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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 1,405 records · Page 78
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Revisit NGC 5466 tidal stream with Gaia , SDSS/SEGUE, and LAMOST

ABSTRACT By mining the data from Gaia Early Data Release 3, Sloan Digital Sky Survey/Sloan Extension for Galactic Understanding and Exploration Data Release 16, and Large Sky Area Multi-Object Fiber Spectroscopic Telescope Data Release 8, 11 member stars of the NGC 5466 tidal stream are detected and 7 of them are newly identified. To reject contaminators, a variety of cuts are applied in sky position, colour–magnitude diagram, metallicity, proper motion, and radial velocity. We compare our data to a mock stream generated by modelling the cluster’s disruption under a smooth Galactic potential plus the Large Magellanic Cloud (LMC). The concordant trends in phase space between the model and observations imply that the stream might have been perturbed by the LMC. The two most distant stars among the 11 detected members trace the stream’s length to 60° of sky, supporting and extending the previous length of 45°. Given that NGC 5466 is so distant and potentially has a longer tail than previously thought, we expect that the NGC 5466 tidal stream could be a useful tool in constraining the Milky Way gravitational field.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

A unique, ring-like radio source with quadrilateral structure detected with machine learning

ABSTRACT We report the discovery of a unique object in the MeerKAT Galaxy Cluster Legacy Survey (MGCLS) using the machine learning anomaly detection framework astronomaly. This strange, ring-like source is 30′ from the MGCLS field centred on Abell 209, and is not readily explained by simple physical models. With an assumed host galaxy at redshift 0.55, the luminosity (1025 W Hz−1) is comparable to powerful radio galaxies. The source consists of a ring of emission 175 kpc across, quadrilateral enhanced brightness regions bearing resemblance to radio jets, two ‘ears’ separated by 368 kpc, and a diffuse envelope. All of the structures appear spectrally steep, ranging from −1.0 to −1.5. The ring has high polarization (25 per cent) except on the bright patches (<10 per cent). We compare this source to the Odd Radio Circles recently discovered in ASKAP data and discuss several possible physical models, including a termination shock from starburst activity, an end-on radio galaxy, and a supermassive black hole merger event. No simple model can easily explain the observed structure of the source. This work, as well as other recent discoveries, demonstrates the power of unsupervised machine learning in mining large data sets for scientifically interesting sources.

Astronomy & Astrophysics↗
DOE OSTI2021

ECO: the Evidence and Conclusion Ontology, an update for 2022

The Evidence and Conclusion Ontology (ECO) is a community resource that provides an ontology of terms used to capture the type of evidence that supports biomedical annotations and assertions. Consistent capture of evidence information with ECO allows tracking of annotation provenance, establishment of quality control measures, and evidence-based data mining. ECO is in use by dozens of data repositories and resources with both specific and general areas of focus. ECO is continually being expanded and enhanced in response to user requests as well as our aim to adhere to community best-practices for ontology development. The ECO support team engages in multiple collaborations with other ontologies and annotating groups. Here we report on recent updates to the ECO ontology itself as well as associated resources that are available through this project. ECO project products are freely available for download from the project website (https://evidenceontology.org/) and GitHub (https://github.com/evidenceontology/evidenceontology). ECO is released into the public domain under a CC0 1.0 Universal license.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters

Abstract With an ever-increasing amount of (meta)genomic data being deposited in sequence databases, (meta)genome mining for natural product biosynthetic pathways occupies a critical role in the discovery of novel pharmaceutical drugs, crop protection agents and biomaterials. The genes that encode these pathways are often organised into biosynthetic gene clusters (BGCs). In 2015, we defined the Minimum Information about a Biosynthetic Gene cluster (MIBiG): a standardised data format that describes the minimally required information to uniquely characterise a BGC. We simultaneously constructed an accompanying online database of BGCs, which has since been widely used by the community as a reference dataset for BGCs and was expanded to 2021 entries in 2019 (MIBiG 2.0). Here, we describe MIBiG 3.0, a database update comprising large-scale validation and re-annotation of existing entries and 661 new entries. Particular attention was paid to the annotation of compound structures and biological activities, as well as protein domain selectivities. Together, these new features keep the database up-to-date, and will provide new opportunities for the scientific community to use its freely available data, e.g. for the training of new machine learning models to predict sequence-structure-function relationships for diverse natural products. MIBiG 3.0 is accessible online at https://mibig.secondarymetabolites.org/.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Combining Machine Learning and Comparative Effectiveness Methodology to Study Primary Care Pharmacotherapy Pathways for Veterans With Depression

Our objective is to demonstrate an innovative method combining machine learning with comparative effectiveness research techniques and to investigate a hitherto unstudied question about the effectiveness of common prescribing patterns. For Operation Enduring Freedom/Operation Iraqi Freedom veterans with major depressive disorder, we generate pharmacotherapy pathways (of antidepressants) using process mining and machine learning. We select the medication episodes that were started at subtherapeutic doses by the first assigned primary care physician and observe the paths that those medication episodes follow. Using 2-stage least squares, we test the effectiveness of starting at a low dose and staying low for longer versus ramping up fast while balancing observable and unobservable characteristics of patients and providers through instrumental variables. We leverage predetermined provider practice patterns as instruments. We collected outpatient pharmacy data for selective serotonin reuptake inhibitors and selective norepinephrine reuptake inhibitors, patient and provider characteristics (as control variables), and the instruments for our cohort. All data were extracted for the period between 2006 and 2020. There is a statistically significant positive effect (0.68, 95% CI 0.11–1.25) of “ramping up fast” on engagement in care. When we examine the effect of “ramping up slow”, we see an insignificant negative impact on engagement in care (−0.82, 95% CI −1.89 to 0.25). As expected, the probability of drop-out also seems to have a negative effect on engagement in care (−0.39, 95% CI −0.94 to 0.17). We further validate these results by testing with medication possession ratios calculated periodically as an alternative engagement in care metric. Our findings contradict the “Start low, go slow” adage, indicating that ramping up the dose of an antidepressant faster has a significantly positive effect on engagement in care for our population.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Prevalence and diversity of TAL effector-like proteins in fungal endosymbiotic Mycetohabitans spp.

EndofungalMycetohabitans(formerlyBurkholderia) spp. rely on a type III secretion system to deliver mostly unidentified effector proteins when colonizing their host fungus,Rhizopus microsporus. The one known secreted effector family fromMycetohabitansconsists of homologues of transcription activator-like (TAL) effectors, which are used by plant pathogenicXanthomonasandRalstoniaspp. to activate host genes that promote disease. These ‘BurkholderiaTAL-like (Btl)’ proteins bind corresponding specific DNA sequences in a predictable manner, but their genomic target(s) and impact on transcription in the fungus are unknown. Recent phenotyping of Btl mutants of twoMycetohabitansstrains revealed that the single Btl in oneMycetohabitans endofungorumstrain enhances fungal membrane stress tolerance, while others in aMycetohabitans rhizoxinicastrain promote bacterial colonization of the fungus. The phenotypic diversity underscores the need to assess the sequence diversity and, given that sequence diversity translates to DNA targeting specificity, the functional diversity of Btl proteins. Using a dual approach to maximize capture of Btl protein sequences for our analysis, we sequenced and assembled nineMycetohabitansspp. genomes using long-read PacBio technology and also mined available short-read Illumina fungal–bacterial metagenomes. We show thatbtlgenes are present across diverseMycetohabitansstrains from Mucoromycota fungal hosts yet vary in sequences and predicted DNA binding specificity. Phylogenetic analysis revealed distinct clades of Btl proteins and suggested thatMycetohabitansmight contain more species than previously recognized. Within our data set, Btl proteins were more conserved acrossM. rhizoxinicastrains than acrossM. endofungorum, but there was also evidence of greater overall strain diversity within the latter clade. Overall, the results suggest that Btl proteins contribute to bacterial–fungal symbioses in myriad ways.

Genetics & Heredity↗
DOE OSTI2020

Phonon spectrum of underdoped HgBa 2 CuO 4+δ investigated by neutron scattering

The cuprates exhibit a prominent charge-density-wave (CDW) instability with a wave vector along [100], i.e., the Cu-O bond direction. Whereas CDW order is most prominent at moderate doping and low temperature, there exists increasing evidence for dynamic charge correlations throughout a large portion of the temperature-doping phase diagram. In particular, the signatures of incipient charge order have been observed as phonon softening and/or broadening near the CDW wave vector approximately halfway through the Brillouin zone. Most of this work is focused on moderately doped cuprates, for which the CDW order is robust, or on optimally doped samples, for which the superconducting transition temperature (T c ) attains its maximum. Here we present a time-of-flight neutron scattering study of phonons in simple-tetragonal HgBa 2 CuO 4+δ (T c = 55 K) at a low doping level where prior work showed the CDW order to be weak. We employ and showcase a new software-based technique that mines a large number of measured Brillouin zones for useful data in order to improve accuracy and counting statistics. Density-functional theory has not provided an accurate description of phonons in HgBa2CuO4+δ, yet we find the right set of parameters to qualitatively reproduce the data. The notable exception is a dispersion minimum in the longitudinal Cu-O bond-stretching branch along [100]. Here, this discrepancy suggests that, while CDW order is weak, there exist significant dynamic charge correlations in the optic phonon range at low doping, near the edge of the superconducting dome.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Polarized Structure Function {sigma}LT from {pi}0 p Electroproduction Data in the Resonance Region at 0.4 GeV2 < Q2 < 1.0 GeV2

The first results on the sigma(LT') structure function in exclusive pi(0)p electroproduction at invariant masses of the final state of 1.5 GeV < W < 1.8 GeV and in the range of photon virtualities 0.4 GeV2 < Q(2) < 1.0 GeV2 were obtained from data on beam spin asymmetries and differential cross sections measured with the CLAS detector at Jefferson Lab. The Legendre moments determined from the sigma(LT') structure function have demonstrated sensitivity to the contributions from the nucleon resonances in the second and third resonance regions. These new data on the beam spin asymmetries in pi(0)p electroproduction extend the opportunities for the extraction of the nucleon resonance electro-excitation amplitudes in the mass range above 1.6 GeV.

Isupov, E. L.↗
DOE OSTI2021

Penrose process for a charged black hole in a uniform magnetic field

Spinning black holes create electromagnetic storms when immersed in ambient magnetic fields, illuminating the otherwise epically dark terrain. In an electromagnetic extension of the Penrose process, tremendous energy can be extracted, boosting the energy of radiating particles far more efficiently than the mechanical Penrose process. We locate the regions from which energy can be mined and demonstrate explicitly that they are no longer restricted to the ergosphere. Here we also show that there can be toroidal regions that trap negative energy particles in orbit around the black hole. We find that the effective charge coupling between the black hole and the superradiant particles decreases as energy is extracted, much like the spin of a black hole decreases in the mechanical analogue. While the effective coupling decreases, the actual charge of the black hole increases in magnitude reaching the energetically-favored Wald value, at which point energy extraction is impeded. We demonstrate the array of orbits for products from the electromagnetic Penrose process.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Spin-Triplet Pairing State Evidenced by Half-Quantum Flux in a Noncentrosymmetric Superconductor

Building future fault-tolerant quantum computers may rely on a basic but so far elusive building-block-type of materials, superconductors with spin-triplet pairing, which were considered to be very rare. Now physicists demonstrate that they can be found in materials with low symmetry, different from most common crystalline materials. The new finding focuses on a particular type of crystals, the structure of which does not have inversion symmetry. For more than a decade, this material class (noncentrosymmetric superconductor) has been inferred to be a potential rich mine of spin-triplet superconductors. It is conceived that the spin-triplet pairing is promised by the broken inversion symmetry, however key experimental evidences remain lacking. Xu et al. applied a newly developed method to examine a prototype noncentrosymmetric superconductor, α-BiPd. Their experiment reveals the presence of the highly unusual half-integer quantization of magnetic flux in polycrystalline rings of α-BiPd, which is a smoking-gun evidence for spin-triplet pairing. This new finding ignites hopes that spin-triplet pairing may be a common presence among the dozens of known noncentrosymmetric superconductors as theoretically expected, which can now be unambiguously identified by the unique phenomenon of half-quantum magnetic flux.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Electron-phonon coupling strength from ab initio frozen-phonon approach

In this work, we propose a fast method for high-throughput screening of potential superconducting materials. The method is based on calculating metallic screening of zone-center phonon modes, which provides an accurate estimate for the electron-phonon coupling strength. This method is complementary to the recently proposed Rigid Muffin Tin (RMT) method, which amounts to integrating the electronphonon coupling over the entire Brillouin zone (as opposed to the zone center), but in a relatively inferior approximation. We illustrate the use of this method by applying it to MgB 2 , where the high-temperature superconductivity is known to be driven largely by the zone-center modes, and compare it to a sister compound AlB 2 . We further illustrate the usage of this descriptor by screening a large number of binary hydrides, for which accurate first-principle calculations of electron-phonon coupling have been recently published. Together with the RMT descriptor, this method opens a way to perform initial high-throughput screening in search of conventional superconductors via machine learning or data mining.

36 MATERIALS SCIENCE↗
DOE OSTI2021

End-to-end orientation estimation from 2D cryo-EM1images

Cryo-electron microscopy (cryo-EM) is a Nobel Prize-winning technique for deter-mining high-resolution 3D structures of biological macromolecules. A 3D structure is reconstructed from hundreds of thousands of noisy 2D projection images. However, existing 3D reconstruction methods are still time-consuming, and one of the major computational bottlenecks is to recover the unknown orientation of the particle in16each 2D image. The dominant methods typically exploit expensive global search on each image to estimate the missing orientations. Here, a novel end-to-end supervised learning method is introduced to directly recover the missing orientations from 2D cryo-EM images. A neural network is used to approximate the mapping from images to orientations. Furthermore, a robust loss function is proposed for optimizing the parameters of the network, which can handle both asymmetric and symmetric 3D structures. Experiments on synthetic datasets with various symmetry types confirm that the neural network is capable of recovering orientations from 2D cryo-EM images, and the results on one real cryo-EM dataset further demonstrate its potential in more challenging imaging conditions.

3D reconstruction↗
DOE OSTI2021

Sentiment Analysis based Error Detection for Large-Scale Systems

Today's large-scale systems such as High Performance Computing (HPC) Systems are designed/utilized towards exascale computing, inevitably decreasing its reliability due to the increasing design complexity. HPC systems conduct extensive logging of their execution behaviour. In this paper, we leverage the inherent meaning behind the log messages and propose a novel sentiment analysis-based approach for the error detection in large-scale systems, by automatically mining the sentiments in the log messages. Our contributions are four-fold. (1) We develop a machine learning (ML) based approach to automatically build a sentiment lexicon, based on the system log message templates. (2) Using the sentiment lexicon, we develop an algorithm to detect system errors. (3) We develop an algorithm to identify the nodes and components with erroneous behaviors, based on sentiment polarity scores. (4) We evaluate our solution vs. other state-of-the-art machine/deep learning algorithms based on three representative supercomputers' system logs. Experiments show that our error detection algorithm can identify error messages with an average MCC score and f -score of 91% and 96% respectively, while state of the art ML/deep learning model (LSTM) obtains only 67% and 84%. To the best of our knowledge, this is the first work leveraging the sentiments embedded in log entries of large-scale systems for system health analysis.

error detection↗
DOE OSTI2022

Automated Metadata Extraction: Challenges and Opportunities

Proper application of the FAIR data principles is what separates a vibrant data ecosystem, in which research data are frequently shared and reused, from a lifeless data graveyard. Automated metadata extraction systems have been proposed as a means of bolstering the findability, interoperability, and reusabil- ity of data repositories with little or no human intervention. These extraction systems mine metadata by crawling a repository and applying lightweight extractors that, for various types of file (e.g., image, CSV file), extract or synthesize relevant attributes. In practice, however, the automated creation of generally useful metadata is fraught with challenges. Data consumers may have different perspectives as to what metadata representations are useful, the standards for recording metadata tend to change over time, and the software model for processing updates can introduce unnecessary human and computational effort. Thus, generalizing extraction for a broad audience of data consumers is a difficult and relatively unsolved problem.In this work, we explore these challenges faced by extraction systems in the context of constructing our own extraction system for science data. We first define the metadata extraction problem and provide context to the issues faced in generalizing metadata. Additionally, we identify potential research directions to help alleviate many of these challenges for all automated extraction systems. Ultimately, this work represents a first step in designing ubiquitous metadata extraction systems that can maximize the value of research data while minimizing the human efforts required in doing so.

Skluzacek, Tyler↗
DOE OSTI2023

Fast Parallel Tensor Times Same Vector for Hypergraphs

Hypergraphs are a popular paradigm to rep- resent complex real-world networks exhibiting multi-way relationships of varying sizes. Mining centrality in hyper- graphs via symmetric adjacency tensors has only recently become computationally feasible for large and complex datasets. To enable scalable computation of these and related hypergraph analytics, here we focus on the Sparse Symmetric Tensor Times Same Vector (S3TTVC) oper- ation. We introduce the Compound Compressed Sparse Symmetric (CCSS) format, an extension of the compact CSS format for hypergraphs of varying hyperedge sizes and present a shared-memory parallel algorithm to compute S3TTVC. We experimentally show S3TTVC computation using the CCSS format achieves better performance than the naive baseline, and is subsequently more performant for hypergraph H-eigenvector centrality.

Shivakumar, Shruti↗
DOE OSTI2023

A Pulse Generation Framework with Augmented Program-aware Basis Gates and Criticality Analysis

Near-term intermediate scale quantum (NISQ) de- vices are subject to considerable noise and short coherence time. Consequently, it is critical to minimize circuit execution latency. Traditionally, each basis gate of a transpiled circuit is decoded into a fixed episode of the device control pulses. Recently, people started to investigate merged pulse generation for customized gates through quantum optimal control (QOC). However, existing QOC approaches face the challenges of (i) restricted search space due to prohibitive compilation overhead; (ii) suboptimal end-to-end performance due to aggressive local optimization and falsely introduced dependency among the customized gates; (iii) inadequate adaptivity towards system calibration, which is critical for NISQ devices. In this work, we propose PAQOC, a novel QOC framework that can (i) automatically detect frequently encountered gate patterns in the logical circuit by modeling the problem as a subgraph mining process and reuse these patterns to enable much larger search space exploration (i.e., program aware); (ii) systemically construct customized gate-set based on the impact to the overall program latency (i.e., criticality-aware); and (iii) quickly adapt to system re-calibration thanks to the small-scale pattern-based gate generation (i.e., adaptivity-aware). PAQOC achieves a good tradeoff between circuit performance and compilation time, allowing fully automatic, single stop, ad- hoc customized pulse generation for more efficient execution of user programs on NISQ devices. Evaluations using fifteen applications show that PAQOC can achieve on average 1.95× speedup of the circuit latency and achieve on average 36.7% reduction in compilation overhead. With PAQOC, circuits can run faster with reduced noise, allowing deeper circuits to be tested within the coherence time of present NISQ platforms.

Chen, Yanhao↗
DOE OSTI2025

SymProp: Scaling Sparse Symmetric Tucker Decomposition via Symmetry Propagation

Sparse symmetric tensors are an important class of tensors, and their decompositions serve as powerful tools for revealing low-rank structures. This paper introduces SymProp, a novel approach for scaling sparse symmetric Tucker decomposition by propagating symmetry through intermediate computations. SymProp optimizes two key computational kernels: Sparse Symmetric Tensor Times Same Matrix chain (S3 TTMc) for Higher-Order Orthogonal Iteration (HOOI) and Sparse Symmetric Tensor Times Same Matrix chain Times Core (S3 TTMcTC) for Higher-Order QR Iteration (HOQRI). Our method employs a metaprogramming-based index iteration approach to efficiently handle the upper triangular parts of intermediate dense symmetric tensors. SymProp achieves up to 50.9× speedup over SPLATT and up to 360.8× over Compressed Sparse Symmetric (CSS) format on the S3 TTMc operation. Moreover, our S3 TTMc and S3 TTMcTC implementations support tensor orders four levels higher than state-of-the-art methods. Our HOQRI demonstrates superior scalability and up to a 33.6× speedup over optimized HOOI. By enabling more scalable Tucker decompositions for higher orders, decomposition ranks, and dimension sizes, SymProp opens new possibilities for analyzing complex hypergraph structures in fields such as network science, data mining, and machine learning.

Li, Zecheng [North Carolina State University]↗
DOE OSTI2024

Distributed Multi-GPU Community Detection on Exascale Computing Platforms

Community detection is a fundamental operation in graph mining, and by uncovering hidden structures and patterns within complex systems it helps solve fundamental problems pertaining to social networks, such as information diffusion, epidemics, and recommender systems. Scaling graph algorithms for massive networks becomes challenging on modern distributed-memory multi-GPU (Graphics Processing Unit) systems due to limitations such as irregular memory access patterns, load imbalances, higher communication-computation ratios, and cross-platform support. We present a novel algorithm HiPDPL-GPU (distributed parallel Louvain) to address these challenges. We conduct experiments involving different partitioning techniques to achieve optimized performance of HiPDPL-GPU on the two largest supercomputers: Frontier and Summit. Remarkably, HiPDPL-GPU processes a graph with 4.2 billion edges in less than 3 minutes using 1024 GPUs. Qualitatively performance of HiPDPL-GPU is similar or better compared to other state-of-the-art CPU- and GPU-based implementations. While prior GPU implementations have predominantly employed CUDA, our first-of-its-kind implementation for community detection is cross-platform, accommodating both AMD and NVIDIA GPUs.

graph algorithms, high performance comptuing↗