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DOE OSTI2026

Finding the missing pieces: filling gaps that impede the translation of omics data into models

High-throughput omics technologies such as DNA sequencing have made the sequencing and computational assembly of microbial genomes recovered from the environment relatively routine. Computational inference of the protein products encoded by these genomes, and the associated biochemical functions, should enable the accurate prediction and modeling of microbial metabolism, organismal interactions, and ecosystem processes. However, a lack of scalable, probabilistic protein annotation tools limits the full potential of modeling for understanding the metabolism and biogeochemical cycles of microbial communities. Our approach to improve inference of protein annotations and metabolic models relied on learning from and emulating expert manual curation, leveraging software engineering and data science best practices to scale up the throughput and accuracy of annotations and metabolic model construction, building software to objectively evaluate different annotation strategies, and more closely linking the protein annotation and metabolic model inference process. Outcomes of this research include several improved or new computational tools, including DRAM (Distilled and Refined Annotation of Metabolism) for annotating microbial genomes with protein function and metabolic traits, CAMPER (Curated Annotations for Microbial Polyphenol Enzymes and Reactions) for annotating key polyphenol metabolisms, EC-Bench for comprehensive and unbiased benchmarking of annotation tools, and several apps available via the DOE Systems Biology Knowledgebase (KBase) for building genome-scale metabolic models. We demonstrate that these tools allow us to scalably annotate and understand thousands of genomes for microbial communities from a variety of systems and test cases, including rivers, thawing permafrost, and gut microbiomes. All of these computational tools are available as open-source software, with most broadly and easily accessible to the scientific community via KBase apps.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2021

Topic Modeling Tool for PeTaL (Periodic Table of Life)

A topic modeling tool is constructed for the purpose of providing insights from biology to the engineer within the framework of PeTaL (Periodic Table of Life). The machine learning text mining tools–latent Dirichlet allocation (LDA) and nonnegative matrix factorization (NMF) with Kullback-Leibler (KL) divergence—are used to provide topic clusters to the user. Topic clusters are the underlying themes of a paper. For the text modeling problem, NMF-KL is the equivalent of probabilistic latent semantic analysis. Both LDA and NMF-KL are top-performing modeling tools. These tools are used to identify biological specimens relevant to the user. Various organisms solve a particular survival problem in nature differently. The topic clusters allow people without domain expertise to find these cross-topic themes in the body of documents and then branch out and examine papers whose target organisms solve the engineer’s problem. Abstracts from the Journal of Experimental Biology were used as input for the clustering tool in addition to a curated set of articles for validation. The tool is able to accept alternate input sources.

Machine learning↗

DOE OSTI2025

AUTOMATIC GENERATION OF EVENT TREES AND FAULT TREES: A MODEL-BASED APPROACH

In the past few decades, increasing complexity in modern engineering systems has been driven by the integration of a large number of components and by the fact that the system operations involve many disciplines (e.g., thermal-hydraulics, plant operations, cyber-security). Current safety/reliability modeling approaches to such systems are labor intensive, difficult to learn, and rely heavily on simplistic Boolean logic to depict failure propagation and accident progression. While these methods serve well for simple systems (i.e., linear causal systems with limited small inter- and intra-system interactions), their results are difficult to verify when modeling complex systems (typically performed through the extensive use of modeling assumptions). The development of new methods is addressed to meet these challenges through a model-based system engineering (MBSE) lens. Under MBSE philosophy, every aspect of the system (form or function) is represented by a model that completely characterizes its architecture or behavior. MBSE approach greatly improves the management of design, analysis and verification of complex systems. An integration of Dynamic Probabilistic Risk Assessment (DPRA) methods with MBSE models is proposed to perform safety/reliability analyses of engineering systems. In particular, MBSE representation of the system (performed using Systems Modeling Language [SysML]) is coupled with DPRA methods to automatically generate event trees and fault trees.

97 - MATHEMATICS AND COMPUTING↗

NASA NTRS2012

A Systems Modeling Approach for Risk Management of Command File Errors

The main cause of commanding errors is often (but not always) due to procedures. Either lack of maturity in the processes, incompleteness of requirements or lack of compliance to these procedures. Other causes of commanding errors include lack of understanding of system states, inadequate communication, and making hasty changes in standard procedures in response to an unexpected event. In general, it's important to look at the big picture prior to making corrective actions. In the case of errors traced back to procedures, considering the reliability of the process as a metric during its' design may help to reduce risk. This metric is obtained by using data from Nuclear Industry regarding human reliability. A structured method for the collection of anomaly data will help the operator think systematically about the anomaly and facilitate risk management. Formal models can be used for risk based design and risk management. A generic set of models can be customized for a broad range of missions.

probabilistic risk↗

NASA NTRS2011

A Model-Based Prognostics Approach Applied to Pneumatic Valves

Within the area of systems health management, the task of prognostics centers on predicting when components will fail. Model-based prognostics exploits domain knowledge of the system, its components, and how they fail by casting the underlying physical phenomena in a physics-based model that is derived from first principles. Uncertainty cannot be avoided in prediction, therefore, algorithms are employed that help in managing these uncertainties. The particle filtering algorithm has become a popular choice for model-based prognostics due to its wide applicability, ease of implementation, and support for uncertainty management. We develop a general model-based prognostics methodology within a robust probabilistic framework using particle filters. As a case study, we consider a pneumatic valve from the Space Shuttle cryogenic refueling system. We develop a detailed physics-based model of the pneumatic valve, and perform comprehensive simulation experiments to illustrate our prognostics approach and evaluate its effectiveness and robustness. The approach is demonstrated using historical pneumatic valve data from the refueling system.

Daigle, Matthew J.↗

NASA NTRS1981

The application of probabilistic design theory to high temperature low cycle fatigue

Metal fatigue under stress and thermal cycling is a principal mode of failure in gas turbine engine hot section components such as turbine blades and disks and combustor liners. Designing for fatigue is subject to considerable uncertainty, e.g., scatter in cycles to failure, available fatigue test data and operating environment data, uncertainties in the models used to predict stresses, etc. Methods of analyzing fatigue test data for probabilistic design purposes are summarized. The general strain life as well as homo- and hetero-scedastic models are considered. Modern probabilistic design theory is reviewed and examples are presented which illustrate application to reliability analysis of gas turbine engine components.

Wirsching, P. H.↗

NASA NTRSDate not supplied

IMPACT, a Tool Suite for Crew Health and Performance System Trade Analyses and Decision Support - Status of Development

Mission planners, systems engineers, and clinicians that support crew health and performance face very difficult choices on upcoming exploration missions. Given that there will be a heavily constrained mass and volume allocation for a medical system on these missions, what medical capability should be manifested to minimize both medical risk and mission risk? Given that not all promising research and technology proposals can be funded, how can proposals be prioritized so that those funded research investments produce the maximum benefit in reducing overall medical risk? The Informing Mission Planning via Analysis of Complex Tradespaces (IMPACT) project seeks to answer these kinds of questions and others to support upcoming exploration missions. IMPACT enables risk-informed and evidence-based trade space analysis for future space vehicles, missions, and systems. This presentation will discuss the long-term HRP and ExMC vision for the larger ecosystem of tools, which include an updated medical database, consisting of an Evidence Library for medical conditions and a medical item database (MedID) for medical resources, dynamic Probabilistic Risk Assessment (PRA) capabilities, System Modeling Language (SysML) models, and contextual data visualizations of output data. IMPACT is the result of a multi-center collaborative effort. The trade space analyses performed by IMPACT can directly inform mission, vehicle, and habitat development by quantifying medical risk, given a design reference mission, crew attributes and a set of medical capabilities. This presentation will update the audience on the development status of the tool suite as it nears its System Acceptance Review (SAR). It will review IMPACT’s constituent parts, briefly discuss typical outputs and outline the plans for transitioning to operations, currently scheduled for later in FY23. Recent development successes on the IMPACT project include the integration of the Medical Extensible Dynamic Probabilistic Risk Assessment Tool (MEDPRAT) v2.0 to accommodate segmented missions with multiple carriers and medical systems, full onboarding of the IMPACT Medical Database (IMPACT-MD), clustering medical resources and skills into medical capabilities and mutually-dependent bundles, and the ability to perform trade analyses on different medical sets, different design reference missions (DRM), with different crew complements and extra-vehicular activity (EVA) schedule.

IMPACT↗

NASA NTRSDate not supplied

Impact, A Tool Suite for Crew Health and Performance System Trade Analyses and Decision to Support - Transition to Operations

Mission planners, systems engineers, and clinicians that support crew health and performance face very difficult choices on upcoming exploration missions. Given that there will be a heavily constrained mass and volume allocation for a medical system on these missions, what medical capability should be manifested to minimize both medical risk and mission risk? Given that not all promising research and technology proposals can be funded, how can proposals be prioritized so that those funded research investments produce the maximum benefit in reducing overall medical risk? The Informing Mission Planning via Analysis of Complex Tradespaces (IMPACT) project seeks to answer these kinds of questions and others to support upcoming exploration missions. IMPACT enables risk-informed and evidence-based trade space analysis for future space vehicles, missions, and systems. This presentation will discuss the long-term HRP and ExMC vision for the larger ecosystem of tools, which include an updated medical database, consisting of an Evidence Library for medical conditions and a medical item database (MedID) for medical resources, dynamic Probabilistic Risk Assessment (PRA) capabilities, System Modeling Language (SysML) models, and contextual data visualizations of output data. IMPACT is the result of a multi-center collaborative effort. The trade space analyses performed by IMPACT can directly inform mission, vehicle, and habitat development by quantifying medical risk, given a design reference mission, crew attributes and a set of medical capabilities. This presentation will update the audience on the development status of the IMPACT tool suite as it comes out of its System Acceptance Review (SAR) and nears Transition to Operations (TTO). It will review IMPACT’s constituent parts, briefly discuss typical outputs, and outline the plans for transitioning to operations, currently scheduled for later in FY24. Recent development successes on the IMPACT project include the integration of the Medical Extensible Dynamic Probabilistic Risk Assessment Tool (MEDPRAT) v2.0 to accommodate segmented missions with multiple carriers and medical systems, full onboarding of the IMPACT Medical Database (IMPACT-MD), clustering medical resources and skills into medical capabilities and mutually-dependent bundles, verification of IMPACT-MD, and the ability to perform trade analyses on different medical sets, different design reference missions (DRM), with different crew complements and extra-vehicular activity (EVA) schedules.

IMPACT↗

NASA NTRSDate not supplied

IMPACT, A Tool Suite for Crew Health and Performance System Trade Analyses and Decision Support- Transition to Operations

Mission planners, systems engineers, and clinicians that support crew health and performance face very difficult choices on upcoming exploration missions. Given that there will be a heavily constrained mass and volume allocation for a medical system on these missions, what medical capability should be manifested to minimize both medical risk and mission risk? Given that not all promising research and technology proposals can be funded, how can proposals be prioritized so that those funded research investments produce the maximum benefit in reducing overall medical risk? The Informing Mission Planning via Analysis of Complex Tradespaces (IMPACT) project seeks to answer these kinds of questions and others to support upcoming exploration missions. IMPACT enables risk-informed and evidence-based trade space analysis for future space vehicles, missions, and systems. This presentation will discuss the long-term HRP and ExMC vision for the larger ecosystem of tools, which include an updated medical database, consisting of an Evidence Library for medical conditions and a medical item database (MedID) for medical resources, dynamic Probabilistic Risk Assessment (PRA) capabilities, System Modeling Language (SysML) models, and contextual data visualizations of output data. IMPACT is the result of a multi-center collaborative effort. The trade space analyses performed by IMPACT can directly inform mission, vehicle, and habitat development by quantifying medical risk, given a design reference mission, crew attributes and a set of medical capabilities. This presentation will update the audience on the development status of the IMPACT tool suite as it comes out of its System Acceptance Review (SAR) and nears Transition to Operations (TTO). It will review IMPACT’s constituent parts, briefly discuss typical outputs, and outline the plans for transitioning to operations, currently scheduled for later in FY24. Recent development successes on the IMPACT project include the integration of the Medical Extensible Dynamic Probabilistic Risk Assessment Tool (MEDPRAT) v2.0 to accommodate segmented missions with multiple carriers and medical systems, full onboarding of the IMPACT Medical Database (IMPACT-MD), clustering medical resources and skills into medical capabilities and mutually-dependent bundles, verification of IMPACT-MD, and the ability to perform trade analyses on different medical sets, different design reference missions (DRM), with different crew complements and extra-vehicular activity (EVA) schedules.

IMPACT↗

NASA NTRS2023

Risk Assessment for Asteroid Impact Threat Scenarios

Asteroid impacts can cause a wide range of damage through multiple potential hazards, from localized blast waves or thermal radiation, to tsunami inundation, to global climatic effects. The level of risk posed by these hazards depends not only upon their extent and severity, but also upon the likelihood of the various damage ranges. Some consequences may be more moderate but very likely, while others may be unlikely but catastrophic. Evaluating the risk from these hazards involves substantial uncertainties across all aspects of the problem, including the properties of the asteroid itself, the specifics of its entry, and the complex high-energy damage physics involved. NASA’s Asteroid Threat Assessment Project performs Probabilistic Asteroid Impact Risk (PAIR) assessments that use fast-running entry and hazard models to evaluate millions of impact cases representing the distributions of these many uncertain parameters. This paper presents current probabilistic asteroid impact risk assessment modeling tools and approaches used for evaluating specific asteroid impact threat cases. We give an overview of the current PAIR model used to support impact threat scenarios and discuss some of the key applications of these assessment in supporting response decisions and planetary defense preparedness. We then present the results and key findings from the recent 2023 PDC hypothetical impact exercise as an example of the primary types of risk results and metrics being developed to inform and support those mitigation and response decisions.

SMD↗

DOE OSTI2025

Enhancing Gaussian Process Surrogates for Optimization and Posterior Approximation via Random Exploration

This paper proposes novel noise-free Bayesian optimization strategies that rely on a random exploration step to enhance the accuracy of Gaussian process surrogate models. The new algorithms retain the ease of implementation of the classical GP-UCB algorithm, but the additional random exploration step accelerates their convergence, nearly achieving the optimal convergence rate. Furthermore, to facilitate Bayesian inference with intractable likelihoods, we propose to utilize optimization iterates for maximum a posteriori estimation to build a Gaussian process surrogate model for the unnormalized log-posterior density. We provide bounds for the Hellinger distance between the true and the approximate posterior distributions in terms of the number of design points. We demonstrate the effectiveness of our Bayesian optimization algorithms in nonconvex benchmark objective functions, in a machine learning hyperparameter tuning problem, and in a black-box engineering design problem. The effectiveness of our posterior approximation approach is demonstrated in two Bayesian inference problems for parameters of dynamical systems.

Bayesian inference↗

DOE OSTI2026

Model-based economic analysis under uncertainty for PFAS treatment by granular activated carbon and ion exchange technologies

Recent drinking water regulations have imposed the need for per- and polyfluoroalkyl substances (PFAS) remediation. In response, treatment facilities may be required to retrofit existing treatment schemes to treat PFAS below maximum contaminant levels (MCLs). Adsorption technologies such as granular activated carbon (GAC) and ion exchange (IX) have been demonstrated to be effective; however, there are limited techno-economic metrics available which provide guidance on technology selection and design for diverse PFAS-containing source water conditions. Process systems engineering (PSE) tools which can traditionally perform these analyses are hindered by the data availability, model validity, and understanding of treatment phenomena for emerging contaminants. This work employs published data regressions, statistical models, process models, techno-economic analyses, and other process systems tools in a model-based uncertainty framework to consider the limitations of emerging contaminant research. Through this analysis framework, economic results are provided as probabilistic distributions based on the uncertainty of the models and diverse conditions that treatment facilities experience.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1987

Probabilistic SSME blades structural response under random pulse loading

The purpose is to develop models of random impacts on a Space Shuttle Main Engine (SSME) turbopump blade and to predict the probabilistic structural response of the blade to these impacts. The random loading is caused by the impact of debris. The probabilistic structural response is characterized by distribution functions for stress and displacements as functions of the loading parameters which determine the random pulse model. These parameters include pulse arrival, amplitude, and location. The analysis can be extended to predict level crossing rates. This requires knowledge of the joint distribution of the response and its derivative. The model of random impacts chosen allows the pulse arrivals, pulse amplitudes, and pulse locations to be random. Specifically, the pulse arrivals are assumed to be governed by a Poisson process, which is characterized by a mean arrival rate. The pulse intensity is modelled as a normally distributed random variable with a zero mean chosen independently at each arrival. The standard deviation of the distribution is a measure of pulse intensity. Several different models were used for the pulse locations. For example, three points near the blade tip were chosen at which pulses were allowed to arrive with equal probability. Again, the locations were chosen independently at each arrival. The structural response was analyzed both by direct Monte Carlo simulation and by a semi-analytical method.

Shiao, Michael↗

NASA NTRSDate not supplied

Impact, a Tool Suite for Crew Health and Performance System Trade Analyses and Decision Support - Status of Development

Mission planners, systems engineers, and clinicians that support crew health and performance face very difficult choices on upcoming exploration missions. Given that there will be a heavily constrained mass and volume allocation for a medical system on these missions, what medical capability should be manifested to minimize both medical risk and mission risk? Given that not all promising research and technology proposals can be funded, how can proposals be prioritized so that those funded research investments produce the maximum benefit in reducing overall medical risk? The Informing Mission Planning via Analysis of Complex Tradespaces (IMPACT) project seeks to answer these kinds of questions and others to support upcoming exploration missions. IMPACT enables risk-informed and evidence-based trade space analysis for future space vehicles, missions, and systems. This presentation will discuss the long-term HRP and ExMC vision for the larger ecosystem of tools, which include an updated medical database (consisting of an Evidence Library for medical conditions and a medical item database (MedID) for medical resources), dynamic Probabilistic Risk Assessment (PRA) capabilities, System Modeling Language (SysML) models, and contextual data visualizations of output data. IMPACT is the result of a multi-center collaborative effort. The trade space analyses performed by IMPACT can directly inform mission, vehicle, and habitat development by quantifying medical risk, given a design reference mission, crew attributes and a set of medical capabilities. This presentation will update the audience on the development status of the tool suite, its constituent parts and the plans for when it will deploy as an operational product, currently scheduled for the end of FY22. Recent development successes on the IMPACT project include the ability to cluster medical resources into medical capabilities and mutually-dependent bundles, the ability to perform trade analyses on different medical sets, different DRMs, and different crew complements, and the ability to specify mission segments as periods of time assigned to one or more members of the crew during which unique mission events occur (e.g., extravehicular activities, surface operations, gravity well adaptations, etc.). IMPACT is gearing up for its verification and validation phase to compile the data package necessary for a successful Transition to Operations (TtO), per the guidance in NPR 8900.1B .

IMPACT↗

DOE OSTI2025

Probabilistic Predictions for Fastener Failure in the Sandia Mechanics Challenge Using the Discrete-Direct Uncertainty Quantification Approach

This paper documents the blind and post-blind analysis predictions for the 2023 Sandia Mechanics Challenge (SMC), which involved predicting the behavior of a threaded fastener joint structure subjected to shock loading. Utilizing repeat sets of fastener calibration data from various experimental configurations including tension, double shear, and joint tension, we developed a library of calibrated models which were propagated through the application model using the Discrete-Direct (DD) uncertainty quantification (UQ) approach. Although the initial blind predictions did not incorporate spare-sample processing to quantify fastener failure probabilities, the analyses yielded reasonable conclusions aligned with experimental results. In the post-blind analysis phase, we focused on enhancing the fidelity of the aluminum constitutive model and innovating the DD approach to obtain probabilistic predictions for fastener failure, particularly when quantities of interest (QoIs) approach their bounds. The improved aluminum model captures the behavior of the cantilever under shock loading more accurately, predicting both partial and complete cracks, although it tends to underpredict failure propagation. The enhanced DD approach facilitates probabilistic predictions that reflect the interdependent failure mechanisms of the fasteners and the cantilever, revealing that while certain fasteners are more likely to fail, the failure does not necessarily follow a progressive pattern. Overall, the post-blind analyses significantly improved the predictive capabilities of the model, providing valuable insights into the SMC application and establishing a robust foundation for informed engineering decisions. The methodology demonstrates a cost-effective and extensible approach suitable for a wide range of applications, highlighting the importance of uncertainty quantification to provide context for engineering decision making.

42 ENGINEERING↗

NASA NTRS2022

Scheduling For Urban Air Mobility Using Safe Learning

This work considers the scheduling problem for Urban Air Mobility (UAM) vehicles travelling between origin-destination pairs with both hard and soft trip deadlines. Each route is described by a discrete probability distribution over trip completion times (or delay) and over interarrival times of requests (or demand) for the route along with a fixed hard or soft deadline. Soft deadlines carry a cost that is incurred when the deadline is missed. An online, safe scheduler is developed that ensures that hard deadlines are never missed and that average cost of missing soft deadlines is minimized. The system is modelled as a Markov Decision Process (MDP) and safe model based learning is used to find the probabilistic distributions over route delays and demand. Monte Carlo Tree Search (MCTS) Earliest Deadline First (EDF) is used to safely explore the learned models in an online fashion and develop a near-optimal non-preemptive scheduling policy. These results are compared with Value Iteration (VI) and MCTS (Random) scheduling solutions.

Urban Air Mobility↗

NASA NTRSDate not supplied

Scheduling for Urban Air Mobility using Safe Learning

Urban Air Mobility↗

DOE OSTI2026

Multidimensional Distributional Neural Network Output Demonstrated in Super‐Resolution of Surface Wind Speed

Accurate quantification of uncertainty in neural network predictions remains a central challenge for scientific applications involving high-dimensional, correlated data. While existing methods capture either aleatoric or epistemic uncertainty, few offer closed-form, multidimensional distributions that preserve spatial correlation while remaining computationally tractable. In this work, we present a framework for training neural networks with a multidimensional Gaussian loss, generating a closed-form predictive distribution over outputs informed by non-identically distributed training data. Our approach captures aleatoric uncertainty by iteratively estimating the means and covariance matrices, and is demonstrated on a super-resolution example out-of-training-sample. We leverage a Fourier representation of the covariance matrix to stabilize network training and preserve spatial correlation. We introduce a novel regularization strategy—referred to as information sharing—that interpolates between image-specific and global covariance estimates, enabling convergence of the super-resolution downscaling network trained on image-specific distributional loss functions. This framework allows for efficient sampling, explicit correlation modeling, and extensions to more complex distribution families all without disrupting prediction performance. We demonstrate the method on a surface wind speed downscaling task and discuss its broader applicability to uncertainty-aware prediction in scientific models.

17 WIND ENERGY↗