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DOE OSTI2024

CrossMP: Enabling Cross-Modality Translation between Single-Cell RNA-Seq and Single-Cell ATAC-Seq through Web-Based Portal

In recent years, there has been a growing interest in profiling multiomic modalities within individual cells simultaneously. One such example is integrating combined single-cell RNA sequencing (scRNA-seq) data and single-cell transposase-accessible chromatin sequencing (scATAC-seq) data. Integrated analysis of diverse modalities has helped researchers make more accurate predictions and gain a more comprehensive understanding than with single-modality analysis. However, generating such multimodal data is technically challenging and expensive, leading to limited availability of single-cell co-assay data. Here, we propose a model for cross-modal prediction between the transcriptome and chromatin profiles in single cells. Our model is based on a deep neural network architecture that learns the latent representations from the source modality and then predicts the target modality. It demonstrates reliable performance in accurately translating between these modalities across multiple paired human scATAC-seq and scRNA-seq datasets. Additionally, we developed CrossMP, a web-based portal allowing researchers to upload their single-cell modality data through an interactive web interface and predict the other type of modality data, using high-performance computing resources plugged at the backend.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Exploring the role of judgement and shared situation awareness when working with AI recommender systems

Abstract AI-advised Decision Making is a form of human-autonomy teaming in which an AI recommender system suggests a solution to a human operator, who is responsible for the final decision. This work seeks to examine the importance of judgement and shared situation awareness between humans and automated agents when interacting together in the form of a recommender systems. We propose manipulating both human judgement and shared situation awareness by providing the human decision maker with relevant information that the automated agent (AI), in the form of a recommender system, uses to generate possible courses of action. This paper presents the results of a two-phase between-subjects study in which participants and a recommender system jointly make a high-stakes decision. We varied the amount of relevant information the participant had, the assessment technique of the proposed solution, and the reliability of the recommender system. Findings indicate that this technique of supporting the human’s judgement and establishing a shared situation awareness is effective in (1) boosting the human decision maker’s situation awareness and task performance, (2) calibrating their trust in AI teammates, and (3) reducing overreliance on an AI partner. Additionally, participants were able to pinpoint the limitations and boundaries of the AI partner’s capabilities. They were able to discern situations where the AI’s recommendations could be trusted versus instances when they should not rely on the AI’s advice. This work proposes and validates a way to provide model-agnostic transparency into recommender systems that can support the human decision maker and lead to improved team performance.

Srivastava, Divya↗

DOE OSTI2021

Genotoxicity evaluation using primary hepatocytes isolated from rhesus macaque ( Macaca mulatta )

Non-human primates (NHPs) have played a vital role in fundamental, pre-clinical, and translational studies because of their high physiological and genetic similarity to humans. We report a method to isolate primary hepatocytes from the livers of rhesus macaques (Macaca mulatta) after in situ whole liver perfusion. Isolated primary macaque hepatocytes (PMHs) were treated with various compounds known to have different pathways of genotoxicity/carcinogenicity and the resulting DNA damage was evaluated using the high-throughput CometChip assay. The comet data were quantified using benchmark dose (BMD) modeling and the BMD50 values for treatments of PMHs were compared with those generated from primary human hepatocytes (PHHs) in our previous study. The results showed that despite varying CYP450 enzyme activities, PMHs had the same sensitivity and specificity as PHHs in detecting four indirect-acting (i.e., requiring metabolic activation) and seven direct-acting genotoxicants/carcinogens, as well as five non-carcinogens that are negative or equivocal for genotoxicity in vivo. The BMD50 estimates and their confidence intervals revealed species differences for DNA damage potency, especially for direct-acting compounds. The present study provides a practical method for maximizing the use of animal tissues by isolating primary hepatocytes from NHPs. Our data support the use of PMHs as a reliable surrogate of PHHs for evaluating the genotoxic hazards of chemical substances for humans.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Data Collection and Analysis Challenges and Mitigation Strategies for Quantitative Human Factors Research Studies in Nuclear Power Plant Modernization

The United States (U.S.) Department of Energy (DOE) Light Water Reactor Sustainability (LWRS) program Plant Modernization Pathway is conducting targeted research and development (R&D) to address aging and reliability concerns with the legacy instrumentation and control and related information systems of the U.S. LWR fleet. In this effort, the application of human factors engineering (HFE) provides an important role in ensuring new digital plant technologies enable broad innovation and business improvement with continued operational safety. Evaluation is a key activity in HFE, which often occurs iteratively through the system design lifecycle. While qualitative methods are important in collecting information of how users perform tasks through observations, quantitative methods are equally important in assessing system design based on performance. In collecting and analyzing this quantitative data, there are notable challenges in the nuclear HFE domain that may threaten the validity and reliability of the inferences made in these studies. Notable challenges include small sample size and limited resources, large error variance and small effect size, an “adding test features to losing degrees of freedom” dilemma, non-normal distribution, and heterogeneity of variance. The results in control room usability studies are often statistically non-significant, which makes it hard to interpret. This work discusses these challenges across different scientific viewpoints and provides real-world examples of these challenges in practice. Collectively, the objective of this work is to position these challenges to the larger data science community as a means of identifying future opportunities to address these issues.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2023

Spatiotemporal features of traffic help reduce automatic accident detection time

Quick and reliable automatic detection of traffic accidents is of paramount importance to save human lives in transportation systems. However, automatically detecting when accidents occur has proven challenging, and minimizing the time to detect accidents (TTDA) by using traditional features in machine learning (ML) classifiers has plateaued. We hypothesize that accidents affect traffic farther from the accident location than previously reported. Therefore, leveraging traffic signatures from neighboring sensors that are adjacent to accidents should help improve their detection. We confirm this hypothesis by using verified ground-truth accident data, traffic data from radar detection system sensors, and light and weather conditions and show that we can minimize the TTDA while maximizing classification performance by considering spatiotemporal features of traffic. Specifically, we compare the performance of different ML classifiers (i.e, logistic regression, random forest, and XGBoost) when controlling for different numbers of neighboring sensors and TTDA horizons. We use data from interstates 75 and 24 in the metropolitan area that surrounds Chattanooga, TN. Our results show that the XGBoost classifier produces the best results by detecting accidents as quickly as 1.0 min after their occurrence with an area under the receiver operating characteristic curve of up to 83% and an average precision of up to 49%. We describe limitations, open challenges, and how the proposed framework can be used for quicker operational accident detection.

33 ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2021

Co-Evolving Climate Models under Uncertainty to Improve Predictive Skill

Focal Area: Predictive modeling through the use of AI techniques and AI-derived model components; the use of AI and other tools to design a prediction system comprising of a hierarchy of models Science Challenge: Advances in modeling of climate and improved observational capabilities have led to great improvements in understanding large-scale historical climate effects. It however remains a challenge to reliably predict the risk of fine-scale regional climate events on human systems even as such risks are on the rise because warmer and wetter climates are more prone to hydrometeorological extremes,

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Learning from Crowds by Modeling Common Confusions

Crowdsourcing provides a practical way to obtain large amounts of labeled data at a low cost. However, the annotation quality of annotators varies considerably, which imposes new challenges in learning a high-quality model from the crowdsourced annotations. In this work, we provide a new perspective to decompose annotation noise into common noise and individual noise and differentiate the source of confusion based on instance difficulty and annotator expertise on a per-instance-annotator basis. We realize this new crowdsourcing model by an end-to-end learning solution with two types of noise adaptation layers: one is shared across annotators to capture their commonly shared confusions, and the other one is pertaining to each annotator to realize individual confusion. To recognize the source of noise in each annotation, we use an auxiliary network to choose from the two noise adaptation layers with respect to both instances and annotators. Extensive experiments on both synthesized and real-world benchmarks demonstrate the effectiveness of our proposed common noise adaptation solution.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2021

Using Qualified On-Site Nuclear Power Plant Simulators in Human Factors Validations of Control Room Upgrades

Existing commercial nuclear power plants (NPPs) are valuable assets in the infrastructure portfolio of the United States (U.S.) because they safely and reliably generate about 1/5th of all the electricity used. The instrumentation and control (I&C) systems in commercial NPPs are the ‘eyes and ears' of the operator, allowing operators to maintain situation awareness, thereby allowing the plant to operate safely and efficiently for all phases of operation. Because the I&C systems in NPPs are still mostly based on analog technologies, which are reliable but not especially cost-effective, upgrading the existing I&C in com-mercial NPPs to new digital I&C is very important. Furthermore, simulators and simulation are critical human factors engineering tools for this I&C modernization work. NPP control room simulators are essential test beds to simulate normal, abnormal, and emergency operations that allow human factors researchers to safely and realistically evaluate early design phase prototypes of the upgraded digital I&C, and validate final as-built digital I&C systems that have been modernized deployed in NPPs. This paper describes research performed using qualified on-site NPP simulators to perform human factors validations of digital I&C control room upgrades.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2023

Deep learning uncertainty quantification for clinical text classification

Machine learning algorithms are expected to work side-by-side with humans in decision-making pipelines. Thus, the ability of classifiers to make reliable decisions is of paramount importance. Deep neural networks (DNNs) represent the state-of-the-art models to address real-world classification. Although the strength of activation in DNNs is often correlated with the network’s confidence, in-depth analyses are needed to establish whether they are well calibrated. In this paper, we demonstrate the use of DNN-based classification tools to benefit cancer registries by automating information extraction of disease at diagnosis and at surgery from electronic text pathology reports from the US National Cancer Institute (NCI) Surveillance, Epidemiology, and End Results (SEER) population-based cancer registries. In particular, we introduce multiple methods for selective classification to achieve a target level of accuracy on multiple classification tasks while minimizing the rejection amount—that is, the number of electronic pathology reports for which the model’s predictions are unreliable. We evaluate the proposed methods by comparing our approach with the current in-house deep learning-based abstaining classifier. Overall, all the proposed selective classification methods effectively allow for achieving the targeted level of accuracy or higher in a trade-off analysis aimed to minimize the rejection rate. On in-distribution validation and holdout test data, with all the proposed methods, we achieve on all tasks the required target level of accuracy with a lower rejection rate than the deep abstaining classifier (DAC). Interpreting the results for the out-of-distribution test data is more complex; nevertheless, in this case as well, the rejection rate from the best among the proposed methods achieving 97% accuracy or higher is lower than the rejection rate based on the DAC. We show that although both approaches can flag those samples that should be manually reviewed and labeled by human annotators, the newly proposed methods retain a larger fraction and do so without retraining—thus offering a reduced computational cost compared with the in-house deep learning-based abstaining classifier.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Human myoblasts differentiate in various mesenchymal lineages and inhibit allogeneic T cell proliferation through an indolamine 2,3 dioxygenase dependent pathway

Muscle stem cells (MuSC) are considered as a reliable source of therapeutic cells to restore diseased muscles. However in most cases, injected MuSC-derived myoblasts are rapidly destroyed by the host immune response, which impairs the beneficial effect. By contrast, human mesenchymal stromal cells (MSC), have been reported to exhibit potent immune regulatory functions. Thus, we investigated, in vitro, the multipotent differentiation- and immunosuppressive capacities of human myoblasts and compared these features with those of human MSC. Myoblasts shared numerous cell surface markers with MSC, including CD73, CD90, CD105 and CD146. Both cell type were negative for HLA-DR and CD45, CD34 and CD31. CD56, a myogenic marker, was expressed by myoblasts exclusively. Myoblasts displayed multipotent potential capabilities with differentiation in chondrocytes, adipocytes and osteoblasts in vitro. Myoblasts also inhibited allogenic T cell proliferation in vitro in a dose dependent manner, very similarly to MSC. This effect was partly mediated via the activation of indolamine 2,3 dioxygenase enzyme (IDO) after IFNγ exposure. Altogether, these data demonstrate that human myoblasts can differentiate in various mesenchymal linages and exhibit powerful immunosuppressive properties in vitro. Such features may open new therapeutic strategies for MuSC-derived myoblasts.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Next-Level Energy Management in Manufacturing: Facility-Level Energy Digital Twin Framework Based on Machine Learning and Automated Data Collection

This research introduces an energy prediction framework at the facility level supported by automated data collection and machine learning models. It investigates whether reducing the prediction time scale allows for applying more complex machine learning techniques and if those techniques improve the prediction accuracy. The primary advantages of this framework lie in its automation of the energy prediction process and its provision of real-time energy data suitable for use in energy dashboards or digital twins. A sitewide dataset was created by combining 15 min energy and daily production data of five shops—assembly, battery, body (electric), body (gas), and paint—from a globally recognized electric vehicle manufacturer. Various machine learning models were evaluated on daily, weekly, and monthly datasets, including, in increasingly complex order: naïve, simple linear regression, net regularized generalized linear regression, principal component regression, k-nearest neighbor, random forest, and Bayesian regularized neural network. Compared to the current state-of-the-art energy consumption prediction for the industrial facility level, this research investigates more complex models and smaller time intervals for higher accuracy. The findings revealed that the more complex monthly models require a minimum of a year and a half of data to operate, while weekly models demand a year of data to achieve improved accuracy. Daily models can operate with only six months of data but exhibit poor performance due to reduced prediction accuracy of production. Key challenges identified include access to reliable, high-quality energy and production data and the initial demand for human labor.

digital twin↗

DOE OSTI2026

An improved dataset for predicting mammal infecting viruses from genetic sequence information

There have been several attempts to develop machine learning (ML) models to identify human infecting viruses from their genomic sequences, with varying degrees of success. Direct comparison between models is problematic, because these models are typically trained and evaluated on different datasets with alternative data splitting schemes, features, and model performance metrics. In this paper we present a standardized dataset of mammal infecting and non-infecting viral pathogens, refined from the previous work of Mollentze et al. to include the latest literature evidence, roughly doubling the number of curated host-virus records available to the community, and new host target labels, primate and mammal. The new host labels were included for several reasons, including previous reports that classification performance is better at broader taxonomic ranks and the idea that there may be more data for primate infection that might serve as a suitable proxy for zoonotic potential and avoidance of false positives for human infection due to absence of evidence. On this dataset, we report the performance of eight machine learning models for predicting mammal-infecting viruses from their genomic sequences. We find that randomly assigning cases in our improved dataset to training/testing sets, when compared to the original assignments into training/testing in Mollentze et al., increases the overall average ROC AUC of prediction of human infection from 0.663 ± 0.070 to 0.784 ± 0.013, consistent with the reduction in phylogenetic distance between train and test sets (relative entropy change from 3.00 to 0.08). The broadest host category of mammal infection can be predicted most reliably at 0.850 ± 0.020. We share our improved dataset and code to enable standardized comparisons of machine learning methods to predict human host infections. Overall, we have presented preliminary evidence that classification of virus host infection is more tractable at higher taxonomic ranks, that unsurprisingly reducing the phylogenetic distance between training and test sets can improve predictive performance, that peptide kmer features appear to be harmful to out of sample model performance, and we are left with the question of whether models for virus host prediction can reasonably be expected to perform well in out of sample scenarios given the likelihood that viruses do not share a common ancestor. Consistent with this concern, when the data is resampled such that there is no overlap between viral families in training and test sets (relative entropy > 24), models perform no better than random chance at prediction of human infection regardless of whether kmers are included (ROC AUC 0.50 ± 0.08) or not (ROC AUC 0.50 ± 0.04).

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Reliable and Efficient Machine Learning (Final Technical Report)

Modern scientific experiments generate massive amounts of data at a pace much faster than humans can manually analyze. While machine learning has revolutionized commercial data analysis (such as recommending movies or recognizing faces), applying these tools to complex scientific discovery is challenging because scientific answers must be precise, interpretable, and adhere to physical laws. The research under this project aims to develop new mathematical tools and computer algorithms specifically designed for scientific applications. Major progress has been made in automatically cleaning and deconstructing messy experimental data, analyzing the visual information of physical phenomena, determining the underlying physical variables, and providing rig orous mathematical analysis of interesting algorithms and concepts widely used in machine learning. This project addressed the critical gap between our ability to generate massive scientific data and our ability to extract interpretable information from it. We established mathematical foundations for Scientific Machine Learning (SciML) aimed at effective data analytics and automated discovery. Our work focused on three core objectives: (1) developing reliable feature extraction methods for dynamic high-dimensional data, (2) establishing mathematical foundations for discovering dynamics via neural networks, and (3) creating rigorous optimization techniques for these models. Key outcomes come from two fronts. On the practical side, they include the development of algorithms that significantly enhance the extraction of signals from field data, as well as the capability to handle situations that exhibit smooth variations or physical stretching due to temperature changes. They also include the creation of an automated framework for discovering fundamental state variables from raw experimental data, demonstrating the ability to identify intrinsic physical dimensions without prior knowledge of the governing laws. On the theoretical front, the research results in theoretical advances in Optimal Transport, a widely used notion in SciML, specifically regarding functions with fixed-size nodal sets, provide sharp bounds relevant to uncertainty quantification. Meanwhile, the outcomes also include the establishment of convergence theories for nonlocal gradient descent methods, enabling robust optimization with noisy data in high-dimensional settings commonly encountered in scientific modeling. The project also helps creating opportunities to train the next generation of researchers, equipping them with the necessary technical skills for today’s workplace and preparing them for future advances.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Special Observing Period (SOP) data for the Year of Polar Prediction site Model Intercomparison Project (YOPPsiteMIP)

The rapid changes occurring in the polar regions require an improved understanding of the processes that are driving these changes. At the same time, increased human activities such as marine navigation, resource exploitation, aviation, commercial fishing, and tourism require reliable and relevant weather information. One of the primary goals of the World Meteorological Organization's Year of Polar Prediction (YOPP) project is to improve the accuracy of numerical weather prediction (NWP) at high latitudes. During YOPP, two Canadian “supersites” were commissioned and equipped with new ground-based instruments for enhanced meteorological and system process observations. Additional pre-existing supersites in Canada, the United States, Norway, Finland, and Russia also provided data from ongoing long-term observing programs. These supersites collected a wealth of observations that are well suited to address YOPP objectives. In order to increase data useability and station interoperability, novel Merged Observatory Data Files (MODFs) were created for the seven supersites over two Special Observing Periods (February to March 2018 and July to September 2018). All observations collected at the supersites were compiled into this standardized NetCDF MODF format, simplifying the process of conducting pan-Arctic NWP verification and process evaluation studies. This paper describes the seven Arctic YOPP supersites, their instrumentation, data collection and processing methods, the novel MODF format, and examples of the observations contained therein. MODFs comprise the observational contribution to the model intercomparison effort, termed YOPP site Model Intercomparison Project (YOPPsiteMIP). All YOPPsiteMIP MODFs are publicly accessible via the YOPP Data Portal (Whitehorse: https://doi.org/10.21343/a33e-j150, Huang et al., 2023a; Iqaluit: https://doi.org/10.21343/yrnf-ck57, Huang et al., 2023b; Sodankylä: https://doi.org/10.21343/m16p-pq17, O'Connor, 2023; Utqiagvik: https://doi.org/10.21343/a2dx-nq55, Akish and Morris, 2023c; Tiksi: https://doi.org/10.21343/5bwn-w881, Akish and Morris, 2023b; Ny-Ålesund: https://doi.org/10.21343/y89m-6393, Holt, 2023; and Eureka: https://doi.org/10.21343/r85j-tc61, Akish and Morris, 2023a), which is hosted by MET Norway, with corresponding output from NWP models.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Advances in PFAS Monitoring and Remediation Using a Functionalized Material Approach

The growing global concerns about the effects to public health from human exposure to per- and polyfluoroalkyl substances (PFAS) motivates the development of strategies for reliable monitoring of PFAS in environmental streams, as well as for their rapid, effective removal if detected. For the continuous PFAS monitoring, an inexpensive, field-deployable, in situ sensor is urgently needed; yet the prevalent in situ techniques often struggle to strike a balance between the practical sensitivity and selectivity demands of the real world. Similarly, for effective PFAS removal, strategies for their fast, selective, and quantitative capture are desired, yet the present commercially available sorbents are unable to meet the requirements of rapid, quantitative capture of all PFAS components, and are notably inefficient in removing the more toxic smaller chains. To address these twin challenges, Pacific Northwest National Laboratory is developing strategies for improved detection and remediation of PFAS. For the rapid, selective, quantitative removal of PFAS from environmental streams, the strategy relies on designing capture probes with exclusively tailored electronic and spatial affinities for the PFAS that are able to selectively capture them from environmental streams. For the in situ detection and quantification of PFAS in complex, multicomponent matrices such as groundwater, the approach relies on the targeted capture of specific PFAS by these PFAS-specific capture probes immobilized on a platform. The platform acts as an electrode to directly measure PFAS concentration through a proportional change in electrical response upon their capture. A combination of optimization of platform design and incorporation of additional, sensitive detection modalities have allowed us to achieve detection limits as low as 0.5 ng/L for detection of PFAS compounds (compared to the 70 ng/L Health Advisory Limit of the U.S. Environmental Protection Agency).

Per- and poly-fluorinated alkyl substances (PFAS),↗

DOE OSTI2020

Advances in PFAS Monitoring and Remediation Using a Functionalized Material Approach - 20080

47 OTHER INSTRUMENTATION↗

DOE OSTI2023

Human and Technology Integration Evaluation of Advanced Automation and Data Visualization

While the existing United States (U.S.) light water reactors are highly reliable, safe, and provide a significant proportion of carbon-free electricity, the cost of operating and maintaining them has become less competitive compared to other electricity generating sources. The reason for the gap in operating and maintenance (O&M) costs can be at least in part attributed to the advent of new digital technologies that other electricity generating industries are currently using. Advanced capabilities including digital instrumentation and control (I&C) systems, advanced automation and analytics, and greater span of data integration (i.e., connectedness) across these non-nuclear plants has transformed the way work is performed and ultimately given them a competitive advantage in terms of the cost required for operating, maintaining, and supporting them. To reduce O&M cost and address obsolescence of the aging I&C infrastructure of the existing U.S. light water reactors, the U.S. Department of Energy (DOE) Light Water Reactor Sustainability (LWRS) Program Plant Modernization Pathway is conducting targeting multidisciplinary research that 1) delivers a sustainable business model to enable a cost-competitive U.S. nuclear industry and 2) is developing technology modernization solutions that address aging and obsolescence challenges. The work described in this report supports these two objectives and describes the demonstration of human and technology integration across recent industry collaborations to support their large-scale digital I&C modifications. This technical report describes the demonstration of the human and technology integration methodology in performing full-scale performance-based human-in-the-loop tests to evaluate plant-specific advanced automation and data visualization applications within these collaborators’ digital modifications. This technical report also documents future applications of human and technology integration that expand beyond main control room modernization and digital I&C upgrades, which have been a central focus to date. Thus, this technical report discusses how to implement human and technology integration across new business opportunities and how to develop an evaluation plan that defines measures and criteria, and documents key assumptions to support full plant modernization.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2024

Photovoltaic Reliability Workshop (PVRW) 2024 Proceedings: Posters

NREL hosts an annual Photovoltaic Reliability Workshop (PVRW) so that solar technology experts can discuss current and future issues in PV reliability. Longer-lasting PV systems make lower-cost solar electricity and have less impact on the environment, human health, and natural resources. PVRW offers a combination of oral presentations, panel discussions with vigorous audience participation, and poster presentations. This document collects posters that were presented at PVRW 2024.

degradation↗