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At least 91 records · Page 5

In Situ Transmission Electron Microscopy: Signal processing challenges and examples

Transmission electron microscopy (TEM) is a powerful tool for imaging material structure and characterizing material chemistry. Recent advances in data collection technology for TEM have enabled high-volume and high-resolution data collection at a microsecond frame rate. Here, taking advantage of these advances in data collection rates requires the development and application of data processing tools, including image analysis, feature extraction, and streaming data processing techniques. In this article, we highlight a few areas in materials science that have benefited from combining signal processing and statistical analysis with data collection capabilities in TEM and present a future outlook on opportunities of integrating signal processing with automated TEM data analysis.

36 MATERIALS SCIENCE↗

TiN Nanoporous Electrode Covered by Single Cell as Bio-Electronic Sensor of Radiation Hazard

Here we demonstrate a simple label-free bio-electronic radiation (ultra-violet) hazard detector based on non-destructive electrical impedance spectroscopy technique with a single living cell as a sensing element. Radiation results in wrong cell’s functioning and, as corollary, cell’s membrane distortion. The latter results in impedance shift for the electrode covered by the cell. The additional sensitivity of impedance shift is achieved by the simultaneous usage of the TiN porous electrodes and adaptive filtering for impedance data processing. The main advantage of the proposed sensor with respect to purely physical and/or chemical sensors is high selectivity: it a priory reacts only on the dangerous for living beings radiation.

36 MATERIALS SCIENCE↗

PESSTO: survey description and products from the first data release by the Public ESO Spectroscopic Survey of Transient Objects

Context. The Public European Southern Observatory Spectroscopic Survey of Transient Objects (PESSTO) began as a public spectroscopic survey in April 2012. PESSTO classifies transients from publicly available sources and wide-field surveys, and selects science targets for detailed spectroscopic and photometric follow-up. PESSTO runs for nine months of the year, January - April and August - December inclusive, and typically has allocations of 10 nights per month. Aims. We describe the data reduction strategy and data products that are publicly available through the ESO archive as the Spectroscopic Survey data release 1 (SSDR1). Methods. PESSTO uses the New Technology Telescope with the instruments EFOSC2 and SOFI to provide optical and NIR spectroscopy and imaging. We target supernovae and optical transients brighter than 20.5m for classification. Science targets are selected for follow-up based on the PESSTO science goal of extending knowledge of the extremes of the supernova population. We use standard EFOSC2 set-ups providing spectra with resolutions of 13-18 Å between 3345-9995 Å. A subset of the brighter science targets are selected for SOFI spectroscopy with the blue and red grisms (0.935-2.53 μm and resolutions 23-33 Å) and imaging with broadband JHKs filters. Results. This first data release (SSDR1) contains flux calibrated spectra from the first year (April 2012-2013). A total of 221 confirmed supernovae were classified, and we released calibrated optical spectra and classifications publicly within 24 h of the data being taken (via WISeREP). The data in SSDR1 replace those released spectra. They have more reliable and quantifiable flux calibrations, correction for telluric absorption, and are made available in standard ESO Phase 3 formats. We estimate the absolute accuracy of the flux calibrations for EFOSC2 across the whole survey in SSDR1 to be typically ~15%, although a number of spectra will have less reliable absolute flux calibration because of weather and slit losses. Acquisition images for each spectrum are available which, in principle, can allow the user to refine the absolute flux calibration. The standard NIR reduction process does not produce high accuracy absolute spectrophotometry but synthetic photometry with accompanying JHKs imaging can improve this. Whenever possible, reduced SOFI images are provided to allow this. Conclusions. Future data releases will focus on improving the automated flux calibration of the data products. The rapid turnaround between discovery and classification and access to reliable pipeline processed data products has allowed early science papers in the first few months of the survey.

79 ASTRONOMY AND ASTROPHYSICS↗

Multi-Dimensional Scaling on Groups

Leveraging the intrinsic symmetries in data for clear and efficient analysis is an important theme in signal processing and other data-driven sciences. A basic example of this is the ubiquity of the discrete Fourier transform which arises from translational symmetry (i.e. time-delay/phase-shift). Particularly important in this area is understanding how symmetries inform the algorithms that we apply to our data. In this paper we explore the behavior of the dimensionality reduction algorithm multi-dimensional scaling (MDS) in the presence of symmetry. We show that understanding the properties of the underlying symmetry group allows us to make strong statements about the output of MDS even before applying the algorithm itself. In analogy to Fourier theory, we show that in some cases only a handful of fundamental ``frequencies'' (irreducible representations derived from the corresponding group) contribute information for the MDS Euclidean embedding.

Dimensionality reduction, Representation theory, D↗

Massive all-atom analysis of 2D materials with quantum properties (Final report)

Improvements in microscopy have enabled the acquisition of data at a scale that is difficult to process manually, making automated machine learning approaches to analyzing experimental images essential. In this project, we developed and applied machine learning (ML) workflows for atomic resolution scanning transmission electron microscopy (STEM) images. This development included improving both methodology as well as generating user-friendly codes. We developed machine learning architectures which, after training, automatically identify the location and types of defects throughout a material. We used these data to produce class-averaged images of 2D atomic coordinates with up to 0.3 pm precision, uncovering the structure and oscillations of long-range strain fields around point defects in WSe 2-2x Te 2x . We also resolved a long-standing problem in this field in the training of ML models, a lack of labeled experimental data, by developing a cycle-GAN that transformed simulated-generated labeled data into labeled data indistinguishable from experiment and therefore suitable for training. This removed the remaining parts of the ML data processing workflow where human intervention was still critical and therefore a bottleneck to working at scale. Codes have been developed and released for this full machine learning workflow. ML approaches to partially automate STEM acquisition were also developed. Finally we applied ML and other advanced data processing methods to several materials science problems in two-dimensional materials, including studying the evolution of hyperuniformity with defect concentration in WSe2, understanding phase transformations in transition metal dichalcogenides during in-situ heating in the STEM, and exploring how 2D interfaces transform from twisted into aligned structures.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Reviews and syntheses: The promise of big diverse soil data, moving current practices towards future potential

Abstract. In the age of big data, soil data are more available and richer than ever, but – outside of a few large soil survey resources – they remain largely unusable for informing soil management and understanding Earth system processes beyond the original study. Data science has promised a fully reusable research pipeline where data from past studies are used to contextualize new findings and reanalyzed for new insight. Yet synthesis projects encounter challenges at all steps of the data reuse pipeline, including unavailable data, labor-intensive transcription of datasets, incomplete metadata, and a lack of communication between collaborators. Here, using insights from a diversity of soil, data, and climate scientists, we summarize current practices in soil data synthesis across all stages of database creation: availability, input, harmonization, curation, and publication. We then suggest new soil-focused semantic tools to improve existing data pipelines, such as ontologies, vocabulary lists, and community practices. Our goal is to provide the soil data community with an overview of current practices in soil data and where we need to go to fully leverage big data to solve soil problems in the next century.

54 ENVIRONMENTAL SCIENCES↗

Challenges in Bioinformatics Workflows for Processing Microbiome Omics Data at Scale

The nascent field of microbiome science is transitioning from a descriptive approach of cataloging taxa and functions present in an environment to applying multi-omics methods to investigate microbiome dynamics and function. A large number of new tools and algorithms have been designed and used for very specific purposes on samples collected by individual investigators or groups. While these developments have been quite instructive, the ability to compare microbiome data generated by many groups of researchers is impeded by the lack of standardized application of bioinformatics methods. Additionally, there are few examples of broad bioinformatics workflows that can process metagenome, metatranscriptome, metaproteome and metabolomic data at scale, and no central hub that allows processing, or provides varied omics data that are findable, accessible, interoperable and reusable (FAIR). Here, we review some of the challenges that exist in analyzing omics data within the microbiome research sphere, and provide context on how the National Microbiome Data Collaborative has adopted a standardized and open access approach to address such challenges.

NMDC, Microbiome↗

ARM Aerosol Measurement Science Group Charter

The Atmospheric Radiation Measurement (ARM) Aerosol Measurement Science Group (AMSG) is tasked with providing enhanced coordination of ARM Climate Research Facility observations of aerosols and atmospheric trace gases with the needs of its users. Its objective is to ensure advanced, well-characterized observational measurements and data products at the spatial and temporal scales necessary for improving climate science and climate model forecasts. The primary function of the AMSG will be to provide strategies to the ARM Technical Director and ARM Chief Operations Officer that can be used to implement a coherent measurement and data processing approach that addresses the priority aerosol science needs of ARM and Atmospheric System Research. The group fulfills the need for an integrated oversight to the planning, coordination, and leadership of aerosol instrumentation selection and deployment, measurement strategy and quality, and data product development from both science and operations perspectives.

Source record↗

Distributed Resources for the Earth System Grid Federation (ESGF) Advanced Management (DREAM). Final Report

Distributed Resources for the Earth System Grid Federation (ESGF) Advanced Management (DREAM) is a proposed system that will enable data from an infinite number of diverse sources to be organized and accessed from anywhere using any handheld or other computer device. The approach offers a powerful roadmap for the creation and integration of a unified knowledge base of an entire ecosystem, including its many geophysical, geographical, social, political, agricultural, energy, transportation, and cyber aspects. The resulting aggregation of data has the potential to generate an informational universe of unprecedented size that has never before been possible due to the prohibitive costs, managerial complexity, and technical barriers associated with ever-changing exponential-growth data flows. We envision that DREAM will accelerate discovery by enabling climate researchers, among other types of researchers, to manage, analyze, and visualize data from earth-scale measurements and simulations. DREAM’s success will be built on proven components that leverage existing services and resources. A key building block for DREAM will be the ESGF, chaired by Dean N. Williams. Expanding on the existing ESGF, the project will ensure that the access, storage, movement, and analysis of the large quantities of data that are processed and produced by diverse science projects can be dynamically distributed with proper resource management. Much of the Office of Science data is currently generated by multiple stand-alone facilities. DREAM can collect data accumulated from these facilities and incorporate it into a fully integrated network accessible from anywhere in the world. The result is a completely new paradigm shift for data management, analysis, and visualization enabling researchers to: Manage their calculations, data, tools, and research results; Ensure that all data are sharable, reproducible and (re)usable—accompanied by appropriate metadata describing its provenance, syntax, and semantics at creation; Advance application performance by selectively adapting APIs and services in response to scientific requirements and architectural complexities; and Provide scalable interactive resource management—navigate data and metadata at multiple levels, provide architecture-aware data integration, analysis and visualization tools. We will engage closely with DOE, NASA, and NOAA science groups working at the leading edge of computing. These engagements—in domains such as biology, climate, and hydrology—will allow us to advance disciplinary science goals and inform our development of technologies that can accelerate discovery across DOE more broadly. We will advertise and promote our technologies via dedicated workshops, tutorials, and sessions at conferences, stand-alone events with broad inter-disciplinary invitation, and engagements with leadership facilities.

54 ENVIRONMENTAL SCIENCES↗

Improving Scientific Data Analysis Through Multi-touch Enabled Interactive Data Visualization with Applications to Neutron Science

Scientific data analysis is an inherently exploratory process that requires flexible human interaction with data visualization and anal- ysis tools. In this paper, we describe challenges in neutron scattering data analysis and present our approach for allowing more effective human interaction. In addition to multi-touch enabled data visualiza- tion techniques, we describe color scale enhancements, layouts, and visual analytics approaches for 3D volume slicing. Since challenges in neutron science are echoed in most scientific fields, we generalize the project objective and present a case for bridging the gap between the latest advances in interactive data visualization and practical scientific scenarios where new critical knowledge is buried in large volumes of complex data.

Steed, Chad↗

South Dakota Region Scientific Deep Dive

EPOC uses the Deep Dive process to discuss and analyze current and planned science use cases and anticipated data output of a particular use case, site, or project to help inform the strategic planning of a campus or regional networking environment. This includes understanding future needs related to network operations, network capacity upgrades, and other technological service investments. A Deep Dive comprehensively surveys major research stakeholders’ plans and processes in order to investigate data management requirements over the next 5–10 years. Questions crafted to explore this space include the following: 1) How, and where, will new data be analyzed and used? 2) How will the process of doing science change over the next 5–10 years? and 3) How will changes to the underlying hardware and software technologies influence scientific discovery? Deep Dives help ensure that key stakeholders have a common understanding of the issues and the actions that a campus or regional network may need to undertake to offer solutions. The EPOC team leads the effort and relies on collaboration with the hosting site or network, and other affiliated entities that participate in the process. EPOC organizes, convenes, executes, and shares the outcomes of the review with all stakeholders

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

System design and prototyping for the CMS Level-1 Trigger at the High-Luminosity LHC

For the High-Luminosity Large Hadron Collider, the trigger and data acquisition system of the CMS experiment will be entirely replaced. Novel design choices have been explored, including ATCA prototyping platforms with SoC controllers and newly available interconnect technologies with serial optical links with data rates up to 28 Gb/s. Trigger analyses will be performed through sophisticated algorithms, including widespread use of Machine Learning, in large FPGAs, such as the Xilinx Ultrascale family. The system will process over 50 Tb/s of detector data with an event rate of 750 kHz. Here, we describe system design and prototyping and review trigger algorithm exemplars.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Aligning NASA Earth Science Data Stewardship with FAIR Principles: Outcomes, Recommendations, and Future Directions

The FAIR Principles—Findable, Accessible, Interoperable, and Reusable—offer a widely accepted framework for improving the sharing and reuse of digital scientific data by both human and machine users. Following these principles is critical for effective scientific data stewardship, broader scientific collaboration, and compliance with federal and agency data policies. This paper, based on the work of NASA’s Open, Free, and FAIR Working Group (O’FAIR WG) under the Earth Science Data Systems Program, presents an overview of how FAIR is being applied within NASA’s Earth science data landscape. It highlights ongoing progress and challenges, identifies FAIR-enabling resources, and offers recommendations and strategic actions to enhance the FAIRness of NASA-funded open and free Earth science data products. The FAIR-enabling resources identified underscore the vital role of NASA's existing enterprise processes, standards, tools, and infrastructures in supporting FAIR implementation. Our findings show strong performance in making NASA Earth science data more findable and accessible. However, further work is needed—especially in enhancing interoperability, so that different systems and tools can better understand and exchange data. This is especially important for enabling machine-driven discovery and analysis. We emphasize the importance of a balanced strategy that combines a centralized, top-down approach—focused on building enterprise-level capabilities and processes—with a decentralized, bottom-up approach driven by discipline-specific needs and community practices. We advocate for coordinated efforts to enhance (meta)data interoperability to facilitate seamless data and information sharing and exchange of Earth science data both within NASA and across other agencies managing Earth science data.

Data Product↗

Complex-valued universal linear transformations and image encryption using spatially incoherent diffractive networks

As an optical processor, a diffractive deep neural network (D2NN) utilizes engineered diffractive surfaces designed through machine learning to perform all-optical information processing, completing its tasks at the speed of light propagation through thin optical layers. With sufficient degrees of freedom, D2NNs can perform arbitrary complex-valued linear transformations using spatially coherent light. Similarly, D2NNs can also perform arbitrary linear intensity transformations with spatially incoherent illumination; however, under spatially incoherent light, these transformations are nonnegative, acting on diffraction-limited optical intensity patterns at the input field of view. Here, we expand the use of spatially incoherent D2NNs to complex-valued information processing for executing arbitrary complex-valued linear transformations using spatially incoherent light. Through simulations, we show that as the number of optimized diffractive features increases beyond a threshold dictated by the multiplication of the input and output space-bandwidth products, a spatially incoherent diffractive visual processor can approximate any complex-valued linear transformation and be used for all-optical image encryption using incoherent illumination. The findings are important for the all-optical processing of information under natural light using various forms of diffractive surface-based optical processors.

36 MATERIALS SCIENCE↗

Using spatial statistical methods to determine an effective minimum detectable activity - 15681

Instrument minimum detectable activity (MDA) is generally established by collecting multiple measurements over time of a single representative background location to estimate a probability distribution of instrument readings. A reading that is considered to be greater than would be expected from the background probability distribution (i.e., a low-probability event) is deemed to be sufficiently unlikely that it must be attributable to added radioactivity and is therefore used as the instrument MDA. An effective MDA can be determined from spatially distributed data that are much lower than the instrument MDA. This has been accomplished using a large number of spatially distributed data points (from a radiation survey) where patterns of elevated survey readings can be distinguished from background at levels. Given the variation of the instrument response and the relatively low regulatory action levels, it is vital to establish MDA thresholds that are well below corrective action levels. Processing of radiological survey data with the use of histogram binning and geo-statistics in enabling pattern recognition can be used to establish effective field MDAs that are much lower than instrument MDAs. (authors)

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

In-depth analysis on parallel processing patterns for high-performance Dataframes

The Data Science domain has expanded monumentally in both research and industry communities during the past decade, predominantly owing to the Big Data revolution. Artificial Intelligence (AI) and Machine Learning (ML) are bringing more complexities to data engineering applications, which are now integrated into data processing pipelines to process terabytes of data. Typically, a significant amount of time is spent on data preprocessing in these pipelines, and hence improving its efficiency directly impacts the overall pipeline performance. The community has recently embraced the concept of Dataframes as the de-facto data structure for data representation and manipulation. However, the most widely used serial Dataframes today (R, pandas) experience performance limitations while working on even moderately large data sets. We believe that there is plenty of room for improvement by taking a look at this problem from a high-performance computing point of view. In a prior publication, we presented a set of parallel processing patterns for distributed dataframe operators and the reference runtime implementation, Cylon. In this paper, we are expanding on the initial concept by introducing a cost model for evaluating the said patterns. Furthermore, we evaluate the performance of Cylon on the ORNL Summit supercomputer.

97 MATHEMATICS AND COMPUTING↗

Fault diagnosis and severity estimation in nuclear power plants - 196

Signed Directed Graph (SDG) is a type of fault diagnosis method with a capability to display the complex relationship between plant parameters and reveal the potential danger and the propagation path when a fault occurs in a nuclear plant. However, the fault diagnosis method based on qualitative SDG model inevitably has a number of disadvantages, and some of these disadvantages include its inability to identify reoccurring faults; ambiguous reasoning that can result in low resolution; performance that relies on the accuracy of the model; slow diagnosis rate for large systems and poor real-time diagnosis, among others. In this paper, we propose an SDG fault diagnosis methodology based on Granular Computing Theory, referred to as Granular Computing Signed Directed Graph (GCSDG). This paper shows how knowledge reduction nature of granular computing based fault diagnosis can simplify the decision table, reduce the allocation of resources, scale-down the complexity of the problem and improve the efficiency of data processing. Then, we estimate the severity of the fault using Back Propagation (BP) neural network approach. The proposed methodology was verified by considering certain faults in the primary loop of a PWR, using PCTRAN. The result shows a considerable improvement in fault diagnosis and the severity estimated serves as a useful information for the operator, providing a firm foundation for further intervention. (authors)

22 GENERAL STUDIES OF NUCLEAR REACTORS↗