We designed our model to navigate challenges such as a limited amount of data with high levels of noise and bias. We first trained and tested the model using data from the UK and the USA, and then tested the generalization ability of the model to many other countries and US states. Remarkably, the trained model makes accurate predictions two months into the future with high levels of accuracy both globally (in 31 countries with high levels of sequencing effort) and at the US-state level. Our model performed substantially better than a widely used forecasting tool, the multinomial regression model implemented in Nextstrain, demonstrating its utility in SARS-CoV-2 monitoring. Assuming a newly emerged lineage is identified and assigned, our test using retrospective data shows that our model is able to identify the dominating lineages 7 weeks in advance on average before they became dominant. Overall, our work demonstrates that transformer models represent a promising approach for SARS-CoV-2 forecasting and pandemic monitoring.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

On operation and control of CW magnetrons for superconducting accelerators

CW magnetrons, developed for industrial RF heaters, were suggested to feed RF cavities of superconducting accelerators due to higher efficiency and lower cost of RF power than provide traditionally used klystrons, IOTs or solid-state amplifiers. RF amplifiers driven by a master oscillator serve as coherent RF sources. CW magnetrons are regenerative RF auto generators with a huge regenerative gain. This causes regenerative instability with a notable noise when a magnetron operates as an auto generator i.e., with the anode voltage above the threshold of self-excitation. Traditionally, an injection locking by a small signal is used for phase stabilization of magnetrons. In this case CW magnetrons with the injection-locked (coherent) oscillations generate a notable level of noise. This may preclude use of CW magnetrons in this mode in the Superconducting RF (SRF) accelerators. This paper reviews PIC modeling and previously obtained experimental results for the operation and control of CW magnetrons, which led to the development of techniques most suitable for various SRF accelerators using forced RF oscillation of magnetrons, when the magnetron is launched by an injected forcing signal, and regenerative noise is suppressed.

Kazakevich, G. [MUONS Inc., Batavia] (ORCID:000000↗

DOE OSTI2020

Fabrication of OMT-Coupled Kinetic Inductance Detector for CMB Detection

Future cosmic microwave background (CMB) experiments, including the large scale ground-based Stage Four CMB Experiment (CMB-S4), satellites, and balloons, aim to map the CMB to an unprecedented precision in order to answer several key questions in cosmology. However, to reach the target noise sensitivity, more than 100,000 detectors will be needed. Arrays of kinetic inductance detectors (KIDs) are a promising alternative for experiments that require large number of detectors due to the intrinsic multiplexing capabilities. We present the fabrication procedure for a prototype planar orthomode transducer (OMT)-coupled multi-color KID array optimized for 220/270 GHz frequency bands. These devices are made from silicon-on-insulator wafers to provide a low-loss substrate for the KIDs. The OMT couples the two polarizations of light from a wide-band feedhorn to separate Nb/SiN/Nb microstrip lines, which are then coupled to Al/Nb lumped-element KIDs (LEKIDs). The silicon on the backside of the OMT is etched away using deep reactive ion etch to release the OMT membrane to enable operation over a wide bandwidth. Finally, the buried oxide is removed underneath the KID capacitors in order to minimize two-level system noise and loss mitigation. We achieved a good yield (> 80%) on our prototype devices.

47 OTHER INSTRUMENTATION↗

DOE OSTI2023

Noise dynamics of quantum annealers: estimating the effective noise using idle qubits

Quantum annealing is a type of analog computation that aims to use quantum mechanical fluctuations in search of optimal solutions of QUBO (quadratic unconstrained binary optimization) or, equivalently, Ising problems. Since NP-hard problems can in general be mapped to Ising and QUBO formulations, the quantum annealing paradigm has the potential to help solve various NP-hard problems. Current quantum annealers, such as those manufactured by D-Wave Systems, Inc. have various practical limitations including the size (number of qubits) of the problem that can be solved, the qubit connectivity, and error due to the environment or system calibration, which can reduce the quality of the solutions. Typically, for an arbitrary problem instance, the corresponding QUBO (or Ising) structure will not natively embed onto the available qubit architecture on the quantum chip. Thus, in these cases, a minor embedding of the problem structure onto the device is necessary. However, minor embeddings on these devices do not always make use of the full sparse chip hardware graph, and a large portion of the available qubits stay unused during quantum annealing. In this work, we embed a disjoint random QUBO on the unused parts of the chip alongside the QUBO to be solved, which acts as an indicator of the solution quality of the device over time. Using experiments on three different D-Wave quantum annealers, we demonstrate that (i) long term trends in solution quality exist on the D-Wave device, and (ii) the unused qubits can be used to measure the current level of noise of the quantum system.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2021

Detection of Outliers in LiDAR Data Acquired by Multiple Platforms over Sorghum and Maize

High-resolution point cloud data acquired with a laser scanner from any platform contain random noise and outliers. Therefore, outlier detection in LiDAR data is often necessary prior to analysis. Applications in agriculture are particularly challenging, as there is typically no prior knowledge of the statistical distribution of points, plant complexity, and local point densities, which are crop-dependent. The goals of this study were first to investigate approaches to minimize the impact of outliers on LiDAR acquired over agricultural row crops, and specifically for sorghum and maize breeding experiments, by an unmanned aerial vehicle (UAV) and a wheel-based ground platform; second, to evaluate the impact of existing outliers in the datasets on leaf area index (LAI) prediction using LiDAR data. Two methods were investigated to detect and remove the outliers from the plant datasets. The first was based on surface fitting to noisy point cloud data via normal and curvature estimation in a local neighborhood. The second utilized the PointCleanNet deep learning framework. Both methods were applied to individual plants and field-based datasets. To evaluate the method, an F-score was calculated for synthetic data in the controlled conditions, and LAI, the variable being predicted, was computed both before and after outlier removal for both scenarios. Results indicate that the deep learning method for outlier detection is more robust than the geometric approach to changes in point densities, level of noise, and shapes. The prediction of LAI was also improved for the wheel-based vehicle data based on the coefficient of determination (R2) and the root mean squared error (RMSE) of the residuals before and after the removal of outliers.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Using soil library hyperspectral reflectance and machine learning to predict soil organic carbon: Assessing potential of airborne and spaceborne optical soil sensing

Soil organic carbon (SOC) is a key variable to determine soil functioning, ecosystem services, and global carbon cycles. Spectroscopy, particularly optical hyperspectral reflectance coupled with machine learning, can provide rapid, efficient, and cost-effective quantification of SOC. However, how to exploit soil hyperspectral reflectance to predict SOC concentration, and the potential performance of airborne and satellite data for predicting surface SOC at large scales remain relatively underknown. Here, this study utilized a continental-scale soil laboratory spectral library (37,540 full-pedon 350–2500 nm reflectance spectra with SOC concentration of 0–780 g·kg –1 across the US) to thoroughly evaluate seven machine learning algorithms including Partial-Least Squares Regression (PLSR), Random Forest (RF), K-Nearest Neighbors (KNN), Ridge, Artificial Neural Networks (ANN), Convolutional Neural Networks (CNN), and Long Short-Term Memory (LSTM) along with four preprocessed spectra, i.e. original, vector normalization, continuum removal, and first-order derivative, to quantify SOC concentration. Furthermore, by using the coupled soil-vegetation-atmosphere radiative transfer model, we simulated twelve airborne and spaceborne hyper/multi-spectral remote sensing data from surface bare soil laboratory spectra to evaluate their potential for estimating SOC concentration of surface bare soils. Results show that LSTM achieved best predictive performance of quantifying SOC concentration for the whole data sets (R 2 = 0.96, RMSE = 30.81 g·kg –1 ), mineral soils (SOC ≤ 120 g·kg –1 , R 2 = 0.71, RMSE = 10.60 g·kg –1 ), and organic soils (SOC > 120 g·kg –1 , R 2 = 0.78, RMSE = 62.31 g·kg –1 ). Spectral data preprocessing, particularly the first-order derivative, improved the performance of PLSR, RF, Ridge, KNN, and ANN, but not LSTM or CNN. We found that the SOC models of mineral and organic soils should be distinguished given their distinct spectral signatures. Finally, we identified that the shortwave infrared is vital for airborne and spaceborne hyperspectral sensors to monitor surface SOC. This study highlights the high accuracy of LSTM with hyperspectral/multispectral data to mitigate a certain level of noise (soil moisture <0.4 m 3 ·m –3 , green leaf area < 0.3 m 2 ·m –2 , plant residue <0.4 m 2 ·m –2 ) for quantifying surface SOC concentration. Forthcoming satellite hyperspectral missions like Surface Biology and Geology (SBG) have a high potential for future global soil carbon monitoring, while high-resolution satellite multispectral fusion data can be an alternative.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Boosting Noise2Inverse via enhanced model selection for denoising computed tomography data

Synchrotron-based x-ray tomographic imaging enables the examination of the internal structure of materials at high spatial and temporal resolution. Experimental constraints can impose dose and time limits on the measurements, introducing a higher level of noise and artifacts in the reconstructed images. Deep learning has emerged as a powerful tool to remove noise from reconstructed images. Recently, the Noise2Inverse method was designed specifically for denoising reconstructed images without requiring paired noisy and clean images. This method creates multiple statistically independent reconstructions used to pair the data in which training involves transforming one reconstruction into the other, and vice versa. Originally designed to be used after a fixed number of epochs, we see in practice that this approach may not produce the optimal model and may unnecessarily waste computational resources. Therefore, we propose an alternative method of identifying the best model during training that aligns with the Noise2Inverse method. During validation, we compare the model output of the multiple reconstructions among each other. We hypothesize that the best model is the one that produces images with the highest similarity, implying a convergence in the predicted material properties and absorption values. To compare model outputs, we consider the absolute error, square error, structural similarity index (SSIM), peak signal-to-noise ratio (PSNR), and cosine similarity. We evaluate our method on two simulated tomography datasets and two, real-world, low-contrast, high-energy x-ray tomography datasets. We show our approach is more effective at determining the best model, up to an increase of 12.50% and 12.53% in SSIM and PSNR, respectively, while only requiring a fifth of the training time compared to the original approach.

CT↗

DOE OSTI2020

Planck intermediate results

We present the NPIPE processing pipeline, which produces calibrated frequency maps in temperature and polarization from data from the Planck Low Frequency Instrument (LFI) and High Frequency Instrument (HFI) using high-performance computers. NPIPE represents a natural evolution of previous Planck analysis efforts, and combines some of the most powerful features of the separate LFI and HFI analysis pipelines. For example, following the LFI 2018 processing procedure, NPIPE uses foreground polarization priors during the calibration stage in order to break scanning-induced degeneracies. Similarly, NPIPE employs the HFI 2018 time-domain processing methodology to correct for bandpass mismatch at all frequencies. In addition, NPIPE introduces several improvements, including, but not limited to: inclusion of the 8% of data collected during repointing manoeuvres; smoothing of the LFI reference load data streams; in-flight estimation of detector polarization parameters; and construction of maximally independent detector-set split maps. For component-separation purposes, important improvements include: maps that retain the CMB Solar dipole, allowing for high-precision relative calibration in higher-level analyses; well-defined single-detector maps, allowing for robust CO extraction; and HFI temperature maps between 217 and 857 GHz that are binned into 0'.9 pixels (Nside = 4096), ensuring that the full angular information in the data is represented in the maps even at the highest Planck resolutions. The net effect of these improvements is lower levels of noise and systematics in both frequency and component maps at essentially all angular scales, as well as notably improved internal consistency between the various frequency channels. Based on the NPIPE maps, we present the first estimate of the Solar dipole determined through component separation across all nine Planck frequencies. The amplitude is (3366.6 ± 2.7) μK, consistent with, albeit slightly higher than, earlier estimates. From the large-scale polarization data, we derive an updated estimate of the optical depth of reionization of τ = 0.051 ± 0.006, which appears robust with respect to data and sky cuts. There are 600 complete signal, noise and systematics simulations of the full-frequency and detector-set maps. As a Planck first, these simulations include full time-domain processing of the beam-convolved CMB anisotropies. The release of NPIPE maps and simulations is accompanied with a complete suite of raw and processed time-ordered data and the software, scripts, auxiliary data, and parameter files needed to improve further on the analysis and to run matching simulations.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

Low-pass spectral analysis of time-resolved serial femtosecond crystallography data

Low-pass spectral analysis (LPSA) is a recently developed dynamics retrieval algorithm showing excellent retrieval properties when applied to model data affected by extreme incompleteness and stochastic weighting. In this work, we apply LPSA to an experimental time-resolved serial femtosecond crystallography (TR-SFX) dataset from the membrane protein bacteriorhodopsin (bR) and analyze its parametric sensitivity. While most dynamical modes are contaminated by nonphysical high-frequency features, we identify two dominant modes, which are little affected by spurious frequencies. The dynamics retrieved using these modes shows an isomerization signal compatible with previous findings. We employ synthetic data with increasing timing uncertainty, increasing incompleteness level, pixel-dependent incompleteness, and photon counting errors to investigate the root cause of the high-frequency contamination of our TR-SFX modes. By testing a range of methods, we show that timing errors comparable to the dynamical periods to be retrieved produce a smearing of dynamical features, hampering dynamics retrieval, but with no introduction of spurious components in the solution, when convergence criteria are met. Using model data, we are able to attribute the high-frequency contamination of low-order dynamical modes to the high levels of noise present in the data. Finally, we propose a method to handle missing observations that produces a substantial dynamics retrieval improvement from synthetic data with a significant static component. Reprocessing of the bR TR-SFX data using the improved method yields dynamical movies with strong isomerization signals compatible with previous findings.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

A comparison of past and present computational methods for shape analysis of double-shell x-ray radiographs

Implosion symmetry is a key requirement in achieving a robust burning plasma in inertial confinement fusion experiments. In double-shell capsule implosions, we are interested in the shape of the inner shell as it pushes on the fuel. Shape analysis is a popular technique for studying said symmetry during implosion. Combinations of filtering and contour-finding algorithms are studied for their promise in reliably recovering Legendre shape coefficients from synthetic radiographs of double-shell capsules with applied levels of noise. A radial lineout max(slope) method when used on an image pre-filtered with non-local means and a variant of the marching squares algorithm are able to recover p 0 , p 2 , and p 4 maxslope Legendre shape coefficients with mean pixel discrepancy errors of 2.81 and 3.06, respectively, for the noisy synthetic radiographs we consider. Here, this improves upon prior radial lineout methods paired with Gaussian filtering, which we show to be unreliable and whose performance is dependent on input parameters that are difficult to estimate.

47 OTHER INSTRUMENTATION↗