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DOE OSTI2025

Energy metric prediction for double insertion mutants via the RoseNet deep learning framework

Studying the structural and functional implications of protein mutations is an important task in computational biology and bioinformatics. We leverage our previously proposed RoseNet neural network architecture to predict energy metrics of proteins with double amino acid insertions or deletions (InDels). We train models on previously generated benchmark datasets containing the exhaustive double InDel mutations for three proteins, as well as an additional three proteins for which ∼145k random mutants, each with two InDels, have been generated. We expand on our previous work by evaluating three additional proteins and analyzing domain features that impact the prediction capabilities of RoseNet. These features include InDels into secondary structures and the solvent accessible surface area (SASA) scores of the residues. We uncover further evidence to support that RoseNet has a higher proficiency of generalizing to unseen residue combinations than unseen insertion positions. We also observe that RoseNet produces higher-quality predictions when inserting into a β-sheet over an α-helix. Additionally, when the insertions fall in an area of high SASA, RoseNet often displays better performance than inserting into areas of low SASA.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

A gated graph transformer for protein complex structure quality assessment and its performance in CASP15

Abstract Motivation Proteins interact to form complexes to carry out essential biological functions. Computational methods such as AlphaFold-multimer have been developed to predict the quaternary structures of protein complexes. An important yet largely unsolved challenge in protein complex structure prediction is to accurately estimate the quality of predicted protein complex structures without any knowledge of the corresponding native structures. Such estimations can then be used to select high-quality predicted complex structures to facilitate biomedical research such as protein function analysis and drug discovery. Results In this work, we introduce a new gated neighborhood-modulating graph transformer to predict the quality of 3D protein complex structures. It incorporates node and edge gates within a graph transformer framework to control information flow during graph message passing. We trained, evaluated and tested the method (called DProQA) on newly-curated protein complex datasets before the 15th Critical Assessment of Techniques for Protein Structure Prediction (CASP15) and then blindly tested it in the 2022 CASP15 experiment. The method was ranked 3rd among the single-model quality assessment methods in CASP15 in terms of the ranking loss of TM-score on 36 complex targets. The rigorous internal and external experiments demonstrate that DProQA is effective in ranking protein complex structures. Availability and implementation The source code, data, and pre-trained models are available at https://github.com/jianlin-cheng/DProQA.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Probabilistic Solar Power Forecasting Using Bayesian Model Averaging

There is rising interest in probabilistic forecasting to mitigate risks from solar power uncertainty, but the numerical weather prediction (NWP) ensembles readily available to system operators are often biased and underdispersed. We propose a Bayesian model averaging (BMA) post-processing method suitable for forecasting power from utility-scale photovoltaic (PV) plants at multiple time horizons up to at least the day-ahead timescale. BMA is a kernel dressing technique for NWP ensembles in which the forecast is a weighted sum of member-specific probability density functions. We tailor BMA for utility-scale PV forecasting by modeling power clipping at the AC inverter rating and advance the theory of BMA with a new beta kernel parameterization that accommodates theoretical constraints not previously addressed. BMA is demonstrated for a case study of 11 utility-scale PV plants in Texas, forecasting at hourly resolution for the complete year 2018. BMA's mixture-model approach mitigates underdispersion of the raw ensemble to significantly improve forecast calibration, while consistently outperforming an ensemble model output statistics (EMOS) parametric approach from the literature. At 4-hour lead time, the BMA post-processing achieves continuous ranked probability skill scores of 2--36% over the raw ensemble, with consistent performance at multiple lead times suitable for power system operations.

14 SOLAR ENERGY↗

DOE OSTI2021

AutoAtlas: Neural Network for 3D Unsupervised Partitioning and Representation Learning

Here we present a novel neural network architecture called AutoAtlas for fully unsupervised partitioning and representation learning of 3D brain Magnetic Resonance Imaging (MRI) volumes. AutoAtlas consists of two neural network components: one neural network to perform multi-label partitioning based on local texture in the volume, and a second neural network to compress the information contained within each partition. We train both of these components simultaneously by optimizing a loss function that is designed to promote accurate reconstruction of each partition, while encouraging spatially smooth and contiguous partitioning, and discouraging relatively small partitions. We show that the partitions adapt to the subject specific structural variations of brain tissue while consistently appearing at similar spatial locations across subjects. AutoAtlas also produces very low dimensional features that represent local texture of each partition. We demonstrate prediction of metadata associated with each subject using the derived feature representations and compare the results to prediction using features derived from FreeSurfer anatomical parcellation. Since our features are intrinsically linked to distinct partitions, we can then map values of interest, such as partition-specific feature importance scores onto the brain for visualization.

42 ENGINEERING↗

DOE OSTI2025

JGI-Trichoderma v1.0

There is a series of Python and bash scripts to parse genomics datasets used to evaluate the coevolution of gene families and the feature importance of gene families using an SVM classifier. - Cover analysis: takes a list of single-copy genes in a set of genomes, aligns and builds the gene trees to determine if two gene families have a signature of covariation with one another. It parses the files to run phykit cover script described here: https://jlsteenwyk.com/PhyKIT/usage/index.html - SVM-classifier: This Python script is an SVM-based genomic classifier designed for biological data analysis. It combines machine learning with feature selection to identify important genomic markers and classify biological samples. Core Functionality: The script uses Support Vector Machines from scikit-learn to classify genomic data, incorporating SelectKBest for automated feature selection and leave-one-out cross-validation for performance assessment. It operates in multiple modes: feature ranking, optimal combination discovery, and sample prediction. Primary Applications: Genomic sample classification and biomarker discovery Feature importance analysis in high-dimensional biological datasets Prediction of sample categories based on genomic profiles Research applications requiring robust classification of biological data Key Advantages: High-dimensional handling: SVMs excel with genomic data's typical high feature-to-sample ratios Integrated feature selection: Reduces noise and computational overhead while identifying key markers Probability estimation: Provides confidence scores essential for biological interpretation Validation robustness: Leave-one-out cross-validation ensures reliable performance metrics Operational flexibility: Multiple analysis modes support different research phases from exploration to prediction

Stecca Steindorff, Andrei [Lawrence Berkeley Natio↗

DOE OSTI2023

Understanding the Uncertainty in the Technical Performance Level Assessment for Wave Energy

In recent years, the design and development of wave energy converters (WECs) has been explored with intense interest, with highly varying design concepts emerging globally across both research enterprises and industry. The design space for WECs is vast - many concepts ranging in functionality, control systems, power development systems, materials, and scale have been ideated and prototyped, but WEC technology has yet to converge. One critical element of the technology trajectory that governs the speed of adoption is the performance of a WEC concept. In analogous but more-established industries (such as aerospace, and environmentally sustainable electronics design), performance assessment is a quantitative method, based on historical data, that is used as an iterative tool to improve the design of these systems early on in the design process. Though more nascent than these approaches, in wave energy R&D, WEC performance has been assessed using the Technology Performance Level (TPL) assessment, which provides designers with a quantitative score, situating a grid-scale WEC concept on a scale from 1-9 (1 being the lowest performance, and 9 being the highest, trending with the oft-used Technology Readiness Level, or TRL). The TPL assessment is designed to be used during design iteration, when a WEC concept is fully ideated, to enable designers to consider potential means of improving the downstream performance of the concept. One concern that may be slowing the adoption of TPL among WEC developers is the inherent uncertainty in the assessment, and how uncertainty in the individual questions asked as part of the assessment may contribute to perceived inaccuracies in the final score. In this work, we explore the uncertainty present in the assessment and quantify this uncertainty using both traditional mathematical operations and a Monte Carlo simulation. Results imply areas of improvement of the TPL assessment, where reducing uncertainty will be most helpful to end users, enabling both TPL practitioners and users to understand with more accuracy those design elements that can be improved to impact device performance most substantively.

techno-economic analysis↗

NASA NTRS2011

Developing Tests of Visual Dependency

Astronauts develop neural adaptive responses to microgravity during space flight. Consequently these adaptive responses cause maladaptive disturbances in balance and gait function when astronauts return to Earth and are re-exposed to gravity. Current research in the Neuroscience Laboratories at NASA-JSC is focused on understanding how exposure to space flight produces post-flight disturbances in balance and gait control and developing training programs designed to facilitate the rapid recovery of functional mobility after space flight. In concert with these disturbances, astronauts also often report an increase in their visual dependency during space flight. To better understand this phenomenon, studies were conducted with specially designed training programs focusing on visual dependency with the aim to understand and enhance subjects ability to rapidly adapt to novel sensory situations. The Rod and Frame test (RFT) was used first to assess an individual s visual dependency, using a variety of testing techniques. Once assessed, subjects were asked to perform two novel tasks under transformation (both the Pegboard and Cube Construction tasks). Results indicate that head position cues and initial visual test conditions had no effect on an individual s visual dependency scores. Subjects were also able to adapt to the manual tasks after several trials. Individual visual dependency correlated with ability to adapt manual to a novel visual distortion only for the cube task. Subjects with higher visual dependency showed decreased ability to adapt to this task. Ultimately, it was revealed that the RFT may serve as an effective prediction tool to produce individualized adaptability training prescriptions that target the specific sensory profile of each crewmember.

Kindrat, Alexandra N.↗

DOE OSTI2020

PersGNN: Applying Topological Data Analysis and Geometric Deep Learning to Structure-Based Protein Function Prediction

Understanding protein structure-function relationships is a key challenge in computational biology, with applications across the biotechnology and pharmaceutical industries. While it is known that protein structure directly impacts protein function, many functional prediction tasks use only protein sequence. In this work, we isolate protein structure to make functional annotations for proteins in the Protein Data Bank in order to study the expressiveness of different structure-based prediction schemes. We present PersGNN - an end-to-end trainable deep learning model that combines graph representation learning with topological data analysis to capture a complex set of both local and global structural features. While variations of these techniques have been successfully applied to proteins before, we demonstrate that our hybridized approach, PersGNN, outperforms either method on its own as well as a baseline neural network that learns from the same information. PersGNN achieves a 9.3% boost in area under the precision recall curve (AUPR) compared to the best individual model, as well as high F1 scores across different gene ontology categories, indicating the transferability of this approach.

Swenson, Nicolas↗

NASA NTRS2023

Leveraging Automated Fiber Placement Computer Aided Process Planning Framework for Defect Validation and Dynamic Layup Strategies

Process planning represents an essential stage of the Automated Fiber Placement (AFP) workflow. It develops useful and efficient machine processes based upon the working material, composite design, and manufacturing resources. The current state of process planning requires a high degree of interaction from the process planner and could greatly benefit from increased automation. Therefore, a list of key steps and functions are created to identify the more difficult and time-consuming phases of process planning. Additionally, a set of metrics must exist by which to evaluate the effectiveness of the manufactured laminate from the machine code created during the Process Planning stage. Layup strategies, in addition to dog ears, stagger shifts, steering constraints, and starting points, represented the group of functions labeled as process optimization and ranked the highest in terms of priority for automation. The laminates resulting from the selected parameters are evaluated through the occurrences of principal defect metrics such as fiber gaps, overlaps, angle deviation and steering violations. This document presents an automated software solution to the layup strategy and starting point selection phase of process planning. A series of ply scenarios are generated with variations of these ply parameters and evaluated according to a set of metrics entered by the Process Planner. These metrics are generated through use of the Analytical Hierarchy Process (AHP), where relative importance between each of the fiber features are defined. The ply scenarios are selected which reduce the overall fiber feature scores based on the defects the Process Planner wishes to minimize.

HiCAM↗

NASA NTRS2010

Functional Mobility Performance and Balance Confidence in Older Adults after Sensorimotor Adaptation Training

Research indicates a main contributor of injury in older adults is from falling. The decline in sensory systems limits information needed to successfully maneuver through the environment. The objective of this study was to determine if prolonged exposure to the realignment of perceptual-motor systems increases adaptability of balance, and if balance confidence improves after training. A total of 16 older adults between ages 65-85 were randomized to a control group (walking on a treadmill while viewing a static visual scene) and an experimental group (walking on a treadmill while viewing a rotating visual scene). Prior to visual exposure, participants completed six trials of walking through a soft foamed obstacle course. Participants came in twice a week for 4 weeks to complete training of walking on a treadmill and viewing the visual scene for 20 minutes each session. Participants completed the obstacle course after training and four weeks later. Average time, penalty, and Activity Balance Confidence Scale scores were computed for both groups across testing times. The older adults who trained, significantly improved their time through the obstacle course F (2, 28) = 9.41, p < 0.05, as well as reduced their penalty scores F (2, 28) = 21.03, p < 0.05, compared to those who did not train. There was no difference in balance confidence scores between groups across testing times F (2, 28) = 0.503, p > 0.05. Although the training group improved mobility through the obstacle course, there were no differences between the groups in balance confidence.

Buccello-Stout, Regina R.↗

NASA NTRS1991

Resolving Sensory Conflict: the Effect of Muscle Vibration on Postural Stability

The otolith-tilt reinterpretation hypothesis (OTTR) proposes that the central nervous system adapts to weightlessness by reinterpreting all otolith input as linear motion. While interpreting otolith input exclusively as linear motion is functionally useful in space, it is maladaptive upon return to Earth. Astronauts have reported experiencing illusory sensations during head movement which contributes to postural instability. The effect is assessed of muscle vibration in combination with a variety of sensory conflicts on postural equilibrium. The equilibrium of six healthy subjects was tested using the EquiTest sensory test protocol, with and without the confounding influence of triceps surea vibration. The data were analyzed with repeated measures with vibration, vision status, and platform status as independent variables. All main effects and an interaction between the presence of vision and platform sway referencing were found to be significant. Overall, a 4.5 pct. decrease in postural stability was observed with vibration. The trend of the difference scores between conditions with and without vibration suggests that vibration is most destabilizing when the triceps surea is able to change length during postural sway (i.e., conditions with a fixed support surface). The impact of sway referencing vision was virtually identical to that of eye closure, providing compelling evidence that sway referencing 'nulls out' useful cues about subject sway.

Layne, Charles S.↗

NASA NTRS1999

The Chancellor's Model School Project (CMSP)

What does it take to create and implement a 7th to 8th grade middle school program where the great majority of students achieve at high academic levels regardless of their previous elementary school backgrounds? This was the major question that guided the research and development of a 7-year long project effort entitled the Chancellor's Model School Project (CMSP) from September 1991 to August 1998. The CMSP effort conducted largely in two New York City public schools was aimed at creating and testing a prototype 7th and 8th grade model program that was organized and test-implemented in two distinct project phases: Phase I of the CMSP effort was conducted from 1991 to 1995 as a 7th to 8th grade extension of an existing K-6 elementary school, and Phase II was conducted from 1995 to 1998 as a 7th to 8th grade middle school program that became an integral part of a newly established 7-12th grade high school. In Phase I, the CMSP demonstrated that with a highly structured curriculum coupled with strong academic support and increased learning time, students participating in the CMSP were able to develop a strong foundation for rigorous high school coursework within the space of 2 years (at the 7th and 8th grades). Mathematics and Reading test score data during Phase I of the project, clearly indicated that significant academic gains were obtained by almost all students -- at both the high and low ends of the spectrum -- regardless of their previous academic performance in the K-6 elementary school experience. The CMSP effort expanded in Phase II to include a fully operating 7-12 high school model. Achievement gains at the 7th and 8th grade levels in Phase II were tempered by the fact that incoming 7th grade students' academic background at the CMSP High School was significantly lower than students participating in Phase 1. Student performance in Phase II was also affected by the broadening of the CMSP effort from a 7-8th grade program to a fully functioning 7-12 high school which as a consequence lessened the focus and structure available to the 7-8th grade students and teachers -- as compared to Phase I. Nevertheless, the CMSP does represent a unique curriculum model for 7th and 8th grade students in urban middle schools. Experience in both Phase I and Phase II of the project allowed the CMSP to be developed and tested along the broad range of parameters and characteristics that embody an operating public school in an urban environment.

Lopez, Gil↗

DOE OSTI2023

A multiplexed bacterial two-hybrid for rapid characterization of protein–protein interactions and iterative protein design

Protein-protein interactions (PPIs) are crucial for biological functions and have applications ranging from drug design to synthetic cell circuits. Coiled-coils have been used as a model to study the sequence determinants of specificity. However, building well-behaved sets of orthogonal pairs of coiled-coils remains challenging due to inaccurate predictions of orthogonality and difficulties in testing at scale. To address this, we develop the next-generation bacterial two-hybrid (NGB2H) method, which allows for the rapid exploration of interactions of programmed protein libraries in a quantitative and scalable way using next-generation sequencing readout. We design, build, and test large sets of orthogonal synthetic coiled-coils, assayed over 8,000 PPIs, and used the dataset to train a more accurate coiled-coil scoring algorithm (iCipa). After characterizing nearly 18,000 new PPIs, we identify to the best of our knowledge the largest set of orthogonal coiled-coils to date, with fifteen on-target interactions. Our approach provides a powerful tool for the design of orthogonal PPIs.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2010

The Walk on Floor Eyes Closed Tandem Step Test as a Quantitative Measure of Ataxia After Space Flight

INTRODUCTION Posture and locomotion are among the functions most affected by space flight. Postflight ataxia can be quantified easily by using the walk on the floor line test with the eyes closed (WOFEC). Data from a modified WOFEC were obtained as part of an ongoing interdisciplinary pre- and postflight study (Functional Task Test, FTT) designed to evaluate both postflight functional performance of astronauts and related physiological changes. METHODS Five astronauts with flight durations of 12 to 16 days participated in this study. Performance measurements were obtained in 2 preflight sessions, on landing day, and 1, 6, and 30 days after landing. The WOFEC test consisted of walking with the feet placed heel to toe in tandem, arms folded across the chest and eyes closed, for 10 steps. A trial was initiated after the eyes were closed and the front foot was aligned with the rear foot. The performance metric was the average percentage of correct steps completed over 3 trials. A step was not counted as correct if the crewmember sidestepped, opened eyes, or paused for more than 3 seconds between steps. Step accuracy was scored independently by 3 examiners. RESULTS Immediately after landing subjects seemed to be unaware of their foot position relative to their body or the floor. The percentage of correct steps was significantly decreased on landing day. Partial recovery was observed the next day, and full recovery to baseline on the sixth day post landing. CONCLUSION These data clearly demonstrate the sensorimotor challenges facing crewmembers after they return from space flight. Although this simple test is intended to complement the FTT battery of tests, it has some stand-alone value as it provides investigators with a means to quantify vestibular ataxia as well as provide instant feedback on postural stability without the use of complex test equipment.

Fisher, E. A.↗

DOE OSTI2021

Differential Credibility of Climate Modes in CMIP6

This work quantitatively evaluates the fidelity with which the northern annular mode (NAM), southern annular mode (SAM), Pacific–North American pattern (PNA), El Niño–Southern Oscillation (ENSO), Pacific decadal oscillation (PDO), Atlantic multidecadal oscillation (AMO), and the first-order mode interactions are represented in Earth system model (ESM) output from the CMIP6 archive. Several skill metrics are used as part of a differential credibility assessment (DCA) of both spatial and temporal characteristics of the modes across ESMs, ESM families, and specific ESM realizations relative to ERA5. The spatial patterns and probability distributions are generally well represented but skill scores that measure the degree to which the frequencies of maximum variance are captured are consistently lower for most ESMs and climate modes. Substantial variability in skill scores manifests across realizations from individual ESMs for the PNA and oceanic modes. Further, the ESMs consistently overestimate the strength of the NAM–PNA first-order interaction and underestimate the NAM–AMO connection. Furthermore, these results suggest that the choice of ESM and ESM realizations will continue to play a critical role in determining climate projections at the global and regional scale at least in the near term.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Machine Learning-Based Identification of the Interface Regions for Coupling Local and Nonlocal Models

Local-nonlocal coupling approaches provide a means to combine the computational efficiency of local models and the accuracy of nonlocal models. However, the coupling process can be challenging, requiring expertise to identify the interface between local and nonlocal regions. Here, this study introduces a machine learning-based approach to automatically detect the regions in which the local and nonlocal models should be used. The method uses loading functions evaluated at grid points to decide the model selection at those points. Training of the networks is based on datasets provided by classes of loading functions for which reference coupling configurations are computed using accurate coupled solutions, where accuracy is measured in terms of the relative error between the solution to the coupling approach and the solution to the nonlocal model. We study two approaches that vary in data structure. The first, the full-domain input data approach, uses the entire load vector and outputs a complete label vector, performing a global classification. The second, a window-based approach, processes loads into windows and addresses the problem as a node-wise classification where each window's central point is classified individually. The classification problems are solved via deep learning algorithms based on convolutional neural networks. The performance of these approaches is studied on one-dimensional numerical examples using F1-scores and accuracy metrics. Notably, the windowing approach achieves an accuracy of 0.96 and an F1-score of 0.97, highlighting its potential to automate coupling processes effectively and enhance computational efficiency in material science applications.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Data-Informed Evaluation Framework for Integrated Energy Systems: Insights from Power, Process Heat, and Hydrogen Production Applications

The multi-criteria decision analysis (MCDA) framework provides a systematic evaluation of the diverse preferences and performance metrics associated with alternative solutions. This approach is advantageous over a single-criterion methodology, which are only valid under conditions that assume ceteris paribus or an "apples-to-apples" comparison. However, selecting suitable technologies for integrated energy systems (IES) can be likened to an "apples-to-oranges" comparison, given the heterogeneous factors at stake. These factors include economics and performance parameters, geological compatibility, and environmental impacts. Consequently, past research has often employed a mixture of qualitative and quantitative criteria tailored to the specific interests of each study. While the method proves effective in handling the intricate interplay of criteria, the resulting rankings and scores can vary from study to study. This inconsistency is introduced from the use of subjectively defined thresholds and weights. As a result, decision-makers frequently find it challenging to establish clear connections between specific criteria and the resulting scores, as the transformation of criteria into ordinal scores results in a substantial loss of information. To address this challenge, we introduce a data-informed IES evaluation framework that offers comprehensive, interpretable, and traceable evaluations backed by quantifiable rationale. First, we identified key IES evaluation criteria from a decade of literature, focusing on relevant IES applications in power, process heat, and hydrogen production. We leveraged state-of-the-art cost estimates from the Idaho National Laboratory (INL) and technical data from 78 reactor designs from the International Atomic Energy Agency (IAEA) and the Organization for Economic Co-operation and Development - Nuclear Energy Agency (OECD-NEA). Lastly, we established thresholds by analyzing the mean, variance, root mean square, and slope of values across alternatives, categorizing the preferences of decision-makers into distinct utility functions, such as linear, saturating, exponential, and stepwise. Our approach yielded two main outcomes: (1) it provided consistent assessments across different stakeholder groups and (2) it visualized uncertainties in the decision-making context via comprehensive sensitivity analysis. To demonstrate the impact of our framework, we conducted case studies on 6 reactor designs (AP1000, NuScale, BWRX-300, Xe-100, eVinci, iMSR) for the three applications. Our data-driven framework proved to be highly effective in addressing heterogenous uncertainties faced by varied decision-makers? preferences and IES applications, as well as cost and technical estimates of advanced reactors.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2024

Data-Informed Evaluation Framework for Integrated Energy Systems: Insights from Power, Process Heat, and Hydrogen Production Applications

29 ENERGY PLANNING, POLICY, AND ECONOMY↗