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DOE OSTI2025

Challenges in predicting protein-protein interactions of understudied viruses: Arenavirus-human interactions

Understanding protein-protein interactions (PPIs) between viruses and host organisms is crucial for uncovering infection mechanisms and identifying potential therapeutic targets. The ability to generalize PPI predictive models across understudied viruses presents a significant challenge. In this work, we use arenavirus-human PPIs to illustrate the difficulties associated with model generalization, which are compounded by a lack of both positive and negative data. We employ a Transfer Learning approach to investigate arenavirus-human PPIs by utilizing models trained on better-studied virus-human and human-human PPIs. Additionally, we curate and assess four types of negative sampling datasets to evaluate their impact on model performance. Despite the overall high accuracies (93–99 %) and AUPRC scores (0.8–0.9) appearing promising, further analysis indicates that these performance metrics can be misleading due to data leakage, data bias, and overfitting, especially concerning under-represented viral proteins. We reveal these gaps and assess the impact of data imbalance using standard k-fold cross-validation and Independent Blind Testing with a Balanced Dataset, resulting in a drop in accuracy below 50 %. We propose a viral protein-specific evaluation framework that categorizes viral proteins into majority and minority classes based on their representation in the dataset, enabling comparison of model performance across these groups using balanced accuracies. This framework offers a more robust evaluation of model generalizability, addressing biases inherent in standard evaluation techniques and paving the way for more reliable PPI prediction models for understudied viruses.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2015

Distributed Space Mission Design for Earth Observation Using Model-Based Performance Evaluation

Distributed Space Missions (DSMs) are gaining momentum in their application to earth observation missions owing to their unique ability to increase observation sampling in multiple dimensions. DSM design is a complex problem with many design variables, multiple objectives determining performance and cost and emergent, often unexpected, behaviors. There are very few open-access tools available to explore the tradespace of variables, minimize cost and maximize performance for pre-defined science goals, and therefore select the most optimal design. This paper presents a software tool that can multiple DSM architectures based on pre-defined design variable ranges and size those architectures in terms of predefined science and cost metrics. The tool will help a user select Pareto optimal DSM designs based on design of experiments techniques. The tool will be applied to some earth observation examples to demonstrate its applicability in making some key decisions between different performance metrics and cost metrics early in the design lifecycle.

Constellation↗

DOE OSTI2021

The Virtual Blast Furnace - An Integrated High Performance Computing Modeling, Simulation, and Visualization Capability for Steel Manufacturing (Final Report)

Many manufacturing industries require substantial capital and utilize energy intensive processes that involve complex phenomena. One example of such an industry is the steel industry, which is the fourth largest energy consuming industry in the U.S. By harnessing the power of High-Performance Computing (HPC) to enhance current simulation and visualization methods in the steel industry, it should be possible to increase resolution and/or decrease time of these methods by a factor of 1000. In this way, information can be obtained in a time frame that is useful for making business and engineering decisions, optimizing manufacturing processes and, ultimately, improving the completeness of U.S. industries. For example, if coke usage in blast furnaces were optimized such that the average coke rate was reduced from 797 lb/net tonne of hot metal (NTHM) to 604 lb/NTHM, costs could be reduced by $894 million/year. Additionally, members of the steel industry need the flexibility to efficiently operate blast furnaces at a range of production rates in order to meet fluctuating market demands. Large scale parameter studies can be utilized to discover workable operating parameters at a range of production rates.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2020

A critical examination of compound stability predictions from machine-learned formation energies

Machine learning has emerged as a novel tool for the efficient prediction of material properties, and claims have been made that machine-learned models for the formation energy of compounds can approach the accuracy of Density Functional Theory (DFT). The models tested in this work include five recently published compositional models, a baseline model using stoichiometry alone, and a structural model. By testing seven machine learning models for formation energy on stability predictions using the Materials Project database of DFT calculations for 85,014 unique chemical compositions, we show that while formation energies can indeed be predicted well, all compositional models perform poorly on predicting the stability of compounds, making them considerably less useful than DFT for the discovery and design of new solids. Most critically, in sparse chemical spaces where few stoichiometries have stable compounds, only the structural model is capable of efficiently detecting which materials are stable. The nonincremental improvement of structural models compared with compositional models is noteworthy and encourages the use of structural models for materials discovery, with the constraint that for any new composition, the ground-state structure is not known a priori. This work demonstrates that accurate predictions of formation energy do not imply accurate predictions of stability, emphasizing the importance of assessing model performance on stability predictions, for which we provide a set of publicly available tests.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Nonlinear modeling and performance analysis of cracked beam microgyroscopes

Cracks constitute a common structural defect in microelectromechanical systems that may arise during manufacturing, mechanical fatigue, or shock loading. Areas weakened by cracks increase the flexibility of the microstructure. Furthermore, depending on the crack severity, the increased flexibility can cause dramatic changes in the static and dynamic behaviors of electrically actuated MEMS. In this study, a numerical investigation of the depth and location of multiple edge cracks on the performance of beam microgyroscopes is conducted. Applying the Griffith strain energy release theorem for an edge crack, the vibrational characteristics of microgyroscopes with multiple cracks including the static deflection, natural frequencies, and mode shapes are studied analytically. Then, the differential quadrature method is employed to model the nonlinear dynamic behaviors of the cracked gyroscope system. Cracks initiated along the driving or sensing directions of the microgyroscope are found to have differing effects on its nonlinear dynamic response. This numerical study reveals that the onset of severe single cracks or a series of multiple cracks can significantly affect the sensitivity of the microgyroscope to base rotations and therefore leads to a degradation in the performance of the damaged MEMS sensor. This study also shows that a potential design approach for broadband microgyroscope systems manufactured with cracks can be proposed.

42 ENGINEERING↗

NASA NTRS2012

Design and Performance of Lift-Offset Rotorcraft for Short-Haul Missions

The design and performance of compound helicopters utilizing lift-offset rotors are examined, in the context of short-haul, medium-size civil and military missions. The analysis tools used are the comprehensive analysis CAMRAD II and the sizing code NDARC. Following correlation of the comprehensive analysis with existing lift-offset aircraft flight test data, the rotor performance model for the sizing code was developed, and an initial estimate was made of the rotor size and key hover and cruise flight conditions. The rotor planform and twist were optimized for those conditions, and the sizing code rotor performance model updated. Two models for estimating the blade and hub weight of lift-offset rotors are discussed. The civil and military missions are described, along with the aircraft design assumptions. The aircraft are sized for 30 passengers or 6600 lb payload, with a range of 300 nm. Civil and military aircraft designs are described for each of the rotor weight models. Disk loading and blade loading were varied to optimize the designs, based on gross weight and fuel burn. The influence of technology is shown, in terms of rotor hub drag and rotor weight.

Johnson, Wayne↗

NASA NTRS2023

A Surface Radiation Balance Data Set from Siple Dome in West Antarctica for Atmospheric and Climate Model Evaluation

A field campaign at Siple Dome in West Antarctica during the austral summer 2019-2020 offers an opportunity to evaluate climate model performance, particularly cloud microphysical simulation. Over Antarctic ice sheets and ice shelves, clouds are a major regulator of the surface energy balance, and in the warm season their presence occasionally induces surface melt that can gradually weaken an ice shelf structure. This dataset from Siple Dome, obtained using transportable and solar-poweredequipment, includes surface energy balance measurements, meteorology and cloud remote sensing. To demonstrate how these data can be used to evaluate model performance, comparisons are made with meteorological reanalysis known to give generally good performance over Antarctica (ERA5). Surface albedo measurements show expected variability with observed cloud amount, and can be used to evaluate a model's snowpack parameterization. One case study discussed involves a squall with northerly winds, during which ERA5 fails to produce cloud cover throughout one of the days. A second case study illustrates how shortwave spectroradiometer measurements that encompass the 1.6-micron atmospheric window reveal cloud phase transitions associated with cloud lifecycle. Here, continuously precipitating mixed-phase clouds become mainly liquid water clouds from local morning through the afternoon, not reproduced by ERA5. We challenge researchers to run their various regional or global models in a manner that has the large-scale meteorology follow the conditions of this field campaign, compare cloud and radiation simulations with this Siple Dome dataset, and potentially investigate why cloud microphysical simulations or other model components might produce discrepancies with these observations.

cloud remote sensing↗

DOE OSTI2023

A Surface Radiation Balance Dataset from Siple Dome in West Antarctica for Atmospheric and Climate Model Evaluation

Abstract A field campaign at Siple Dome in West Antarctica during the austral summer 2019/20 offers an opportunity to evaluate climate model performance, particularly cloud microphysical simulation. Over Antarctic ice sheets and ice shelves, clouds are a major regulator of the surface energy balance, and in the warm season their presence occasionally induces surface melt that can gradually weaken an ice shelf structure. This dataset from Siple Dome, obtained using transportable and solar-powered equipment, includes surface energy balance measurements, meteorology, and cloud remote sensing. To demonstrate how these data can be used to evaluate model performance, comparisons are made with meteorological reanalysis known to give generally good performance over Antarctica (ERA5). Surface albedo measurements show expected variability with observed cloud amount, and can be used to evaluate a model’s snowpack parameterization. One case study discussed involves a squall with northerly winds, during which ERA5 fails to produce cloud cover throughout one of the days. A second case study illustrates how shortwave spectroradiometer measurements that encompass the 1.6- μ m atmospheric window reveal cloud phase transitions associated with cloud life cycle. Here, continuously precipitating mixed-phase clouds become mainly liquid water clouds from local morning through the afternoon, not reproduced by ERA5. We challenge researchers to run their various regional or global models in a manner that has the large-scale meteorology follow the conditions of this field campaign, compare cloud and radiation simulations with this Siple Dome dataset, and potentially investigate why cloud microphysical simulations or other model components might produce discrepancies with these observations. significance statement Antarctica is a critical region for understanding climate change and sea level rise, as the great ice sheets and the ice shelves are subject to increasing risk as global climate warms. Climate models have difficulties over Antarctica, particularly with simulation of cloud properties that regulate snow surface melting or refreezing. Atmospheric and climate-related field work has significant challenges in the Antarctic, due to the small number of research stations that can support state-of-the-art equipment. Here we present new data from a suite of transportable and solar-powered instruments that can be deployed to remote Antarctic sites, including regions where ice shelves are most at risk, and we demonstrate how key components of climate model simulations can be evaluated against these data.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS2017

Comparative Study of Three Reconnection X Line Models at the Earth's Dayside Magnetopause Using in Situ Observations

This work examines the large-scale aspects of magnetic field reconnection at the Earth's dayside magnetopause. We use two sets of reconnection events, which are identified mostly by the in situ detection of accelerated and Alfvenic plasma flows. We intercompare three analytical models that predict the reconnection X line location and orientation, namely, the Trattner et al. (2007) and Swisdak and Drake (2007) models and also a modified version of the component merging model. In the first set of reconnection observations, we show three fortuitous, quasi-simultaneous dayside magnetopause crossing events where two widely separated spacecraft detect reconnection signatures, and the X line location and orientation can be inferred from the observations. We compare X line model predictions to those inferred from observations. These three reconnection events indicate the presence of an extended (greater than 7 Earth radii in length), component-type reconnection X line on Earth's dayside magnetopause connecting and structuring the reconnection signatures at locations far apart. In the second set of reconnection events, we analyze the X line models' performance in predicting the observed reconnection outflow direction, i.e., its north-south and/or east-west senses, in a total of 75 single, rather than multiple and quasi-simultaneous, magnetopause crossing events, where reconnection-associated plasma flows were clearly present. We found that the Swisdak and Drake's (2007) X line model performs slightly better, albeit not statistically significant, when predicting both accelerated plasma flow north-south and east-west components in 73% and 53% of the cases, respectively, as compared to the Trattner et al. (2007) model (70% north-south and 42% east-west) and the modified component merging model (66% north-south and 50% east-west).

Souza, V. M.↗

DOE OSTI2024

Impact of Color Space and Color Resolution on Vehicle Recognition Models

In this study, we analyze both linear and nonlinear color mappings by training on versions of a curated dataset collected in a controlled campus environment. We experiment with color space and color resolution to assess model performance in vehicle recognition tasks. Color encodings can be designed in principle to highlight certain vehicle characteristics or compensate for lighting differences when assessing potential matches to previously encountered objects. The dataset used in this work includes imagery gathered under diverse environmental conditions, including daytime and nighttime lighting. Experimental results inform expectations for possible improvements with automatic color space selection through feature learning. Moreover, we find there is only a gradual decrease in model performance with degraded color resolution, which suggests the need for simplified data collection and processing. By focusing on the most critical features, we could see improved model generalization and robustness, as the model becomes less prone to overfitting to noise or irrelevant details in the data. Such a reduction in resolution will lower computational complexity, leading to quicker training and inference times.

47 OTHER INSTRUMENTATION↗

DOE OSTI2021

Automated prediction of lattice parameters from X-ray powder diffraction patterns

A key step in the analysis of powder X-ray diffraction (PXRD) data is the accurate determination of unit-cell lattice parameters. This step often requires significant human intervention and is a bottleneck that hinders efforts towards automated analysis. This work develops a series of one-dimensional convolutional neural networks (1D-CNNs) trained to provide lattice parameter estimates for each crystal system. A mean absolute percentage error of approximately 10% is achieved for each crystal system, which corresponds to a 100- to 1000-fold reduction in lattice parameter search space volume. The models learn from nearly one million crystal structures contained within the Inorganic Crystal Structure Database and the Cambridge Structural Database and, due to the nature of these two complimentary databases, the models generalize well across chemistries. A key component of this work is a systematic analysis of the effect of different realistic experimental non-idealities on model performance. It is found that the addition of impurity phases, baseline noise and peak broadening present the greatest challenges to learning, while zero-offset error and random intensity modulations have little effect. However, appropriate data modification schemes can be used to bolster model performance and yield reasonable predictions, even for data which simulate realistic experimental non-idealities. In order to obtain accurate results, a new approach is introduced which uses the initial machine learning estimates with existing iterative whole-pattern refinement schemes to tackle automated unit-cell solution.

42 ENGINEERING↗

DOE OSTI2026

Search for HH → bbτ⁺τ⁻ Using Run 3 Scouting Data Analyze b-tagging and tau-tagging Performance with Unified Particle Transformer

B-tagging and tau-tagging performances play an important role in the search for the rare event HH → bbτ⁺τ⁻. A transformer-based neural network, Unified Particle Transformer, is applied for both tagging tasks, and Run 3 proton–proton collision scouting data at center-of-mass energy of 13.6 TeV is used. The scouting data stream accepts events at a much higher rate compared to traditional triggers, but stores only the objects reconstructed in the trigger, no low-level detector information. Therefore, existing taggers trained for the offline event reconstruction cannot be used. Analysis of the SoftMax plots, ROC/AUC curves, confusion matrix, accuracy and losses are used to evaluate model performance. Specifically, the tagging efficiency of the signal and misidentification probability across multiple background processes are compared for varying working points. Different training samples with distinct distributions of jet flavors are utilized and related model performances are analyzed. Interpretability methods, such as Integrated Gradients, may further be applied to study the input features’ influence on the model’s decisions, providing insights into potential improvements.

Chen, Blair [Purdue U., West Lafayette; Fermilab]↗

DOE OSTI2020

Multimodel validation of single wakes in neutral and stratified atmospheric conditions

Previous research has revealed the need for a validation study that considers several wake quantities and code types so that decisions on the trade-off between accuracy and computational cost can be well informed and appropriate to the intended application. In addition to guiding code choice and setup, rigorous model validation exercises are needed to identify weaknesses and strengths of specific models and guide future improvements. Here, we consider 13 approaches to simulating wakes observed with a nacelle-mounted lidar at the Scaled Wind Technology Facility (SWiFT) under varying atmospheric conditions. We find that some of the main challenges in wind turbine wake modeling are related to simulating the inflow. In the neutral benchmark, model performance tracked as expected with model fidelity, with large-eddy simulations performing the best. In the more challenging stable case, steady-state Reynolds-averaged Navier–Stokes simulations were found to outperform other model alternatives because they provide the ability to more easily prescribe noncanonical inflows and their low cost allows for simulations to be repeated as needed. Dynamic measurements were only available for the unstable benchmark at a single downstream distance. These dynamic analyses revealed that differences in the performance of time-stepping models come largely from differences in wake meandering. This highlights the need for more validation exercises that take into account wake dynamics and are able to identify where these differences come from: mesh setup, inflow, turbulence models, or wake-meandering parameterizations. In addition to model validation findings, we summarize lessons learned and provide recommendations for future benchmark exercises.

17 WIND ENERGY↗

NASA NTRSDate not supplied

Marin County Wildland Fires: Examining Fuel Load and Land Cover Change to Inform Fire Prevention and Suppression Decisions in Marin County, CA

Heightened occurrence of severe wildfires in the Western United States is increasing the need to better understand regions of high potential wild fire severity and develop methodologies for identifying the best locations for fuels reduction and active wildfire suppression, especially in populated regions such as Marin County, California. Marin County, located in the San Francisco Bay Area, has had significant development in the wildland-urban interface and periods of highly wildfire-prone conditions. The NASA DEVELOP team collaborated with Fire Foundry, a Marin-based fire service work force development program, to develop new models to assist with fire management. Using data from Sentinel-2A, Planet Scope, ECOSTRESS, a county-wide LiDAR mapping effort, Landsat 7 Enhanced Thematic Mapper (ETM+), and Landsat 8 Operational Land Imager (OLI), the team developed several input data layers to three models evaluating wild fire severity. One model performed a suitability analysis with weights based on scientific literature, another utilized machine learning based on past fires in Marin and neighboring Sonoma County to predict the difference normalized burn ratio, and the third inputted data layers into the Flam Map tool, which outputs risk categories. The team compared model outputs and, using the best-fit model, performed fuzzy logic analysis to identify specific locations where a fire break could be constructed to interrupt the progress of an active fire. These tools were proven useful and will assist partners in preparing for and managing an active wildfire event.

Suhani Dalal↗

NASA NTRS2009

Information Presentation

The goal of the Information Presentation Directed Research Project (DRP) is to address design questions related to the presentation of information to the crew. In addition to addressing display design issues associated with information formatting, style, layout, and interaction, the Information Presentation DRP is also working toward understanding the effects of extreme environments encountered in space travel on information processing. Work is also in progress to refine human factors-based design tools, such as human performance modeling, that will supplement traditional design techniques and help ensure that optimal information design is accomplished in the most cost-efficient manner. The major areas of work, or subtasks, within the Information Presentation DRP for FY10 are: 1) Displays, 2) Controls, 3) Procedures and Fault Management, and 4) Human Performance Modeling. The poster will highlight completed and planned work for each subtask.

Holden, Kritina L.↗

NASA NTRS2024

Future CH4 Budgets as Modelled By A Fully Coupled Earth System Model Using Prescribed GHG Concentrations vs. Interactive CH4 Sources and Sinks

We have used the NASA Goddard Institute for Space Studies (GISS) Earth system model GISS-E2.1 to study the future budgets and trends of global and regional CH4 under different emission scenarios. GISS-E2.1 is one of the few ESMs that can be driven by anthropogenic CH4 emissions, as well as interactive natural sources such as wetlands, and can simulate the tropospheric CH4 chemistry. In frame of the recent short-lived climate forcers (SLCFs) assessment by the Arctic Monitoring and Assessment Programme (AMAP), we used the GISS-E2.1 model with prescribed long-lived greenhouse gas (GHG) concentrations. In the present study, we have supplemented these simulations using the interactive CH4 sources and sinks in order to quantify the model performance and the sensitivity to CH4 sources and sinks. We have used the Current Legislation (CLE) and the Maximum Feasible Reduction (MFR) emission scenarios from the Eclipse V6b emission database to simulate the future chemical composition and climate impacts from 2015 to 2050. We have also simulated 1995-2014 in order to evaluate the model performance following the AMAP-SLCF protocol. The prescribed GHG version underestimates the Global Atmospheric Watch (GAW) surface CH4 observations during the period between 1995 and 2023 by 1% [-8.4%-2.0%], with a correlation (r) of 0.71 [-0.41 0.99]. The largest underestimations are over the continental emission regions such as North America, Europe, and Asia, while biases are smallest over oceans. On the other hand, the simulation with interactive sources and sinks underestimates the GAW observations more than the prescribed simulation, by 18.5% [-25% -10.4%], with a lower r of 0.36 [-0.82 0.93]. Opposite to the prescribed simulation, the biases are largest over oceans and smaller over the continents, however they are still larger over land than the prescribed simulation. The interactive simulation, with large sources virtually over land and strong sink over oceans, has a land/ocean ratio larger than 1 while the prescribed simulation has this ratio equal to 1 as it distributes the global prescribed CH4 concentration equally in longitude over a given latitude. This clearly shows that the interactive sources and sinks should be represented in models in order to realistically simulate the chemical composition and the oxidative capacity of the atmosphere. As expected, the MFR scenario simulates lower global surface CH4 concentrations and burdens compared to the CLE scenario, however in both cases, global surface CH4 and burden continue to increase through 2050 compared to present day. In the CLE scenario, increases are largest over the equatorial belt, in particular over India and East China, while the MFR scenario shows increases over the whole Southern Hemisphere, however much smaller compared to CLE. Finally, the interactive simulation shows that the chemical CH4 sink increases in the CLE scenario, while it slightly decreases in the MFR, leading to a larger CH4 lifetime in the MFR scenario compared to in the CLE scenario.

CH4↗

NASA NTRS2007

Observations on Cost Modeling and Performance Measurement of Long Term Archives

This paper describes a prototype suite of Excel-based tools that could be used for estimating lifecycle costs for newly planned or modified long-term archival facilities. These tools may also prove valuable for monitoring the long-term performance of such facilities once operational. Cost estimation is by analogy, using statistical curve-fitting techniques across a database of comparable data activities. The database currently includes 29 operational data centers ranging from small (2 FTEs) to large (66 FTEs), and is readily expandable to include additional activities specifically involving data preservation and added value. Each comparable data center is described in terms of its staffing, throughput workload, archival and distribution requirements, levels of user service, overall complexity, degree of automation, and other data, comprising 94 distinct descriptors in all. The descriptors were developed by normalizing heterogeneous data from the various centers and mapping them into an Excel framework consistent with the OAIS reference model. A user-friendly tool is provided for generating input to and updating the comparables database. This tool can also be used to benchmark the performance (in terms of cost versus throughput) of an operational data center, and to update the staffing, cost and workload data on a periodic basis. The comparables database could thus provide a history of staffing and throughput over time, as a means of performance monitoring and providing feedback for continuous improvement. Ancillary tools are also provided for performing "what-if' cost exercises for planning purposes, and for graphical display of data and results. We provide a high-level description of the tools; present our experiences and observations on gathering the information and maintaining the database; and discuss how this tool set might be applied to long term archives.

Fontaine, Kathy↗

NASA NTRS2018

Low Reynolds Number Airfoil Evaluation for the Mars Helicopter Rotor

The present research is aimed at providing a performance model for the Mars Helicopter (MH), to understand the complexity of the flow, and future regions of improvement. The Martian atmosphere's low density and the MH's relatively small rotor result in very low chord-based Reynolds number flows, Rec = O(10(exp 3)-10(exp 4)). The low density and subcritical Reynolds number reduce the lifting force and lifting efficiency, respectively. The high drag coefficients in subcritical flow, especially for thicker sections, are attributed to laminar separation from the rear of the airfoil. The goal is to generate a performance model for the MH rotor for a free wake analysis, since the computational budget for a complete Navier-Stokes solution for a rotating body-fitted rotor is substantial. In this study, a RANS-based approach is used to generate the airfoil deck using OVERFLOW with stitched experimental data for very high angles of attack. The model is presented through airfoil data tables (C81 files) that are used by comprehensive rotor analysis codes such as CAMRADII, or the mid-fidelity CFD solver RotCFD. These codes have proven to provide accurate performance predictions for all rotor operations at only a fraction of the computational expense of three- dimensional body-fitted viscous grids.

Koning, Witold J. K.↗