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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

DL-TODA: A Deep Learning Tool for Omics Data Analysis

Metagenomics is a technique for genome-wide profiling of microbiomes; this technique generates billions of DNA sequences called reads. Given the multiplication of metagenomic projects, computational tools are necessary to enable the efficient and accurate classification of metagenomic reads without needing to construct a reference database. The program DL-TODA presented here aims to classify metagenomic reads using a deep learning model trained on over 3000 bacterial species. A convolutional neural network architecture originally designed for computer vision was applied for the modeling of species-specific features. Using synthetic testing data simulated with 2454 genomes from 639 species, DL-TODA was shown to classify nearly 75% of the reads with high confidence. The classification accuracy of DL-TODA was over 0.98 at taxonomic ranks above the genus level, making it comparable with Kraken2 and Centrifuge, two state-of-the-art taxonomic classification tools. DL-TODA also achieved an accuracy of 0.97 at the species level, which is higher than 0.93 by Kraken2 and 0.85 by Centrifuge on the same test set. Application of DL-TODA to the human oral and cropland soil metagenomes further demonstrated its use in analyzing microbiomes from diverse environments. Compared to Centrifuge and Kraken2, DL-TODA predicted distinct relative abundance rankings and is less biased toward a single taxon.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

A Data-Driven Framework for Direct Local Tensile Property Prediction of Laser Powder Bed Fusion Parts

This article proposes a generalizable, data-driven framework for qualifying laser powder bed fusion additively manufactured parts using part-specific in situ data, including powder bed imaging, machine health sensors, and laser scan paths. To achieve part qualification without relying solely on statistical processes or feedstock control, a sequence of machine learning models was trained on 6299 tensile specimens to locally predict the tensile properties of stainless-steel parts based on fused multi-modal in situ sensor data and a priori information. A cyberphysical infrastructure enabled the robust spatial tracking of individual specimens, and computer vision techniques registered the ground truth tensile measurements to the in situ data. The co-registered 230 GB dataset used in this work has been publicly released and is available as a set of HDF5 files. The extensive training data requirements and wide range of size scales were addressed by combining deep learning, machine learning, and feature engineering algorithms in a relay. The trained models demonstrated a 61% error reduction in ultimate tensile strength predictions relative to estimates made without any in situ information. Lessons learned and potential improvements to the sensors and mechanical testing procedure are discussed.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Deep-Learning-Based Segmentation of Keyhole in In-Situ X-ray Imaging of Laser Powder Bed Fusion

In laser powder bed fusion processes, keyholes are the gaseous cavities formed where laser interacts with metal, and their morphologies play an important role in defect formation and the final product quality. The in-situ X-ray imaging technique can monitor the keyhole dynamics from the side and capture keyhole shapes in the X-ray image stream. Keyhole shapes in X-ray images are then often labeled by humans for analysis, which increasingly involves attempting to correlate keyhole shapes with defects using machine learning. However, such labeling is tedious, time-consuming, error-prone, and cannot be scaled to large data sets. To use keyhole shapes more readily as the input to machine learning methods, an automatic tool to identify keyhole regions is desirable. In this paper, a deep-learning-based computer vision tool that can automatically segment keyhole shapes out of X-ray images is presented. The pipeline contains a filtering method and an implementation of the BASNet deep learning model to semantically segment the keyhole morphologies out of X-ray images. The presented tool shows promising average accuracy of 91.24% for keyhole area, and 92.81% for boundary shape, for a range of test dataset conditions in Al6061 (and one AliSi10Mg) alloys, with 300 training images/labels and 100 testing images for each trial. Prospective users may apply the presently trained tool or a retrained version following the approach used here to automatically label keyhole shapes in large image sets.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Vegetation Detection Using Deep Learning and Conventional Methods

Land cover classification with the focus on chlorophyll-rich vegetation detection plays an important role in urban growth monitoring and planning, autonomous navigation, drone mapping, biodiversity conservation, etc. Conventional approaches usually apply the normalized difference vegetation index (NDVI) for vegetation detection. In this paper, we investigate the performance of deep learning and conventional methods for vegetation detection. Two deep learning methods, DeepLabV3+ and our customized convolutional neural network (CNN) were evaluated with respect to their detection performance when training and testing datasets originated from different geographical sites with different image resolutions. A novel object-based vegetation detection approach, which utilizes NDVI, computer vision, and machine learning (ML) techniques, is also proposed. The vegetation detection methods were applied to high-resolution airborne color images which consist of RGB and near-infrared (NIR) bands. RGB color images alone were also used with the two deep learning methods to examine their detection performances without the NIR band. The detection performances of the deep learning methods with respect to the object-based detection approach are discussed and sample images from the datasets are used for demonstrations.

58 GEOSCIENCES↗
DOE OSTI2025

Data Quality Monitoring for the Hadron Calorimeters Using Transfer Learning for Anomaly Detection

The proliferation of sensors brings an immense volume of spatio-temporal (ST) data in many domains, including monitoring, diagnostics, and prognostics applications. Data curation is a time-consuming process for a large volume of data, making it challenging and expensive to deploy data analytics platforms in new environments. Transfer learning (TL) mechanisms promise to mitigate data sparsity and model complexity by utilizing pre-trained models for a new task. Despite the triumph of TL in fields like computer vision and natural language processing, efforts on complex ST models for anomaly detection (AD) applications are limited. In this study, we present the potential of TL within the context of high-dimensional ST AD with a hybrid autoencoder architecture, incorporating convolutional, graph, and recurrent neural networks. Motivated by the need for improved model accuracy and robustness, particularly in scenarios with limited training data on systems with thousands of sensors, this research investigates the transferability of models trained on different sections of the Hadron Calorimeter of the Compact Muon Solenoid experiment at CERN. The key contributions of the study include exploring TL’s potential and limitations within the context of encoder and decoder networks, revealing insights into model initialization and training configurations that enhance performance while substantially reducing trainable parameters and mitigating data contamination effects.

47 OTHER INSTRUMENTATION↗
DOE OSTI2023

High-Throughput Field Plant Phenotyping: A Self-Supervised Sequential CNN Method to Segment Overlapping Plants

High-throughput plant phenotyping—the use of imaging and remote sensing to record plant growth dynamics—is becoming more widely used. The first step in this process is typically plant segmentation, which requires a well-labeled training dataset to enable accurate segmentation of overlapping plants. However, preparing such training data is both time and labor intensive. To solve this problem, we propose a plant image processing pipeline using a self-supervised sequential convolutional neural network method for in-field phenotyping systems. This first step uses plant pixels from greenhouse images to segment nonoverlapping in-field plants in an early growth stage and then applies the segmentation results from those early-stage images as training data for the separation of plants at later growth stages. The proposed pipeline is efficient and self-supervising in the sense that no human-labeled data are needed. We then combine this approach with functional principal components analysis to reveal the relationship between the growth dynamics of plants and genotypes. We show that the proposed pipeline can accurately separate the pixels of foreground plants and estimate their heights when foreground and background plants overlap and can thus be used to efficiently assess the impact of treatments and genotypes on plant growth in a field environment by computer vision techniques. This approach should be useful for answering important scientific questions in the area of high-throughput phenotyping.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Identification of Galaxy Shreds in Large Photometric Catalogs Using Convolutional Neural Networks

Contamination from galaxy fragments, identified as sources, is a major issue in large photometric galaxy catalogs. In this paper, we prove that this problem can be easily addressed with computer vision techniques. We use image cutouts to train a convolutional neural network (CNN) to identify cataloged sources that are in reality just star-formation regions and/or shreds of larger galaxies. The CNN reaches an accuracy ~98% on our testing data sets. We apply this CNN to galaxy catalogs from three among the largest surveys available today: the Sloan Digital Sky Survey, the DESI Legacy Imaging Surveys, and the Panoramic Survey Telescope and Rapid Response System Survey. We find that, even when strict selection criteria are used, all catalogs still show a ~5% level of contamination from galaxy shreds. Our CNN gives a simple yet effective solution to clean galaxy catalogs from these contaminants.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2017

Pseudo-automatic Determination of Coronal Mass Ejections’ Kinematics in 3D

Coronal mass ejection (CME) events are among the main drivers of geomagnetic disturbances, and hence play a central role in the Sun–Earth system. Their monitoring and, in particular, the determination of their speed and direction of propagation are key issues for the forecasting of space weather near to Earth. We have implemented a method to track CME events in three dimensions by combining triangulation and tie-pointing analysis with a supervised computer vision algorithm. This novel approach does not rely on any geometric constraint, and eliminates the need for visual identification of the CME boundaries. We applied our method to 17 CME events observed simultaneously by the twin Solar Terrestrial Relations Observatory ( STEREO ) COR2 coronagraph imagers from 2008 December to 2011 November in order to obtain their 3D kinematical characterization (i.e., the velocity vector) along with their morphological properties. About ten of these events have already been analyzed using other methodologies. In these cases, we carried out a thorough comparison with our results and found that, in spite of the different nature and spatial coverage range of the other methods with respect to CORSET3D, the majority of the results agree. We found, however, that three events exhibited discrepancies in the magnitude of the velocity vector, four in the longitudinal direction of propagation, and in only one case was there a discrepancy in latitude. The discrepancies appeared in those cases where quasi-simultaneous, quasi-co-located events were observed in the coronagraphs’ fields of view.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Benchmarking a Tunable Quantum Neural Network on Trapped-Ion and Superconducting Hardware

We implement a quantum generalization of a neural network on trapped-ion and IBM superconducting quantum computers to classify MNIST images, a common benchmark in computer vision. The network feedforward involves qubit rotations whose angles depend on the results of measurements in the previous layer. The network is trained via simulation, but inference is performed experimentally on quantum hardware. The classical-to-quantum correspondence is controlled by an interpolation parameter, $a$, which is zero in the classical limit. Increasing $a$ introduces quantum uncertainty into the measurements, which is shown to improve network performance at moderate values of the interpolation parameter. We then focus on particular images that fail to be classified by a classical neural network but are detected correctly in the quantum network. For such borderline cases, we observe strong deviations from the simulated behavior. We attribute this to physical noise, which causes the output to fluctuate between nearby minima of the classification energy landscape. Such strong sensitivity to physical noise is absent for clear images. We further benchmark physical noise by inserting additional single-qubit and two-qubit gate pairs into the neural network circuits. Our work provides a springboard toward more complex quantum neural networks on current devices: while the approach is rooted in standard classical machine learning, scaling up such networks may prove classically non-simulable and could offer a route to near-term quantum advantage.

FOS: Physical sciences↗
DOE OSTI2026

RU Net for Automatic Characterization of TRISO Fuel Cross Sections

TRistructural ISOtropic (TRISO) particle fuel is a type of nuclear fuel known for its high-temperature and high-burnup performance. Each sub-millimeter diameter TRISO particle consists of uranium-oxycarbide (UCO) or UO2 fuel kernel, coated with buffer, inner pyrolytic carbon (IPyC), silicon carbide (SiC), and outer pyrolytic carbon (OPyC) layers. The SiC layer acts as the main containment barrier for the TRISO particle to retain the fission products, while the IPyC and OPyC layers provide additional barriers to the release of fission products, especially fission gases. During irradiation, phenomena like kernel swelling, buffer densification, and IPyC fracture may impact fuel performance. Post-irradiation microscopy on entire compact cross sections or samples of individual particles deconsolidated from compacts is often used to identify these irradiation-induced changes in morphology. However, each fuel compact generally contains thousands of TRISO particles. To get statistical information on these phenomena, it is cumbersome work if done manually. For example, to get information about swelling/densification behaviors of different layers or kernels after irradiation, researchers previously manually measured the perimeter of each TRISO layer in hundreds of particles after four rounds of iterative grinding and polishing encompassing more than 2000 cross-section images for a total of four fuel compacts. To attempt to reduce the subjectivity inherent in that process and accelerate data analysis, we conducted a study on the automatic TRISO layer segmentation on cross-sectional microscopic images using Convolutional Neural Networks (CNNs). CNNs are a class of machine learning algorithms specifically designed for processing structured grid data that have gained popularity in recent years due to their remarkable performance in various computer vision tasks, including image classification, object detection, and image segmentation. In this research, we have generated the large irradiated TRISO layer dataset with more than 2000 cross-section TRISO microscopic images and the corresponding annotated images. Based on these annotated images, we have employed different CNNs for automatic segmentation of different TRISO layers. These include RU-Net (developed in this study), as well as three existing architectures: U-Net, Residual Network (ResNet), and Attention U-Net. The preliminary results show that the model based on RU-Net has the best performance in terms of intersection-over-union (IoU). Through the aid of these CNN models, we can expedite the analysis of TRISO particle cross-sections, significantly reducing the manual labor involved and improving the objectivity of the segmentation results.

Convolutional Neural Networks↗
DOE OSTI2023

A semi-Lagrangian method for detecting and tracking deep convective clouds in geostationary satellite observations

Automated methods for the detection and tracking of deep convective clouds in geostationary satellite imagery have a vital role in both the forecasting of severe storms and research into their behaviour. Studying the interactions and feedbacks between multiple deep convective clouds (DCC), however, poses a challenge for existing algorithms due to the necessary compromise between false detection and missed detection errors. We utilise an optical flow method to determine the motion of deep convective clouds in GOES-16 ABI imagery in order to construct a semi-Lagrangian framework for the motion of the cloud field, independently of the detection and tracking of cloud objects. The semi-Lagrangian framework allows severe storms to be simultaneously detected and tracked in both spatial and temporal dimensions. For the purpose of this framework we have developed a novel Lagrangian convolution method and a number of novel implementations of morphological image operations that account for the motion of observed objects. These novel methods allow the accurate extension of computer vision techniques to the temporal domain for moving objects such as DCCs. By combining this framework with existing methods for detecting DCCs (including detection of growing cores through cloud top cooling and detection of anvil clouds using brightness temperature), we show that the novel framework enables reductions in errors due to both false and missed detections compared to any of the individual methods, reducing the need to compromise when compared with existing frameworks. The novel framework enables the continuous tracking of anvil clouds associated with detected deep convection after convective activity has stopped, enabling the study of the entire life cycle of DCCs and their associated anvils. Furthermore, we expect this framework to be applicable to a wide range of cases including the detection and tracking of low-level clouds and other atmospheric phenomena. In addition, this framework may be used to combine observations from multiple sources, including satellite observations, weather radar and reanalysis model data.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

ClimateNet: an expert-labeled open dataset and deep learning architecture for enabling high-precision analyses of extreme weather

Abstract. Identifying, detecting, and localizing extreme weather events is a crucial first step in understanding how they may vary under different climate change scenarios. Pattern recognition tasks such as classification, object detection, and segmentation (i.e., pixel-level classification) have remained challenging problems in the weather and climate sciences. While there exist many empirical heuristics for detecting extreme events, the disparities between the output of these different methods even for a single event are large and often difficult to reconcile. Given the success of deep learning (DL) in tackling similar problems in computer vision, we advocate a DL-based approach. DL, however, works best in the context of supervised learning – when labeled datasets are readily available. Reliable labeled training data for extreme weather and climate events is scarce. We create “ClimateNet” – an open, community-sourced human-expert-labeled curated dataset that captures tropical cyclones (TCs) and atmospheric rivers (ARs) in high-resolution climate model output from a simulation of a recent historical period. We use the curated ClimateNet dataset to train a state-of-the-art DL model for pixel-level identification – i.e., segmentation – of TCs and ARs. We then apply the trained DL model to historical and climate change scenarios simulated by the Community Atmospheric Model (CAM5.1) and show that the DL model accurately segments the data into TCs, ARs, or “the background” at a pixel level. Further, we show how the segmentation results can be used to conduct spatially and temporally precise analytics by quantifying distributions of extreme precipitation conditioned on event types (TC or AR) at regional scales. The key contribution of this work is that it paves the way for DL-based automated, high-fidelity, and highly precise analytics of climate data using a curated expert-labeled dataset – ClimateNet. ClimateNet and the DL-based segmentation method provide several unique capabilities: (i) they can be used to calculate a variety of TC and AR statistics at a fine-grained level; (ii) they can be applied to different climate scenarios and different datasets without tuning as they do not rely on threshold conditions; and (iii) the proposed DL method is suitable for rapidly analyzing large amounts of climate model output. While our study has been conducted for two important extreme weather patterns (TCs and ARs) in simulation datasets, we believe that this methodology can be applied to a much broader class of patterns and applied to observational and reanalysis data products via transfer learning.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

A New Reflected Target Optical Assessment System: Stage 1 Development Results

NREL has completed stage 1 development of an indoor optical measurement tool for fully assembled heliostats and single facets. This tool began as an indoor version of NREL’s outdoor Non-Intrusive Optical (NIO) measurement technique [1]. It uses similar techniques to other available tools (deflectometry, photogrammetry, etc.), but is designed to require very little infrastructure, labor, and time to set up and collect surface slope and canting measurements, making it a valuable tool for quality assurance and laboratory measurement of heliostat optics. It accomplishes this by using computer vision, photogrammetry, and multiple images stitched together to minimize the printed target size and required setup precision. This adaptable setup is useful for taking measurements at a variety of heliostat pointing angles, and for measuring fully assembled heliostats on the assembly line. In this paper, we describe the methodology behind the measurement system, present an initial analysis of its uncertainty and sensitivity, and compare it with established optical measurement systems.

Kesseli, Devon (ORCID:0000000193113036)↗
DOE OSTI2015

An Evaluation of Image Based Techniques for Early Wildfire Detection and Fuel Mapping

Few events can cause the catastrophic impact to ecology, infrastructure, and human safety of a wildland fire along the wildland urban interface. The suppression of natural wildland fires over the past decade has caused a buildup of dry, dead surface fuels: a condition that, coupled with the right weather conditions, can cause large destructive wildfires that are capable of threatening both ancient tree stands and manmade infrastructure. Firefighters use fire danger models to determine staffing needs on high fire risk days; however models are only as effective as the spatial and temporal density of their observations. OKFIRE, an Oklahoma initiative created by a partnership between Oklahoma State University and the University of Oklahoma, has proven that fire danger assessments close to the fire – both geographically and temporally – can give firefighters a significant increase in their situational awareness while fighting a wildland fire. This paper investigates several possible solutions for a small Unmanned Aerial System (UAS) which could gather information useful for detecting ground fires and constructing fire danger maps. Multiple fire detection and fuel mapping programs utilize satellites, manned aircraft, and large UAS equipped with hyperspectral sensors to gather useful information. Their success provides convincing proof of the utility that could be gained from low-altitude UAS gathering information at the exact time and place firefighters and land managers are interested in. Close proximity, both geographically and operationally, to the end can reduce latency times below what could ever be possible with satellite observation. This paper expands on recent advances in computer vision, photogrammetry, and infrared and color imagery to develop a framework for a next-generation UAS which can assess fire danger and aid firefighters in real time as they observe, contain, or extinguish wildland fires. It also investigates the impact information gained by this system could have on pre-fire risk assessments through the development of very high resolution fuel maps.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2015

Evidence of Long Range Dependence and Self-similarity in Urban Traffic Systems

Transportation simulation technologies should accurately model traffic demand, distribution, and assignment parame- ters for urban environment simulation. These three param- eters significantly impact transportation engineering bench- mark process, are also critical in realizing realistic traffic modeling situations. In this paper, we model and charac- terize traffic density distribution of thousands of locations around the world. The traffic densities are generated from millions of images collected over several years and processed using computer vision techniques. The resulting traffic den- sity distribution time series are then analyzed. It is found using the goodness-of-fit test that the traffic density dis- tributions follows heavy-tail models such as Log-gamma, Log-logistic, and Weibull in over 90% of analyzed locations. Moreover, a heavy-tail gives rise to long-range dependence and self-similarity, which we studied by estimating the Hurst exponent (H). Our analysis based on seven different Hurst estimators strongly indicate that the traffic distribution pat- terns are stochastically self-similar (0.5 H 1.0). We believe this is an important finding that will influence the design and development of the next generation traffic simu- lation techniques and also aid in accurately modeling traffic engineering of urban systems. In addition, it shall provide a much needed input for the development of smart cities.

long range dependence↗
DOE OSTI2016

Learning Weight Uncertainty with Stochastic Gradient MCMC for Shape Classification

Learning the representation of shape cues in 2D & 3D objects for recognition is a fundamental task in computer vision. Deep neural networks (DNNs) have shown promising performance on this task. Due to the large variability of shapes, accurate recognition relies on good estimates of model uncertainty, ignored in traditional training of DNNs, typically learned via stochastic optimization. This paper leverages recent advances in stochastic gradient Markov Chain Monte Carlo (SG-MCMC) to learn weight uncertainty in DNNs. It yields principled Bayesian interpretations for the commonly used Dropout/DropConnect techniques and incorporates them into the SG-MCMC framework. Extensive experiments on 2D & 3D shape datasets and various DNN models demonstrate the superiority of the proposed approach over stochastic optimization. Our approach yields higher recognition accuracy when used in conjunction with Dropout and Batch-Normalization.

convolutional neural network↗
DOE OSTI2017

AN INDUCTIVE MAPPING WITH CONVOLUTIONAL REPRESENTATIONS FOR HUMAN SETTLEMENT DETECTION: PRELIMINARY RESULTS

Undoubtedly, deep convolutional learning methods continue to improve performance in image-level classification for computer vision and remote sensing applications. However, the spatio-temporal nature of remote sensing imagery offers other interesting challenges in multiscale image understanding. Emerging opportunities include seeking fine-grained and neighborhood mapping with overhead imagery. Limitations due to lack of relevant scale ground-truth often mandates that these challenges are pursued as disjoint. We test this premise and explore representation spaces from a single deep convolutional network and their visualization to argue for a unified feature extraction framework. The objective is to utilize and re-purpose trained feature extractors without the need for network retraining on three remote sensing tasks i.e. superpixel mapping, pixel-level segmentation and semantic based image visualization. By leveraging the same convolutional feature extractors and viewing them as visual information extractors that encode different image representation spaces, we demonstrate surprising potential on multiscale experiments that incorporate edge-level details up to semantic-level informationWe test this premise and explore representation spaces from a single deep convolutional network and their visualization to argue for a novel unified feature extraction framework. The objective is to utilize and re-purpose trained feature extractors without the need for network retraining on three remote sensing tasks i.e. superpixel mapping, pixel-level segmentation and semantic based image visualization. By leveraging the same convolutional feature extractors and viewing them as visual information extractors that encode different image representation spaces, we demonstrate a preliminary inductive transfer learning potential on multiscale experiments that incorporate edge-level details up to semantic-level informationWe test this premise and explore representation spaces from a single deep convolutional network and their visualization to argue for a novel unified feature extraction framework. The objective is to utilize and re-purpose trained feature extractors without the need for network retraining on three remote sensing tasks i.e. superpixel mapping, pixel-level segmentation and semantic based image visualization. By leveraging the same convolutional feature extractors and viewing them as visual information extractors that encode different image representation spaces, we demonstrate a preliminary inductive transfer learning potential on multiscale experiments that incorporate edge-level details up to semantic-level information.

Lunga, Dalton↗
DOE OSTI2020

Graph Neural Networks for Particle Reconstruction in High Energy Physics detectors

Pattern recognition problems in high energy physics are notably different from traditional machine learning applications in computer vision. Reconstruction algorithms identify and measure the kinematic properties of particles produced in high energy collisions and recorded with complex detector systems. Two critical applications are the reconstruction of charged particle trajectories in tracking detectors and the reconstruction of particle showers in calorimeters. These two problems have unique challenges and characteristics, but both have high dimensionality, high degree of sparsity, and complex geometric layouts. Graph Neural Networks (GNNs) are a relatively new class of deep learning architectures which can deal with such data effectively, allowing scientists to incorporate domain knowledge in a graph structure and learn powerful representations leveraging that structure to identify patterns of interest. In this work we demonstrate the applicability of GNNs to these two diverse particle reconstruction problems.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗