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At least 433 records · Page 24
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Smart pixel sensors: towards on-sensor filtering of pixel clusters with deep learning

Highly granular pixel detectors allow for increasingly precise measurements of charged particle tracks. Next-generation detectors require that pixel sizes will be further reduced, leading to unprecedented data rates exceeding those foreseen at the High- Luminosity Large Hadron Collider. Signal processing that handles data incoming at a rate of $\mathcal{O}$(40 MHz) and intelligently reduces the data within the pixelated region of the detector at rate will enhance physics performance at high luminosity and enable physics analyses that are not currently possible. Using the shape of charge clusters deposited in an array of small pixels, the physical properties of the traversing particle can be extracted with locally customized neural networks. In this first demonstration, we present a neural network that can be embedded into the on-sensor readout and filter out hits from low momentum tracks, reducing the detector's data volume by 57.1%–75.7%. The network is designed and simulated as a custom readout integrated circuit with 28 nm CMOS technology and is expected to operate at less than 300 μW with an area of less than 0.2 mm 2 . The temporal development of charge clusters is investigated to demonstrate possible future performance gains, and there is also a discussion of future algorithmic and technological improvements that could enhance efficiency, data reduction, and power per area.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2025

Clustering at Massive Scale

ClaMS provides hierarchical clustering technology for use on massive, high-dimensional datasets that require distributed memory for processing. The algorithm employed is inspired by the popular HDBSCAN algorithm but makes use of computational kernels better suited for distributed computing. ClaMS is built on scalable nearest neighbor graph construction, metric forest completion, and approximate minimum spanning tree techniques.

Stanley, ThomasA [Lawrence Livermore National Labo↗
DOE OSTI2021

Neutrino event selection in the MicroBooNE liquid argon time projection chamber using Wire-Cell 3D imaging, clustering, and charge-light matching

An accurate and efficient event reconstruction is required to realize the full scientific capability of liquid argon time projection chambers (LArTPCs). The current and future neutrino experiments that rely on massive LArTPCs create a need for new ideas and reconstruction approaches. Wire-Cell, proposed in recent years, is a novel tomographic event reconstruction method for LArTPCs. The Wire-Cell 3D imaging approach capitalizes on charge, sparsity, time, and geometry information to reconstruct a topology-agnostic 3D image of the ionization electrons prior to pattern recognition. A second novel method, the many-to-many charge-light matching, then pairs the TPC charge activity to the detected scintillation light signal, thus enabling a powerful rejection of cosmic-ray muons in the MicroBooNE detector. A robust processing of the scintillation light signal and an appropriate clustering of the reconstructed 3D image are fundamental to this technique. In this paper, we describe the principles and algorithms of these techniques and their successful application in the MicroBooNE experiment. A quantitative evaluation of the performance of these techniques is presented. Using these techniques, a 95% efficient pre-selection of neutrino charged-current events is achieved with a 30-fold reduction of non-beam-coincident cosmic-ray muons, and about 80% of the selected neutrino charged-current events are reconstructed with at least 70% completeness and 80% purity.

3D imaging↗
DOE OSTI2024

Forming a database to study reversed magnetic shear from the National Spherical Torus eXperiment using machine learning

Achieving a long-lived reversed magnetic shear (RMS) target plasma in the National Spherical Torus eXperiment Upgrade will require developing various sustainment scenarios. To help with the ongoing plasma control efforts, the development of a new analysis for the motional Stark effect (MSE) diagnostic using a machine learning algorithm, namely, MSE-ML, is described. MSE-ML will be used to identify patterns during RMS discharges, some of which suffer magnetohydrodynamic (MHD) events resulting in current redistribution and monotonic q-profiles. A database consisting of q and magnetic shear profiles is being constructed primarily based on the existing National Spherical Torus eXperiment data with equilibrium reconstructions constrained by the magnetic field pitch angle profile measured using the multi-channel MSE diagnostic. An unsupervised k-means clustering of the data is developed to study the RMS formation as a function of time. The initial clustering from the q-profiles shows significant differences in both amplitude and the duration of the RMS period. As a goal, the clustering results that detect and distinguish shots with substantial and sustained RMS are to be used as a preprocessing step in a supervised algorithm to identify the underlying conditions that lead to long-lasting improved confinement with RMS. Another aim of the MSE-ML study is to identify precursors of RMS-destroying MHD events in either derived data such as the q-profile or directly measured data such as the magnetic field pitch angle profile.

Uzun-Kaymak, I. U. (ORCID:0000000276251493)↗
DOE OSTI2022

Toward Accurate Modeling of Galaxy Clustering on Small Scales: Constraining the Galaxy-halo Connection with Optimal Statistics

Applying halo models to analyze the small-scale clustering of galaxies is a proven method for characterizing the connection between galaxies and their host halos. Such works are often plagued by systematic errors or limited to clustering statistics that can be predicted analytically. In this work, we employ a numerical mock-based modeling procedure to examine the clustering of Sloan Digital Sky Survey DR7 galaxies. We apply a standard halo occupation distribution (HOD) model to dark matter only simulations with a ΛCDM cosmology. To constrain the theoreStical models, we utilize a combination of galaxy number density and selected scales of the projected correlation function, redshift-space correlation function, group multiplicity function, average group velocity dispersion, mark correlation function, and counts-in-cells statistics. We design an algorithm to choose an optimal combination of measurements that yields tight and accurate constraints on our model parameters. Compared to previous work using fewer clustering statistics, we find a significant improvement in the constraints on all parameters of our halo model for two different luminosity-threshold galaxy samples. Most interestingly, we obtain unprecedented high-precision constraints on the scatter in the relationship between galaxy luminosity and halo mass. However, our best-fit model results in significant tension (>4σ) for both samples, indicating the need to add second-order features to the standard HOD model. To guarantee the robustness of these results, we perform an extensive analysis of the systematic and statistical errors in our modeling procedure, including a first of its kind study of the sensitivity of our constraints to changes in the halo mass function due to baryonic physics.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Multi-channel Imager Algorithm (MIA): A novel cloud-top phase classification algorithm

The current Geostationary Operational Environmental Satellites (GOES-16 and 17) cloud-top phase classification algorithm is based primarily on empirical thresholds at multiple wavelengths that have varying absorption capabilities for water and ice. The performance of current GOES-16 cloud-top phase product largely depends on the accuracy of the selection of reflectance ratios. Here this study aims at presenting a novel cloud-top phase classification algorithm (the Multi-channel Imager Algorithm, MIA) that provides a more judicious selection of relationships between channels using a supervised K-mean clustering method on multi-channel Red-Green-Blue images. The K-mean clustering method works analogously to how human eyes separate different colors in a microphysical color rendering set of satellite images, which differentiates water, ice and unclassified thin clouds. For water phase, cloud-top temperature information is used to further distinguish supercooled water. To evaluate the performance of the MIA, an extensive comparison with Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP), Moderate Resolution Imaging Spectroradiometer, and current GOES-16 cloud-top phase products is conducted, using CALIOP as the benchmark. Compared to the current GOES-16 cloud-top phase product, MIA demonstrates a substantial improvement in phase classification, where hit rate increases from 69% to 76% over the Continental United States and 58% to 66% over the full disk domain.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

A k-mer based approach for classifying viruses without taxonomy identifies viral associations in human autism and plant microbiomes

Viruses are an underrepresented taxa in the study and identification of microbiome constituents; however, they play an essential role in health, microbiome regulation, and transfer of genetic material. Only a few thousand viruses have been isolated, sequenced, and assigned a taxonomy, which limits the ability to identify and quantify viruses in the microbiome. Additionally, the vast diversity of viruses represents a challenge for classification, not only in constructing a viral taxonomy, but also in identifying similarities between a virus’ genotype and its phenotype. However, the diversity of viral sequences can be leveraged to classify their sequences in metagenomic and metatranscriptomic samples, even if they do not have a taxonomy. To identify and quantify viruses in transcriptomic and genomic samples, we developed a dynamic programming algorithm for creating a classification tree out of 715,672 metagenome viruses. To create the classification tree, we clustered proportional similarity scores generated from the k-mer profiles of each of the metagenome viruses to create a database of metagenomic viruses. The resulting Kraken2 database of the metagenomic viruses can be found here: https://www.osti.gov/biblio/1615774 and is compatible with Kraken2. We then integrated the viral classification database with databases created with genomes from NCBI for use with ParaKraken (a parallelized version of Kraken provided in Supplemental Zip 1), a metagenomic/transcriptomic classifier. To illustrate the breadth of our utility for classifying metagenome viruses, we analyzed data from a plant metagenome study identifying genotypic and compartment specific differences between two Populus genotypes in three different compartments. We also identified a significant increase in abundance of eight viral sequences in post mortem brains in a human metatranscriptome study comparing Autism Spectrum Disorder patients and controls. We also show the potential accuracy for classifying viruses by utilizing both the JGI and NCBI viral databases to identify the uniqueness of viral sequences. Finally, we validate the accuracy of viral classification with NCBI databases containing viruses with taxonomy to identify pathogenic viruses in known COVID-19 and cassava brown streak virus infection samples. Our method represents the compulsory first step in better understanding the role of viruses in the microbiome by allowing for a more complete identification of sequences without taxonomy. Better classification of viruses will improve identifying associations between viruses and their hosts as well as viruses and other microbiome members. Despite the lack of taxonomy, this database of metagenomic viruses can be used with any tool that utilizes a taxonomy, such as Kraken, for accurate classification of viruses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Community detection in hypergraphs via mutual information maximization

Abstract The hypergraph community detection problem seeks to identify groups of related vertices in hypergraph data. We propose an information-theoretic hypergraph community detection algorithm which compresses the observed data in terms of community labels and community-edge intersections. This algorithm can also be viewed as maximum-likelihood inference in a degree-corrected microcanonical stochastic blockmodel. We perform the compression/inference step via simulated annealing. Unlike several recent algorithms based on canonical models, our microcanonical algorithm does not require inference of statistical parameters such as vertex degrees or pairwise group connection rates. Through synthetic experiments, we find that our algorithm succeeds down to recently-conjectured thresholds for sparse random hypergraphs. We also find competitive performance in cluster recovery tasks on several hypergraph data sets.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

GPU-based Image Compression for Efficient Compositing in Distributed Rendering Applications

Visualizations of large-scale data sets are often created on graphics clusters that distribute the rendering task amongst many processes. When using real-time GPU-based graphics algorithms, the most time-consuming aspect of distributed rendering is typically the com-positing phase - combining all partial images from each rendering process into the final visualization. Compo siting requires image data to be copied off the GPU and sent over a network to other processes. While compression has been utilized in existing distributed rendering compositors to reduce the data being sent over the network, this compression tends to occur after the raw images are transferred from the GPU to main memory. In this paper, we present work that leverages OpenGL / CUDA interoperability to compress raw images on the GPU prior to transferring the data to main memory. This approach can significantly reduce the device-to-host data transfer time, thus enabling more efficient compositing of images generated by distributed rendering applications.

Lipinksi, Riley↗
DOE OSTI2020

Kraken2 Metagenomic Virus Database

The Database: Kraken2 [1] database built from a classification tree containing over 700k metagenomic viruses from JGI IMG/VR [2]. (1) Wood, D. E., Lu, J., and Langmead, B. (2019). Improved metagenomic analysis with Kraken 2. Genome Biol., 20(1), 1–13. doi: 10.1186/s13059-019-1891-0 (2) Paez-Espino D, Chen I-MA, Palaniappan K, Ratner A, Chu K, Szeto E, et al. IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses. Nucleic Acids Res. 2017;45:D457-65. For Paper: Title: A k-mer based approach for virus classification in metatranscriptomic and metagenomic samples identifies viral associations in the Populus phytobiome and autism brains Abstract Background Viruses are an underrepresented taxa in the study and identification of microbiome constituents; however, they play an important role in health, microbiome regulation, and transfer of genetic material. Only a few thousand viruses have been isolated, sequenced, and assigned a taxonomy, which further limits the ability to identify and quantify viruses in the microbiome. Additionally, the vast diversity of viruses represents a challenge for classification, not only in constructing a viral taxonomy, but also in identifying similarities between a virus' genotype and its phenotype. However, the diversity of viral sequences can be leveraged to classify their sequences in metagenomic and metatranscriptomic samples. Methods To identify viruses in transcriptomic and genomic samples, we developed a dynamic programming algorithm for creating a classification tree out of 715,672 metagenome viruses. To create the classification tree, we clustered proportional similarity scores generated from the k-mer profiles of each of the metagenome viruses. We then integrated the viral classification tree with the NCBI taxonomy for use with ParaKraken, a metagenomic/transcriptomic classifier. Results To illustrate the breadth of our utility for classifying viruses with ParaKraken, we analyzed data from a plant metagenome study identifying the differences between two Populus genotypes in three different compartments and on a human metatranscriptome study identifying the differences between Autism Spectrum Disorder patients and controls in post mortem brain biopsies. In the Populus study, we identified genotype and compartment specific viral signatures, while in the Autism study we identified a significant increased abundance of eight viral sequences in Autism brain biopsies. Conclusion Viruses represent an important aspect of the microbiome. The ability to classify viruses represents the first step in being able to better understand their role in the microbiome. The viral classification method presented here allows for more complete identification of viral sequences for use in identifying associations between viruses and the host and viruses and other microbiome members. Acknowledgements and Funding This research used resources of the Oak Ridge Leadership Computing Facility at the Oak Ridge National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-00OR22725. This research was also supported by the Plant-Microbe Interfaces Scientific Focus Area in the Genomic Science Program, the Office of Biological and Environmental Research (BER) in the U.S. Department of Energy Office of Science, and by the Department of Energy, Laboratory Directed Research and Development funding (ProjectID 8321), at the Oak Ridge National Laboratory. Oak Ridge National Laboratory is managed by UT-Battelle, LLC, for the US DOE under contract DE-AC05-00OR22725. This research used resources of the Compute and Data Environment for Science (CADES).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Summer Proceedings 2019

The Computer Science Research Institute (CSRI) brings university faculty and students to Sandia for focused collaborative research on Department of Energy (DOE) computer and computational science problems. The institute provides an opportunity for university researchers to learn about problems in computer and computational science at DOE laboratories. Participants conduct leading-edge research, interact with scientists and engineers at the laboratories, and help transfer results of their research to programs at the labs. Some specific CSRI research interest areas are: scalable solvers, optimization, adaptivity and mesh refinement, graph-based, discrete, and combinatorial algorithms, uncertainty estimation, mesh generation, dynamic load-balancing, virus and other malicious-code defense, visualization, scalable cluster computers and heterogeneous computers, data-intensive computing, environments for scalable computing, parallel input/output, advanced architectures, and theoretical computer science. The CSRI Summer Program includes the organization of a weekly seminar series and the publication of this summer proceedings.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

CSRI Summer Proceedings 2020

The Computer Science Research Institute (CSRI) brings university faculty and students to Sandia for focused collaborative research on Department of Energy (DOE) computer and computational science problems. The institute provides an opportunity for university researchers to learn about problems in computer and computational science at DOE laboratories. Participants conduct leading-edge research, interact with scientists and engineers at the laboratories, and help transfer results of their research to programs at the labs. Some specific CSRI research interest areas are: scalable solvers, optimization, adaptivity and mesh refinement, graph-based, discrete, and combinatorial algorithms, uncertainty estimation, mesh generation, dynamic load-balancing, virus and other malicious-code defense, visualization, scalable cluster computers, data-intensive computing, environments for scalable computing, parallel input/output, advanced architectures, and theoretical computer science. The CSRI Summer Program is organized by CSRI and typically includes the organization of a weekly seminar series and the publication of a summer proceedings. In 2020, the CSRI summer program was executed completely virtually; all student interns worked from home, due to the COVID-19 pandemic.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Baryon acoustic oscillation theory and modelling systematics for the DESI 2024 results

This paper provides a comprehensive overview of how fitting of baryon acoustic oscillations (BAO) is carried out within the upcoming Dark Energy Spectroscopic Instrument’s (DESI) 2024 results using its DR1 data set, and the associated systematic error budget from theory and modelling of the BAO. We derive new results showing how non-linearities in the clustering of galaxies can cause potential biases in measurements of the isotropic (⁠α iso ⁠) and anisotropic (⁠α ap ) BAO distance scales, and how these can be effectively removed with an appropriate choice of reconstruction algorithm. We then demonstrate how theory leads to a clear choice for how to model the BAO and develop, implement, and validate a new model for the remaining smooth-broad-band (i.e. without BAO) component of the galaxy clustering. Finally, we explore the impact of all remaining modelling choices on the BAO constraints from DESI using a suite of high-precision simulations, arriving at a set of best practices for DESI BAO fits, and an associated theory and modelling systematic error. Overall, our results demonstrate the remarkable robustness of the BAO to all our modelling choices and motivate a combined theory and modelling systematic error contribution to the post-reconstruction DESI BAO measurements of no more than 0.1 per cent (0.2 per cent) for its isotropic (anisotropic) distance measurements. We expect the theory and best practices laid out to here to be applicable to other BAO experiments in the era of DESI and beyond.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Hypercane

Automatically summarizing a collection of documents requires analyzing their features using various operations. Hypercane is a framework for building algorithms for sampling files from a collection. Sampling is a vital part of automatic summarization. Hypercane ties together many existing third-party libraries. These libraries include those for processing web resources, natural language processing for analyzing text and filtering documents, and machine learning for clustering summarization candidates. A user can run up to more than 70 operations on a corpus in the order of their choosing. Through these operations, they can create custom automatic summarization algorithms to help them process the corpus of their choice. Details of the algorithms possible with Hypercane are available in Jones 2021. Details of running Hypercane are available in Jones et al.; 2021.

Jones, Shawn↗
DOE OSTI2020

Reliable photometric membership (RPM) of galaxies in clusters – I. A machine learning method and its performance in the local universe

ABSTRACT We introduce a new method to determine galaxy cluster membership based solely on photometric properties. We adopt a machine learning approach to recover a cluster membership probability from galaxy photometric parameters and finally derive a membership classification. After testing several machine learning techniques (such as stochastic gradient boosting, model averaged neural network and k-nearest neighbours), we found the support vector machine algorithm to perform better when applied to our data. Our training and validation data are from the Sloan Digital Sky Survey main sample. Hence, to be complete to $M_r^* + 3$, we limit our work to 30 clusters with $z$phot-cl ≤ 0.045. Masses (M200) are larger than $\sim 0.6\times 10^{14} \, \mathrm{M}_{\odot }$ (most above $3\times 10^{14} \, \mathrm{M}_{\odot }$). Our results are derived taking in account all galaxies in the line of sight of each cluster, with no photometric redshift cuts or background corrections. Our method is non-parametric, making no assumptions on the number density or luminosity profiles of galaxies in clusters. Our approach delivers extremely accurate results (completeness, C $\sim 92{\rm{ per\ cent}}$ and purity, P $\sim 87{\rm{ per\ cent}}$) within R200, so that we named our code reliable photometric membership. We discuss possible dependencies on magnitude, colour, and cluster mass. Finally, we present some applications of our method, stressing its impact to galaxy evolution and cosmological studies based on future large-scale surveys, such as eROSITA, EUCLID, and LSST.

Lopes, Paulo A. A.↗
DOE OSTI2020

ReaxFF molecular dynamics simulations of electrolyte–water systems at supercritical temperature

We have performed ReaxFF molecular dynamics simulations of alkali metal–chlorine pairs in different water densities at supercritical temperature (700 K) to elucidate the structural and dynamical properties of the system. The radial distribution function and the angular distribution function explain the inter-ionic structural and orientational arrangements of atoms during the simulation. The coordination number of water molecules in the solvation shell of ions increases with an increase in the radius of ions. We find that the self-diffusion coefficient of metal ions increases with a decrease in density under supercritical conditions due to the formation of voids within the system. The hydrogen bond dynamics has been interpreted by the residence time distribution of various ions, which shows Li+ having the highest water retaining capability. The void distribution within the system has been analyzed by using the Voronoi polyhedra algorithm providing an estimation of void formation within the system at high temperatures. We observe the formation of salt clusters of Na+ and K+ at low densities due to the loss of dielectric constants of ions. The diffusion of ions gets altered dramatically due to the formation of voids and nucleation of ions in the system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

On the Robustness of Network Community Structure Under Addition of Edges

Communities represent important functional modules in networked systems. A key goal in preserving such communities is understanding their robustness under perturbations. Previous research has studied the impact of node removals and edge removals on the community structure. However, the impact of edge additions on the robustness of the community structure is relatively unknown. Edge additions or false positive edges may simulate measurement errors or external exceptional events that threaten the functionality of networked systems. Here, we study the impact of edge additions on the community structure using Lancichinetti-Fortunato-Radicchi (LFR) benchmark networks. We show that, for a fixed network size, the impact of edge additions is greater on networks with initially weak community structure than on networks with strongly clustered structures. In addition, we find that the perception of the impact is also dependent on the community detection algorithm used to uncover communities. In particular, we found that modularity-based methods such as Leiden and Louvain are less affected than information-theoretic and message passing-based methods such as Infomap and Label Propagation. Our results demonstrate that edge addition can (a) significantly impact the community structure of networks based on their initial conditions, and (b) the perception of the impact is dependent on the community detection algorithm used. We describe limitations, open challenges, and how this methodology can inform the design of resilient networked systems under edge additions.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

The Circular Velocity Curve of the Milky Way from 5–25 kpc Using Luminous Red Giant Branch Stars

We present a sample of 254,882 luminous red giant branch (LRGB) stars selected from the APOGEE and LAMOST surveys. By combining photometric and astrometric information from the Two Micron All Sky Survey and Gaia survey, the precise distances of the sample stars are determined by a supervised machine-learning algorithm: the gradient-boosted decision trees. To test the accuracy of the derived distances, member stars of globular clusters (GCs) and open clusters are used. The tests by cluster member stars show a precision of about 10% with negligible zero-point offsets, for the derived distances of our sample stars. The final sample covers a large volume of the Galactic disk(s) and halo of 0 < R < 30 kpc and |Z| ≤ 15 kpc. The rotation curve (RC) of the Milky Way across the radius of 5 ≲ R ≲ 25 kpc has been accurately measured with ~54,000 stars of the thin disk population selected from the LRGB sample. The derived RC shows a weak decline along R with a gradient of -1.83 ± 0.02 (stat.) ± 0.07 (sys.) km s -1 kpc -1 , in excellent agreement with the results measured by previous studies. The circular velocity at the solar position, yielded by our RC is 234.04 ± 0.08 (stat.) ± 1.36 (sys.) km s -1 , again in great consistency with other independent determinations. From the newly constructed RC, as well as constraints from other data, we have constructed a mass model for our Galaxy, yielding a mass of the dark matter halo of M 200 = (8.05 ± 1.15) × 10 11 M ⊙ with a corresponding radius of R 200 = 192.37 ± 9.24 kpc and a local dark matter density of 0.39 ± 0.03 GeV cm -3 .

79 ASTRONOMY AND ASTROPHYSICS↗