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DOE OSTI2021

Deciphering enhancer sequence using thermodynamics-based models and convolutional neural networks

Abstract Deciphering the sequence-function relationship encoded in enhancers holds the key to interpreting non-coding variants and understanding mechanisms of transcriptomic variation. Several quantitative models exist for predicting enhancer function and underlying mechanisms; however, there has been no systematic comparison of these models characterizing their relative strengths and shortcomings. Here, we interrogated a rich data set of neuroectodermal enhancers in Drosophila, representing cis- and trans- sources of expression variation, with a suite of biophysical and machine learning models. We performed rigorous comparisons of thermodynamics-based models implementing different mechanisms of activation, repression and cooperativity. Moreover, we developed a convolutional neural network (CNN) model, called CoNSEPT, that learns enhancer ‘grammar’ in an unbiased manner. CoNSEPT is the first general-purpose CNN tool for predicting enhancer function in varying conditions, such as different cell types and experimental conditions, and we show that such complex models can suggest interpretable mechanisms. We found model-based evidence for mechanisms previously established for the studied system, including cooperative activation and short-range repression. The data also favored one hypothesized activation mechanism over another and suggested an intriguing role for a direct, distance-independent repression mechanism. Our modeling shows that while fundamentally different models can yield similar fits to data, they vary in their utility for mechanistic inference. CoNSEPT is freely available at: https://github.com/PayamDiba/CoNSEPT.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

PayamDiba/CoNSEPT

Deciphering the sequence-function relationship encoded in enhancers holds the key to interpreting non-coding variants and understanding mechanisms of transcriptomic variation. Several quantitative models exist for predicting enhancer function and underlying mechanisms; however, there has been no systematic comparison of these models characterizing their relative strengths and shortcomings. Here, we interrogated a rich data set of neuroectodermal enhancers in Drosophila, representing cis- and trans- sources of expression variation, with a suite of biophysical and machine learning models. We performed rigorous comparisons of thermodynamics-based models implementing different mechanisms of activation, repression and cooperativity. Moreover, we developed a convolutional neural network (CNN) model, called CoNSEPT, that learns enhancer ‘grammar’ in an unbiased manner. CoNSEPT is the first general-purpose CNN tool for predicting enhancer function in varying conditions, such as different cell types and experimental conditions, and we show that such complex models can suggest interpretable mechanisms. We found model-based evidence for mechanisms previously established for the studied system, including cooperative activation and short-range repression. The data also favored one hypothesized activation mechanism over another and suggested an intriguing role for a direct, distance-independent repression mechanism. Our modeling shows that while fundamentally different models can yield similar fits to data, they vary in their utility for mechanistic inference.

Dibaeinia, Payam↗

DOE OSTI2022

High-Throughput Microfluidics Platform for Intracellular Delivery and Sampling of Biomolecules from Live Cells

Nondestructive cell membrane permeabilization systems enable the intracellular delivery of exogenous biomolecules for cell engineering tasks as well as the temporal sampling of cytosolic contents from live cells for the analysis of dynamic processes. Here, in this paper, we report a microwell array format live-cell analysis device (LCAD) that can perform localized-electroporation induced membrane permeabilization, for cellular delivery or sampling, and directly interfaces with surface-based biosensors for analyzing the extracted contents. We demonstrate the capabilities of the LCAD via an automated high-throughput workflow for multimodal analysis of live-cell dynamics, consisting of quantitative measurements of enzyme activity using self-assembled monolayers for MALDI mass spectrometry (SAMDI) and deep-learning enhanced imaging and analysis. By combining a fabrication protocol that enables robust assembly and operation of multilayer devices with embedded gold electrodes and an automated imaging workflow, we successfully deliver functional molecules (plasmid and siRNA) into live cells at multiple time-points and track their effect on gene expression and cell morphology temporally. Furthermore, we report sampling performance enhancements, achieving saturation levels of protein tyrosine phosphatase activity measured from as few as 60 cells, and demonstrate control over the amount of sampled contents by optimization of electroporation parameters using a lumped model. Lastly, we investigate the implications of cell morphology on electroporation-induced sampling of fluorescent molecules using a deep-learning enhanced image analysis workflow.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Overview of International Activities in Hydrogen System Safety in IEA Hydrogen TCP Task 43

Safety and reliability have long been recognized as key issues for the development, commercialization, and implementation of new technologies and infrastructure, and hydrogen systems are no exception to this rule. Reliability engineering, quantitative risk assessment (QRA), and knowledge exchange each play a key role in proactive addressing safety - before problems happen - and help us learn from problems if they happen. Many international research activities are focusing on both reliability and risk assessment for hydrogen systems. However, the element of knowledge exchange is sometimes less visible. To support international collaboration and knowledge exchange, the International Energy Agency (IEA) convened a new Technology Collaboration Program, "Task 43: Safety and Regulatory Aspects of Emerging Large Scale Hydrogen Energy Applications" started in June 2022. Within Task 43, Subtask E focuses on Hydrogen Systems Safety. This paper discusses the structure of the Hydrogen Systems Safety subtask and the aligned activities and introduces opportunities for future work.

HYDROGEN↗

NASA NTRSDate not supplied

Machine-learning Solution for Automatic Spacesuit Motion Recognition and Measurement from Conventional Video

Extravehicular Activity (EVA) spacesuits exhibit unique movement patterns due to their design characteristics. Mobility assessments using traditional motion capture systems are cost prohibitive and not feasible for some training conditions (e.g., simulated lunar outdoor terrain). This paper aims to present the ongoing development of machine learning solutions to quantify suit motions from conventional videos without special sensors or hardware. Given the fast growth in deep/machine learning technologies, external expertise was sought from open-source communities. This was expected to accelerate development and provide more cost-effective, time-saving solutions. This work was selected for a NASA Crowdsourcing project through an agency-wide solicitation. Partnerships were formed with the NASA JSC Center of Excellence for Collaborative Innovation and an execution crowdsourcing platform partner to solicit framework developments from external contenders. NASA provided contenders with video clips of spacesuits and simultaneously measured motion capture data during EVA simulation tasks. The contenders used this data to train and develop generalized algorithms to predict motions. At the end of the crowdsourcing event, five solutions were selected from 250 submissions. Each submission was tested and scored using video clips not previously disclosed to the contenders. The scoring metrics measured how well the algorithm detected the suit shape, the 2D suit joint detection accuracy, and 3D joint detection accuracy. The winning solution was able to achieve roughly 85% prediction accuracy (weighted combination of scoring metrics). Overall, the algorithms could efficiently detect various types of spacesuits and motions across different EVA simulation environments such as the Neutral Buoyancy Lab (NBL). However, 3D joint identification is less reliable when parts of the suit were obstructed in the image. After continued improvements and validation, the fully developed system will enable EVA stakeholders to quantify suit kinematic patterns, which can help optimize suit, hardware, and task designs.

Linh Vu↗

DOE OSTI2021

Machine Learning of Bacterial Transcriptomes Reveals Responses Underlying Differential Antibiotic Susceptibility

In vitro antibiotic susceptibility testing often fails to accurately predict in vivo drug efficacies, in part due to differences in the molecular composition between standardized bacteriologic media and physiological environments within the body. Here, we investigate the interrelationship between antibiotic susceptibility and medium composition in Escherichia coli K-12 MG1655 as contextualized through machine learning of transcriptomics data. Application of independent component analysis, a signal separation algorithm, shows that complex phenotypic changes induced by environmental conditions or antibiotic treatment are directly traced to the action of a few key transcriptional regulators, including RpoS, Fur, and Fnr. Integrating machine learning results with biochemical knowledge of transcription factor activation reveals medium-dependent shifts in respiration and iron availability that drive differential antibiotic susceptibility. By extension, the data generation and data analytics workflow used here can interrogate the regulatory state of a pathogen under any measured condition and can be applied to any strain or organism for which sufficient transcriptomics data are available.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2010

Operational Lessons Learned from the Ares I-X Flight Test

The Ares I-X flight test, launched in 2009, is the first test of the Ares I crew launch vehicle. This development flight test evaluated the flight dynamics, roll control, and separation events, but also provided early insights into logistical, stacking, launch, and recovery operations for Ares I. Operational lessons will be especially important for NASA as the agency makes the transition from the Space Shuttle to the Constellation Program, which is designed to be less labor-intensive. The mission team itself comprised only 700 individuals over the life of the project compared to the thousands involved in Shuttle and Apollo missions; while missions to and beyond low-Earth orbit obviously will require additional personnel, this lean approach will serve as a model for future Constellation missions. To prepare for Ares I-X, vehicle stacking and launch infrastructure had to be modified at Kennedy Space Center's Vehicle Assembly Building (VAB) as well as Launch Complex (LC) 39B. In the VAB, several platforms and other structures designed for the Shuttle s configuration had to be removed to accommodate the in-line, much taller Ares I-X. Vehicle preparation activities resulted in delays, but also in lessons learned for ground operations personnel, including hardware deliveries, cable routing, transferred work and custodial paperwork. Ares I-X also proved to be a resource challenge, as individuals and ground service equipment (GSE) supporting the mission also were required for Shuttle or Atlas V operations at LC 40/41 at Cape Canaveral Air Force Station. At LC 39B, several Shuttle-specific access arms were removed and others were added to accommodate the in-line Ares vehicle. Ground command, control, and communication (GC3) hardware was incorporated into the Mobile Launcher Platform (MLP). The lightning protection system at LC 39B was replaced by a trio of 600-foot-tall towers connected by a catenary wire to account for the much greater height of the vehicle. Like Shuttle, Ares I-X will be stacked on a MLP and rolled out to the pad on a Saturn-era crawler-transporter. While Ares I-X was only held in place by the four hold-down posts on its aft skirt during rollout, a new vehicle stabilization system (VSS) attached to the vertical service structure kept the vehicle from undue swaying prior to launch at the pad, LC 39B. Following the launch, the flight test vehicle first stage was recovered with the aid of new parachutes resized to accommodate the five-segment-long first stage, which had a much greater length and mass than the Shuttle s reusable solid rocket boosters. After splashdown, recovery divers exercised extra care when handling the first stage to ensure that the flight data recorders in the fifth segment simulator were not damaged by exposure to sea water. The data recovered from the Ares I-X flight test will be very valuable in verifying the predicted environments and models used to design the vehicle. Lessons learned from Ares I-X will be shared with the Ares Projects through written and verbal reports and through integration of mission team members into the Project workforce.

Davis, Stephan R.↗

DOE OSTI2023

Machine-Learning-Based Rotating Detonation Engine Diagnostics: Evaluation for Application in Experimental Facilities

Real-time monitoring of combustion behavior is a crucial step toward actively controlled rotating detonation engine (RDE) operation in laboratory and industrial environments. Various machine learning methods have been developed to advance diagnostic efficiencies from conventional postprocessing efforts to real-time methods. Here this work evaluates and compares conventional techniques alongside convolutional neural network (CNN) architectures trained in previous studies, including image classification, object detection, and time series classification, according to metrics affecting diagnostic feasibility, external applicability, and performance. Real-time, capable diagnostics are deployed and evaluated using an altered experimental setup. Image-based CNNs are applied to externally provided images to approximate dataset restrictions. Image classification using high-speed chemiluminescence images and time series classification using high-speed flame ionization and pressure measurements achieve classification speeds enabling real-time diagnostic capabilities, averaging laboratory-deployed diagnostic feedback rates of 4–5 Hz. Object detection achieves the most refined resolution of 20 μs in postprocessing. Image and time series classification require the additional correlation of sensor data, extending their time-step resolutions to 80 ms. Comparisons show that no single diagnostic approach outperforms its competitors across all metrics. This finding justifies the need for a machine learning portfolio containing a host of networks to address specific needs throughout the RDE research community.

33 ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2024

Time Series Foundation Models and Deep Learning Architectures for Earthquake Temporal and Spatial Nowcasting

Advancing the capabilities of earthquake nowcasting, the real-time forecasting of seismic activities, remains crucial for reducing casualties. This multifaceted challenge has recently gained attention within the deep learning domain, facilitated by the availability of extensive earthquake datasets. Despite significant advancements, the existing literature on earthquake nowcasting lacks comprehensive evaluations of pre-trained foundation models and modern deep learning architectures; each focuses on a different aspect of data, such as spatial relationships, temporal patterns, and multi-scale dependencies. This paper addresses the mentioned gap by analyzing different architectures and introducing two innovative approaches called Multi Foundation Quake and GNNCoder. We formulate earthquake nowcasting as a time series forecasting problem for the next 14 days within 0.1-degree spatial bins in Southern California. Earthquake time series are generated using the logarithm energy released by quakes, spanning 1986 to 2024. Our comprehensive evaluations demonstrate that our introduced models outperform other custom architectures by effectively capturing temporal-spatial relationships inherent in seismic data. The performance of existing foundation models varies significantly based on the pre-training datasets, emphasizing the need for careful dataset selection. However, we introduce a novel method, Multi Foundation Quake, that achieves the best overall performance by combining a bespoke pattern with Foundation model results handled as auxiliary streams.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS2012

Free-Flight Terrestrial Rocket Lander Demonstration for NASA's Autonomous Landing and Hazard Avoidance Technology (ALHAT) System

The Autonomous Landing Hazard Avoidance Technology (ALHAT) Project is chartered to develop and mature to a Technology Readiness Level (TRL) of six an autonomous system combining guidance, navigation and control with terrain sensing and recognition functions for crewed, cargo, and robotic planetary landing vehicles. The ALHAT System must be capable of identifying and avoiding surface hazards to enable a safe and accurate landing to within tens of meters of designated and certified landing sites anywhere on a planetary surface under any lighting conditions. Since its inception in 2006, the ALHAT Project has executed four field test campaigns to characterize and mature sensors and algorithms that support real-time hazard detection and global/local precision navigation for planetary landings. The driving objective for Government Fiscal Year 2012 (GFY2012) is to successfully demonstrate autonomous, real-time, closed loop operation of the ALHAT system in a realistic free flight scenario on Earth using the Morpheus lander developed at the Johnson Space Center (JSC). This goal represents an aggressive target consistent with a lean engineering culture of rapid prototyping and development. This culture is characterized by prioritizing early implementation to gain practical lessons learned and then building on this knowledge with subsequent prototyping design cycles of increasing complexity culminating in the implementation of the baseline design. This paper provides an overview of the ALHAT/Morpheus flight demonstration activities in GFY2012, including accomplishments, current status, results, and lessons learned. The ALHAT/Morpheus effort is also described in the context of a technology path in support of future crewed and robotic planetary exploration missions based upon the core sensing functions of the ALHAT system: Terrain Relative Navigation (TRN), Hazard Detection and Avoidance (HDA), and Hazard Relative Navigation (HRN).

Rutishauser, David K.↗

NASA NTRS2008

A Sample of What We Have Learned from A-Train Cloud Measurements

The A-train active sensors CloudSat and CALIPSO provide detailed information about cloud vertical structure. Coarse vertical information can also be obtained from a combination of passive sensors (e.g. cloud liquid water content from AMSR-E, cloud ice properties from MLS and HIRDLS, cloud-top pressure from MODIS and AIRS, and UVNISINear IR absorption and scattering from OMI, MODIS, and POLDER). In addition, the wide swaths of instruments such as MODIS, AIRS, OMI, POLDER, and AMSR-E can be exploited to create estimates of the three-dimensional cloud extent. We will show how data fusion from A-train sensors can be used, e.g., to detect and map the presence of multiple layer/phase clouds. Ultimately, combined cloud information from Atrain instruments will allow for estimates of heating and radiative flux at the surface as well as UV/VIS/Near IR trace-gas absorption at the overpass time on a near-global daily basis. CloudSat has also dramatically improved our interpretation of visible and UV passive measurements in complex cloudy situations such as deep convection and multiple cloud layers. This has led to new approaches for unique and accurate constituent retrievals from A-train instruments. For example, ozone mixing ratios inside tropical deep convective clouds have recently been estimated using the Aura Ozone Monitoring Instrument (OMI). Field campaign data from TC4 provide additional information about the spatial variability and origin of trace-gases inside convective clouds. We will highlight some of the new applications of remote sensing in cloudy conditions that have been enabled by the synergy between the A-train active and passive sensors.

Joiner, Joanna↗

DOE OSTI2022

Incorporating polar field data for improved solar flare prediction

In this paper, we consider incorporating data associated with the sun’s north and south polar field strengths to improve solar flare prediction performance using machine learning models. When used to supplement local data from active regions on the photospheric magnetic field of the sun, the polar field data provides global information to the predictor. While such global features have been previously proposed for predicting the next solar cycle’s intensity, in this paper we propose using them to help classify individual solar flares. We conduct experiments using HMI data employing four different machine learning algorithms that can exploit polar field information. Additionally, we propose a novel probabilistic mixture of experts model that can simply and effectively incorporate polar field data and provide on-par prediction performance with state-of-the-art solar flare prediction algorithms such as the Recurrent Neural Network (RNN). Our experimental results indicate the usefulness of the polar field data for solar flare prediction, which can improve Heidke Skill Score (HSS2) by as much as 10.1%.

79 ASTRONOMY AND ASTROPHYSICS↗

NASA NTRS2004

The PMDP Roadmap

NASA's complex and highly technical missions rely on effective project teams and managers. Since 1993, through its Project Management Development Process (PMDP), the Academy of Program and Project Leadership (APPL) has offered direction to the Agency's project practitioners as they advance in their careers. PMDP helps identify and sequence professional experiences, courses, and other project-based learning experiences that support individual career goals and center activities by outlining competencies at four levels of development. The result is that PMDP provides NASA project practitioners with a road map to the knowledge and competencies appropriate for their job and the jobs to which they aspire. Plus, new this year, APPL has rolled out its electronic Project Management Development Process (ePMDP) tool, a learning management system that includes a dynamic presentation of the PMDP levels, competency areas, competency organizational structures, Individual Development Plans (IDP), and online PMDP enrollment. APPL's website, www.appl.nasa.gov, provides access to ePMDP as well as other online resources for NASA practitioners enrolled in the Project Management Development Process.

Source record↗

DOE OSTI2022

Geochemistry and Multiomics Data Differentiate Streams in Pennsylvania Based on Unconventional Oil and Gas Activity

Unconventional oil and gas (UOG) extraction is increasing exponentially around the world, as new technological advances have provided cost-effective methods to extract hard-to-reach hydrocarbons. While UOG has increased the energy output of some countries, past research indicates potential impacts in nearby stream ecosystems as measured by geochemical and microbial markers. Here, we utilized a robust data set that combines 16S rRNA gene amplicon sequencing (DNA), metatranscriptomics (RNA), geochemistry, and trace element analyses to establish the impact of UOG activity in 21 sites in northern Pennsylvania. These data were also used to design predictive machine learning models to determine the UOG impact on streams. We identified multiple biomarkers of UOG activity and contributors of antimicrobial resistance within the order Burkholderiales. Furthermore, we identified expressed antimicrobial resistance genes, land coverage, geochemistry, and specific microbes as strong predictors of UOG status. Of the predictive models constructed (n = 30), 15 had accuracies higher than expected by chance and area under the curve values above 0.70. The supervised random forest models with the highest accuracy were constructed with 16S rRNA gene profiles, metatranscriptomics active microbial composition, metatranscriptomics active antimicrobial resistance genes, land coverage, and geochemistry (n = 23). The models identified the most important features within those data sets for classifying UOG status. These findings identified specific shifts in gene presence and expression, as well as geochemical measures, that can be used to build robust models to identify impacts of UOG development.

16S rRNA↗

DOE OSTI2020

The Spatiotemporal Evolution of Granular Microslip Precursors to Laboratory Earthquakes

Laboratory earthquake experiments provide important observational constraints for our understanding of earthquake physics. Here we leverage continuous waveform data from a network of piezoceramic sensors to study the spatial and temporal evolution of microslip activity during a shear experiment with synthetic fault gouge. We combine machine learning techniques with ray theoretical seismology to detect, associate, and locate tens of thousands of microslip events within the gouge layer. Microslip activity is concentrated near the center of the system but is highly variable in space and time. While microslip activity rate increases as failure approaches, the spatiotemporal evolution can differ substantially between stick-slip cycles. These results illustrate that even within a single, well-constrained laboratory experiment, the dynamics of earthquake nucleation can be highly complex.

58 GEOSCIENCES↗

DOE OSTI2023

The LSST AGN Data Challenge: Selection Methods

Abstract Development of the Rubin Observatory Legacy Survey of Space and Time (LSST) includes a series of Data Challenges (DCs) arranged by various LSST Scientific Collaborations that are taking place during the project's preoperational phase. The AGN Science Collaboration Data Challenge (AGNSC-DC) is a partial prototype of the expected LSST data on active galactic nuclei (AGNs), aimed at validating machine learning approaches for AGN selection and characterization in large surveys like LSST. The AGNSC-DC took place in 2021, focusing on accuracy, robustness, and scalability. The training and the blinded data sets were constructed to mimic the future LSST release catalogs using the data from the Sloan Digital Sky Survey Stripe 82 region and the XMM-Newton Large Scale Structure Survey region. Data features were divided into astrometry, photometry, color, morphology, redshift, and class label with the addition of variability features and images. We present the results of four submitted solutions to DCs using both classical and machine learning methods. We systematically test the performance of supervised models (support vector machine, random forest, extreme gradient boosting, artificial neural network, convolutional neural network) and unsupervised ones (deep embedding clustering) when applied to the problem of classifying/clustering sources as stars, galaxies, or AGNs. We obtained classification accuracy of 97.5% for supervised models and clustering accuracy of 96.0% for unsupervised ones and 95.0% with a classic approach for a blinded data set. We find that variability features significantly improve the accuracy of the trained models, and correlation analysis among different bands enables a fast and inexpensive first-order selection of quasar candidates.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2023

Solving multiphysics-based inverse problems with learned surrogates and constraints

Abstract Solving multiphysics-based inverse problems for geological carbon storage monitoring can be challenging when multimodal time-lapse data are expensive to collect and costly to simulate numerically. We overcome these challenges by combining computationally cheap learned surrogates with learned constraints. Not only does this combination lead to vastly improved inversions for the important fluid-flow property, permeability, it also provides a natural platform for inverting multimodal data including well measurements and active-source time-lapse seismic data. By adding a learned constraint, we arrive at a computationally feasible inversion approach that remains accurate. This is accomplished by including a trained deep neural network, known as a normalizing flow, which forces the model iterates to remain in-distribution, thereby safeguarding the accuracy of trained Fourier neural operators that act as surrogates for the computationally expensive multiphase flow simulations involving partial differential equation solves. By means of carefully selected experiments, centered around the problem of geological carbon storage, we demonstrate the efficacy of the proposed constrained optimization method on two different data modalities, namely time-lapse well and time-lapse seismic data. While permeability inversions from both these two modalities have their pluses and minuses, their joint inversion benefits from either, yielding valuable superior permeability inversions and CO 2 plume predictions near, and far away, from the monitoring wells.

Yin, Ziyi (ORCID:0000000250248771)↗

DOE OSTI2025

Subspace-Driven Learning for Anomaly Detection in Process Transients

Nuclear power plant (NPP) monitoring and diagnostic centers are actively investigating and implementing automated anomaly detection algorithms to help plants catch anomalies sooner, thereby preventing or reducing the duration of unexpected shutdowns. Current machine learning-based anomaly detection methods are expected to be highly effective during stable, full-power operations because NPPs typically operate as baseload power generators, meaning there are extensive operating data available from plant equipment. However, it is expected that anomaly detection methods will face significant challenges during transient conditions (i.e., when power output falls below full power) because plants only occasionally operate at these lower power levels, generating sparse transient operational data, and resulting in false alarms or missed detections. Here, to address this issue, transfer learning is used, which for this problem leverages knowledge (in the form of learned features) from stable, full-power operations to improve detection accuracy during transient conditions, even with limited data. In this effort, a novel subspace approach is developed to transfer a subset of the data features from full power operation to transients. This approach is validated through experiments using synthetic data and was found to outperform two baseline transfer learning approaches in anomaly detection performance across a range of amounts of transient data used in the training process.

46 - INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AN↗