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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

Hydroacoustic Assessment of Behavioral Responses by Fish Passing Near an Operating Tidal Turbine in the East River, New York

An important environmental issue facing the marine and hydrokinetic energy industry is whether fish that encounter underwater energy devices are likely to be struck and injured by moving components, primarily rotating turbine blades. The automated analysis of nearly 3 weeks of multibeam hydroacoustics data identified about 35,000 tracks of fish passing a tidal turbine in the East River, New York. These tracks included both individual fish and schools during periods with the turbine absent, the turbine present and operating, and the turbine present but not operating. The density of fish in the sampled area when the turbine was absent was roughly twice the density observed when the turbine was in place, particularly when the turbine was operating. This suggests that some avoidance occurred before fish were close enough to the turbine to be observed by the hydroacoustics system. Various measures of swimming behavior (direction, velocity, and linearity) were calculated for each track and evaluated for indication of behavioral responses to turbine presence and operation. Fish tracks were grouped based on tidal cycle, current velocity, and swimming direction and were evaluated with respect to turbine presence and operation and with respect to distance from the turbine. Nonparametric tests (Kolmogorov–Smirnov test) and multivariate analysis (canonical discriminant analysis) found significant differences among groups with respect to turbine presence and operation, suggesting that some fish responded to the turbine by adjusting swimming behavior, such as making small adjustments to swimming direction and velocity as they passed near the turbine. We found no evidence that fish were being struck by rotating blades, but there did appear to be large-scale avoidance initiated out of the range of the hydroacoustics detection system. Furthermore, more study is needed to determine whether such avoidance behavior has significant ramifications for normal fish movement patterns, bioenergetics, seasonal migrations, and predator exposure.

13 HYDRO ENERGY↗
DOE OSTI2013

Quantification of organ motion based on an adaptive image-based scale invariant feature method

Purpose: The availability of corresponding landmarks in IGRT image series allows quantifying the inter and intrafractional motion of internal organs. In this study, an approach for the automatic localization of anatomical landmarks is presented, with the aim of describing the nonrigid motion of anatomo-pathological structures in radiotherapy treatments according to local image contrast.Methods: An adaptive scale invariant feature transform (SIFT) was developed from the integration of a standard 3D SIFT approach with a local image-based contrast definition. The robustness and invariance of the proposed method to shape-preserving and deformable transforms were analyzed in a CT phantom study. The application of contrast transforms to the phantom images was also tested, in order to verify the variation of the local adaptive measure in relation to the modification of image contrast. The method was also applied to a lung 4D CT dataset, relying on manual feature identification by an expert user as ground truth. The 3D residual distance between matches obtained in adaptive-SIFT was then computed to verify the internal motion quantification with respect to the expert user. Extracted corresponding features in the lungs were used as regularization landmarks in a multistage deformable image registration (DIR) mapping the inhale vs exhale phase. The residual distances between the warped manual landmarks and their reference position in the inhale phase were evaluated, in order to provide a quantitative indication of the registration performed with the three different point sets.Results: The phantom study confirmed the method invariance and robustness properties to shape-preserving and deformable transforms, showing residual matching errors below the voxel dimension. The adapted SIFT algorithm on the 4D CT dataset provided automated and accurate motion detection of peak to peak breathing motion. The proposed method resulted in reduced residual errors with respect to standard SIFT, providing a motion description comparable to expert manual identification, as confirmed by DIR.Conclusions: The application of the method to a 4D lung CT patient dataset demonstrated adaptive-SIFT potential as an automatic tool to detect landmarks for DIR regularization and internal motion quantification. Future works should include the optimization of the computational cost and the application of the method to other anatomical sites and image modalities.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2015

A “loop” shape descriptor and its application to automated segmentation of airways from CT scans

Purpose: A novel shape descriptor is presented to aid an automated identification of the airways depicted on computed tomography (CT) images. Methods: Instead of simplifying the tubular characteristic of the airways as an ideal mathematical cylindrical or circular shape, the proposed “loop” shape descriptor exploits the fact that the cross sections of any tubular structure (regardless of its regularity) always appear as a loop. In implementation, the authors first reconstruct the anatomical structures in volumetric CT as a three-dimensional surface model using the classical marching cubes algorithm. Then, the loop descriptor is applied to locate the airways with a concave loop cross section. To deal with the variation of the airway walls in density as depicted on CT images, a multiple threshold strategy is proposed. A publicly available chest CT database consisting of 20 CT scans, which was designed specifically for evaluating an airway segmentation algorithm, was used for quantitative performance assessment. Measures, including length, branch count, and generations, were computed under the aid of a skeletonization operation. Results: For the test dataset, the airway length ranged from 64.6 to 429.8 cm, the generation ranged from 7 to 11, and the branch number ranged from 48 to 312. These results were comparable to the performance of the state-of-the-art algorithms validated on the same dataset. Conclusions: The authors’ quantitative experiment demonstrated the feasibility and reliability of the developed shape descriptor in identifying lung airways.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Design of machine learning models with domain experts for automated sensor selection for energy fault detection

Data-driven techniques that extract insights from sensor data reduce the cost of improving system energy performance through fault detection and system health monitoring. To lower cost barriers to widespread deployment, a methodology is proposed that takes advantage of existing sensor data, encodes expert knowledge about the application system to create ‘virtual sensors’ and applies statistical and mathematical methods to reduce the time required for manual configurations. The approach combines sensor data points with encoded expert knowledge that is generic to the application system but independent of a particular deployment, thereby reducing the need to tailor to individual deployments. Additionally, this paper not only presents a method that detects faults from measured energy data, but also (1) describes an engagement method with experts in the energy system domain to identify data, (2) integrates domain knowledge with the data, (3) automatically selects from among the large pool of potential input data, and (4) uses machine learning to automatically build a data-driven fault detection model. Demonstration on a commercial building chiller plant shows that only a small number of virtual sensors is necessary for fault detection with high accuracy rates. This corresponds to the use of only five out of 52 original sensor data points features. With as few as four features, classification F1 scores exceed 90% on the training set and 80% on the testing set. The results are implementable and realizable using off-the-shelf tools. The goal is to design with domain experts an energy monitoring system that can be configured once and then widely deployed with little additional cost or effort.

47 OTHER INSTRUMENTATION↗
DOE OSTI2022

Automated identification of local contamination in remote atmospheric composition time series

Abstract. Atmospheric observations in remote locations offer a possibility of exploring trace gas and particle concentrations in pristine environments. However, data from remote areas are often contaminated by pollution from local sources. Detecting this contamination is thus a central and frequently encountered issue. Consequently, many different methods exist today to identify local contamination in atmospheric composition measurement time series, but no single method has been widely accepted. In this study, we present a new method to identify primary pollution in remote atmospheric datasets, e.g., from ship campaigns or stations with a low background signal compared to the contaminated signal. The pollution detection algorithm (PDA) identifies and flags periods of polluted data in five steps. The first and most important step identifies polluted periods based on the derivative (time derivative) of a concentration over time. If this derivative exceeds a given threshold, data are flagged as polluted. Further pollution identification steps are a simple concentration threshold filter, a neighboring points filter (optional), a median, and a sparse data filter (optional). The PDA only relies on the target dataset itself and is independent of ancillary datasets such as meteorological variables. All parameters of each step are adjustable so that the PDA can be “tuned” to be more or less stringent (e.g., flag more or fewer data points as contaminated). The PDA was developed and tested with a particle number concentration dataset collected during the Multidisciplinary drifting Observatory for the Study of Arctic Climate (MOSAiC) expedition in the central Arctic. Using strict settings, we identified 62 % of the data as influenced by local contamination. Using a second independent particle number concentration dataset also collected during MOSAiC, we evaluated the performance of the PDA against the same dataset cleaned by visual inspection. The two methods agreed in 94 % of the cases. Additionally, the PDA was successfully applied to a trace gas dataset (CO2), also collected during MOSAiC, and to another particle number concentration dataset, collected at the high-altitude background station Jungfraujoch, Switzerland. Thus, the PDA proves to be a useful and flexible tool to identify periods affected by local contamination in atmospheric composition datasets without the need for ancillary measurements. It is best applied to data representing primary pollution. The user-friendly and open-access code enables reproducible application to a wide suite of different datasets. It is available at https://doi.org/10.5281/zenodo.5761101 (Beck et al., 2021).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Flux REaction TArget Prioritization (Flux RETAP) v1

Metabolic engineering is evolving rapidly as a result of new advances in synthetic biology and automation, as well as the irruption of machine learning (ML). ML has been shown to provide the predictive power synthetic biology lacked and needed, and to be able to effectively guide the metabolic engineering process. However, current technical limitations prevent the independent application of ML approaches to metabolic engineering without the use of previous biological knowledge in the form of a prioritized list of desirable engineering targets. Here, we present FluxRETAP, a simple and computationally inexpensive method that leverages the prior mechanistic knowledge embedded in genome-scale metabolic models (GSMs) for suggesting targets for genetic overexpression, downregulation or deletion, with the final goal of increasing metabolite production. FluxRETAP captured 100% of reaction targets experimentally verified to improve Escherichia coli isoprenol production in the literature accessible to us, 50% of targets that experimentally improved taxadiene production in E. coli and ~60% of genetic targets from a verified minimal constrained cut-set in Pseudomonas putida while providing additional high priority targets that could be tested. Overall, FluxRETAP is an efficient algorithm for identifying a prioritized list of testable genetic and reaction targets which can also be utilized in ML pipelines.

Czajka, Jeffrey [Battelle Memorial Institute, Paci↗
DOE OSTI2016

Development and Validation of a Polarimetric-MCScene 3D Atmospheric Radiation Model

Polarimetric measurements can substantially enhance the ability of both spectrally resolved and single band imagery to detect the proliferation of weapons of mass destruction, providing data for locating and identifying facilities, materials, and processes of undeclared and proliferant nuclear weapons programs worldwide. Unfortunately, models do not exist that efficiently and accurately predict spectral polarized signatures for the materials of interest embedded in complex 3D environments. Having such a model would enable one to test hypotheses and optimize both the enhancement of scene contrast and the signal processing for spectral signature extraction. The Phase I set the groundwork for development of fully validated polarimetric spectral signature and scene simulation models. This has been accomplished 1. by (a) identifying and downloading state-of-the-art surface and atmospheric polarimetric data sources, (b) implementing tools for generating custom polarimetric data, and (c) identifying and requesting US Government funded field measurement data for use in validation; 2. by formulating an approach for upgrading the radiometric spectral signature model MODTRAN to generate polarimetric intensities through (a) ingestion of the polarimetric data, (b) polarimetric vectorization of existing MODTRAN modules, and (c) integration of a newly developed algorithm for computing polarimetric multiple scattering contributions; 3. by generating an initial polarimetric model that demonstrates calculation of polarimetric solar and lunar single scatter intensities arising from the interaction of incoming irradiances with molecules and aerosols; 4. by developing a design and implementation plan to (a) automate polarimetric scene construction and (b) efficiently sample polarimetric scattering and reflection events, for use in a to be developed polarimetric version of the existing first-principles synthetic scene simulation model, MCScene; and 5. by planning a validation field measurement program in collaboration with the Remote Sensing and Exploitation group at Sandia National Laboratories (SNL) in which data from their ongoing polarimetric field and laboratory measurement program will be shared and, to the extent allowed, tailored for model validation in exchange for model predictions under conditions and for geometries outside of their measurement domain.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗
DOE OSTI2018

Recurrent Neural Network Language Models for Open Vocabulary Event-Level Cyber Anomaly Detection

Automated analysis methods are crucial aids for monitoring and defending a network to protect the sensitive or confidential data it hosts. This work introduces a flexible, powerful, and unsupervised approach to detecting anomalous behavior in computer and network logs; one that largely eliminates domain-dependent feature engineering employed by existing methods. By treating system logs as threads of interleaved ``sentences'' (event log lines) to train online unsupervised neural network language models, our approach provides an adaptive model of normal network behavior. We compare the effectiveness of both standard and bidirectional recurrent neural network language models at detecting malicious activity within network log data. Extending these models, we introduce a tiered recurrent architecture, which provides context by modeling sequences of users' actions over time. Compared to isolation forests and Principal Components Analysis (PCA), two popular anomaly detection algorithms, we observe superior performance on the Los Alamos National Laboratory Cyber Security dataset. For log-line-level predictions, our best performing character-based model provides test set anomaly scores ranking red team events in the 98th percentile on average, and yields 0.97 area under the receiver operator characteristic curve, demonstrating the strong fine-grained anomaly detection performance of this approach on open vocabulary logging sources.

Cyber Analysis, Deep Learning, language analysis, ↗
DOE OSTI2018

Soft Robotic Glove System for Wearable Haptic Teleoperation - 18373

Managing nuclear waste is a difficult, dangerous, and costly task. Teleoperation of robotic operators is an important functionality for this application, allowing robotic devices to operate in dangerous environments while still leveraging the existing abilities and technical knowledge of human workers. One difficulty in implementing effective teleoperation systems is that human operators rely on more senses beside sight: in particular, touch. The sense of touch could provide significant benefits for teleoperation, preventing environmental mishaps that could cost millions of dollars. To help remedy this problem, we present a soft haptic feedback glove system. The primary functionality of this system is to provide tactile and force feedback on the user's hands. This was achieved using custom cylindrical pneumatic actuators. These actuators consist of plastic sheeting folded into a hollow-walled cylinder which is connected to a pressure source. When pressurized, the cylinder walls expand and the cylinder straightens, with the force being related to the pressure. The glove system has one of these actuators over each of the user's three main fingers (index, middle, and thumb), where pressurizing the actuator applies a reaction force to the finger of the user, mimicking the resistance of a grasped object. The expansion of these actuators also causes them to physically press against the user's fingers, giving them the feeling of contact. To demonstrate the usability of this system, we implemented a virtual environment in V-REP simulating the interactions between a robotic Jaco Arm and a floating ball. This simulation receives hand and figure positions from the haptic glove and used them to drive the state of the simulated Jaco Arm. In response to the interactions between the Jaco and the floating ball, the simulation returns commands to the glove, instructing it to pressurize or depressurize its actuators as appropriate, allowing the user to feel the ball in their hand. We tested users in their ability to prevent the ball from floating away using this system with and without the haptic feedback. Results show that the addition of haptic feedback significantly improved the ability of users to interact precisely with the environment. We also used the finger positions of the haptic glove to control a physical robotic hand, and demonstrated the system's usability for control of real robots, though the lack of sensors on the robot made providing the tactile feedback impractical. However, there is more to grasping and holding an object than just the feeling of contact and the resistance to closing one's hand. The weight of the object will apply forces to the user's other joints as they hold it. To this end, we added a haptic feedback device for the user's wrist, a technique that can be generalized to the user's other joints. This is made up of reverse Pneumatic Artificial Muscles (rPAMs) stretching across the wrist between mounts on the hand and forearm. These rPAM actuators are tubes of silicone wrapped in thread such that they extend when pressurized. This extension can apply torque on the user's wrist, mimicking the feeling of gravity, or allowing the simulation of additional contact forces (such as the user's hand impacting an object). We tested this wrist device independently using a simulated path-following experiment. Users showed a significant improvement in performance when aided by haptic feedback during sinusoidal path experiments, demonstrating the usability of this approach. We then integrated the two systems, further demonstrating the usability of this approach. This project represents the first step towards a more effective robotic teleoperation system, allowing skilled human workers to perform tasks more effectively while remaining out of danger. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2023

Final Technical Report

Statement of the problem or situation that is being addressed in your application. The DOE and its national laboratories developed the Home Energy Score™ (HES) to encourage homeowners to improve their energy performance, lower costs and to share energy information through the MLS listing, appraisal, and financing channels. While the HES is an instrumental tool, it is currently underutilized and consists of technical, structural and sector barriers which need to be addressed in order to scale and many energy efficiency contractors are understandably overwhelmed by the added time and effort and lack of incentive to sell and deliver deep retrofit projects while simultaneously meeting the DOE HES program requirements; consequently, contractors may decide to forgo participation. Home Energy Rating System (HERS) Raters have the opportunity to play the critical Assessor role in producing a Home Energy Score (HES); this role has immense potential but currently is unfulfilled. Lastly, while utilities are interested in their customer base achieving greater energy efficiency, especially to help offset growing residential loads in states like California that are accelerating electrification, utilities do not have access to the market actors who are on the front line of influence to homeowners or review and approve their permits: HERS Raters, assessors, contractors and building departments. General statement of how this problem is being addressed: ConSol will integrate the Home Energy Score™ (HES) to its State of California, approved home energy rating services (HERS) platform (CHEERS) to develop a single tool for contractors nationwide to assess, record and install recommended cost, energy, and emissions saving measures to the 140 million single-family homes throughout the U.S. and 14 million homes in California (CHEERS+HES). The CHEERS high fidelity energy code permitting data will be integrated with HES for simple, accurate, easy-to-use home energy estimation and analysis and will directly gain access to the retrofit and renovations markets with the same upgraded platform. This innovative project will assist the utilities in supporting existing homes in their jurisdictions with HES and develop measures to improve energy efficiency and reduce emissions. How is this problem being addressed? What is the overall project approach? In effort to expand the Home Energy Score™ (HES) by increasing the use of aggregable home energy asset data, ConSol proposes to integrate the DOE HES via Application Programming Interface (API) to its State of California approved home energy rating services platform (CHEERS). Once the CHEERS platform and HES are integrated (CHEERS+HES), this enhanced platform will be instantly available and actively deployed via Phase 1 pilot to HERS Raters, assessors and contractors in California to market-test the solution, understand the rate of adoption and identify opportunities for improvement prior to scaling nationally. The CHEERS high fidelity energy code permitting data will be integrated with HES for simple, accurate, easy-to-use home energy estimation and analysis and will directly gain access to the retrofit and renovations markets with the same upgraded platform. This innovative project will assist the building industry and homeowners with an easy-to-use assessment if energy and carbon impacts of existing homes, and assist the utilities in supporting existing homes in their jurisdictions with HES to improve energy efficiency and reduce emissions. What is to be done in Phase I? During Phase I of this proposed project, ConSol will (1) design software architecture that links CHEERS to the Home Energy ScoreTM via API, (2) solicit partnership from one or more California utilities for a regional pilot, (3) test the new software with its HERS Raters and contractor network in the partnership utility jurisdiction, (4) launch a pilot version of the newly developed software with HERS Raters and contractors in the utility territory, and (5) explore California’s GoGreen energy efficiency homeowner lending program in parallel with the pilot. Commercial Applications and Other Benefits. Summarize the future applications or public benefits if the project is carried over into Phase II or Phase III and beyond. The CHEERS+HES commercialized product will be ready for national market scale following a successful Phase 1 performance. The CHEERS+HES adoption is estimated to reach a 5% adoption growth rate versus the 110,000 baseline, starting in Year 1 after Phase I completion, and continuing each year. As a direct benefit to the DOE, CHEERS will set a goal of 100,000 Home Energy Score assessments for existing home alterations within the first 10 years following Phase 1 performance. The technical benefits of this proposed project include the harmonized, automated, and seamless integration of the DOE HES into the widely used and market leading California energy registry, CHEERS. The social benefits include the aggregate energy, cost and GHG savings by allowing the broader public streamlined access to the CHEERS+HES measurement and the energy efficiency recommended measures that may result. Key Words: Home Energy ScoreTM (HES); Application Programming Interface (API); Home Energy Rating Services (HERS); HERS Raters; contractors; assessors; existing homes, energy asset data; cost, energy, and emissions saving measures; energy code (Title 24) compliance; document repository; utilities; pilot; newly developed software; energy efficiency; homeowner. Summary for Members of Congress: The DOE Home Energy Score™ (HES) is a tool to encourage homeowners to improve their energy performance, lower costs and share energy information but is underutilized and consists of barriers which need to be addressed in order to scale. In effort to expand the HES, CHEERS, Inc. will integrate the HES to its State of California, approved home energy rating services (HERS) platform (CHEERS) to develop a single tool for contractors nationwide to assess, record and install recommended cost, energy, and emissions saving measures to the 140 million single-family homes throughout the U.S. and 14 million homes in California.

Application Programming Interface (API)↗
DOE OSTI2016

A SPATIOTEMPORAL APPROACH FOR HIGH RESOLUTION TRAFFIC FLOW IMPUTATION

Along with the rapid development of Intelligent Transportation Systems (ITS), traffic data collection technologies have been evolving dramatically. The emergence of innovative data collection technologies such as Remote Traffic Microwave Sensor (RTMS), Bluetooth sensor, GPS-based Floating Car method, automated license plate recognition (ALPR) (1), etc., creates an explosion of traffic data, which brings transportation engineering into the new era of Big Data. However, despite the advance of technologies, the missing data issue is still inevitable and has posed great challenges for research such as traffic forecasting, real-time incident detection and management, dynamic route guidance, and massive evacuation optimization, because the degree of success of these endeavors depends on the timely availability of relatively complete and reasonably accurate traffic data. A thorough literature review suggests most current imputation models, if not all, focus largely on the temporal nature of the traffic data and fail to consider the fact that traffic stream characteristics at a certain location are closely related to those at neighboring locations and utilize these correlations for data imputation. To this end, this paper presents a Kriging based spatiotemporal data imputation approach that is able to fully utilize the spatiotemporal information underlying in traffic data. Imputation performance of the proposed approach was tested using simulated scenarios and achieved stable imputation accuracy. Moreover, the proposed Kriging imputation model is more flexible compared to current models.

Han, Lee↗
DOE OSTI2013

A measurement technique to determine the calibration accuracy of an electromagnetic tracking system to radiation isocenter

Purpose: To present and characterize a measurement technique to quantify the calibration accuracy of an electromagnetic tracking system to radiation isocenter.Methods: This technique was developed as a quality assurance method for electromagnetic tracking systems used in a multi-institutional clinical hypofractionated prostate study. In this technique, the electromagnetic tracking system is calibrated to isocenter with the manufacturers recommended technique, using laser-based alignment. A test patient is created with a transponder at isocenter whose position is measured electromagnetically. Four portal images of the transponder are taken with collimator rotations of 45° 135°, 225°, and 315°, at each of four gantry angles (0°, 90°, 180°, 270°) using a 3 × 6 cm{sup 2} radiation field. In each image, the center of the copper-wrapped iron core of the transponder is determined. All measurements are made relative to this transponder position to remove gantry and imager sag effects. For each of the 16 images, the 50% collimation edges are identified and used to find a ray representing the rotational axis of each collimation edge. The 16 collimator rotation rays from four gantry angles pass through and bound the radiation isocenter volume. The center of the bounded region, relative to the transponder, is calculated and then transformed to tracking system coordinates using the transponder position, allowing the tracking system's calibration offset from radiation isocenter to be found. All image analysis and calculations are automated with inhouse software for user-independent accuracy. Three different tracking systems at two different sites were evaluated for this study.Results: The magnitude of the calibration offset was always less than the manufacturer's stated accuracy of 0.2 cm using their standard clinical calibration procedure, and ranged from 0.014 to 0.175 cm. On three systems in clinical use, the magnitude of the offset was found to be 0.053 ± 0.036, 0.121 ± 0.023, and 0.093 ± 0.013 cm.Conclusions: The method presented here provides an independent technique to verify the calibration of an electromagnetic tracking system to radiation isocenter. The calibration accuracy of the system was better than the 0.2 cm accuracy stated by the manufacturer. However, it should not be assumed to be zero, especially for stereotactic radiation therapy treatments where planning target volume margins are very small.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2024

NuQKD: A Modular Quantum Key Distribution Simulation Framework for Engineering Applications

Abstract An experimental Quantum Key Distribution (QKD) implementation requires advanced costly hardware, unavailable in most research environments, making protocol testing and performance evaluation complicated. This has been a major motivation for the development of QKD simulation frameworks, to allow researchers to obtain insight before proceeding into practical implementations. Several simulators have been introduced over the recent years. However, only four are publicly available, only one of which models equipment imperfections. Currently, no open‐source simulator includes all following capabilities: channel attenuation modelling, equipment imperfections and effects on key rates, estimation of elapsed time during classical and quantum‐ channel processes, use of truly random binary sequences for qubits and measurement bases, shared ‐bit fraction customization. In this paper, we present NuQKD, an open‐ source modular, intuitive simulator, featuring all the above capabilities. NuQKD establishes communication between two computer terminals, accepts custom user inputs (iterations, raw key size, attacker interception rate etc.) and evaluates the sifted key, Quantum Bit Error Rate (QBER), elapsed communication time, and more. NuQKD capabilities include optical fiber and free ‐space simulation, modeling of equipment/channel imperfections, bitstrings from True Random Number Generators, decoy‐state protocol support, and automated evaluation of performance metrics. We expect NuQKD to enable convenient and accurate representation of actual experimental conditions.

Gkouliaras, Konstantinos↗
DOE OSTI2022

Artificial intelligence based analysis of nanoindentation load–displacement data using a genetic algorithm

In this work, we developed an automated tool, Nanoindentation Neo package for the analysis of nanoindentation load–displacement curves using a Genetic Algorithm (GA) applied to the Oliver-Pharr method (Oliver et al.,1992). For some materials, such as polycrystalline isotropic graphites, Least Squares Fitting (LSF) of the unload curve can produce unrealistic fit parameters. These graphites exhibit sharply peaked unloading curves not easily fit using the LSF, which tends to overestimate the indenter tip geometry parameter. To tackle this problem, we extended our general materials characterization tool Neo for EXAFS analysis (Terry et al., 2021) to fit nanoindentation data. Nanoindentation Neo automatically processes and analyzes nanoindentation data with minimal user input while producing meaningful fit parameters. GA, a robust metaheuristic method, begins with a population of temporary solutions using model parameters called chromosomes; from these we evaluate a fitness value for each solution, and select the best solutions to mix with random solutions producing the next generation. A mutation operator then modifies existing solutions by random perturbations, and the optimal solution is selected. We tested the GA method using Silica and Al reference standards. We fit samples of graphite and a high entropy alloy (HEA) consisting of BCC and FCC phases.

42 ENGINEERING↗
DOE OSTI2023

HOLISMOKES IX. Neural network inference of strong-lens parameters and uncertainties from ground-based images

Modeling of strong gravitational lenses is a necessity for further applications in astrophysics and cosmology. With the large number of detections in current and upcoming surveys, such as the Rubin Legacy Survey of Space and Time (LSST), it is pertinent to investigate automated and fast analysis techniques beyond the traditional and time-consuming Markov chain Monte Carlo sampling methods. Building upon our (simple) convolutional neural network (CNN), we present here another CNN, specifically a residual neural network (ResNet), that predicts the five mass parameters of a singular isothermal ellipsoid (SIE) profile (lens center x and y, ellipticity e x and e y , Einstein radius θ E ) and the external shear (γ ext, 1 , γ ext, 2 ) from ground-based imaging data. In contrast to our previous CNN, this ResNet further predicts the 1σ uncertainty for each parameter. To train our network, we use our improved pipeline to simulate lens images using real images of galaxies from the Hyper Suprime-Cam Survey (HSC) and from the Hubble Ultra Deep Field as lens galaxies and background sources, respectively. We find very good recoveries overall for the SIE parameters, especially for the lens center in comparison to our previous CNN, while significant differences remain in predicting the external shear. From our multiple tests, it appears that most likely the low ground-based image resolution is the limiting factor in predicting the external shear. Given the run time of milli-seconds per system, our network is perfectly suited to quickly predict the next appearing image and time delays of lensed transients. Therefore, we use the network-predicted mass model to estimate these quantities and compare to those values obtained from our simulations. Unfortunately, the achieved precision allows only a first-order estimate of time delays on real lens systems and requires further refinement through follow-up modeling. Nonetheless, our ResNet is able to predict the SIE and shear parameter values in fractions of a second on a single CPU, meaning that we are able to efficiently process the huge amount of galaxy-scale lenses expected in the near future.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

FluxRETAP: a REaction TArget Prioritization genome-scale modeling technique for selecting genetic targets

MOTIVATION: Metabolic engineering is rapidly evolving as a result of new advances in synthetic biology tools and automation platforms that enable high throughput strain construction, as well as the development of machine learning tools (ML) for biology. However, selecting genetic engineering targets that effectively guide the metabolic engineering process is still challenging. ML can provide predictive power for synthetic biology, but current technical limitations prevent the independent use of ML approaches without previous biological knowledge. RESULTS: Here, we present FluxRETAP, a simple and computationally inexpensive method that leverages the prior mechanistic knowledge embedded in genome-scale models for suggesting targets for genetic overexpression, downregulation or deletion, with the final goal of increasing the production of a desired metabolite. This method can provide a list of desirable engineering targets that can be combined with current ML pipelines. FluxRETAP captured 100% of reaction targets experimentally verified to improve Escherichia coli isoprenol production, 50% of targets that experimentally improved taxadiene production in E. coli and ∼60% of genetic targets from a verified minimal constrained cut-set in Pseudomonas putida, while providing additional high priority targets that could be tested. Overall, FluxRETAP is an efficient algorithm for identifying a prioritized list of testable genetic and reaction targets. AVAILABILITY AND IMPLEMENTATION: FluxRETAP is implemented in python and released under the creative commons license. The implementation and code are freely available at: https://github.com/JBEI/FluxRETAP.

Czajka, Jeffrey J↗
DOE OSTI2024

AXI4MLIR: User-Driven Automatic Host Code Generation for Custom AXI-Based Accelerators

Tensor algebra operations represent an important class of algorithms used across many applications, including machine learning, scientific computing, and data analytics. As a result, the efficient generation of custom accelerators for tensor operations has received increased attention. Previous efforts have produced automated tools enabling users to prototype and explore optimized accelerators. However, little effort has been focused on the host-accelerator interaction in these tools. Efficient use of hardware accelerators requires knowledge about the accelerator's capabilities (operations, data formats, and opcode support), the host CPU microarchitecture (e.g., memory hierarchy), the host-accelerator interface, and the application's features (which code regions should be mapped onto an accelerator). Manually rewriting the original applications to facilitate improved custom accelerator mapping is an error-prone and time-consuming endeavor. To cope with this, we propose AXI4MLIR, a new framework to automatically generate and optimize the communication between the host CPU and arbitrary accelerators that implement linear algebra algorithms. AXI4MLIR extends the MLIR compiler framework to automatically generate efficient host-accelerator driver code for accelerators with AXI-based interfaces. Our compiler extensions enable automatic driver code generation while carefully considering the host's memory hierarchy and target accelerator features. To demonstrate the flexibility and utility of AXI4MLIR, we test it with diverse use cases that include different types of accelerators, tiling scenarios, and dataflow schemes. We compare our experimental results to manual implementations of host-accelerator driver code and find that our approach can reduce CPU cache references by 56% and deliver up to a 1.65x speedup.

Bohm Agostini, Nicolas↗
DOE OSTI2016

acdc – Automated Contamination Detection and Confidence estimation for single-cell genome data

Abstract Background A major obstacle in single-cell sequencing is sample contamination with foreign DNA. To guarantee clean genome assemblies and to prevent the introduction of contamination into public databases, considerable quality control efforts are put into post-sequencing analysis. Contamination screening generally relies on reference-based methods such as database alignment or marker gene search, which limits the set of detectable contaminants to organisms with closely related reference species. As genomic coverage in the tree of life is highly fragmented, there is an urgent need for a reference-free methodology for contaminant identification in sequence data. Results We present acdc, a tool specifically developed to aid the quality control process of genomic sequence data. By combining supervised and unsupervised methods, it reliably detects both known and de novo contaminants. First, 16S rRNA gene prediction and the inclusion of ultrafast exact alignment techniques allow sequence classification using existing knowledge from databases. Second, reference-free inspection is enabled by the use of state-of-the-art machine learning techniques that include fast, non-linear dimensionality reduction of oligonucleotide signatures and subsequent clustering algorithms that automatically estimate the number of clusters. The latter also enables the removal of any contaminant, yielding a clean sample. Furthermore, given the data complexity and the ill-posedness of clustering, acdc employs bootstrapping techniques to provide statistically profound confidence values. Tested on a large number of samples from diverse sequencing projects, our software is able to quickly and accurately identify contamination. Results are displayed in an interactive user interface. Acdc can be run from the web as well as a dedicated command line application, which allows easy integration into large sequencing project analysis workflows. Conclusions Acdc can reliably detect contamination in single-cell genome data. In addition to database-driven detection, it complements existing tools by its unsupervised techniques, which allow for the detection of de novo contaminants. Our contribution has the potential to drastically reduce the amount of resources put into these processes, particularly in the context of limited availability of reference species. As single-cell genome data continues to grow rapidly, acdc adds to the toolkit of crucial quality assurance tools.

59 BASIC BIOLOGICAL SCIENCES↗