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At least 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

NMR Spectroscopy for Protein Higher Order Structure Similarity Assessment in Formulated Drug Products

Peptide and protein drug molecules fold into higher order structures (HOS) in formulation and these folded structures are often critical for drug efficacy and safety. Generic or biosimilar drug products (DPs) need to show similar HOS to the reference product. The solution NMR spectroscopy is a non-invasive, chemically and structurally specific analytical method that is ideal for characterizing protein therapeutics in formulation. However, only limited NMR studies have been performed directly on marketed DPs and questions remain on how to quantitively define similarity. Here, NMR spectra were collected on marketed peptide and protein DPs, including calcitonin-salmon, liraglutide, teriparatide, exenatide, insulin glargine and rituximab. The 1D 1 H spectral pattern readily revealed protein HOS heterogeneity, exchange and oligomerization in the different formulations. Principal component analysis (PCA) applied to two rituximab DPs showed consistent results with the previously demonstrated similarity metrics of Mahalanobis distance (D M ) of 3.3. The 2D 1 H- 13 C HSQC spectral comparison of insulin glargine DPs provided similarity metrics for chemical shift difference (Δδ) and methyl peak profile, i.e., 4 ppb for 1 H, 15 ppb for 13 C and 98% peaks with equivalent peak height. Finally, 2D 1 H- 15 N sofast HMQC was demonstrated as a sensitive method for comparison of small protein HOS. The application of NMR procedures and chemometric analysis on therapeutic proteins offer quantitative similarity assessments of DPs with practically achievable similarity metrics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Predicting Short-Term Deformation in the Central Valley Using Machine Learning

Land subsidence caused by excessive groundwater pumping in Central Valley, California, is a major issue that has several negative impacts such as reduced aquifer storage and damaged infrastructures which, in turn, produce an economic loss due to the high reliance on crop production. This is why it is of utmost importance to routinely monitor and assess the surface deformation occurring. Two main goals that this paper attempts to accomplish are deformation characterization and deformation prediction. The first goal is realized through the use of Principal Component Analysis (PCA) applied to a series of Interferomtric Synthetic Aperture Radar (InSAR) images that produces eigenimages displaying the key characteristics of the subsidence. Water storage changes are also directly analyzed by the use of data from the Gravity Recovery and Climate Experiment (GRACE) twin satellites and the Global Land Data Assimilation System (GLDAS). The second goal is accomplished by building a Long Short-Term Memory (LSTM) model to predict short-term deformation after developing an InSAR time series using LiCSBAS, an open-source InSAR time series package. The model is applied to the city of Madera and produces better results than a baseline averaging model and a one dimensional convolutional neural network (CNN) based on a mean squared error metric showing the effectiveness of machine learning in deformation prediction as well as the potential for incorporation in hazard mitigation models. The model results can directly aid policy makers in determining the appropriate rate of groundwater withdrawal while maintaining the safety and well-being of the population as well as the aquifers’ integrity.

58 GEOSCIENCES↗
DOE OSTI2020

Dimensionality Reduction of SDSS Spectra with Variational Autoencoders

High-resolution galaxy spectra contain much information about galactic physics, but the high dimensionality of these spectra makes it difficult to fully utilize the information they contain. We apply variational autoencoders (VAEs), a nonlinear dimensionality reduction technique, to a sample of spectra from the Sloan Digital Sky Survey (SDSS). In contrast to principal component analysis (PCA), a widely used technique, VAEs can capture nonlinear relationships between latent parameters and the data. We find that a VAE can reconstruct the SDSS spectra well with only six latent parameters, outperforming PCA with the same number of components. Different galaxy classes are naturally separated in this latent space, without class labels having been given to the VAE. The VAE latent space is interpretable because the VAE can be used to make synthetic spectra at any point in latent space. For example, making synthetic spectra along tracks in latent space yields sequences of realistic spectra that interpolate between two different types of galaxies. Using the latent space to find outliers may yield interesting spectra: in our small sample, we immediately find unusual data artifacts and stars misclassified as galaxies. In this exploratory work, we show that VAEs create compact, interpretable latent spaces that capture nonlinear features of the data. While a VAE takes substantial time to train (≈1 day for 48,000 spectra), once trained, VAEs can enable the fast exploration of large astronomical data sets.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

New Measurements of the Lyα Forest Continuum and Effective Optical Depth with LyCAN and DESI Y1 Data

Abstract We present the Ly α Continuum Analysis Network (LyCAN), a convolutional neural network that predicts the unabsorbed quasar continuum within the rest-frame wavelength range of 1040–1600 Å based on the red side of the Ly α emission line (1216–1600 Å). We developed synthetic spectra based on a Gaussian mixture model representation of nonnegative matrix factorization (NMF) coefficients. These coefficients were derived from high-resolution, low-redshift ( z < 0.2) Hubble Space Telescope/Cosmic Origins Spectrograph (COS) quasar spectra. We supplemented this COS-based synthetic sample with an equal number of DESI Year 5 mock spectra. LyCAN performs extremely well on testing sets, achieving a median error in the forest region of 1.5% on the DESI mock sample, 2.0% on the COS-based synthetic sample, and 4.1% on the original COS spectra. LyCAN outperforms principal component analysis (PCA) and NMF-based prediction methods using the same training set by 40% or more. We predict the intrinsic continua of 83,635 DESI Year 1 spectra in the redshift range of 2.1 ≤ z ≤ 4.2 and perform an absolute measurement of the evolution of the effective optical depth. This is the largest sample employed to measure the optical depth evolution to date. We fit a power law of the form τ ( z ) = τ 0 ( 1 + z ) γ to our measurements and find τ 0 = (2.46 ± 0.14) × 10 −3 and γ = 3.62 ± 0.04. Our results show particular agreement with high-resolution, ground-based observations around z = 2, indicating that LyCAN is able to predict the quasar continuum in the forest region with only spectral information outside the forest.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

The development of rainfall retrievals from radar at Darwin

Abstract. The U.S. Department of Energy Atmospheric Radiation Measurement program Tropical Western Pacific site hosted a C-band polarization (CPOL) radar in Darwin, Australia. It provides 2 decades of tropical rainfall characteristics useful for validating global circulation models. Rainfall retrievals from radar assume characteristics about the droplet size distribution (DSD) that vary significantly. To minimize the uncertainty associated with DSD variability, new radar rainfall techniques use dual polarization and specific attenuation estimates. This study challenges the applicability of several specific attenuation and dual-polarization-based rainfall estimators in tropical settings using a 4-year archive of Darwin disdrometer datasets in conjunction with CPOL observations. This assessment is based on three metrics: statistical uncertainty estimates, principal component analysis (PCA), and comparisons of various retrievals from CPOL data. The PCA shows that the variability in R can be consistently attributed to reflectivity, but dependence on dual-polarization quantities was wavelength dependent for 1 10mmh-1. Rainfall estimates during these conditions primarily originate from deep convective clouds with median drop diameters greater than 1.5 mm. An uncertainty analysis and intercomparison with CPOL show that a Colorado State University blended technique for tropical oceans, with modified estimators developed from video disdrometer observations, is most appropriate for use in all cases, such as when 1 10mmh-1 (deeper convective rain).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Prediction of DIII-D Pedestal Structure from Externally Controllable Parameters

The sharp increase of pressure at the edge of a high confinement mode (H-mode) plasma, the pedestal, strongly impacts overall plasma performance. Predicting the pedestal is a necessity to control and optimize tokamak operations. An experimental data-driven machine learning (ML) approach is presented that predicts the pedestal heights and widths of electron density (ne) and electron temperature (Te) profiles as well as the separatrix ne from externally controllable parameters such as the plasma shape, heating method and power, and gas puff rate and integrated gas puff. The OMFIT framework was used with DIII-D data to efficiently, robustly, and automatically build a database of pedestal parameters to train machine learning models. Database creation was enabled by the search engine tool for DIII-D data, TokSearch, which parallelizes data fetching, enabling fast searches through basic signals of thousands of DIII-D shots and selection of relevant time intervals. Principal Component Analysis (PCA) separated the database into three clusters that represent classes of plasma shapes that are regularly used in DIII-D. The most important parameters for setting the pedestal structure were plasma current (Ip), toroidal magnetic field (Bφ), neutral beam heating power (PNBI) and shaping quantities. The Deep Jointly Informed Neural Networks (DJINN) algorithm was applied to identify suitable neural network (NN) architectures that appropriately capture the features of the pedestal database. Separate NNs were implemented for each pedestal parameter, and ensembling methods were used to improve the prediction accuracy and allowed estimation of the prediction uncertainty. The pedestal predictions of the test dataset lie within the measurement uncertainties of the pedestal parameters. The NN outperformed simple Linear Regression (LR) analysis, indicating non-linear dependencies in the pedestal structure. The presented achievements illustrate a promising path for future research, using feature extraction to infer experimental trends and thereby improve pedestal models as well as deploying NN for a fast pedestal prediction in DIII-D scenario development.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
NASA NTRS1985

Martian Fretted Terrain Morphometry Interpreted Using Principal Components Analysis

Martian fretted terrain is an extensive area of complex topography characterized by smooth, flat-floor valleys and mesas separated by abrupt escarpments along the boundary of heavily cratered uplands. The Deuteronilus-Protonilus region of the fretted terrain between latitude 35 degrees N and 50 degrees N and between 305 degrees W and 350 degrees W longitude was selected for quantitative landform study with the use of principal components analysis (PCA). The morphometry of upland mesa remnants and debris aprons was digitized with respect to latitude, longitude, and distance from the cratered terrain boundary (CTB). The PCA demonstrates that there are definable spatial variations in morphology with respect to longitude and latitude which suggest that the degradation along the CTB proceeded toward the southwest. The PCA also showed that there are organized relationships within the fretted landforms irrespective of their location. Finally, PCA indicated that an orientation of the degraded mesas exists which may be controlled by structure.

Kochell, R. C.↗
NASA NTRS1985

Determining Mineral Types and Abundances from Reflectance Measurements

Mineral types and their abundances were quantitatively determined from laboratory reflectance spectra using principal components analysis (PCA). PCA reduced the measured spectral dimensionality and allowed testing the uniqueness and validity of spectral mixing models. In addition to interpreting absorption bands, in this new approach we interpreted variations in the overall spectral curves in terms of physical processes, namely changes in mixtures of minerals, in particle size and in illumination geometry. Application of this approach to reflectances of planetary surfaces allows interpretation to be extended to quantitative determinations of mineral types and abundances.

Smith, M. O.↗
NASA NTRS1984

A comparison of the usefulness of canonical analysis, principal components analysis, and band selection for extraction of features from TMS data for landcover analysis

Three feature extraction methods, canonical analysis (CA), principal component analysis (PCA), and band selection, have been applied to Thematic Mapper Simulator (TMS) data in order to evaluate the relative performance of the methods. The results obtained show that CA is capable of providing a transformation of TMS data which leads to better classification results than provided by all seven bands, by PCA, or by band selection. A second conclusion drawn from the study is that TMS bands 2, 3, 4, and 7 (thermal) are most important for landcover classification.

Boyd, R. K.↗
NASA NTRS1991

Psychophysical evaluation of three-dimensional auditory displays

Work during this reporting period included the completion of our research on the use of principal components analysis (PCA) to model the acoustical head related transfer functions (HRTFs) that are used to synthesize virtual sources for three dimensional auditory displays. In addition, a series of studies was initiated on the perceptual errors made by listeners when localizing free-field and virtual sources. Previous research has revealed that under certain conditions these perceptual errors, often called 'confusions' or 'reversals', are both large and frequent, thus seriously comprising the utility of a 3-D virtual auditory display. The long-range goal of our work in this area is to elucidate the sources of the confusions and to develop signal-processing strategies to reduce or eliminate them.

Wightman, Frederic L.↗
NASA NTRS1993

Fourier domain target transformation analysis in the thermal infrared

Remote sensing uses of principal component analysis (PCA) of multispectral images include band selection and optimal color selection for display of information content. PCA has also been used for quantitative determination of mineral types and abundances given end member spectra. The preliminary results of the investigation of target transformation PCA (TTPCA) in the fourier domain to both identify end member spectra in an unknown spectrum, and to then calculate the relative concentrations of these selected end members are presented. Identification of endmember spectra in an unknown sample has previously been performed through bandmatching, expert systems, and binary classifiers. Both bandmatching and expert system techniques require the analyst to select bands or combinations of bands unique to each endmember. Thermal infrared mineral spectra have broad spectral features which vary subtly with composition. This makes identification of unique features difficult. Alternatively, whole spectra can be used in the classification process, in which case there is not need for an expert to identify unique spectra. Use of binary classifiers on whole spectra to identify endmember components has met with some success. These techniques can be used, along with a least squares fit approach on the endmembers identified, to derive compositional information. An alternative to the approach outlined above usese target transformation in conjunction with PCA to both identify and quantify the composition of unknown spectra. Preprocessing of the library and unknown spectra into the fourier domain, and using only a specific number of the components, allows for significant data volume reduction while maintaining a linear relationship in a Beer's Law sense. The approach taken here is to iteratively calculate concentrations, reducing the number of endmember components until only non-negative concentrations remain.

Anderson, D. L.↗
NASA NTRS1994

Regional climates in the GISS general circulation model: Surface air temperature

One of the more viable research techniques into global climate change for the purpose of understanding the consequent environmental impacts is based on the use of general circulation models (GCMs). However, GCMs are currently unable to reliably predict the regional climate change resulting from global warming, and it is at the regional scale that predictions are required for understanding human and environmental responses. Regional climates in the extratropics are in large part governed by the synoptic-scale circulation and the feasibility of using this interscale relationship is explored to provide a way of moving to grid cell and sub-grid cell scales in the model. The relationships between the daily circulation systems and surface air temperature for points across the continental United States are first developed in a quantitative form using a multivariate index based on principal components analysis (PCA) of the surface circulation. These relationships are then validated by predicting daily temperature using observed circulation and comparing the predicted values with the observed temperatures. The relationships predict surface temperature accurately over the major portion of the country in winter, and for half the country in summer. These relationships are then applied to the surface synoptic circulation of the Goddard Institute for Space Studies (GISS) GCM control run, and a set of surface grid cell temperatures are generated. These temperatures, based on the larger-scale validated circulation, may now be used with greater confidence at the regional scale. The generated temperatures are compared to those of the model and show that the model has regional errors of up to 10 C in individual grid cells.

Hewitson, Bruce↗
NASA NTRS1998

Diagnostics and Active Control of Aircraft Interior Noise

This project deals with developing advanced methods for investigating and controlling interior noise in aircraft. The work concentrates on developing and applying the techniques of Near Field Acoustic Holography (NAH) and Principal Component Analysis (PCA) to the aircraft interior noise dynamic problem. This involves investigating the current state of the art, developing new techniques and then applying them to the particular problem being studied. The knowledge gained under the first part of the project was then used to develop and apply new, advanced noise control techniques for reducing interior noise. A new fully active control approach based on the PCA was developed and implemented on a test cylinder. Finally an active-passive approach based on tunable vibration absorbers was to be developed and analytically applied to a range of test structures from simple plates to aircraft fuselages.

Fuller, C. R.↗
NASA NTRS2001

Oleoresin, Chemistry and Spectral Reflectance in "Stressed" Lodgepole and White Bark Pine, Mammoth Mountain, California

Development of methods to identify the physical and chemical character of materials on the earth's surface is one of the foci of hyperspectral remote sensing activities. Enhancing the ability to elucidate changes in foliar chemistry that relate to the health of a plant is a benefit to plant physiologists, foresters, and plant ecologists, as well as geologist and environmental scientists. Vegetation covers the landscape throughout the temperate and tropical regions of the earth. The existence of vegetation in these areas presents special problems to remote sensing systems since geologic bedrock and alteration zones are masked. At times, however, alterations in the soil/sediment geochemical environment result in foliar chemical changes that are detectable via remote sensing. Examples include monitoring of chlorophyll reflectance/fluorescence and equivalent water thickness indices as indicators of drought-induced plant stress. Another processing and interpretation approach used with hyperspectral data has been principal components analysis (PCA). Rowan et al. used PCA to identify absorption feature patterns obtained from vegetated areas with discrete bedrock geology or mineralization as the substrate. Many researchers highlight the need to advance our ability for hyperspectral imaging in vegetated areas as a near-term priority.

Hickey, James C.↗
NASA NTRS2002

General Aviation Interior Noise: Source/Path Identification - Part 1

There were two primary objectives of the research effort reported herein. The first objective was to identify and evaluate noise source/path identification technology applicable to single engine propeller driven aircraft that can be used to identify interior noise sources originating from structure-borne engine/propeller vibration, airborne propeller transmission, airborne engine exhaust noise, and engine case radiation. The approach taken to identify the contributions of each of these possible sources was first to conduct a Principal Component Analysis (PCA) of an in-flight noise and vibration database acquired on a Cessna Model 182E aircraft. The second objective was to develop and evaluate advanced technology for noise source ranking of interior panel groups such as the aircraft windshield, instrument panel, firewall, and door/window panels within the cabin of a single engine propeller driven aircraft. The technology employed was that of Acoustic Holography (AH). AH was applied to the test aircraft by acquiring a series of in-flight microphone array measurements within the aircraft cabin and correlating the measurements via PCA. The source contributions of the various panel groups leading to the array measurements were then synthesized by solving the inverse problem using the boundary element model.

Unruh, James F.↗
NASA NTRS2002

Spectral Data Reduction via Wavelet Decomposition

The greatest advantage gained from hyperspectral imagery is that narrow spectral features can be used to give more information about materials than was previously possible with broad-band multispectral imagery. For many applications, the new larger data volumes from such hyperspectral sensors, however, present a challenge for traditional processing techniques. For example, the actual identification of each ground surface pixel by its corresponding reflecting spectral signature is still one of the most difficult challenges in the exploitation of this advanced technology, because of the immense volume of data collected. Therefore, conventional classification methods require a preprocessing step of dimension reduction to conquer the so-called "curse of dimensionality." Spectral data reduction using wavelet decomposition could be useful, as it does not only reduce the data volume, but also preserves the distinctions between spectral signatures. This characteristic is related to the intrinsic property of wavelet transforms that preserves high- and low-frequency features during the signal decomposition, therefore preserving peaks and valleys found in typical spectra. When comparing to the most widespread dimension reduction technique, the Principal Component Analysis (PCA), and looking at the same level of compression rate, we show that Wavelet Reduction yields better classification accuracy, for hyperspectral data processed with a conventional supervised classification such as a maximum likelihood method.

Kaewpijit, S.↗
NASA NTRS1998

Feature Extraction of Event-Related Potentials Using Wavelets: An Application to Human Performance Monitoring

This report describes the development and evaluation of mathematical models for predicting human performance from discrete wavelet transforms (DWT) of event-related potentials (ERP) elicited by task-relevant stimuli. The DWT was compared to principal components analysis (PCA) for representation of ERPs in linear regression and neural network models developed to predict a composite measure of human signal detection performance. Linear regression models based on coefficients of the decimated DWT predicted signal detection performance with half as many f ree parameters as comparable models based on PCA scores. In addition, the DWT-based models were more resistant to model degradation due to over-fitting than PCA-based models. Feed-forward neural networks were trained using the backpropagation,-, algorithm to predict signal detection performance based on raw ERPs, PCA scores, or high-power coefficients of the DWT. Neural networks based on high-power DWT coefficients trained with fewer iterations, generalized to new data better, and were more resistant to overfitting than networks based on raw ERPs. Networks based on PCA scores did not generalize to new data as well as either the DWT network or the raw ERP network. The results show that wavelet expansions represent the ERP efficiently and extract behaviorally important features for use in linear regression or neural network models of human performance. The efficiency of the DWT is discussed in terms of its decorrelation and energy compaction properties. In addition, the DWT models provided evidence that a pattern of low-frequency activity (1 to 3.5 Hz) occurring at specific times and scalp locations is a reliable correlate of human signal detection performance.

Trejo, Leonard J.↗
NASA NTRS2002

Decomposition-Based Failure Mode Identification Method for Risk-Free Design of Large Systems

When designing products, it is crucial to assure failure and risk-free operation in the intended operating environment. Failures are typically studied and eliminated as much as possible during the early stages of design. The few failures that go undetected result in unacceptable damage and losses in high-risk applications where public safety is of concern. Published NASA and NTSB accident reports point to a variety of components identified as sources of failures in the reported cases. In previous work, data from these reports were processed and placed in matrix form for all the system components and failure modes encountered, and then manipulated using matrix methods to determine similarities between the different components and failure modes. In this paper, these matrices are represented in the form of a linear combination of failures modes, mathematically formed using Principal Components Analysis (PCA) decomposition. The PCA decomposition results in a low-dimensionality representation of all failure modes and components of interest, represented in a transformed coordinate system. Such a representation opens the way for efficient pattern analysis and prediction of failure modes with highest potential risks on the final product, rather than making decisions based on the large space of component and failure mode data. The mathematics of the proposed method are explained first using a simple example problem. The method is then applied to component failure data gathered from helicopter, accident reports to demonstrate its potential.

Tumer, Irem Y.↗