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At least 469 records · Page 26

Developing an Open Source, Reusable Platform for Distributed Collaborative Information Management in the Early Detection Research Network

For the past decade, the NASA Jet Propulsion Laboratory, in collaboration with Dartmouth University has served as the center for informatics for the Early Detection Research Network (EDRN). The EDRN is a multi-institution research effort funded by the U.S. National Cancer Institute (NCI) and tasked with identifying and validating biomarkers for the early detection of cancer. As the distributed network has grown, increasingly formal processes have been developed for the acquisition, curation, storage, and dissemination of heterogeneous research information assets, and an informatics infrastructure has emerged. In this paper we discuss the evolution of EDRN informatics, its success as a mechanism for distributed information integration, and the potential sustainability and reuse benefits of emerging efforts to make the platform components themselves open source. We describe our experience transitioning a large closed-source software system to a community driven, open source project at the Apache Software Foundation, and point to lessons learned that will guide our present efforts to promote the reuse of the EDRN informatics infrastructure by a broader community.

Early Detection Research Network (EDRN)↗

In situ quantum verification of polarization-stabilized optical channels

The active stabilization of polarization channels is a task of growing importance as quantum networks move to deployed demonstrations over existing fiber infrastructure. However, the uniquely strict requirements for high-fidelity qubit transmission complicate the extent to which classical solutions may apply to future quantum networks, particularly in terms of recognizing noise sources present in low-flux, nonunitary channels. Here we introduce an in situ benchmarking approach that augments a classical polarization tracking system, limited to unitary correction, with simultaneously transmitted quantum light for ancilla-assisted process tomography of the full quantum map. Implemented in a quantum local-area network, our method uses the reconstructed map both to validate the classical compensation and to expose noise sources it fails to capture. A sliding measurement window that continuously updates the estimated quantum process further increases sensitivity to rapid channel fluctuations. Our results should unlock new opportunities for in situ channel characterization in quantum-classical coexistence networks.

Stevens, Matthew L [Arizona State University]↗

Multisensor Machine Learning to Retrieve High Spatiotemporal Resolution Land Surface Temperature

Climate change is making heat waves more frequent, long-lasting, and severe. While multiple satellite types provide data to monitor surface temperature, geostationary (GEO) sensors provide near-continuous, continental-scale observations which can better capture the diurnal variability of land surface temperature (LST) than intermittent observations from low-earth orbit (LEO) sensors. However, standard products from GEO satellites are available at coarsened spatial and temporal resolutions compared to the native sensor resolution. Using datasets from the NASA Earth Exchange, we leveraged co-located, co-temporal observations from LEO and GEO satellites to learn a data-driven mapping using a convolutional neural network. The resulting NASA Earth eXchange Artificial Intelligence LST (NEXAI-LST) achieved a mean absolute error of 1.73 K relative to the target LEO product and improves on both spatial and temporal resolution [2 km, 10 minute] compared to the GEO full disk standard product [10 km, hourly]. In validation against measurements from a ground-based sensor network, NEXAI-LST achieves similar or better fit than both LEO and GEO standard products, while depending none of the prior knowledge of land surface and atmospheric states required by physical-statistical models. Further, application of the model to unseen LEO and GEO satellites demonstrates robust generalization of the model across spatial region, time of day, and sensor. In support of NASA’s open-source science initiative, we make our NEXAI-LST product, model, and codes available to facilitate data exploration and further studies.

Kate Marie Duffy↗

64x64 Analog Input Array for 3-Dimensional Neural Network Processor

In pattern recognition and classification for spatio-temporal problems, one of the most challenging tasks is to provide a good and valid solution in real-time. Because of time constraints, software-based neural network approaches may not be suitable for practical use. Hardware solutions seem to be good candidates for this class of problems. Currently, the Three Dimensional Analog Neural Network (3-DANN) is an effective approach to solving spatio-temporal problems in three-dimensional hardware.

spatio-temporal 3-DANN Three Dimensional Analog Ne↗

Demonstrating the Operational Value of Atmospheric Infrared Sounder (AIRS) Retrieved Profiles in the Pre-Convective Environment

The Short-term Prediction Research and Transition Center (SPoRT) is a collaborative partnership between NASA and operational forecasting partners, including a number of National Weather Service offices. SPoRT provides real-time NASA products and capabilities to its partners to address specific operational forecast challenges. One operational forecast challenge is forecasting convective weather in data-void regions such as large bodies of water (e.g. Gulf of Mexico). To address this forecast challenge, SPoRT produces a twice-daily three-dimensional analysis that blends a model first-guess from the Advanced Research Weather Research and Forecasting (WRF-ARW) model with retrieved profiles from the Atmospheric Infrared Sounder (AIRS) -- a hyperspectral sounding instrument aboard NASA's Aqua satellite that provides temperature and moisture profiles of the atmosphere. AIRS profiles are unique in that they give a three dimensional view of the atmosphere that is not available through the current rawinsonde network. AIRS has two overpass swaths across North America each day, one valid in the 0700-0900 UTC timeframe and the other in the 1900-2100 UTC timeframe. This is helpful because the rawinsonde network only has data from 0000 UTC and 1200 UTC at specific land-based locations. Comparing the AIRS analysis product with control analyses that include no AIRS data demonstrates the value of the retrieved profiles to situational awareness for the pre-convective (and convective) environment. In an attempt to verify that the AIRS analysis was a good representation of the vertical structure of the atmosphere, both the AIRS and control analyses are compared to a Rapid Update Cycle (RUC) analysis used by operational forecasters. Using guidance from operational forecasters, convective available potential energy (CAPE) was determined to be a vital variable in making convective forecasts and is used herein to demonstrate the utility of the AIRS profiles in changing the vertical thermodynamic structure of the atmosphere in the pre-convective and convective environment. CAPE is an important metric because of it is a quantitative measure of atmospheric stability, which is necessary information when forecasting for convective weather. Case studies from the summer of 2010 were examined, and most impact from the AIRS retrieved profiles occurred over the data-void Gulf of Mexico with fields of convective potential closer to the RUC than the CNTL. Mixed results were found when AIRS retrieved profiles were used over land, so more cases need to be examined to determine whether AIRS would be an effective tool over land. Additional analyses of problematic convective forecasts over the Gulf Coast will be needed to determine the operational impact of AIRS. SPoRT eventually plans to transition the AIRS product to select Weather Forecast Office (WFO) partners, pending the outcome of these additional analyses.

Kozlowski, Danielle M.↗

Variance Decomposition of MEDLI2 Reconstructed Heating Using Neural Networks

The Mars Entry, Descent, and Landing Instrumentation (MEDLI2) sensor suite collected data during entry of the Mars 2020 Perseverance rover into Mars’ atmosphere. This suite included a network of MEDLI2 Instrumented Sensor Plugs (MISPs). Each MISP was comprised of a cylinder made of Thermal Protection System (TPS) material with 1-3 embedded thermocouples (TCs), and it was flush mounted into the heatshield or backshell. Data from these in-depth TCs were used to reconstruct the aeroheating environment of the vehicle throughout entry. Surface heating was posed as an inverse problem, with the goal of estimating the surface heating by minimizing an objective function of the difference between MISP temperature measurements during flight and the temperature predictions derived from the Fully Implicit Ablation and Thermal response (FIAT) program. Given an aerothermal environment, FIAT calculates the material response and provides in-depth temperatures throughout the TPS material. To achieve the reverse, an internal tool called FIAT_Opt runs through multiple different environments until the output temperature at the TC depth closely matches the flight data. 95% confidence intervals on the reconstructed surface heating were obtained using Monte Carlo analysis, in which uncertainties in the thermocouple depth and the TPS material properties (e.g., density, thermal conductivity, heat capacity, emissivity) based on flight-lot material testing were included. A variance decomposition method using Sobol indices was employed to assess the sensitivity of the reconstructed peak heating to the TC placement and material property uncertainties. Variance decomposition was found to require tens of thousands of FIAT_Opt runs in order for the Sobol indices to converge. With a single FIAT_Opt run taking on the order of 40 minutes, the required number of computations would take months to complete, even if using multiple CPUs. To mitigate this problem, three machine learning models (ridge regression with cross-validation, random forest regression, and a deep neural network) were trained and tested using the 2000 Monte Carlo runs that were already completed. A subset of 1600 runs were used to train the model (i.e., training set), while the remaining 400 runs were used as the test set. The predictions from the deep neural network (DNN) on the test set showed nearly perfect agreement to the actual values computed with FIAT_Opt (R2 > 0.99). Using the DNN as a surrogate model, the variance decomposition using 50,000 runs was completed within minutes. The resulting Sobol indices showed that the reconstructed peak surface heating was most sensitive to the uncertainties in the thermal conductivity (ST = 0.37) and heat capacity (ST = 0.26). This method can be leveraged to provide requirements for material property measurements needed to improve the accuracy of surface heating prediction and ultimately lead to the reduction of design margins in the future. This presentation will include background on the MEDLI2 suite; the method used for inverse heating estimation; the way that material property uncertainties were accounted for using Monte Carlo analysis; a brief background on variance decomposition; the motivation for using machine learning in this context; how a neural network was trained on the data to enable variance decomposition in a fraction of the time; and the variance decomposition results for one of the MISPs.

Hannah Alpert↗

NASA Orbital Debris Large-Object Baseline Population in ORDEM 3.0

The NASA Orbital Debris Program Office (ODPO) has created and validated high fidelity populations of the debris environment for the latest Orbital Debris Engineering Model (ORDEM 3.0). Though the model includes fluxes of objects 10 um and larger, this paper considers particle fluxes for 1 cm and larger debris objects from low Earth orbit (LEO) through Geosynchronous Transfer Orbit (GTO). These are validated by several reliable radar observations through the Space Surveillance Network (SSN), Haystack, and HAX radars. ORDEM 3.0 populations were designed for the purpose of assisting, debris researchers and sensor developers in planning and testing. This environment includes a background derived from the LEO-to-GEO ENvironment Debris evolutionary model (LEGEND) with a Bayesian rescaling as well as specific events such as the FY-1C anti-satellite test, the Iridium 33/Cosmos 2251 accidental collision, and the Soviet/Russian Radar Ocean Reconnaissance Satellite (RORSAT) sodium-potassium droplet releases. The environment described in this paper is the most realistic orbital debris population larger than 1 cm, to date. We describe derivations of the background population and added specific populations. We present sample validation charts of our 1 cm and larger LEO population against Space Surveillance Network (SSN), Haystack, and HAX radar measurements.

Krisco, Paula H.↗

Evaluation of Modeling NO2 Concentrations Driven by Satellite-Derived and Bottom-Up Emission Inventories Using In-Situ Measurements Over China

Chemical transport models together with emission inventories are widely used to simulate NO2 concentrations over China, but validation of the simulations with in situ measurements has been extremely limited. Here we use ground measurements obtained from the air quality monitoring network recently developed by the Ministry of Environmental Protection of China to validate modeling surface NO2 concentrations from the CHIMERE regional chemical transport model driven by the satellite-derived DECSO and the bottom-up MIX emission inventories. We applied a correction factor to the observations to account for the interferences of other oxidized nitrogen compounds (NOz), based on the modeled ratio of NO2 to NOz. The model accurately reproduces the spatial variability in NO2 from in situ measurements, with a spatial correlation coefficient of over 0.7 for simulations based on both inventories. A negative and positive bias is found for the simulation with the DECSO (slopeD0.74 and 0.64 for the daily mean and daytime only) and the MIX (slopeD1.3 and 1.1) inventories, respectively, suggesting an underestimation and overestimation of NOx emissions from corresponding inventories. The bias between observed and modeled concentrations is reduced, with the slope dropping from 1.3 to 1.0 when the spatial distribution of NOx emissions in the DECSO inventory is applied as the spatial proxy for the MIX inventory, which suggests an improvement of the distribution of emissions between urban and suburban or rural areas in the DECSO inventory compared to that used in the bottom-up inventory. A rough estimate indicates that the observed concentrations, from sites predominantly placed in the populated urban areas, may be 10-40% higher than the corresponding model grid cell mean. This reduces the estimate of the negative bias of the DECSO-based simulation to the range of -30 to 0% on average and more firmly establishes that the MIX inventory is biased high over major cities. The performance of the model is comparable over seasons, with a slightly worse spatial correlation in summer due to the difficulties in resolving the more active NOx photochemistry and larger concentration gradients in summer by the model. In addition, the model well captures the daytime diurnal cycle but shows more significant disagreement between simulations and measurements during nighttime, which likely produces a positive model bias of about 15% in the daily mean concentrations. This is most likely related to the uncertainty in vertical mixing in the model at night.

NO2 modelling↗

Lidar Validation Measurements at the NOAA Mauna Loa Observatory NDACC Station

NASA's Goddard Space Flight Center (GSFC) transported two lidar instruments to the NOAA facility at the Mauna Loa Observatory (MLO) on the Big Island of Hawaii, to participate in an official, extended validation campaign. This site is situated 11,141 ft. above sea level on the side of the mountain. The observatory has been making atmospheric measurements regularly since the 1950's, and has hosted the GSFC Stratospheric Ozone (STROZ) Lidar and the GSFC Aerosol and Temperature (AT) Lidar on several occasions, most recently between November, 2012 and November, 2015. The purpose of this extended deployment was to participate in Network for the Detection of Atmospheric Composition Change (NDACC) Validation campaigns with the JPL Stratospheric Ozone Lidar and the NOAA Temperature, Aerosol and Water Vapor instruments as part of the routine NDACC Validation Protocol.

Lidar↗

Component Importance and Interdependence Analysis for Transmission, Distribution and Communication Systems

For critical infrastructure restoration planning, the real-time scheduling and coordination of system restoration efforts, the key in decision-making is to prioritize those critical components that are out of service during the restoration. For this purpose, there is a need for component importance analysis. While it has been investigated extensively for individual systems, component importance considering interdependence among transmission, distribution and communication (T&D&C) systems has not been systematically analyzed and widely adopted. In this study, we propose a component importance assessment method in the context of interdependence between T&D&C networks. Analytic methods for multilayer networks and a set of metrics have been applied for assessing the component importance and interdependence between T&D&C networks based on their physical characteristics. The proposed methodology is further validated with integrated synthetic Illinois regional transmission, distribution, and communication (T&D&C) systems, the results reveal the unique characteristics of component/node importance, which are strongly affected by the network topologies and cross-domain node mapping.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Analyses of GWAS signal using GRIN identify additional genes contributing to suicidal behavior

Genome-wide association studies (GWAS) identify genetic variants underlying complex traits but are limited by stringent genome-wide significance thresholds. We present GRIN (Gene set Refinement through Interacting Networks), which increases confidence in the expanded gene set by retaining genes strongly connected by biological networks when GWAS thresholds are relaxed. GRIN was validated on both simulated interrelated gene sets as well as multiple GWAS traits. From multiple GWAS summary statistics of suicide attempt, a complex phenotype, GRIN identified additional genes that replicated across independent cohorts and retained biologically interrelated genes despite a relaxed significance threshold. We present a conceptual model of how these retained genes interact through neurobiological pathways that may influence suicidal behavior, and identify existing drugs associated with these pathways that would not have been identified under traditional GWAS thresholds. We demonstrate GRIN’s utility in boosting GWAS results by increasing the number of true positive genes identified from GWAS results.

60 APPLIED LIFE SCIENCES↗

Geometry-complete diffusion for 3D molecule generation and optimization

Abstract Generative deep learning methods have recently been proposed for generating 3D molecules using equivariant graph neural networks (GNNs) within a denoising diffusion framework. However, such methods are unable to learn important geometric properties of 3D molecules, as they adopt molecule-agnostic and non-geometric GNNs as their 3D graph denoising networks, which notably hinders their ability to generate valid large 3D molecules. In this work, we address these gaps by introducing the Geometry-Complete Diffusion Model (GCDM) for 3D molecule generation, which outperforms existing 3D molecular diffusion models by significant margins across conditional and unconditional settings for the QM9 dataset and the larger GEOM-Drugs dataset, respectively. Importantly, we demonstrate that GCDM’s generative denoising process enables the model to generate a significant proportion of valid and energetically-stable large molecules at the scale of GEOM-Drugs, whereas previous methods fail to do so with the features they learn. Additionally, we show that extensions of GCDM can not only effectively design 3D molecules for specific protein pockets but can be repurposed to consistently optimize the geometry and chemical composition of existing 3D molecules for molecular stability and property specificity, demonstrating new versatility of molecular diffusion models. Code and data are freely available on GitHub .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Deep Learning for Multigroup Cross-Section Representation in Two-Step Core Calculations

Here we investigate using deep learning, a type of machine-learning algorithm employing multiple layers of artificial neurons, for the mathematical representation of multigroup cross sections for use in the Griffin reactor multiphysics code for two-step deterministic neutronics calculations. A three-dimensional fuel element typical of a high-temperature gas reactor as well as a two-dimensional sodium-cooled fast reactor lattice are modeled using the Serpent Monte Carlo code, and multigroup macroscopic cross sections are generated for various state parameters to produce a training data set and a separate validation data set. A fully connected, feedforward neural network is trained using the open-source PyTorch machine-learning framework, and its accuracy is compared against the standard piecewise linear interpolation model. Additionally, we provide in this work a generic technique for propagating the cross-section model errors up to the k eff using sensitivity coefficients with the first-order uncertainty propagation rule. Quantifying the eigenvalue error due to the cross-section regression errors is especially practical for appropriately selecting the mathematical representation of the cross sections. We demonstrate that the artificial neural network model produces lower errors and therefore enables better accuracy relative to the piecewise linear model when the cross sections exhibit nonlinear dependencies; especially when a coarse grid is employed, where the errors can be halved by the artificial neural network. However, for linearly dependent multigroup cross sections as found for the sodium-cooled fast reactor case, a simpler linear regression outperforms deeper networks.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Six Machine-Learning Methods for Predicting Hospital-Stay Duration for Patients with Sepsis: A Comparative Study

Sepsis is a life-threatening medical condition that, if not treated promptly, can result in tissue damage, organ failure, and death. According to the Centers for Disease Control, about 270,000 individuals die of sepsis in the US each year. Further, sepsis expenditures accounted for 13% of total US hospital costs in 2013, totaling more than $24 billion. Our project objectives were to determine if Machine Learning algorithms could reliably predict hospital stay duration for patients with sepsis. The data set we used has been de-identified and is freely available through the BupaR package. The data includes 1050 cases, 15214 events, and 16 types of actions related to sepsis patient care. First, we used process mining to determine how long each patient was in the hospital. Using BupaR’s functions, we created several process model graphs. These process models depict the movement of patients at a hospital and provide duration data for each patent case. Second, we identified outlier data and created two dataset versions: one with and one without outliers. We then applied the following analysis methods: Linear Regression, Random Forest, K-Nearest Neighbors, Neural Networks, XGBoost, and lightGBM. We compared the model validations for the six machine learning models using the same data-splitting method. We found that the XGBoost model had the best prediction accuracy of 73.9 percent for cases with outliers, and 79 percent for cases without outliers. We also found that the lightGBM model had the lowest mean absolute error between prediction and actual duration in days with 3.66 days for the case with outliers, and 2.4 days for the case without outliers. These two models outperformed the other four models. This work will be enhanced in the future by exploring new prediction algorithms and comparing them with the results of this study.

Chen, Lingtao↗

Eucalyptus grandis MYB‐Like and RAN‐Like Zinc Finger Proteins Display Dual Roles in Regulating Plant Immunity and Symbiosis Pathways

Plant roots live in constant contact with diverse microbes in the soil. Plant fitness, therefore, relies on signaling pathways that mount an effective immune response against pathogens while fostering mutualistic symbioses. Plant pathways, and specifically immune genes that may act as "switches," discriminating between pathogenic or mutualistic fungi, remain largely unknown. Using Eucalyptus grandis as a model system, we investigate alterations to the root transcriptomic landscape during pre-symbiosis with either the pathogen Armillaria luteobubalina or the mutualistic fungus Pisolithus microcarpus. Comparative analyses identified three strongly counter-regulated genes that may act as immune switches to accommodate or to repress fungal colonization. We characterized two of these, a MYB-like and RAN-like zinc finger protein, using a transgenic approach and demonstrated that they have bifunctional roles in the regulation of cell death and a hypersensitive-like response, depending on the lifestyle of the associated fungus. Using co-expression network analysis, we identified hypothetical pathways correlated to these genes. We functionally validated these predictions using plants with transgenic roots with increased or decreased transcription of these genes, thereby showing the power of co-expression networks as an a priori approach to identify key immune response pathways in plants. Overall, our results demonstrate that prior to physical contact with microbes, MYB-like and RAN-like zinc finger proteins are key regulators of plant immune signaling that respond to fungal signals and enable or repress symbiotic establishment.

mycorrhizal fungi↗

The Value of Information From Horizontal Distributed Acoustic Sensing Compared to Multicomponent Geophones Via Machine Learning

Abstract Faults play an important role in recharging many geothermal reservoirs, and seismic information can image the locations of these faults. The value of information (VOI) metric is used to objectively quantify and compare the value of two types of seismic receiver data via a machine learning approach. The demonstrated VOI methodology is novel by including spatial models from seismic data and obtaining the information statistics from machine learning. Our two-dimensional numerical experiments compare images created from sparsely spaced (80 m), two-component geophone sampling to high spatial resolution (1 m), single-component DAS. We used a three-fold cross validation of a U-Net convolutional neural networks to achieve average classification statistics. The results suggest that when horizontal sources are utilized, geophones and DAS identify reflectors and non-reflectors at roughly the same rate. The average F1 score for horizontal DAS is 0.939 and 0.931 for geophones. For images created from a vertical source, DAS performed marginally better (F1 = 0.919) than geophones (F1 = 0.877). Our transferrable methodology can provide guidance on which acquisition scenarios can improve images of important structures in the subsurface and present an efficient method for obtaining reliability statistics from high-dimensional, spatial data.

Energy & Fuels↗

AI-Powered Knowledge Graphs for Neuromorphic and Energy-Efficient Computing

The surge in scientific literature obscures breakthroughs and hinders the discovery of new research paths. We propose an artificial intelligence (AI) powered framework using large language models (LLMs) and knowledge graphs (KGs) to automate parts of scientific discovery, focusing on energy-efficient AI circuits. Our hybrid approach combines LLMs, structured data, and ontology-based reasoning to construct a comprehensive knowledge graph that integrates insights across computational neuroscience, spiking neuron models, learning rules, architectural motifs, and neuromorphic device technologies. This multi-domain representation enables the generation of hypotheses that connect biological function with implementable, energy-efficient hardware architectures. Using KG embeddings and graph neural networks, the framework generates hypotheses for novel circuits, validates them through optimization on exascale HPC systems, and with tools like SuperNeuro and Fugu, the most promising designs will be prototyped in hardware. This open-source system aims to accelerate discoveries and bridging neuroscience with hardware innovation, drive collaboration, and unlock new opportunities in low-power AI computing.

Gautam, Ashish [ORNL]↗

Reactive Flows in Porous Media: Challenges in Theoretical and Numerical Methods

We review theoretical and computational research, primarily from the past 10 years, addressing the flow of reactive fluids in porous media. The focus is on systems where chemical reactions at the solid–fluid interface cause dissolution of the surrounding porous matrix, creating nonlinear feedback mechanisms that can often lead to greatly enhanced permeability. Here, we discuss insights into the evolution of geological forms that can be inferred from these feedback mechanisms, as well as some geotechnical applications such as enhanced oil recovery, hydraulic fracturing, and carbon sequestration. Until recently, most practical applications of reactive transport have been based on Darcy-scale modeling, where averaged equations for the flow and reactant transport are solved. We summarize the successes and limitations of volume averaging, which leads to Darcy-scale equations, as an introduction to pore-scale modeling. Pore-scale modeling is computationally intensive but offers new insights as well as tests of averaging theories and pore-network models. We include recent research devoted to validation of pore-scale simulations, particularly the use of visual observations from microfluidic experiments.

wormhole formation↗