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DOE OSTI2019

Machine learning framework for assessment of microbial factory performance

Metabolic models can estimate intrinsic product yields for microbial factories, but such frameworks struggle to predict cell performance (including product titer or rate) under suboptimal metabolism and complex bioprocess conditions. On the other hand, machine learning, complementary to metabolic modeling necessitates large amounts of data. Building such a database for metabolic engineering designs requires significant manpower and is prone to human errors and bias. We propose an approach to integrate data-driven methods with genome scale metabolic model for assessment of microbial bio-production (yield, titer and rate). Using engineered E. coli as an example, we manually extracted and curated a data set comprising about 1200 experimentally realized cell factories from ~100 papers. We furthermore augmented the key design features (e.g., genetic modifications and bioprocess variables) extracted from literature with additional features derived from running the genome-scale metabolic model iML1515 simulations with constraints that match the experimental data. Then, data augmentation and ensemble learning (e.g., support vector machines, gradient boosted trees, and neural networks in a stacked regressor model) are employed to alleviate the challenges of sparse, non-standardized, and incomplete data sets, while multiple correspondence analysis/principal component analysis are used to rank influential factors on bio-production. The hybrid framework demonstrates a reasonably high cross-validation accuracy for prediction of E.coli factory performance metrics under presumed bioprocess and pathway conditions (Pearson correlation coefficients between 0.8 and 0.93 on new data not seen by the model).

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

A Climate Data Record (CDR) for the global terrestrial water budget: 1984–2010

Closing the terrestrial water budget is necessary to provide consistent estimates of budget components for understanding water resources and changes over time. Given the lack of in situ observations of budget components at anything but local scale, merging information from multiple data sources (e.g., in situ observation, satellite remote sensing, land surface model, and reanalysis) through data assimilation techniques that optimize the estimation of fluxes is a promising approach. Conditioned on the current limited data availability, a systematic method is developed to optimally combine multiple available data sources for precipitation ( P ), evapotranspiration (ET), runoff ( R ), and the total water storage change (TWSC) at 0.5° spatial resolution globally and to obtain water budget closure (i.e., to enforce P -ET- R -TWSC = 0) through a constrained Kalman filter (CKF) data assimilation technique under the assumption that the deviation from the ensemble mean of all data sources for the same budget variable is used as a proxy of the uncertainty in individual water budget variables. The resulting long-term (1984–2010), monthly 0.5° resolution global terrestrial water cycle Climate Data Record (CDR) data set is developed under the auspices of the National Aeronautics and Space Administration (NASA) Earth System Data Records (ESDRs) program. This data set serves to bridge the gap between sparsely gauged regions and the regions with sufficient in situ observations in investigating the temporal and spatial variability in the terrestrial hydrology at multiple scales. The CDR created in this study is validated against in situ measurements like river discharge from the Global Runoff Data Centre (GRDC) and the United States Geological Survey (USGS), and ET from FLUXNET. The data set is shown to be reliable and can serve the scientific community in understanding historical climate variability in water cycle fluxes and stores, benchmarking the current climate, and validating models.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Measurements of the 27 Al(α,n) Thick Target Yield near Threshold

In this work, we present results from direct measurements of the 27 Al(α,n) thick-target yield from laboratory incident energies E α ≈ 3 to 5 MeV, performed with the 3 HeBF 3 Giant Barrel (HeBGB) neutron detector at the Edwards Accelerator Laboratory. Our measurements have a small energy cadence in order to address discrepancies and sparseness of thick-target-yield data sets existing for this energy region. We find general agreement with existing data sets, including yields derived from cross-section data, while resolving a discrepancy between existing thick-target-yield data sets for E α ≈ 4–5 MeV. However, for E α < 3.5 MeV, our results are substantially lower than previous thick-target-yield data and somewhat larger than yields calculated from existing cross-section data. Our data complete the energy range needed for estimates of the 27 Al(α,n) contribution to neutrino and dark matter detector backgrounds and result in increased viability of 27 Al(α,n) as a plasma diagnostic tool at fusion facilities such as the National Ignition Facility.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2017

Gene and transcript abundances of bacterial type III secretion systems from the rumen microbiome are correlated with methane yield in sheep

Background: Ruminants are important contributors to global methane emissions via microbial fermentation in their reticulo-rumens. This study is part of a larger program, characterising the rumen microbiomes of sheep which vary naturally in methane yield (g CH4/kg DM/day) and aims to defne diferences in microbial communities, and in gene and transcript abundances that can explain the animal methane phenotype. Methods: Rumen microbiome metagenomic and metatranscriptomic data were analysed by Gene Set Enrichment, sparse partial least squares regression and the Wilcoxon Rank Sum test to estimate correlations between specifc KEGG bacterial pathways/genes and high methane yield in sheep. KEGG genes enriched in high methane yield sheep were reassembled from raw reads and existing contigs and analysed by MEGAN to predict their phylogenetic origin. Protein coding sequences from Succinivibrio dextrinosolvens strains were analysed using Efective DB to predict bacterial type III secreted proteins. The efect of S. dextrinosolvens strain H5 growth on methane formation by rumen methanogens was explored using co-cultures. Results: Detailed analysis of the rumen microbiomes of high methane yield sheep shows that gene and transcript abundances of bacterial type III secretion system genes are positively correlated with methane yield in sheep. Most of the bacterial type III secretion system genes could not be assigned to a particular bacterial group, but several genes were afliated with the genus Succinivibrio, and searches of bacterial genome sequences found that strains of S. dextrinosolvens were part of a small group of rumen bacteria that encode this type of secretion system. In co-culture experiments, S. dextrinosolvens strain H5 showed a growth-enhancing efect on a methanogen belonging to the order Methanomassiliicoccales, and inhibition of a representative of the Methanobrevibacter gottschalkii clade. Conclusions: This is the frst report of bacterial type III secretion system genes being associated with high methane emissions in ruminants, and identifes these secretions systems as potential new targets for methane mitigation research. The effects of S. dextrinosolvens on the growth of rumen methanogens in co-cultures indicate that bacteriamethanogen interactions are important modulators of methane production in ruminant animals.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Convolutional neural network based non-iterative reconstruction for accelerating neutron tomography *

Abstract Neutron computed tomography (NCT), a 3D non-destructive characterization technique, is carried out at nuclear reactor or spallation neutron source-based user facilities. Because neutrons are not severely attenuated by heavy elements and are sensitive to light elements like hydrogen, neutron radiography and computed tomography offer a complementary contrast to x-ray CT conducted at a synchrotron user facility. However, compared to synchrotron x-ray CT, the acquisition time for an NCT scan can be orders of magnitude higher due to lower source flux, low detector efficiency and the need to collect a large number of projection images for a high-quality reconstruction when using conventional algorithms. As a result of the long scan times for NCT, the number and type of experiments that can be conducted at a user facility is severely restricted. Recently, several deep convolutional neural network (DCNN) based algorithms have been introduced in the context of accelerating CT scans that can enable high quality reconstructions from sparse-view data. In this paper, we introduce DCNN algorithms to obtain high-quality reconstructions from sparse-view and low signal-to-noise ratio NCT data-sets thereby enabling accelerated scans. Our method is based on the supervised learning strategy of training a DCNN to map a low-quality reconstruction from sparse-view data to a higher quality reconstruction. Specifically, we evaluate the performance of two popular DCNN architectures—one based on using patches for training and the other on using the full images for training. We observe that both the DCNN architectures offer improvements in performance over classical multi-layer perceptron as well as conventional CT reconstruction algorithms. Our results illustrate that the DCNN can be a powerful tool to obtain high-quality NCT reconstructions from sparse-view data thereby enabling accelerated NCT scans for increasing user-facility throughput or enabling high-resolution time-resolved NCT scans.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2018

Sparse recovery of undersampled intensity patterns for coherent diffraction imaging at high X-ray energies

Coherent X-ray photons with energies higher than 50 keV offer new possibilities for imaging nanoscale lattice distortions in bulk crystalline materials using Bragg peak phase retrieval methods. However, the compression of reciprocal space at high energies typically results in poorly resolved fringes on an area detector, rendering the diffraction data unsuitable for the three-dimensional reconstruction of compact crystals. To address this problem, we propose a method by which to recover fine fringe detail in the scattered intensity. This recovery is achieved in two steps: multiple undersampled measurements are made by in-plane sub-pixel motion of the area detector, then this data set is passed to a sparsity-based numerical solver that recovers fringe detail suitable for standard Bragg coherent diffraction imaging (BCDI) reconstruction methods of compact single crystals. The key insight of this paper is that sparsity in a BCDI data set can be enforced by recognising that the signal in the detector, though poorly resolved, is band-limited. This requires fewer in-plane detector translations for complete signal recovery, while adhering to information theory limits. Lastly, we use simulated BCDI data sets to demonstrate the approach, outline our sparse recovery strategy, and comment on future opportunities.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Exact Gaussian processes for massive datasets via non-stationary sparsity-discovering kernels

Abstract A Gaussian Process (GP) is a prominent mathematical framework for stochastic function approximation in science and engineering applications. Its success is largely attributed to the GP’s analytical tractability, robustness, and natural inclusion of uncertainty quantification. Unfortunately, the use of exact GPs is prohibitively expensive for large datasets due to their unfavorable numerical complexity of $$O(N^3)$$ O ( N 3 ) in computation and $$O(N^2)$$ O ( N 2 ) in storage. All existing methods addressing this issue utilize some form of approximation—usually considering subsets of the full dataset or finding representative pseudo-points that render the covariance matrix well-structured and sparse. These approximate methods can lead to inaccuracies in function approximations and often limit the user’s flexibility in designing expressive kernels. Instead of inducing sparsity via data-point geometry and structure, we propose to take advantage of naturally-occurring sparsity by allowing the kernel to discover—instead of induce—sparse structure. The premise of this paper is that the data sets and physical processes modeled by GPs often exhibit natural or implicit sparsities, but commonly-used kernels do not allow us to exploit such sparsity. The core concept of exact, and at the same time sparse GPs relies on kernel definitions that provide enough flexibility to learn and encode not only non-zero but also zero covariances. This principle of ultra-flexible, compactly-supported, and non-stationary kernels, combined with HPC and constrained optimization, lets us scale exact GPs well beyond 5 million data points.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Predicting Drug Effects from High-dimensional Asymmetric Drug Data Sets using Graph Neural Networks: A Comprehensive Analysis of Multi-target Drug Effect Prediction

Graph neural networks (GNNs) have emerged as one of the most effective Machine learning (ML) techniques for drug effect prediction from drug molecular graphs. Despite having immense potential, GNN models lack performance when using data sets that contain high dimensional asymmetrically co-occurrent drug effects as targets with complex correlations between them. Training individual learning models for each drug effect and incorporating every prediction result for a wide spectrum of drug effects is beyond practicality. Such an implication provides a testbed to address this challenge as multi-target prediction problems, aiming to predict all drug effects at a time. We develop standard and hybrid graph neural networks (GNNs)to perform two separate tasks that are multi-regression for continuous values and multi-label classification for categorical values contained in our data sets. Since this step makes the target data even more sparse and introduces asymmetric label co-occurrence, the learning of multi-label classification models becomes difficult and heavily impacts the GNN's performance. To address these challenges, we propose a new data oversampling technique to improve multi-label classification performances on all the given imbalanced molecular graph data sets. Using the technique, we improve the data imbalance ratio of the drug effects better than before while protecting the data set's integrity. Finally, we evaluate multi-label classification performance using the best-performant hybrid GNN model on all the oversampled data sets obtained from the proposed oversampling technique. These results outperform those of other ML models including GNN models when they are trained on the original data sets or oversampled data sets using MLSMOTE (a well-known oversampling technique) in all evaluation metrics precision, recall, and F1 score by a significant margin.

Bose, Avishek [ORNL]↗

DOE OSTI2019

A Novel Sparse Compositional Technique Reveals Microbial Perturbations

ABSTRACT The central aims of many host or environmental microbiome studies are to elucidate factors associated with microbial community compositions and to relate microbial features to outcomes. However, these aims are often complicated by difficulties stemming from high-dimensionality, non-normality, sparsity, and the compositional nature of microbiome data sets. A key tool in microbiome analysis is beta diversity, defined by the distances between microbial samples. Many different distance metrics have been proposed, all with varying discriminatory power on data with differing characteristics. Here, we propose a compositional beta diversity metric rooted in a centered log-ratio transformation and matrix completion called robust Aitchison PCA. We demonstrate the benefits of compositional transformations upstream of beta diversity calculations through simulations. Additionally, we demonstrate improved effect size, classification accuracy, and robustness to sequencing depth over the current methods on several decreased sample subsets of real microbiome data sets. Finally, we highlight the ability of this new beta diversity metric to retain the feature loadings linked to sample ordinations revealing salient intercommunity niche feature importance. IMPORTANCE By accounting for the sparse compositional nature of microbiome data sets, robust Aitchison PCA can yield high discriminatory power and salient feature ranking between microbial niches. The software to perform this analysis is available under an open-source license and can be obtained at https://github.com/biocore/DEICODE ; additionally, a QIIME 2 plugin is provided to perform this analysis at https://library.qiime2.org/plugins/q2-deicode .

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

A sparse Gaussian sigmoid basis function approximation of hyperspectral data for detection of solids

We define a new characterization of emissivity and reflectance curves for compositional exploitation of hyperspectral data. Here, our method decomposes each spectrum into a sparse set of Gaussian sigmoid components using penalized regression. Detection is based on the combination of Gaussian sigmoid components unique to a target material. Focusing on the presence of spectral upslopes and downslopes rather than spectral correlations makes detection more robust to both target variation and spectral variability from atmosphere and background encountered during the collection process. We present simulation studies that demonstrate the potential to reduce false positive rates without compromising sensitivity. Characterization of long–wave infrared (LWIR) experimental data validates our method using minerals of different particle sizes, measurement angles, and collection conditions.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Applying Waveform Correlation to Reduce Seismic Analyst Workload Due to Repeating Mining Blasts

Agencies that monitor for underground nuclear tests are interested in techniques that automatically characterize mining blasts to reduce the human analyst effort required to produce high–quality event bulletins. Waveform correlation is effective in finding similar waveforms from repeating seismic events, including mining blasts. We report the results of an experiment to detect and identify mining blasts for two regions, Wyoming (U.S.A.) and Scandinavia, using waveform templates recorded by multiple International Monitoring System stations of the Preparatory Commission for the Comprehensive Nuclear–Test–Ban Treaty Organization (CTBTO PrepCom) for up to 10 yr prior to the time of interest. We discuss approaches for template selection, threshold setting, and event detection that are specialized for characterizing mining blasts using a sparse, global network. We apply the approaches to one week of data for each of the two regions to evaluate the potential for establishing a set of standards for waveform correlation processing of mining blasts that can be generally applied to operational monitoring systems with a sparse network. Here, we compare candidate events detected with our processing methods to the Reviewed Event Bulletin of the International Data Centre to assess potential reduction in analyst workload.

58 GEOSCIENCES↗

DOE OSTI2022

Dynamic signal recovery in distribution grids using compressive lossy measurements

Distribution system state estimation requires reliable aggregation of the measured data. However, the large volume of the measured data imposes a significant stress on the underlying communication infrastructure. With the challenges associated with measurement availability, current distribution systems are typically unobservable. To cope with the unobservability issue, compressive sensing theory allows us to recover system state information from a small number of measurements provided the states of the distribution system exhibit sparsity. In this paper, we evaluate the robustness of an updated Kalman filtered modified compressive sensing (KF-ModCS) technique that dynamically estimates the grid states using a small fraction of measured data. In practice, measurements used for sparsity based state estimation may also be intermittent due to communication network induced losses. Further, to understand the effect of packet losses on KF-ModCS, we provide an upper bound for the expected variances of the state estimation error for a given rate of information loss. This upper bound is further improved if the support set of the sparse signal that characterizes the state dynamics does not change over time and/or the reduced model is observable. Simulations based on two practical data sets collected from actual customers in a distribution grid validate the theoretical results.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2020

Recursive Dynamic Compressive Sensing in Smart Distribution Systems

With a transition to a smarter grid, we are witnessing a significant growth in smart metering infrastructure and sensor deployment in the distribution system. The underlying communication infrastructure is stressed due to the large volume of data that is generated by the smart meters/sensors. Furthermore, real time operations such as state estimation and control are impaired due to the lack of reliable aggregation of the data. In this paper, we exploit the underlying sparsity in grid data to implement two recursive dynamic compressive sensing (CS) approaches-streaming modified weighted-`1 CS and Kalman filtered CS. These approaches aim to reconstruct the sparse signal using the current underdetermined measurements and the prior information about the sparse signal and its support set. Slow signal and support change is in distribution grid data is validated using Pecan Street data. Both the IEEE 34 node test feeder system and PecanStreet data are considered as two examples to validate the superior performance of the two recursive CS techniques relative to classic CS.

Karimi, Hazhar Sufi↗

DOE OSTI2022

Bayesian-based response expansion and uncertainty quantification using sparse measurement sets

Systems subjected to dynamic loads often require monitoring of their vibrational response, but limitations on the total number and placement of the measurement sensors can hinder the data-collection process. Here, we present an indirect approach to estimate a system’s full-field dynamic response, including all uninstrumented locations, using response measurements from sensors sparsely located on the system. This approach relies on Bayesian inference that utilizes a system model to estimate the full-field response and quantify the uncertainty in these estimates. By casting the estimation problem in the frequency domain, this approach utilizes the modal frequency response functions as a natural, frequency-dependent weighting scheme for the system mode shapes to perform the expansion. This frequency-dependent weighting scheme enables an accurate expansion, even with highly correlated mode shapes that may arise from spatial aliasing due to the limited number of sensors, provided these correlated modes do not have natural frequencies that are closely spaced. Furthermore, the inherent regularization mechanism that arises in this Bayesian-based procedure enables the utilization of the full set of system mode shapes for the expansion, rather than any reduced subset. This approach can produce estimates when considering a single realization of the measured responses, and with some modification, it can also produce estimates for power spectral density matrices measured from many realizations of the responses from statistically stationary random processes. A simply supported beam provides an initial numerical validation, and a cylindrical test article excited by acoustic loads in a reverberation chamber provides experimental validation.

42 ENGINEERING↗

DOE OSTI2018

Developing Intensity-Duration-Frequency (IDF) Curves From Satellite-Based Precipitation: Methodology and Evaluation

Given the continuous advancement in the retrieval of precipitation from satellites, it is important to develop methods that incorporate satellite-based precipitation data sets in the design and planning of infrastructure. This is because in many regions around the world, in situ rainfall observations are sparse and have insufficient record length. A handful of studies examined the use of satellite-based precipitation to develop intensity-duration-frequency (IDF) curves; however, they have mostly focused on small spatial domains and relied on combining satellite-based with ground-based precipitation data sets. In this study, we explore this issue by providing a methodological framework with the potential to be applied in ungauged regions. This framework is based on accounting for the characteristics of satellite-based precipitation products, namely, adjustment of bias and transformation of areal to point rainfall. The latter method is based on previous studies on the reverse transformation (point to areal) commonly used to obtain catchment-scale IDF curves. The paper proceeds by applying this framework to develop IDF curves over the contiguous United States (CONUS); the data set used is Precipitation Estimation from Remotely Sensed Information Using Artificial Neural Networks – Climate Data Record (PERSIANN-CDR). IDFs are then evaluated against National Oceanic and Atmospheric Administration (NOAA) Atlas 14 to provide a quantitative estimate of their accuracy. Results of this work show that median errors are in the range of (17–22%), (6–12%), and (3–8%) for one-day, two-day and three-day IDFs, respectively, and return periods in the range (2–100) years. Furthermore, a considerable percentage of satellite-based IDFs lie within the confidence interval of NOAA Atlas 14.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Development of the Senseiver for efficient field reconstruction from sparse observations

Abstract The reconstruction of complex time-evolving fields from sensor observations is a grand challenge. Frequently, sensors have extremely sparse coverage and low-resource computing capacity for measuring highly nonlinear phenomena. While numerical simulations can model some of these phenomena using partial differential equations, the reconstruction problem is ill-posed. Data-driven-strategies provide crucial disambiguation, but these suffer in cases with small amounts of data, and struggle to handle large domains. Here we present the Senseiver, an attention-based framework that excels in reconstructing complex spatial fields from few observations with low overhead. The Senseiver reconstructs n -dimensional fields by encoding arbitrarily sized sparse sets of inputs into a latent space using cross-attention, producing uniform-sized outputs regardless of the number of observations. This allows efficient inference by decoding only a sparse set of output observations, while a dense set of observations is needed to train. This framework enables training of data with complex boundary conditions and extremely large fine-scale simulations. We build on the Perceiver IO by enabling training models with fewer parameters, which facilitates field deployment, and a training framework that allows a flexible number of sensors as input, which is critical for real-world applications. We show that the Senseiver advances the state-of-the-art of field reconstruction in many applications.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Non-linear relationships between daily temperature extremes and US agricultural yields uncovered by global gridded meteorological datasets

Global agricultural commodity markets are highly integrated among major producers. Prices are driven by aggregate supply rather than what happens in individual countries in isolation. Furthermore, estimating the effects of weather-induced shocks on production, trade patterns and prices hence requires a globally representative weather data set. Recently, two data sets that provide daily or hourly records, GMFD and ERA5-Land, became available. Starting with the US, a data rich region, we formally test whether these global data sets are as good as more fine-scaled country-specific data in explaining yields and whether they estimate similar response functions. While GMFD and ERA5-Land have lower predictive skill for US corn and soybeans yields than the fine-scaled PRISM data, they still correctly uncover the underlying non-linear temperature relationship. All specifications using daily temperature extremes under any of the weather data sets outperform models that use a quadratic in average temperature. Correctly capturing the effect of daily extremes has a larger effect than the choice of weather data. In a second step, focusing on Sub Saharan Africa, a data sparse region, we confirm that GMFD and ERA5-Land have superior predictive power to CRU, a global weather data set previously employed for modeling climate effects in the region.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Stellar kinematics of dwarf galaxies from multi-epoch spectroscopy: application to Triangulum II

ABSTRACT We present new MMT/Hectochelle spectroscopic measurements for 257 stars observed along the line of sight to the ultrafaint dwarf galaxy Triangulum II (Tri II). Combining results from previous Keck/DEIMOS spectroscopy, we obtain a sample that includes 16 likely members of Tri II, with up to 10 independent redshift measurements per star. To this multi-epoch kinematic data set, we apply methodology that we develop in order to infer binary orbital parameters from sparsely sampled radial velocity curves with as few as two epochs. For a previously identified (spatially unresolved) binary system in Tri II, we infer an orbital solution with period $296.0_{-3.3}^{+3.8} \rm ~ d$, semimajor axis $1.12^{+0.41}_{-0.24}\rm ~au$, and systemic velocity $-380.0 \pm 1.7 \rm ~km ~s^{-1}$ that we then use in the analysis of Tri II’s internal kinematics. Despite this improvement in the modelling of binary star systems, the current data remain insufficient to resolve the velocity dispersion of Tri II. We instead find a 95 per cent confidence upper limit of $\sigma _{v} \lesssim 3.4 \rm ~km~s^{-1}$.

Buttry, Rachel (ORCID:0000000155017609)↗