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DOE OSTI2020

Systematic Comparison of High-throughput Single-Cell and Single-Nucleus Transcriptomes during Cardiomyocyte Differentiation

A comprehensive reference map of all cell types in the human body is necessary for improving our understanding of fundamental biological processes and in diagnosing and treating disease. High-throughput single-cell RNA sequencing techniques have emerged as powerful tools to identify and characterize cell types in complex and heterogeneous tissues. However, extracting intact cells from tissues and organs is often technically challenging or impossible, for example in heart or brain tissue. Single-nucleus RNA sequencing provides an alternative way to obtain transcriptome profiles of such tissues. To systematically assess the differences between high-throughput single-cell and single-nuclei RNA-seq approaches, we compared Drop-seq and DroNc-seq, two microfluidic-based 3' RNA capture technologies that profile total cellular and nuclear RNA, respectively, during a time course experiment of human induced pluripotent stem cells (iPSCs) differentiating into cardiomyocytes. Clustering of timeseries transcriptomes from Drop-seq and DroNc-seq revealed six distinct cell types, five of which were found in both techniques. Furthermore, single-cell trajectories reconstructed from both techniques reproduced expected differentiation dynamics. We then applied DroNc-seq to postmortem heart tissue to test its performance on heterogeneous human tissue samples. Our data confirm that DroNcseq yields similar results to Drop-seq on matched samples and can be successfully used to generate reference maps for the human cell atlas.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

SCITUNE: Aligning Large Language Models with Human-Curated Scientific Multimodal Instructions

Instruction finetuning is a popular paradigm to align large language models (LLM) with human intent. Despite its popularity, this idea is less explored in improving the LLMs to align existing foundation models with scientific disciplines, concepts and goals. In this work, we present SciTune as a tuning framework to improve the ability of LLMs to follow scientific multimodal instructions. To test our methodology, we use a human-generated scientific instruction tuning dataset and train a large multimodal model LLaMA-SciTune that connects a vision encoder and LLM for science-focused visual and language understanding. LLaMA-SciTune significantly outperforms the state-of-the-art models in the generated figure types and captions in multiple scientific multimodal benchmarks. In comparison to the models that are fine-tuned with machine generated data only, LLaMA-SciTune surpasses human performance on average and in many sub-categories on the ScienceQA benchmark.

• Artificial intelligence (AI) / machine learning ↗

DOE OSTI2024

An Approach to Dynamic Human Reliability Analysis and Its Data Collection Framework

Human reliability analysis (HRA) is a method for evaluating human errors in a variety of complex systems such as nuclear power plants, military systems, aircraft, and chemical plants. Most HRA methods currently used by regulatory institutes or utilities are called static HRA and are carried out by simple worksheets or simple calculators. To date, there are many unsolved or intrinsic challenges in static HRA. For example, existing static HRA does not realistically model and evaluate human actions as they would be performed at actual systems. There is no method with HRA to objectively estimate the time required for human actions despite being essential to HRA processes. In addition, many HRA methods still rely on a dataset generated prior to the 1980s, from unrelated industry experience or simply from expert judgment. Accordingly, this study attempted to research how to overcome the challenges of existing HRA via dynamic risk assessment (a.k.a., simulation-based or computation-based risk assessment) techniques. First, this study developed a dynamic HRA method, named as PRocedure-based Investigation Method of EMRALD Risk Assessment – HRA (PRIMERA-HRA). The PRIMERA-HRA mainly concentrates on providing HRA analysts with specific guidelines on how to reasonably model human actions, assign human reliability data and evaluate output of simulation within a dynamic probabilistic risk assessment tool, called as Event Modeling Risk Assessment using Linked Diagrams (EMRALD). Second, this study also developed a module for performance shaping factors (i.e., the key concept in HRA quantification) applicable to dynamic HRA, then implemented it based on PRIMERA-HRA within the EMRALD tool. Third, this study developed an HRA data collection framework to support dynamic HRA, called as Simplified Human Error Experimental Program (SHEEP). Originally, the SHEEP study aimed to support static HRA and its data collection, but recently extended the scope to the new technologies such as dynamic HRA or HRA for advanced reactors. SHEEP focuses on the use of data collected from simplified simulators to complement—but not replace—data collection studies using full-scope simulators and actual operators. To date, many experiments were conducted under the SHEEP framework. Multiple analyses, such as human performance analysis, human error analysis, task complexity analysis, learning effect analysis and time distribution analysis, were also carried out using the collected data. Then, based on the major insights, an approach to inferring full-scope data based on simplified simulator data was proposed. The PRIMERA-HRA and SHEEP research are expected to evaluate human actions more realistically than existing static HRA, provide an opportunity to collect more HRA data with reasonable cost and labor, then contribute to enhance the quality of HRA.

99 - GENERAL AND MISCELLANEOUS↗

DOE OSTI2024

An Approach to Dynamic Human Reliability Analysis and Its Data Collection Framework

99 - GENERAL AND MISCELLANEOUS↗

DOE OSTI2016

A model-based scatter artifacts correction for cone beam CT

Purpose: Due to the increased axial coverage of multislice computed tomography (CT) and the introduction of flat detectors, the size of x-ray illumination fields has grown dramatically, causing an increase in scatter radiation. For CT imaging, scatter is a significant issue that introduces shading artifact, streaks, as well as reduced contrast and Hounsfield Units (HU) accuracy. The purpose of this work is to provide a fast and accurate scatter artifacts correction algorithm for cone beam CT (CBCT) imaging. Methods: The method starts with an estimation of coarse scatter profiles for a set of CBCT data in either image domain or projection domain. A denoising algorithm designed specifically for Poisson signals is then applied to derive the final scatter distribution. Qualitative and quantitative evaluations using thorax and abdomen phantoms with Monte Carlo (MC) simulations, experimental Catphan phantom data, and in vivo human data acquired for a clinical image guided radiation therapy were performed. Scatter correction in both projection domain and image domain was conducted and the influences of segmentation method, mismatched attenuation coefficients, and spectrum model as well as parameter selection were also investigated. Results: Results show that the proposed algorithm can significantly reduce scatter artifacts and recover the correct HU in either projection domain or image domain. For the MC thorax phantom study, four-components segmentation yields the best results, while the results of three-components segmentation are still acceptable. The parameters (iteration number K and weight β) affect the accuracy of the scatter correction and the results get improved as K and β increase. It was found that variations in attenuation coefficient accuracies only slightly impact the performance of the proposed processing. For the Catphan phantom data, the mean value over all pixels in the residual image is reduced from −21.8 to −0.2 HU and 0.7 HU for projection domain and image domain, respectively. The contrast of the in vivo human images is greatly improved after correction. Conclusions: The software-based technique has a number of advantages, such as high computational efficiency and accuracy, and the capability of performing scatter correction without modifying the clinical workflow (i.e., no extra scan/measurement data are needed) or modifying the imaging hardware. When implemented practically, this should improve the accuracy of CBCT image quantitation and significantly impact CBCT-based interventional procedures and adaptive radiation therapy.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

Instantiation of HCML Demonstrating Bayesian Predictive Modeling for Attentional Control

The research team developed models of Attentional Control (AC) that are unique to existing modeling approaches in the literature. The goal was to enable the research team to (1) make predictions about AC and human performance in real-world scenarios and (2) to make predictions about individual characteristics based on human data. First, the team developed a proof-of-concept approach for representing an experimental design and human subjects data in a Bayesian model, then demonstrated an ability to draw inferences about conditions of interest relevant to real-world scenarios. Ultimately, this effort was successful, and we were able to make reasonable (meaning supported by behavioral data) inferences about conditions of interest to develop a risk model for AC (where risk is defined as a mismatch between AC and attentional demand). The team additionally defined a path forward for a human-constrained machine learning (HCML) approach to make predictions about an individual's state based on performance data. The effort represents a successful first step in both modeling efforts and serves as a basis for future work activities. Numerous opportunities for future work have been defined.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Automating Anomaly Detection for Target systems at Spallation Neutron Source

The Spallation Neutron Source (SNS) at Oak Ridge National Laboratory, produces the world’s most intense pulse neutrons beams. An accelerated proton beam is directed into a mercury target to generate neutrons via spallation. The target system accounted for over 40% of the overall downtime of the facility in 2022. Thus, early detection in anomalies in the target systems can enable taking corrective actions to avoid failures and reduce downtime. Fault prognostics and anomaly detection in accelerators, both at SNS and outside, has largely focused on the beam side. This paper presents one the first studies exploring leveraging machine learning to automate the detection of anomalies in the target system. The target system consists of over 30 different interconnected subsystems, and the present work focuses on the mercury process system as a use case. Analyzing data from 28 process variables from 2022 and 2023, tree-based and reconstruction-based algorithms are employed to detect anomalies in archived data. The algorithms detected previously unreported anomalies, several of which were deemed alert worthy by human experts, particularly those found by reconstruction-based algorithms. Using data from each production run in the accelerator increased the generalizability of the models in time. Efforts are now underway to implement a workflow for incorporating human feedback to update the models and evaluating performance on unseen data. The models will eventually be integrated into the existing System Tracking and Reliability system with a web interface for automated anomaly detection and reporting along with a pathway for incorporating human feedback for model updates.

Raj, Anant [ORNL] (ORCID:0000000306711244)↗

DOE OSTI2023

An Experimental Investigation of Students’ Learning Effects When Using a Simplified Nuclear Simulator

Securing enough data has been a main challenge in human reliability analysis (HRA). Many researchers and institutes have made a lot of efforts for collecting HRA data to produce reasonable human error probabilities (HEPs) as well as reduce the uncertainty of HRA quantification. Representatively, U.S. Nuclear Regulatory Commission (U.S. NRC), Korea Atomic Energy Research Institute (KAERI) and Idaho National Laboratory (INL) have led lots of empirical research regarding the HRA data collection. The U.S. NRC and KAERI have mainly carried out full-scope simulator research collecting HRA data through experiments using full-scope simulators with actual operators. In contrast, INL has experimentally collected the data using simplified simulators and student operators. INL has proposed the Simplified Human Error Experimental Program (SHEEP) framework to complement full-scope data collection efforts by suggesting a way to infer full-scope data based on experimental data collected from students operating simplified simulators, specifically the Rancor Microworld Simulator (Rancor) and the Compact Nuclear Simulator (CNS). The aim of the SHEEP framework is to lower the entry point for collecting useful HRA data by securing large sample sizes at a reasonable amount of cost and labor while also guaranteeing a high degree of freedom when designing experiments. The authors’ previous research investigated whether data collected from the SHEEP framework could support a representative full-scope study. Besides, human performance differences between professional and student operators when using Rancor and CNS have been analyzed to understand the lack of fidelity of the simplified simulators and student operators within the SHEEP study. As a follow up research, this study experimentally investigates students’ learning effects and the performance trends over a certain period when using Rancor. This study aims to find out 1) how much training or education is required to collect HRA data from non-experts (i.e., students) when using Rancor and 2) how much differences there are in human performance measures between students and professional operators. In this study, a longitudinal experiment is developed. The four experiment trials with two weeks interval are carried out for sixteen undergraduate students majoring nuclear engineering at Chosun University. Totally four scenarios randomly selected from ten Rancor scenarios are used in each experiment trial. Four human performance measurements (i.e., workload, situation awareness, time and error) are considered in the experiment. Lastly, the trend of students’ performance is compared with operator data having been collected from the previous experiment.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2020

AI-Science for Performance Optimization and Diagnosis of Science Instrument Federations

Next generation of science workflows are expected to be executed over complex federations composed of supercomputers, science instruments, storage systems and networks, with new additions of the edge and cloud systems and services. The sheer complexity of these multi-domain federations makes it hard to manage them and optimize their performance, as small impedance mismatches (that can dynamically develop between systems) could drastically degrade the entire federation performance. Recent proliferation of Software Defined Everything (SDX) technologies combined with containerization frameworks provide custom instruments that can monitor and collect critical measurements at various levels to support diagnoses and performance optimization; but their data too enormous for human operators and analysts to process and generate decisions. Machine Learning (ML) methods that extract critical parameters, relationships and trends from the data offer general solutions. Artificial Intelligence (AI) and ML methods must be custom-developed for these problems based on solid, rigorous foundations, since black-box approaches are often ineffective and unsound.We propose to develop comprehensive AI-Science for the performance of science federations to (i) monitor and control storage, networks, experiments, and computing systems across multiple domains via softwarization layers, at speeds and scales orders of magnitude superior to current practice, (ii) optimally realize and orchestrate complex workflows with high performance by using dynamic state and performance estimation methods, and (iii) aggregate measurements across sites and time to develop infrastructure-level profiles, optimizations and diagnoses using AI-Science based on foundational principles from ML, game theory, and information fusion areas.

Rao, Nageswara↗

DOE OSTI2024

Proteomics identifies complement protein signatures in patients with alcohol-associated hepatitis

Diagnostic challenges continue to impede development of effective therapies for successful management of alcohol-associated hepatitis (AH), creating an unmet need to identify noninvasive biomarkers for AH. In murine models, complement contributes to ethanol-induced liver injury. Therefore, we hypothesized that complement proteins could be rational diagnostic/prognostic biomarkers in AH. Here, we performed a comparative analysis of data derived from human hepatic and serum proteome to identify and characterize complement protein signatures in severe AH (sAH). The quantity of multiple complement proteins was perturbed in liver and serum proteome of patients with sAH. Multiple complement proteins differentiated patients with sAH from those with alcohol cirrhosis (AC) or alcohol use disorder (AUD) and healthy controls (HCs). Serum collectin 11 and C1q binding protein were strongly associated with sAH and exhibited good discriminatory performance among patients with sAH, AC, or AUD and HCs. Furthermore, complement component receptor 1-like protein was negatively associated with pro-inflammatory cytokines. Additionally, lower serum MBL associated serine protease 1 and coagulation factor II independently predicted 90-day mortality. In summary, meta-analysis of proteomic profiles from liver and circulation revealed complement protein signatures of sAH, highlighting a complex perturbation of complement and identifying potential diagnostic and prognostic biomarkers for patients with sAH.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

Light Water Reactor Sustainability Program: Use of Time Distributions to Predict Operator Procedure Performance in Dynamic Human Reliability Analysis

The Human Unimodel for Nuclear Technology to Enhance Reliability (HUNTER) framework affords software capable of conducting human reliability analysis (HRA) using a dynamic approach built around operating procedures (OPs) from nuclear power plants (NPPs). Previous HUNTER reports document the development of this software tool, the coupling of HUNTER to the simulator code, the collection of operator performance data by using simulators to calibrate HUNTER models, and linking HUNTER to probabilistic risk assessment (PRA) software. The present report largely addresses two topics. The first is a new function in HUNTER called the HUNTER Procedure Performance Predictor (P3). HUNTER P3 uses HUNTER’s built in Monte Carlo tools featuring human performance variability to identify potential error traps in procedures. The second topic is time distribution analysis to generate time inputs for dynamic HRA. The current analysis was performed to investigate time distributions for task primitives, which are the minimum task unit of analysis used in dynamic HRA modeling. Using the time distribution data, the elapsed time for human actions in an extended loss of AC power (ELAP) scenario is then investigated. Time data and prediction are essential for modeling procedure performance.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2020

Data analysis and modeling pipelines for controlled networked social science experiments

There is large interest in networked social science experiments for understanding human behavior at-scale. Significant effort is required to perform data analytics on experimental outputs and for computational modeling of custom experiments. Moreover, experiments and modeling are often performed in a cycle, enabling iterative experimental refinement and data modeling to uncover interesting insights and to generate/refute hypotheses about social behaviors. The current practice for social analysts is to develop tailor-made computer programs and analytical scripts for experiments and modeling. This often leads to inefficiencies and duplication of effort. In this work, we propose a pipeline framework to take a significant step towards overcoming these challenges. Our contribution is to describe the design and implementation of a software system to automate many of the steps involved in analyzing social science experimental data, building models to capture the behavior of human subjects, and providing data to test hypotheses. The proposed pipeline framework consists of formal models, formal algorithms, and theoretical models as the basis for the design and implementation. We propose a formal data model, such that if an experiment can be described in terms of this model, then our pipeline software can be used to analyze data efficiently. The merits of the proposed pipeline framework is elaborated by several case studies of networked social science experiments.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

SPIDARman: System-Level Physics-Informed Detection of Anomalies in Reactor Collected Data Considering Human Errors

In nuclear power plants (NPPs), anomalies arising from sensors or human errors (HEs) can undermine the performance and reliability of plant operations. Anomaly detection models can be employed to detect sensor errors and HEs. Additionally, physics-informed machine learning models can utilize the known physics of the system, as described by mathematical equations, to ensure that sensor values are consistent with physical laws. Hence, we propose SPIDARman: System-level Physics-Informed Detection of Anomalies in Reactor Collected Data Considering Human Errors, a holistic physics-informed anomaly detection approach based on generative adversarial networks (GANs) to detect anomalies in both automatically collected sensor data and manually collected surveillance data. Here we test our approach on data collected from a flow loop testbed, showcasing its potential to detect anomalies. Results demonstrate that the proposed model performs better than the baseline GAN-based models in detecting sensor and surveillance anomalies, suggesting the potential of physics-informed anomaly detection GAN models in NPPs.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

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 OSTI2019

Toward adaptive decision support for assessing infrastructure system resilience using hidden performance measures

The understanding of resilience is an emerging topic within the study of risks affecting distributed transportation infrastructure systems. Although recent studies have explored the quantification of system resilience, there has been limited research aimed at understanding the role of multiple performance measures, geographies, and modeling uncertainties within the assessment of resilience and associated decision-making. Under real-world conditions, there is an increased burden on analysts for translating observed system data (from human and electronic sensor observations) into the estimation of system performance that may not be directly observable. This paper addresses these issues using a scenario-based risk modeling approach to understand: 1) resilience of complex systems, often in cases of hidden (not readily observable) measures of performance, 2) resilience sensitivity to modeling uncertainties in event and system characteristics, and 3) resilience sensitivity to the measurement of performance across multiple dimensions. The methods in this paper integrate uncertainty-driven risk and probabilistic modeling within a multi-state Markov approach. This study contributes to the state-of-the-art by developing methodologies for assessing community perceptions of infrastructure system resilience using observable factors and inferring possibly hidden performance measures for facilitating adaptive decision-support. The methods are demonstrated with hypothetical spatiotemporal data for the Washington, District of Columbia and Baltimore, Maryland urban regions in the United States against evacuation-causing and shelter-in-place disruptive scenarios across multiple system performance dimensions. The analysis results may be useful for risk managers, supply chain analysts, emergency decision-makers, and the general public.

Infrastructure System Resilience, Risk Management,↗

DOE OSTI2015

A preliminary regional PBPK model of lung metabolism for improving species dependent descriptions of 1,3-butadiene and its metabolites

1,3-Butadiene (BD), a volatile organic chemical (VOC), is used in synthetic rubber production and other industrial processes. It is detectable at low levels in ambient air as well as in tobacco smoke and gasoline vapors. Inhalation exposures to high concentrations of BD have been associated with lung cancer in both humans and experimental animals, although differences in species sensitivity have been observed. Metabolically active lung cells such as Pulmonary Type I and Type II epithelial cells and club cells (Clara cells) 1 are potential targets of BD metabolite-induced toxicity. Metabolic capacities of these cells, their regional densities, and distributions vary throughout the respiratory tract as well as between species and cell types. Here we present a physiologically based pharmacokinetic (PBPK) model for BD that includes a regional model of lung metabolism, based on a previous model for styrene, to provide species-dependent descriptions of BD metabolism in the mouse, rat, and human. Since there are no in vivo data on BD pharmacokinetics in the human, the rat and mouse models were parameterized to the extent possible on the basis of in vitro metabolic data. Where it was necessary to use in vivo data, extrapolation from rat to mouse was performed to evaluate the level of uncertainty in the human model. A kidney compartment and description of downstream metabolism were also included in the model to allow for eventual use of available urinary and blood biomarker data in animals and humans to calibrate the model for estimation of BD exposures and internal metabolite levels. Results from simulated inhalation exposures to BD indicate that incorporation of differential lung region metabolism is important in describing species differences in pulmonary response and that these differences may have implications for risk assessments of human exposures to BD.

1,3-Butadiene↗

DOE OSTI2025

A mathematical approach to using the forgetting curve to evaluate experience and training factors in human reliability analysis

Traditional human reliability analysis (HRA) methods have difficulty dealing with the dynamic nature of factors such as time and rely on static and expert-judgment-based assessments of performance-shaping factors (PSFs) across limited levels. In this study, we introduce a mathematical approach for dynamically evaluating the experience and training PSF. Our proposed method integrates the psychological concept of the “forgetting curve” to evaluate how PSFs are impacted by the number of trainings and the time elapsed since training. To confirm the validity of the model, we provide experimental data fitted by identifying the quantitative relationship between training and human performance. This research enables dynamic and objective assessments, thus reducing reliance on subjective expert judgment and improving the accuracy of HRA.

99 - GENERAL AND MISCELLANEOUS↗

DOE OSTI2021

Multi defect detection and analysis of electron microscopy images with deep learning

Electron microscopy is widely used to explore defects in crystal structures, but human detecting of defects is often time-consuming, error-prone, and unreliable, and is not scalable to large numbers of images or real-time analysis. In this work, we discuss the application of machine learning approaches to find the location and geometry of different defect clusters in irradiated steels. We show that a deep learning based Faster R-CNN analysis system has a performance comparable to human analysis with relatively small training data sets. Furthermore, this study proves the promising ability to apply deep learning to assist the development of automated microscopy data analysis even when multiple features are present and paves the way for fast, scalable, and reliable analysis systems for massive amounts of modern electron microscopy data.

36 MATERIALS SCIENCE↗