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At least 793 records · Page 44

Methods for safely sharing dual-use genetic data

Background: Some genetic data has dual-use potential. Sharing pathogen data has shown tremendous value. For example therapeutic development and lineage tracking during the COVID pandemic. This data sharing is complicated by the fact that these data have the potential to be used for harm. The genome sequence of a pathogen can be used to enable malicious genetic engineering approaches or to recreate the pathogen from synthetic DNA. Standard data security methods can be applied to genetic data, but when data is shared between institutions, ensuring appropriate security can be difficult. Sensitive data that is shared internationally among a wide array of institutions can be especially difficult to control. Methods for securely storing and sharing genetic data with potential for dual-use are needed to mitigate this potential harm.Results: Here we propose new methods that allow genetic data to be shared in a data format that prevents a nefarious actor from accessing sensitive aspects of the data. Our methods obfuscate raw sequence data by pooling reads from different samples. This approach can ensure that data is secure while stored and during electronic transfer. We demonstrate that by pooling raw sequence data from multiple samples of the same organism, the ability to fully reconstruct any individual sample is prevented. In the pooled data, most genomic information remains, but reads or mutations cannot be directly attributed to any individual sample. To further restrict access to information, regions of a genome can be removed from the reads.Conclusion: Our methods obscure genomic information within raw sequence reads. This method can allow genetic data to be stored and shared while preventing a nefarious actor from being able to perfectly reconstruct an organism. Broad-scale sequence information remains, while fine scale details about specific samples are difficult or impossible to reconstruct. Our software is available at https://github.com/Geneinfosec-Inc/ReadMixer.

59 BASIC BIOLOGICAL SCIENCES↗

DKDP /potassium dideuterium phosphate/ light valves

The use of potassium dideuterium phosphate (DKDP) light valves for optical data processing is discussed. The operating principles and structure of optically and electron beam addressed DKDPs are compared, and specifications for both devices given. Optically addressed DKDPs are capable of higher resolution and contrast, but both systems represent viable real time spatial light modulators adaptable to optical processing. Examples of real time data processing performed by the DKDPs include: image addition and subtraction; reduction of noise introduced by scattered light in recording media; reconstruction of computer generated and acoustic holograms; reconstruction of synthetic aperture radar data; retrieval of three-dimensional information in X-ray diagnoses; radar signal processing and display; and optical pattern recognition and correlation of images, which has applications for missile guidance systems.

Casasent, D.↗

SWIPE: Spectral Water Inversion Processor and Emulator

Degradation of Earth’s inland water resources due to anthropogenic perturbations and climate anomalies at both local and global scales continues to place human health at substantial risk. There is now a growing necessity to develop pragmatic approaches that allow timely and effective extrapolation of local processes, to spatially resolved global products, and to promote operational and sustainable resource policy management. This presentation will be discussing the progress made developing SWIPE: Spectral Water Inversion Processor and Emulator. SWIPE is a platform for advanced modeling of coastal and inland aquatic habitats. The goal is create a comprehensive and cohesive system to leverage recent advancements in computation and machine learning to develop a synthetic training ground for sensitivity studies and algorithm development. The four principal facets of SWIPE include: 1. Advanced two-layer coated sphere bio-optical modeling and GPU radiative transfer modeling, 2. Big Data involving massive synthetic spectral libraries of optical properties of various global aquatic particles, surface reflectance, and top-of-atmosphere reflectance, all at hyperspectral resolution leveraging high-end computing systems at NASA Ames Research Center, 3. Deep Learning for algorithm development for water quality inversion of concentrations of common biogeophysical variables as well as optics, full uncertainty characterization by water type, and forward emulation, and lastly, 4. Image Processing for application of developed retrieval algorithms for both hyperspectral and multispectral sensors with experimental corrections for global adjacency, noise, sunglint, and benthic reflectance. This presentation will demonstrate the Equivalent Algal Populations (EAP) two-layer coated sphere scattering model which has been used develop spectral libraries of hyperspectral inherent optical properties of roughly 80 species of phytoplankton, covering 15 different classes and nine taxonomic functional types. The EAP model was also used to derive spectral properties of 10 different non-algal particle functional types. Examples of how the SMART-G (Speed-up Monte-carlo Advanced Radiative Transfer using GPU) radiative transfer code is used to model optically complex aquatic signals will be presented and discussed in the context of creating a massive synthetic database which can leverage the full power of next generation machine learning techniques and high end computing for water quality inversion. We will discuss our active investigation in things like appropriate model architectures, dimensionality reduction techniques such as PCA and autoencoders, uncertainty quantification and abstaining, and which variables actually benefit most from hyperspectral information versus multispectral resolution. We are also curious about questions relating to cost/benefit analysis in terms of computation resources, neural network complexity, and data volumes. Answers to these questions will hopefully elaborate on cost efficiency for potential future sensor design considerations.

SWIPE↗

The data-driven future of high-energy-density physics

High-energy-density physics is the field of physics concerned with studying matter at extremely high temperatures and densities. Such conditions produce highly nonlinear plasmas, in which several phenomena that can normally be treated independently of one another become strongly coupled. The study of these plasmas is important for our understanding of astrophysics, nuclear fusion and fundamental physics—however, the nonlinearities and strong couplings present in these extreme physical systems makes them very difficult to understand theoretically or to optimize experimentally. Here we argue that machine learning models and data-driven methods are in the process of reshaping our exploration of these extreme systems that have hitherto proved far too nonlinear for human researchers. Furthermore, from a fundamental perspective, our understanding can be improved by the way in which machine learning models can rapidly discover complex interactions in large datasets. From a practical point of view, the newest generation of extreme physics facilities can perform experiments multiple times a second (as opposed to approximately daily), thus moving away from human-based control towards automatic control based on real-time interpretation of diagnostic data and updates of the physics model. To make the most of these emerging opportunities, we suggest proposals for the community in terms of research design, training, best practice and support for synthetic diagnostics and data analysis.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Understanding Crew Decision-Making in the Presence of Complexity: A Flight Simulation Experiment

Crew decision making and response have long been leading causal and contributing factors associated with aircraft accidents. Further, it is anticipated that future aircraft and operational environments will increase exposure to risks related to these factors if proactive steps are not taken to account for ever-increasing complexity. A flight simulation study was designed to collect data to help in understanding how complexity can, or may, be manifest. More specifically, an experimental apparatus was constructed that allowed for manipulation of information complexity and uncertainty, while also manipulating operational complexity and uncertainty. Through these manipulations, and the aid of experienced airline pilots, several issues have been discovered, related most prominently to the influence of information content, quality, and management. Flight crews were immersed in an environment that included new operational complexities suggested for the future air transportation system as well as new technological complexities (e.g. electronic flight bags, expanded data link services, synthetic and enhanced vision systems, and interval management automation). In addition, a set of off-nominal situations were emulated. These included, for example, adverse weather conditions, traffic deviations, equipment failures, poor data quality, communication errors, and unexpected clearances, or changes to flight plans. Each situation was based on one or more reference events from past accidents or incidents, or on a similar case that had been used in previous developmental tests or studies. Over the course of the study, 10 twopilot airline crews participated, completing over 230 flights. Each flight consisted of an approach beginning at 10,000 ft. Based on the recorded data and pilot and research observations, preliminary results are presented regarding decision-making issues in the presence of the operational and technological complexities encountered during the flights.

Young, Steven D.↗

Data-driven time-scale separation of ODE right-hand sides using dynamic mode decomposition and time delay embedding

Multi-physics simulation often involves multiple different scales. The ARKODE ODE solver package in the SUNDIALS library addresses multi-scale problems with a multi-rate time-integrator that can work with a right-hand side that has fast scale and slow scale components. In this report, we use dynamic mode decomposition and time delay embedding to extract the fast and slow components of the right-hand sides of a simple ODE from data. We then use the extracted components to solve the ODE with ARKODE. Finally, to move towards a real-world use case, we attempt to extract fast and slow scale dynamics from synthetic seismic modeling data.

97 MATHEMATICS AND COMPUTING↗

Height reconstruction techniques for synthetic aperture lidar systems

The data-processing techniques and acquisition modes of a synthetic aperture lidar (SAL) instrument operating at optical wavelengths are closely related to the analogous modes of a synthetic aperture radar (SAR) instrument operating at microwave frequencies. It is consequently natural to explore the applicability of SAR processing techniques to SAL sensors. In this paper, we examine the feasibility of adopting SAR height-reconstruction techniques with SAL sensors to obtain high-resolution 3-D imagery at optical wavelengths.

synthetic aperture lidar (SAL)↗

A multiscale recurrent neural network model for predicting energy production from geothermal reservoirs

Optimization of energy production from geothermal reservoirs requires reliable prediction of energy production performance under alternative operation and development scenarios. Traditionally, reservoir simulation models are used for the evaluation and screening of alternative production and development plans. However, simulation models require extensive data collection and modeling efforts and are time-consuming to build, run, and update. Data-driven predictive models, on the other hand, can serve as efficient prediction tools that can be used for decision support and management of daily operations and surveillance activities. Data-driven models become particularly attractive when a reservoir simulation model for a field does not exist and/or is difficult to build. Machine learning (ML)-based data-driven models that have recently become popular in several fields exploit statistical patterns and relations in training data to generate predictions. As such, they tend to perform better in interpolation problems (that is, prediction within the training data range) than when they are used to extrapolate beyond the training data. Production data from geothermal reservoirs tend to exhibit short-term variabilities as well as long-term trends, such as monotonically declining production temperatures. Capturing both short-term features and long-term trends with ML-based models is not trivial. We evaluate the use of recurrent neural networks (RNN) for the prediction of energy production from geothermal reservoirs. RNN is a class of ML architectures that are used to represent and predict sequential/dynamic data. Thus, it can be challenging to apply RNN to problems where long-term trends must be captured and extrapolation beyond the training data range is needed. We introduce the multiscale RNN architecture to extend the application of RNN to detect and predict both short-term variabilities and long-term trends in geothermal data. The developed architecture consists of a long-term component to only capture low-frequency data patterns, and a short-term component to detect features with higher frequency and more nonlinearity. The final prediction is obtained by combining the long-term and short-term predictions. Both synthetic and field data are used to evaluate the presented multiscale RNN model. The prediction performance of the multiscale RNN is compared against those obtained from the regular RNN and the autoregressive (AR) model. The results suggest that the multiscale architecture improves the long-term prediction performance of the regular RNN and enhances its robustness against noise.

15 GEOTHERMAL ENERGY↗

Bayesian analysis for estimating statistical parameter distributions of elasto-viscoplastic material models

High temperature design methods rely on constitutive models for inelastic deformation and failure typically calibrated against the mean of experimental data without considering the associated scatter. Variability may arise from the experimental data acquisition process, from heat-to-heat material property variations, or both and need to be accurately captured to predict parameter bounds leading to efficient component design. Applying the Bayesian Markov Chain Monte Carlo (MCMC) method to produce statistical models capturing the underlying uncertainty in the experimental data is an area of ongoing research interest. This work varies aspects of the Bayesian MCMC method and explores their effect on the posterior parameter distributions for a uniaxial elasto-viscoplastic damage model using synthetically generated reference data. From our analysis with the uniaxial inelastic model we determine that an informed prior distribution including different types of test conditions results in more accurate posterior parameter distributions. The parameter posterior distributions, however, do not improve when increasing the number of similar experimental data. Additionally, changing the amount of scatter in the data affects the quality of the posterior distributions, especially for the less sensitive model parameters. Moreover, we perform a sensitivity study of the model parameters against the likelihood function prior to the Bayesian analysis. The results of the sensitivity analysis help to determine the reliability of the posterior distributions and reduce the dimensionality of the problem by fixing the insensitive parameters. The comprehensive study described in this work demonstrates how to efficiently apply the Bayesian MCMC methodology to capture parameter uncertainties in high temperature inelastic material models. Quantifying these uncertainties in inelastic models will improve high temperature engineering design practices and lead to safer, more effective component designs.

42 ENGINEERING↗

3D orthorhombic earth model effects on seismic source characterization

Most earth materials are anisotropic with regard to seismic wave-speeds, especially materials such as shales, or where oriented fractures are present. However, the base assumption for many numerical simulations is to treat earth materials as isotropic media. This is done for simplicity, the apparent weakness of anisotropy in the far field, and the lack of well-characterized anisotropic material properties for input into numerical simulations. One approach for addressing the higher complexity of actual geologic regions is to model the material as an orthorhombic medium. We have developed an explicit time-domain, finite-difference (FD) algorithm for simulating three-dimensional (3D) elastic wave propagation in a heterogeneous orthorhombic medium. The objective of this research is to investigate the errors and biases that result from modeling a non-isotropic medium as an isotropic medium. This is done by computing “observed data” by using synthetic, anisotropic simulations with the assumption of an orthorhombic, anisotropic earth model. Green’s functions for an assumed isotropic earth model are computed and then used an inversion designed to estimate moment tensors with the “observed” data. One specific area of interest is how shear waves, which are introduced in an anisotropic model even for an isotropic explosion, affect the characterization of seismic sources when isotropic earth assumptions are made. This work is done in support of the modeling component of the Source Physics Experiment (SPE), a series of underground chemical explosions at the Nevada National Security Site (NNSS).

58 GEOSCIENCES↗

Elastohydrodynamic analysis using a power law pressure-viscosity relation

An isothermal elastohydrodynamic (EHD) inlet analysis of the Grubin type which considers a power law pressure-viscosity relation and a finite pressure at the inlet edge of the Hertzian contact zone was performed. Comparisons made with published X-ray EHD film thickness data for a synthetic paraffinic oil and when conventional EHD theory showed that the present theory exhibits a slightly stronger film thickness load dependence than do previous isothermal EHD theories but far less than that exhibited by the measured data.

Loewenthal, S. H.↗

Magellan SAR processing algorithm and H/W design

The SAR (synthetic-aperture radar) data-processing algorithm to be used for the Magellan mission is described. Radar system design, SAR data characteristics, and hardware (H/W) constraints, which are critical to the processing algorithm design, are highlighted. Data flow and the H/W architecture are given to show the real-time data processing capability. Simulation results obtained from processing the synthetic point-target echos are presented to demonstrate the performance of the processing algorithm.

Chen, M.↗

The SMAP and Copernicus Sentinel 1A/B Microwave Active-Passive High Resolution Surface Soil Moisture Product and Its Applications

SMAP project released a new enhanced high-resolution (3km and 1 km) soil moisture active-passive product. This product is obtained by combining the SMAP radiometer data and the Sentinel-1A and -1B Synthetic Aperture Radar (SAR) data. The approach used for this product draws heavily from the heritage SMAP active-passive algorithm. Modifications in the SMAP active-passive algorithm are done to accommodate the Copernicus Program's Sentinel-1A and -1B multi-angular C-band SAR data. Assessment of the SMAP and Sentinel active-passive algorithm has been conducted and results show feasibility of estimating surface soil moisture at high-resolution in regions with low vegetation density (~< 3 kg/sq.m). A new version of this product is released to public in May 2018. This high resolution (3 km and 1 km) soil moisture product with reasonable accuracy of 0.05 m3/m3 is useful for agriculture, flood mapping, watershed/rangeland management, and ecological/hydrological applications.

microwave remote sensing↗

Inverse methods for assessing ship-of-opportunity networks and estimating circulation and winds from tropical expendable bathythermograph data

Inverse methods for estimating the surface ciculation of the equatorial Pacific by combining a linear reduced-gravity shallow-water model with the Tropical Ocean-Global Atmosphere ship-of-opportunity expendable bathythermograph (TOGA SOP XBT) observing program are examined. It is demonstrated that a simple linear model of the upper circulation of the equatorial Pacific can be successfully used as a weak constraint when smoothing the TOGA SOP XBT data. A circulation is sought as the weighted least squares fit to the dynamics and the data. The solution method is an expansion in representer functions, and the generalized inverse problem is thereby reduced from a functional problem to an algebraic problem for the coefficients of the representer. A specific inverse calculation using synthetic forcing and data is presented.

Bennett, Andrew F.↗

From RNNs to Foundation Models: An Empirical Study on Commercial Building Energy Consumption

Accurate short-term energy consumption forecasting for commercial buildings is crucial for smart grid operations. While smart meters and deep learning models enable forecasting using past data from multiple buildings, data heterogeneity from diverse buildings can reduce model performance. The impact of increasing dataset heterogeneity in time series forecasting, while keeping size and model constant, is understudied. We tackle this issue using the ComStock dataset, which provides synthetic energy consumption data for U.S. commercial buildings. Two curated subsets, identical in size and region but differing in building type diversity, are used to assess the performance of various time series forecasting models, including finetuned open-source foundation models (FMs). The results show that dataset heterogeneity and model architecture have a greater impact on post-training forecasting performance than the parameter count. Moreover, despite the higher computational cost, finetuned FMs demonstrate competitive performance compared to base models trained from scratch.

commercial buildings↗

Aeroacoustic Study of a Subscale Large Civil Transport (STAR) Model – Part 2: Validation of Simulated Results

Aeroacoustic measurements of the 26%-scale, semispan Boeing 777-200 Subsonic Transport Aeroacoustic Research (STAR) model tested in the NASA Ames Research Center 40- by 80-foot wind tunnel were used to ascertain the efficacy of high-fidelity simulations to accurately predict noise from the landing gear of large commercial transports. The simulations, conducted with the lattice Boltzmann solver PowerFLOW®, used a digital replica of the STAR model with or without main landing gear deployed and slats and flaps set to their highest deflection angles to represent aircraft during landing. The computations were performed at a Mach number of 0.21, Reynolds number of 8.2 million based on the model mean aerodynamic chord, and other conditions prevalent during the STAR model test. Measured and computed surface pressures were in very good agreement at most port locations on the model, as were global force coefficients, indicating that the simulations captured the impact of main gear deployment on inboard flap loading. Noise sources produced by the main landing gear and high-lift devices were determined via source localization maps generated with CLEAN from synthetic and experimental data. In general, very good agreement between predicted and measured acoustic source location and relative strength was observed in the maps. Comparisons of far-field noise spectra obtained from the CLEAN deconvolution maps showed remarkable agreement between synthetic and experimental broadband noise at low and medium frequencies. Main landing gear sources for model-scale frequencies above 7,000 Hz could not be resolved with the spatial resolution used during the simulations.

airframe noise↗

Using synthetic infrared spectra derived from n/k optical constants for standoff detection of chemical deposits

We report results from a recent field experiment to test the validity of using physics-based synthetic infrared spectra to serve as endmembers in a spectral database targeted at chemical deposits. Specifically, the optical constants n and k, (the real and imaginary part of the refractive index) were used to first model infrared reflectance spectra for different thicknesses of chemical layers (e.g. acetaminophen, methylphosphonic acid – MPA, etc.) on various conducting and insulating substrates such as aluminum, wood, and glass. In the experimental portion of the research, thin films of the solid and liquid analytes were deposited onto such substrates to form micron-thick layers of the analytes at different thicknesses: Standoff data from an imaging instrument were then recorded and analyzed to not only identify the different analytes, but also quantify the layer/deposit thickness. To gauge success, the detection results using the synthetic data were compared to the results from hemispherical reflectance (HRF) spectra that were collected for the same sample planchets measured in the field via standoff methods. Preliminary results indicate good agreement between the synthetic reference data as compared to the lab-measured HRF data in terms of their ability to quantitatively reduce longwave infrared data. Specifically, modeled IR spectra for acetaminophen on an aluminum planchet at various thicknesses (1, 2, 5, 10, 15, and 20 µm) were synthesized and compared with standoff field reflectance data as well as HRF laboratory reflectance spectra for two samples: a 5.2 µm- and 12.8 µm-thick layer of acetaminophen on aluminum. Using a first-order approximation, analysis of the field data estimates the thicknesses of the samples to be 2 and 10 µm for the two samples, respectively, while the HRF laboratory data yields thickness estimates of between 5-10 µm and 10 µm, respectively. Both yield reasonable estimates, with the uncertainty most likely due to factors yet to be accounted for in the synthetic spectra such as light scattering.

complex index of refraction, optical constants, hy↗

A novel algorithm for sea surface height estimation using complex SAR data

A method of extracting sea height information from Synthetic Aperture Radar (SAR) complex data was studied. A fundamental SAR ocean imaging model for gravity waves showed that information about the long wave is present in the SAR complex data, especially its phase. Phase demodulation algorithm followed by linear regression and filtering was employed. Only the latter two steps incorporated a priori information that might be available. A relatively simplified simulation indicated that the finite bandwidth of the SAR system imposed the apparently most serious limitation. A preliminary application to SEASAT-SAR complex imagery was encouraging. Information about the long wave, if incorporated into a more sophisticated phase demodulation structure, i.e., at an earlier point in the algorithm, could conceivably mitigate this bandwidth limitation.

Harger, R. O.↗