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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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At least 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Application of a deep learning semantic segmentation model to helium bubbles and voids in nuclear materials

Imaging nanoscale radiation-induced defects using the transmission electron microscope (TEM) is a key factor in the successful implementation of materials for nuclear energy structural applications. Analyzing each defect in a TEM micrograph is currently a manual task. To identify the defects in a single image can take anywhere from 15 min to an hour and a project can require the analysis of anywhere from tens to ≥ 100 images. Here, we use artificial intelligence (AI) models to automate this task. For simplification, we evaluated images with only a single type of defect; helium bubbles. Additionally, we performed semantic segmentation of these helium bubble defects in electron microscopy images of irradiated FeCrAl alloys using a deep learning DefectSegNet model. This model, which was previously used to classify crystal defects, is inspired by the classic DenseNet and U-Net image segmentation models. It claims high spatial resolution, but has poor performance at object boundaries. Our paper improves the DefectSegNet model’s application by adding two new features. First, the DefectSegNet model is applied not only to perform calculation pixel-wise but also object (or feature) wise. Because object-wise metrics are directly relevant to our final goal of detecting bubbles, whereas pixel-wise classification is only an intermediate step, it is an important part of our study. Second, a distance map loss (DML) function has been added to increase its performance at object boundaries. It is crucial to accurately represent defects boundaries, especially bubbles, in order to track the bubble-induced swelling caused by irradiation. The boundary-focused DML function is also compared to other loss functions like Cross-entropy, Weighted Binary Cross Entropy (WBCE), Dice and Intersection over Union (IOU). Finally, by incorporating new features, we found a marked improvement on segmentation quality and better shape preservation at the boundaries and areas of the bubbles.

42 ENGINEERING↗
DOE OSTI2019

Deep Learning for Semantic Segmentation of Defects in Advanced STEM Images of Steels

Crystalline materials exhibit long-range ordered lattice unit, within which resides nonperiodic structural features called defects. These crystallographic defects play a vital role in determining the physical and mechanical properties of a wide range of material systems. While computer vision has demonstrated success in recognizing feature patterns in images with well defined contrast, automated identification of nanometer scale crystallographic defects in electron micrographs governed by complex contrast mechanism is still a challenging task. Here, building upon an advanced defect imaging mode that offers high feature clarity, we introduce DefectSegNet - a new convolutional neural network (CNN) architecture that performs semantic segmentation of three common crystallographic defects in structural alloys: dislocation lines, precipitates and voids. Results from supervised training of a small set of high-quality defect images of steels show high pixel-wise accuracy across all three types of defects: 91.60 ± 1.77% on dislocations, 93.39 ± 1.00% on precipitates, and 98.85 ± 0.56% on voids. We discuss the sources of uncertainties in CNN prediction, and the training data in terms of feature density, representation and homogeneity and their effects on deep learning performance. Further defect quantification using DefectSegNet prediction outperforms human expert average, presenting a promising new workflow for fast and statistically meaningful quantification of materials defects.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Real-time semantic segmentation on FPGAs for autonomous vehicles with hls4ml

In this paper, we investigate how field programmable gate arrays can serve as hardware accelerators for real-time semantic segmentation tasks relevant for autonomous driving. Considering compressed versions of the ENet convolutional neural network architecture, we demonstrate a fully-on-chip deployment with a latency of 4.9 ms per image, using less than 30% of the available resources on a Xilinx ZCU102 evaluation board. The latency is reduced to 3 ms per image when increasing the batch size to ten, corresponding to the use case where the autonomous vehicle receives inputs from multiple cameras simultaneously. We show, through aggressive filter reduction and heterogeneous quantization-aware training, and an optimized implementation of convolutional layers, that the power consumption and resource utilization can be significantly reduced while maintaining accuracy on the Cityscapes dataset.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2013

Accelerating semantic graph databases on commodity clusters

We are developing a full software system for accelerating semantic graph databases on commodity cluster that scales to hundreds of nodes while maintaining constant query throughput. Our framework comprises a SPARQL to C++ compiler, a library of parallel graph methods and a custom multithreaded runtime layer, which provides a Partitioned Global Address Space (PGAS) programming model with fork/join parallelism and automatic load balancing over a commodity clusters. We present preliminary results for the compiler and for the runtime.

commodity clusters↗
DOE OSTI2016

InteGO2: A web tool for measuring and visualizing gene semantic similarities using Gene Ontology

Here, the Gene Ontology (GO) has been used in high-throughput omics research as a major bioinformatics resource. The hierarchical structure of GO provides users a convenient platform for biological information abstraction and hypothesis testing. Computational methods have been developed to identify functionally similar genes. However, none of the existing measurements take into account all the rich information in GO. Similarly, using these existing methods, web-based applications have been constructed to compute gene functional similarities, and to provide pure text-based outputs. Without a graphical visualization interface, it is difficult for result interpretation. As a result, we present InteGO2 , a web tool that allows researchers to calculate the GO-based gene semantic similarities using seven widely used GO-based similarity measurements. Also, we provide an integrative measurement that synergistically integrates all the individual measurements to improve the overall performance. Using HTML5 and cytoscape.js, we provide a graphical interface in InteGO2 to visualize the resulting gene functional association networks. In conclusion, InteGO2 is an easy-to-use HTML5 based web tool. With it, researchers can measure gene or gene product functional similarity conveniently, and visualize the network of functional interactions in a graphical interface.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

BioHackathon 2015: Semantics of data for life sciences and reproducible research

We report on the activities of the 2015 edition of the BioHackathon, an annual event that brings together researchers and developers from around the world to develop tools and technologies that promote the reusability of biological data. We discuss issues surrounding the representation, publication, integration, mining and reuse of biological data and metadata across a wide range of biomedical data types of relevance for the life sciences, including chemistry, genotypes and phenotypes, orthology and phylogeny, proteomics, genomics, glycomics, and metabolomics. We describe our progress to address ongoing challenges to the reusability and reproducibility of research results, and identify outstanding issues that continue to impede the progress of bioinformatics research. We share our perspective on the state of the art, continued challenges, and goals for future research and development for the life sciences Semantic Web.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Open Data and Deep Semantic Segmentation for Automated Extraction of Building Footprints

Advances in machine learning and computer vision, combined with increased access to unstructured data (e.g., images and text), have created an opportunity for automated extraction of building characteristics, cost-effectively, and at scale. These characteristics are relevant to a variety of urban and energy applications, yet are time consuming and costly to acquire with today’s manual methods. Several recent research studies have shown that in comparison to more traditional methods that are based on features engineering approach, an end-to-end learning approach based on deep learning algorithms significantly improved the accuracy of automatic building footprint extraction from remote sensing images. However, these studies used limited benchmark datasets that have been carefully curated and labeled. How the accuracy of these deep learning-based approach holds when using less curated training data has not received enough attention. The aim of this work is to leverage the openly available data to automatically generate a larger training dataset with more variability in term of regions and type of cities, which can be used to build more accurate deep learning models. In contrast to most benchmark datasets, the gathered data have not been manually curated. Thus, the training dataset is not perfectly clean in terms of remote sensing images exactly matching the ground truth building’s foot-print. A workflow that includes data pre-processing, deep learning semantic segmentation modeling, and results post-processing is introduced and applied to a dataset that include remote sensing images from 15 cities and five counties from various region of the USA, which include 8,607,677 buildings. The accuracy of the proposed approach was measured on an out of sample testing dataset corresponding to 364,000 buildings from three USA cities. The results favorably compared to those obtained from Microsoft’s recently released US building footprint dataset.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS2020

Automated Cardiovascular Pathology Assessment using Semantic Segmentation and Ensemble Learning

Cardiac magnetic resonance imaging provides high spatial resolution, enabling improved extraction of important functional and morphological features for cardiovascular disease staging. Segmentation of ventricular cavities and myocardium in cardiac cine sequencing provides a basis to quantify cardiac measures such as ejection fraction. A method is presented that curtails the expense and observer bias of manual cardiac evaluation by combining semantic segmentation and disease classification into a fully automatic processing pipeline. The initial processing element consists of a robust dilated convolutional neural network architecture for voxel-wise segmentation of the myocardium and ventricular cavities. The resulting comprehensive volumetric feature matrix captures diagnostic clinical procedure data and is utilized by the final processing element to model a cardiac pathology classifier. Our approach evaluated anonymized cardiac images from a training data set of 100 patients (4 pathology groups, 1 healthy group, 20 patients per group) examined at the University Hospital of Dijon. The top average Dice index scores achieved were 0.940, 0.886, 0.849 for structure segmentation of the left ventricle (LV), myocardium and right ventricle (RV) respectively. A 5-ary pathology classification accuracy of 90% was recorded on an independent test set using the trained model. Performance results demonstrate potential for advanced machine learning methods to deliver accurate, efficient and reproducible cardiac pathological assessment.

Semantic Segmentation↗
DOE OSTI2019

ADVANCED-STEM-BASED DEEP LEARNING FOR SEMANTIC SEGMENTATION OF DEFECTS IN STEELS

In this work, we developed a novel deep convolutional neural network (DCNN) model, called DefectNet, for robust and automated semantic segmentation of three crystallographic defects including line dislocations, precipitates and voids commonly observed in structural metals and alloys. In previous work, we established an experimental protocol for a diffraction contrast imaging scanning transmission electron microscopy (DCI STEM) technique and tailored it specifically for imaging defects in popular iron-based structural alloy. Thus, the DefectNet was trained over a small but high-quality DCI STEM defect image sets of a HT-9 martensitic steel before and after neutron irradiation for 111.8 dpa at 412°C. For the defect quantification that typically takes at least half an hour even for an expert, with a good model the machine learning algorithm can produce more reproducible and reliable quantification in a few seconds. This work demonstrates the feasibility of using deep learning algorithms for fast and accurate defect quantitative analysis.

Machine Learning, Radiation effects, Image analysi↗
DOE OSTI2026

NuGraph2 with context-aware inputs: physics-inspired improvements in semantic segmentation

Graph neural networks have recently shown strong promise for event reconstruction tasks in Liquid Argon Time Projection Chambers, yet their performance remains limited for underrepresented classes of particles, such as Michel electrons. In this work, we investigate physics-informed strategies to improve semantic segmentation within the NuGraph2 architecture. We explore three complementary approaches: (i) enriching the input representation with context-aware features derived from detector geometry and track continuity, (ii) introducing auxiliary decoders to capture class-level correlations, and (iii) incorporating energy-based regularization terms motivated by Michel electron energy distributions. Experiments on MicroBooNE public datasets show that physics-inspired feature augmentation yields the largest gains, particularly boosting Michel electron precision and recall by disentangling overlapping latent space regions. In contrast, auxiliary decoders and energy-regularization terms provided limited improvements, partly due to the hit-level nature of NuGraph2, which lacks explicit particle- or event-level representations. Our findings highlight that embedding physics context directly into node-level inputs is more effective than imposing task-specific auxiliary losses, and suggest that future hierarchical architectures such as NuGraph3, with explicit particle- and event-level reasoning, will provide a more natural setting for advanced decoders and physics-based regularization. The code for this work is publicly available on Github at https://github.com/vitorgrizzi/nugraph_phys/tree/main_phys.

Other Experiments↗
DOE OSTI2022

PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology

PDBx/mmCIF, Protein Data Bank Exchange (PDBx) macromolecular Crystallographic Information Framework (mmCIF), has become the data standard for structural biology. With its early roots in the domain of small-molecule crystallography, PDBx/mmCIF provides an extensible data representation that is used for deposition, archiving, remediation, and public dissemination of experimentally determined three-dimensional (3D) structures of biological macromolecules by the Worldwide Protein Data Bank (wwPDB, wwpdb.org). Extensions of PDBx/mmCIF are similarly used for computed structure models by ModelArchive (modelarchive.org), integrative/hybrid structures by PDB-Dev (pdb-dev.wwpdb.org), small angle scattering data by Small Angle Scattering Biological Data Bank SASBDB (sasbdb.org), and for models computed generated with the AlphaFold 2.0 deep learning software suite (alphafold.ebi.ac.uk). Community-driven development of PDBx/mmCIF spans three decades, involving contributions from researchers, software and methods developers in structural sciences, data repository providers, scientific publishers, and professional societies. Having a semantically rich and extensible data framework for representing a wide range of structural biology experimental and computational results, combined with expertly curated 3D biostructure data sets in public repositories, accelerates the pace of scientific discovery. Herein, we describe the architecture of the PDBx/mmCIF data standard, tools used to maintain representations of the data standard, governance, and processes by which data content standards are extended, plus community tools/software libraries available for processing and checking the integrity of PDBx/mmCIF data. Use cases exemplify how the members of the Worldwide Protein Data Bank have used PDBx/mmCIF as the foundation for its pipeline for delivering Findable, Accessible, Interoperable, and Reusable (FAIR) data to many millions of users worldwide.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A deep learning approach for semantic segmentation of unbalanced data in electron tomography of catalytic materials

In computed TEM tomography, image segmentation represents one of the most basic tasks with implications not only for 3D volume visualization, but more importantly for quantitative 3D analysis. In case of large and complex 3D data sets, segmentation can be an extremely difficult and laborious task, and thus has been one of the biggest hurdles for comprehensive 3D analysis. Heterogeneous catalysts have complex surface and bulk structures, and often sparse distribution of catalytic particles with relatively poor intrinsic contrast, which possess a unique challenge for image segmentation, including the current state-of-the-art deep learning methods. To tackle this problem, we apply a deep learning-based approach for the multi-class semantic segmentation of a γ-Alumina/Pt catalytic material in a class imbalance situation. Specifically, we used the weighted focal loss as a loss function and attached it to the U-Net’s fully convolutional network architecture. We assessed the accuracy of our results using Dice similarity coefficient (DSC), recall, precision, and Hausdorff distance (HD) metrics on the overlap between the ground-truth and predicted segmentations. Our adopted U-Net model with the weighted focal loss function achieved an average DSC score of 0.96 ± 0.003 in the γ-Alumina support material and 0.84 ± 0.03 in the Pt NPs segmentation tasks. We report an average boundary-overlap error of less than 2 nm at the 90th percentile of HD for γ-Alumina and Pt NPs segmentations. The complex surface morphology of γ-Alumina and its relation to the Pt NPs were visualized in 3D by the deep learning-assisted automatic segmentation of a large data set of high-angle annular dark-field (HAADF) scanning transmission electron microscopy (STEM) tomography reconstructions.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Semantic integration of clinical laboratory tests from electronic health records for deep phenotyping and biomarker discovery

Electronic Health Record (EHR) systems typically define laboratory test results using the Laboratory Observation Identifier Names and Codes (LOINC) and can transmit them using Fast Healthcare Interoperability Resource (FHIR) standards. LOINC has not yet been semantically integrated with computational resources for phenotype analysis. Here, we provide a method for mapping LOINC-encoded laboratory test results transmitted in FHIR standards to Human Phenotype Ontology (HPO) terms. We annotated the medical implications of 2923 commonly used laboratory tests with HPO terms. Using these annotations, our software assesses laboratory test results and converts each result into an HPO term. We validated our approach with EHR data from 15,681 patients with respiratory complaints and identified known biomarkers for asthma. Finally, we provide a freely available SMART on FHIR application that can be used within EHR systems. Our approach allows readily available laboratory tests in EHR to be reused for deep phenotyping and exploits the hierarchical structure of HPO to integrate distinct tests that have comparable medical interpretations for association studies.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning

Abstract Motivation Creating knowledge bases and ontologies is a time consuming task that relies on manual curation. AI/NLP approaches can assist expert curators in populating these knowledge bases, but current approaches rely on extensive training data, and are not able to populate arbitrarily complex nested knowledge schemas. Results Here we present Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES), a Knowledge Extraction approach that relies on the ability of Large Language Models (LLMs) to perform zero-shot learning and general-purpose query answering from flexible prompts and return information conforming to a specified schema. Given a detailed, user-defined knowledge schema and an input text, SPIRES recursively performs prompt interrogation against an LLM to obtain a set of responses matching the provided schema. SPIRES uses existing ontologies and vocabularies to provide identifiers for matched elements. We present examples of applying SPIRES in different domains, including extraction of food recipes, multi-species cellular signaling pathways, disease treatments, multi-step drug mechanisms, and chemical to disease relationships. Current SPIRES accuracy is comparable to the mid-range of existing Relation Extraction methods, but greatly surpasses an LLM’s native capability of grounding entities with unique identifiers. SPIRES has the advantage of easy customization, flexibility, and, crucially, the ability to perform new tasks in the absence of any new training data. This method supports a general strategy of leveraging the language interpreting capabilities of LLMs to assemble knowledge bases, assisting manual knowledge curation and acquisition while supporting validation with publicly-available databases and ontologies external to the LLM. Availability and implementation SPIRES is available as part of the open source OntoGPT package: https://github.com/monarch-initiative/ontogpt.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Radio galaxy zoo EMU: towards a semantic radio galaxy morphology taxonomy

We present a novel natural language processing (NLP) approach to deriving plain English descriptors for science cases otherwise restricted by obfuscating technical terminology. We address the limitations of common radio galaxy morphology classifications by applying this approach. We experimentally derive a set of semantic tags for the Radio Galaxy Zoo EMU (Evolutionary Map of the Universe) project and the wider astronomical community. We collect 8486 plain English annotations of radio galaxy morphology, from which we derive a taxonomy of tags. The tags are plain English. The result is an extensible framework, which is more flexible, more easily communicated, and more sensitive to rare feature combinations, which are indescribable using the current framework of radio astronomy classifications.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Semantic segmentation with a sparse convolutional neural network for event reconstruction in MicroBooNE

We present the performance of a semantic segmentation network, SparseSSNet, that provides pixel-level classification of MicroBooNE data. The MicroBooNE experiment employs a liquid argon time projection chamber for the study of neutrino properties and interactions. SparseSSNet is a submanifold sparse convolutional neural network, which provides the initial machine learning based algorithm utilized in one of MicroBooNE's ν e -appearance oscillation analyses. The network is trained to categorize pixels into five classes, which are re-classified into two classes more relevant to the current analysis. The output of SparseSSNet is a key input in further analysis steps. This technique, used for the first time in liquid argon time projection chambers data and is an improvement compared to a previously used convolutional neural network, both in accuracy and computing resource utilization. Here, the accuracy achieved on the test sample is ≥ 99%. For full neutrino interaction simulations, the time for processing one image is ≈ 0.5 sec, the memory usage is at 1 GB level, which allows utilization of most typical CPU worker machine.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2022

Semantic Property Graph for Scalable Knowledge Graph Analytics

Graphs are a natural and fundamental representation to describe entities, relationships, activities, and evolution of complex systems. Many domains such as communication, citation, procurement, biology, social media, and transportation can be modeled as a set of entities and their relationships. Resource Description Framework (RDF) and Labeled Property Graph (LPG) are two of the most used data models to encode information in a graph. Both models are similar in terms of using basic graph elements such as nodes and edges but differ in terms of the modeling approach, expressibility, serialization, and target applications. RDF is a flexible data exchange model for expressing information about entities but it tends to a have high memory footprint and inefficient storage, which does not make it a natural choice to perform scalable graph analytics. In contrast, LPG has gained traction as a reliable model to perform scalable graph analytic tasks such as sub-graph matching, network alignment, and real-time knowledge graph query. It provides efficient storage, fast traversal, and flexibility to model various real-world domains. At the same time, the LPG lacks the support of a formal knowledge representation such as an ontology to provide automated knowledge inference. We propose Semantic Property Graph (SPG) as a logical projection of reified RDF into the LPG model. SPG continues to use RDF ontology to define the type hierarchy of the projected graph and validate it against a given ontology. We present a framework to convert reified RDF graphs into SPG using two different computing environments. We also present cloud-based graph migration capabilities using Amazon Web Services.

Purohit, Sumit↗
DOE OSTI2024

DaYu: Optimizing Distributed Scientific Workflows by Decoding Dataflow Semantics and Dynamics

The combination of ever-growing scientific datasets and distributed workflow complexity creates I/O performance bottlenecks due to data volume, velocity, and variety. Although the increasing use of descriptive data formats (e.g., HDF5, netCDF) helps organize these datasets, it also creates obscure bottlenecks due to the need to translate high level operations into file addresses and then into low-level I/O operations. To address this challenge, we introduce DaYu, a method and toolset for analyzing (a) semantic relationships between logical datasets and file addresses, (b) how dataset operations translate into I/O, and (c) the combination across entire workflows. DaYu's analysis and visualization enables identification of critical bottlenecks and reasoning about remediation. We describe our methodology and propose optimization guidelines. Evaluation on scientific workflows demonstrates up to 3.7x performance improvements in I/O time for obscure bottlenecks. The time and storage overhead for DaYu's time-ordered data is typically under 0.2% of runtime and 0.25% of data volume, respectively.

Tang, Meng↗