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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Next-generation yeast-two-hybrid analysis with Y2H-SCORES identifies novel interactors of the MLA immune receptor

Protein-protein interaction networks are one of the most effective representations of cellular behavior. In order to build these models, high-throughput techniques are required. Next-generation interaction screening (NGIS) protocols that combine yeast two-hybrid (Y2H) with deep sequencing are promising approaches to generate interactome networks in any organism. However, challenges remain to mining reliable information from these screens and thus, limit its broader implementation. Here, we present a computational framework, designated Y2H-SCORES, for analyzing high-throughput Y2H screens. Y2H-SCORES considers key aspects of NGIS experimental design and important characteristics of the resulting data that distinguish it from RNA-seq expression datasets. Three quantitative ranking scores were implemented to identify interacting partners, comprising: 1) significant enrichment under selection for positive interactions, 2) degree of interaction specificity among multi-bait comparisons, and 3) selection of in-frame interactors. Using simulation and an empirical dataset, we provide a quantitative assessment to predict interacting partners under a wide range of experimental scenarios, facilitating independent confirmation by one-to-one bait-prey tests. Simulation of Y2H-NGIS enabled us to identify conditions that maximize detection of true interactors, which can be achieved with protocols such as prey library normalization, maintenance of larger culture volumes and replication of experimental treatments. Y2H-SCORES can be implemented in different yeast-based interaction screenings, with an equivalent or superior performance than existing methods. Proof-of-concept was demonstrated by discovery and validation of novel interactions between the barley nucleotide-binding leucine-rich repeat (NLR) immune receptor MLA6, and fourteen proteins, including those that function in signaling, transcriptional regulation, and intracellular trafficking.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Score-based deterministic density sampling

We propose a deterministic sampling framework using Score-Based Transport Modeling for sampling an unnormalized target density π given only its score ∇ log π. Our method approximates the Wasserstein gradient flow on KL($f_t$∥π) by learning the time-varying score ∇ log $f_t$ on the fly using score matching. While having the same marginal distribution as Langevin dynamics, our method produces smooth deterministic trajectories, resulting in monotone noise-free convergence. We prove that our method dissipates relative entropy at the same rate as the exact gradient flow, provided sufficient training. Numerical experiments validate our theoretical findings: our method converges at the optimal rate, has smooth trajectories, and is often more sample efficient than its stochastic counterpart. Experiments on high-dimensional image data show that our method produces high-quality generations in as few as 15 steps and exhibits natural exploratory behavior. The memory and runtime scale linearly in the sample size.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

A novel methodology to integrate outcomes regarding perioperative pain experience into a composite score: Prediction model development and validation

Abstract Background An integrated score that globally assesses perioperative pain experience and rationally weights each component has not yet been developed. Methods A development dataset specific to adult Chinese patients undergoing orthopaedic surgery was obtained from PAIN OUT (1985 qualified patients of 2244). A more recent validation dataset obeying the same conditions was obtained from the Chinese Anaesthesia Shared‐database Platform (1004 qualified patients of 1032). Outcomes were assessed using the International Pain Outcomes Questionnaire (IPO‐Q), which comprises key patient‐level outcomes of perioperative pain management, including pain experience and perceptions of care. Using principal component analysis and regression models, a composite score (CS) was inferred to integrate pain experience. The discrimination of the CS for dissatisfaction and desire for more pain treatment was compared with that of the worst pain score. Results A CS was developed from the 12 items of the IPO‐Q regarding pain experience. The weight for calculating the CS was worst pain 11, least pain 17, time spent in severe pain 11, interference with activity in bed 9, interference with breathing deeply or coughing 10, interference with sleep 9, anxiety 12, helplessness 12, nausea 0, drowsiness 2, itch 5 and dizziness 2. In external validation, the CS indicated superior discrimination to the worst pain in predicting dissatisfaction ( p < 0.001) and desire for more pain treatment ( p < 0.001). Conclusions This study introduced a methodology to integrate outcomes regarding perioperative pain experience into a CS, which was based on the weight of each item. Significance This novel methodology sheds additional light on the riveting issue of carefully integrating several measures into a composite endpoint, which may be useful for quality improvement purposes when addressing the impact of a change in clinical practice.

Jiang, Bailin↗
DOE OSTI2024

A Corrected Score Function Framework for Modelling Circadian Gene Expression

Many biological processes display oscillatory behaviour based on an approximately 24 h internal timing system specific to each individual. One process of particular interest is gene expression, for which several circadian transcriptomic studies have identified associations between gene expression during a 24 h period and an individual's health. A challenge with analysing data from these studies is that each individual's internal timing system is offset relative to the 24 h day-night cycle, where day–night cycle time is recorded for each collected sample. Laboratory procedures can accurately determine each individual's offset and determine the internal time of sample collection. However, these laboratory procedures are labour-intensive and expensive. Here, in this paper, we propose a corrected score function framework to obtain a regression model of gene expression given internal time when the offset of each individual is too burdensome to determine. A feature of this framework is that it does not require the probability distribution generating offsets to be symmetric with a mean of zero. Simulation studies validate the use of this corrected score function framework for cosinor regression, which is prevalent in circadian transcriptomic studies. Illustrations with data from three circadian transcriptomic studies further demonstrate that the proposed framework consistently mitigates bias relative to using a score function that does not account for this offset.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

The Clinical Cell-Cycle Risk (CCR) score Is Associated With Metastasis After Radiation Therapy and Provides Guidance on When to Forgo Combined Androgen Deprivation Therapy With Dose-Escalated Radiation

The clinical cell-cycle risk (CCR) score, which combines the University of California, San Francisco's Cancer of the Prostate Risk Assessment (CAPRA) and the cell cycle progression (CCP) molecular score, has been validated to be prognostic of disease progression for men with prostate cancer. This study evaluated the ability of the CCR score to prognosticate the risk of metastasis in men receiving dose-escalated radiation therapy (RT) with or without androgen deprivation therapy (ADT).

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2020

Incorporating uncertainty for enhanced leaderboard scoring and ranking in data competitions

Data competitions have become a popular and cost-effective approach for crowdsourcing versatile solutions from diverse expertise. Current practice relies on the simple leaderboard scoring based on a given set of competition data for ranking competitors and distributing the prize. However, a disadvantage of this practice in many competitions is that a slight difference in the scores due to the natural variability of the observed data could result in a much larger difference in the prize amounts. In this article, we propose a new strategy to quantify the uncertainty in the rankings and scores from using different data sets that share common characteristics with the provided competition data. By using a bootstrap approach to generate many comparable data sets, the new method has four advantages over current practice. Furthermore, during the competition, it provides a mechanism for competitors to get feedback about the uncertainty in their relative ranking. After the competition, it allows the host to gain a deeper understanding of the algorithm performance and their robustness across representative data sets. It also offers a transparent mechanism for prize distribution to reward the competitors more fairly with superior and robust performance. Finally, it has the additional advantage of being able to explore what results might have looked like if competition goals evolved from their original choices. The implementation of the strategy is illustrated with a real data competition hosted by Topcoder on urban radiation search.

42 ENGINEERING↗
DOE OSTI2020

Exploit, Malware And Vulnerability Scoring Application

Exploit, Malware and Vulnerability (EMV) is a way for users to create and use their own scoring schema against various configurations they might be scoring cyber issues against. This application was created to take the EMV process and develop a GUI to accomplish this task. EMV application is customizable and configurable, interfaces with STIX objects and allows exporting scored objects.

Priest, ZacharyM↗
DOE OSTI2023

New machine learning techniques for simulation-based inference: InferoStatic nets, kernel score estimation, and kernel likelihood ratio estimation

We propose an intuitive, machine-learning approach to multiparameter inference, dubbed the InferoStatic Networks (ISN) method, to model the score and likelihood ratio estimators in cases when the probability density can be sampled but not computed directly. The ISN uses a backend neural network that models a scalar function called the inferostatic potential \varphi φ . In addition, we introduce new strategies, respectively called Kernel Score Estimation (KSE) and Kernel Likelihood Ratio Estimation (KLRE), to learn the score and the likelihood ratio functions from simulated data. We illustrate the new techniques with some toy examples and compare to existing approaches in the literature. We mention en passant some new loss functions that optimally incorporate latent information from simulations into the training procedure.

Kong, Kyoungchul↗
DOE OSTI2022

Method for Generating Expert Derived Confidence Scores

We executed a pilot demonstration of a methodology for developing a new confidence metric to help operators calibrate their trust in ML event classifiers. This confidence metric was derived from domain expert judgment and was accompanied with a qualitative description describing the reason for each confidence rating. After learning the boundaries of an ML’s performance by studying a subset of events an SME rated his confidence in the ML’s ability to classify similar events and provided an explanation for his ratings. To demonstrate this methodology, we developed our expert driven confidence scores for the ML event classifier within the ESAMS. Next, we assessed the accuracy of the human expert confidence scores relative to the ML’s uncertainty quantification scores. This report includes a description of our methodology, summary of our findings and future directions.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

SCORE (Synthesis of COnsists as Rolling Energy microgrids) (Final Technical Report)

The SCORE toolset is an open source, web-based application to assess the impact of new powering technologies on railroad performance, specifically technologies capable of both putting power into the rail (motive force) and taking power from the rail (regeneration). SCORE’s primary goal is generate trade studies to analyze different powering and train make-up options to minimize energy usage and greenhouse gas generation. At the core of generating these trade spaces is calculating the optimal powering policy for the train given the makeup of the train, the route, and time constraints. This paper presents details on the algorithms used in SCORE to compute this powering policies that is fast and accurate, discusses its implementation in an Energy-Longitudinal Train Dynamics (E-LTD) model, compares it to naïve approaches, and demonstrates its use across a variety of train/route pairs.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2023

Characterizing Families of Spectral Similarity Scores and Their Use Cases for Gas Chromatography–Mass Spectrometry Small Molecule Identification

Metabolomics provides a unique snapshot into the world of small molecules and the complex biological processes that govern the human, animal, plant, and environmental ecosystems encapsulated by the One Health modeling framework. However, this “molecular snapshot” is only as informative as the number of metabolites confidently identified within it. The spectral similarity (SS) score is traditionally used to identify compound(s) in mass spectrometry approaches to metabolomics, where spectra are matched to reference libraries of candidate spectra. Unfortunately, there is little consensus on which of the dozens of available SS metrics should be used. This lack of standard SS score creates analytic uncertainty and potentially leads to issues in reproducibility, especially as these data are integrated across other domains. In this work, we use metabolomic spectral similarity as a case study to showcase the challenges in consistency within just one piece of the One Health framework that must be addressed to enable data science approaches for One Health problems. Here, using a large cohort of datasets comprising both standard and complex datasets with expert-verified truth annotations, we evaluated the effectiveness of 66 similarity metrics to delineate between correct matches (true positives) and incorrect matches (true negatives). We additionally characterize the families of these metrics to make informed recommendations for their use. Our results indicate that specific families of metrics (the Inner Product, Correlative, and Intersection families of scores) tend to perform better than others, with no single similarity metric performing optimally for all queried spectra. This work and its findings provide an empirically-based resource for researchers to use in their selection of similarity metrics for GC-MS identification, increasing scientific reproducibility through taking steps towards standardizing identification workflows.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

New Machine Learning Techniques for Simulation-Based Inference: InferoStatic Nets, Kernel Score Estimation, and Kernel Likelihood Ratio Estimation

We propose an intuitive, machine-learning approach to multiparameter inference, dubbed the InferoStatic Networks (ISN) method, to model the score and likelihood ratio estimators in cases when the probability density can be sampled but not computed directly. The ISN uses a backend neural network that models a scalar function called the inferostatic potential $\varphi$. In addition, we introduce new strategies, respectively called Kernel Score Estimation (KSE) and Kernel Likelihood Ratio Estimation (KLRE), to learn the score and the likelihood ratio functions from simulated data. We illustrate the new techniques with some toy examples and compare to existing approaches in the literature. We mention en passant some new loss functions that optimally incorporate latent information from simulations into the training procedure.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Application of Banking Scoring and Rating for Coherent Risk Measures in Electricity Systems ABSCORES

This project developed a framework for asset and system risk management that can be incorporated into current electricity system operations to improve economic efficiency and establish an Electric Assets Risk Bureau. We leveraged scoring and ratings from banking and financial institutions alongside current optimization methods in dispatching power systems to help system operators and electricity markets schedule resources. This approach is based on the observation that there are major discrepancies between the power scheduled by a system operator and the actual power generated/consumed. These discrepancies—exacerbated by unplanned contingencies (e.g., natural disasters)—are caused by multiple factors, including the different financial, environmental and risk preferences of power producers, consumers, and aggregators. We developed a framework that counteracts two failures in electricity system operations: imperfect information and missing markets for products. The technical approach included five tasks. Tasks 1 and 2 supported the development of risk scores at the asset level with historical data collected for this project. Tasks 3, 4, and 5 incorporated scoring into decision-making at the system level. The proposed effort achieved PERFORM's Program Objectives because the proposed outputs and algorithms do not exist in the electricity industry and are an innovative approach to managing risk. Since the acknowledged need to better assess and act upon risk profiles for grid assets has not been met by the industry, this project will also impact ARPA-E's Mission Areas, including improving energy efficiency and giving the U.S. a technological lead in advanced energy technologies.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2021

A time-varying vulnerability index for COVID-19 in New Mexico, USA using generalized propensity scores

The coronavirus disease (COVID-19) pandemic has highlighted systemic inequities in the United States and resulted in a larger burden of negative social outcomes for marginalized communities. New Mexico, a state in the southwestern US, has a unique population with a large racial minority population and a high rate of poverty that may make communities more vulnerable to negative social outcomes from COVID-19. To identify which communities may be at the highest relative risk, we created a county-level vulnerability index. After the first COVID-19 case was reported in New Mexico on March 11, 2020, we fit a generalized propensity score model that incorporates sociodemographic factors to predict county-level viral exposure and thus, the generic risk to negative social outcomes such as unemployment or mental health impacts. We used four static sociodemographic covariates important for the state of New Mexico—population, poverty, household size, and minority population—and weekly cumulative case counts to iteratively run our model each week and normalize the exposure score to create a time-varying vulnerability index. We found the relative vulnerability between counties varied in the first eight weeks from the initial COVID-19 case before stabilizing. This framework for creating a location-specific vulnerability index in response to an ongoing disaster may be used as a quick, deployable metric to inform health policy decisions such as allocating state resources to the county level.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Ice Phase Classification Made Easy with Score-Based Denoising

Accurate identification of ice phases is essential for understanding various physicochemical phenomena. However, such classification for structures simulated with molecular dynamics is complicated by the complex symmetries of ice polymorphs and thermal fluctuations. For this purpose, both traditional order parameters and data-driven machine learning approaches have been employed, but they often rely on expert intuition, specific geometric information, or large training data sets. In this work, we present an unsupervised phase classification framework that combines a score-based denoiser model with a subsequent model-free classification method to accurately identify ice phases. Further, the denoiser model is trained on perturbed synthetic data of ideal reference structures, eliminating the need for large data sets and labeling efforts. The classification step utilizes the smooth overlap of atomic position (SOAP) descriptors as the atomic fingerprint, ensuring Euclidean symmetries and transferability to various structural systems. Our approach achieves a remarkable 100% accuracy in distinguishing ice phases of test trajectories using only seven ideal reference structures of ice phases as model inputs. This demonstrates the generalizability of the score-based denoiser model in facilitating phase identification for complex molecular systems. The proposed classification strategy can be broadly applied to investigate structural evolution and phase identification for a wide range of materials, offering new insights into the fundamental understanding of water and other complex systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

A Unified Analytical Method Greenness Score ( uAMGS ) Quantifies How Microscopic Imaging Is Greener Than Conventional Liquid Chromatography

Green chemistry is a set of principles for assessing, developing, and implementing methods that are safer, more efficient, and less detrimental to the environment. The analytical method greenness score (AMGS) is one of many metrics that attempt to evaluate traditional liquid chromatography (LC) based on the energy consumption of the instrument and the safety, health risks, and environmental impact of the solvents employed. Unfortunately, in practice, the AMGS is primarily focused on traditional separation methods in the pharmaceutical industry and is not amenable to cutting-edge separation science, including miniaturization. To broaden this scope, the unified Analytical Method Greenness Score (uAMGS) is presented here, which clarifies and expands on the underlying mathematics and incorporates both dimensional and uncertainty analysis, enabling its application to a broader range of analytical techniques. The uAMGS is used to compare the greenness of two distinct methods: single-molecule microscopy (SMM) and high-performance liquid chromatography (HPLC), which were used to collect equivalent data. uAMGS determines that SMM is significantly greener than HPLC due primarily to decreased solvent consumption. Overall, the uAMGS should allow chemists ranging from undergraduates to industrial PhDs to assess the greenness of a wide range of separations.

chemical separations↗
DOE OSTI2026

Development and Validation of the Near-Miss Safety Score (NMSS) Framework for Heavy-Duty Vehicle Safety Assessment

Heavy-duty commercial vehicles present unique safety challenges due to their size, articulation dynamics, and operational complexity. As Advanced Driver Assistance Systems (ADAS) and Automated Driving Systems (ADS) become more common in Class 8 tractor-trailers, traditional crash-based metrics are no longer sufficient to evaluate safety performance. This study introduces the Near-Miss Safety Score (NMSS)—a quantitative, physics-informed framework developed as a leading indicator of safety for advanced commercial vehicle technologies. NMSS quantifies how close a vehicle or operator comes to a collision or safety-critical event by integrating vehicle kinematics (relative distance, velocity, and acceleration) with driver or system response latency and time-to-collision. A modifier function adjusts the base score for vehicle-specific and environmental factors such as trailer articulation, load distribution, braking condition, and roadway environment. The framework enables systematic evaluation of ADAS/ADS performance under a range of operational and degraded conditions. By capturing near-miss dynamics rather than relying on crash data, NMSS provides a proactive approach to risk assessment, accelerates technology validation, and enhances interpretability for regulators and fleet operators. The proposed NMSS was validated using data collected from a motorcoach platform, demonstrating the framework’s applicability to heavy-duty safety evaluation and performance benchmarking. Results and key insights are presented in this paper.

Siekmann, Adam [ORNL] (ORCID:0000000284653935)↗
DOE OSTI2022

Realistic galaxy image simulation via score-based generative models

ABSTRACT We show that a denoising diffusion probabilistic model (DDPM), a class of score-based generative model, can be used to produce realistic mock images that mimic observations of galaxies. Our method is tested with Dark Energy Spectroscopic Instrument (DESI) grz imaging of galaxies from the Photometry and Rotation curve OBservations from Extragalactic Surveys (PROBES) sample and galaxies selected from the Sloan Digital Sky Survey. Subjectively, the generated galaxies are highly realistic when compared with samples from the real data set. We quantify the similarity by borrowing from the deep generative learning literature, using the ‘Fréchet inception distance’ to test for subjective and morphological similarity. We also introduce the ‘synthetic galaxy distance’ metric to compare the emergent physical properties (such as total magnitude, colour, and half-light radius) of a ground truth parent and synthesized child data set. We argue that the DDPM approach produces sharper and more realistic images than other generative methods such as adversarial networks (with the downside of more costly inference), and could be used to produce large samples of synthetic observations tailored to a specific imaging survey. We demonstrate two potential uses of the DDPM: (1) accurate inpainting of occluded data, such as satellite trails, and (2) domain transfer, where new input images can be processed to mimic the properties of the DDPM training set. Here we ‘DESI-fy’ cartoon images as a proof of concept for domain transfer. Finally, we suggest potential applications for score-based approaches that could motivate further research on this topic within the astronomical community.

79 ASTRONOMY AND ASTROPHYSICS↗