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At least 91 records · Page 5

General-Purpose Bayesian Tensor Learning With Automatic Rank Determination and Uncertainty Quantification

A major challenge in many machine learning tasks is that the model expressive power depends on model size. Low-rank tensor methods are an efficient tool for handling the curse of dimensionality in many large-scale machine learning models. The major challenges in training a tensor learning model include how to process the high-volume data, how to determine the tensor rank automatically, and how to estimate the uncertainty of the results. While existing tensor learning focuses on a specific task, this paper proposes a generic Bayesian framework that can be employed to solve a broad class of tensor learning problems such as tensor completion, tensor regression, and tensorized neural networks. We develop a low-rank tensor prior for automatic rank determination in nonlinear problems. Our method is implemented with both stochastic gradient Hamiltonian Monte Carlo (SGHMC) and Stein Variational Gradient Descent (SVGD). We compare the automatic rank determination and uncertainty quantification of these two solvers. We demonstrate that our proposed method can determine the tensor rank automatically and can quantify the uncertainty of the obtained results. We validate our framework on tensor completion tasks and tensorized neural network training tasks.

Bayesian inference↗

Deactivation and decommissioning web log analysis using big data technology - 15710

The D and D Knowledge Management Information Tool (D and D KM- IT) is a web-based knowledge management information tool built for the D and D user community. Big data is a massive volume of structured and unstructured datasets which is so large that it's difficult to process using traditional database techniques. Web logs are the repository of files which are generated automatically for any operation on the web site. Web log files generated from the D and D KM-IT will be processed using the Apache Hadoop Framework to extract meaningful data. Hadoop is an open-source software framework for storing and processing big data in a distributed environment on large clusters of commodity hardware. Hadoop framework consists of two main layers: Hadoop distributed file system (HDFS) and the Execution engine (MapReduce). Automatic parallelization and distribution; clean and simple programming abstraction. Implementation: Web log files from the D and D KM-IT server are fetched using Apache Flume and loaded into the Hadoop distributed file system. Using the Apache Hcatalog tool, the web log data is parsed and converted into a structured table format. A Pig program is developed to query the tables to retrieve and store the significant information onto the HDFS. The extracted data is fed to business visualization tools such as Microsoft Excel for analysis and reporting. Results The reports generated through the web log data processing will be analyzed to improve the usability and performance of the D and D KM-IT. Conclusion/Future Work: User keyword information can be explored to add new trending topics to the D and D KM-IT application. Statistics generated can be compared to analysis reports from existing analytical tools.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Identifying COVID-19 cases and extracting patient reported symptoms from Reddit using natural language processing

We used social media data from “covid19positive” subreddit, from 03/2020 to 03/2022 to identify COVID-19 cases and extract their reported symptoms automatically using natural language processing (NLP). We trained a Bidirectional Encoder Representations from Transformers classification model with chunking to identify COVID-19 cases; also, we developed a novel QuadArm model, which incorporates Question-answering, dual-corpus expansion, Adaptive rotation clustering, and mapping, to extract symptoms. Our classification model achieved a 91.2% accuracy for the early period (03/2020-05/2020) and was applied to the Delta (07/2021–09/2021) and Omicron (12/2021–03/2022) periods for case identification. We identified 310, 8794, and 12,094 COVID-positive authors in the three periods, respectively. The top five common symptoms extracted in the early period were coughing (57%), fever (55%), loss of sense of smell (41%), headache (40%), and sore throat (40%). During the Delta period, these symptoms remained as the top five symptoms with percent authors reporting symptoms reduced to half or fewer than the early period. During the Omicron period, loss of sense of smell was reported less while sore throat was reported more. Our study demonstrated that NLP can be used to identify COVID-19 cases accurately and extracted symptoms efficiently.

60 APPLIED LIFE SCIENCES↗

Estimation of the time for steam generator trip due to cyber intrusions

The time required to trip a pressurized water reactor (PWR) by inserting malicious signals into its steam generator (SG) control system has been studied using the Generic PWR (GPWR) Simulator. A semi-analytical model is developed to approximately reproduce the simulator response and understand the dynamics of the control unit. A series of two proportional-integral controllers determines control action according to preset constants, the readings from the feedwater level sensor, and those from feedwater and steam flowrate transmitters. It is observed that the most important factor that determines whether a trip will occur is how much additional water is added to or withheld from the SG over time compared to normal operating conditions. In order to determine the effects of control action on the SG, changes in mass inventory are considered. This approach models the SG water level as a function of mass inventory and has a backward temporal memory. A Python interface is developed for the GPWR framework to automatically simulate different spoofing scenarios and post-process the related data. We observe that the trip times predominantly depend on flow mismatch and/or level errors. Controller parameters, including the integral time and gain constants, either speed up or slow down the rate of progression to a trip setpoint but do not cause a trip by themselves. The reactor can trip on a high-level signal when the reading crosses above 78%, increased from its reference level of 57%, or a low-level reading when it is below 25%. The present results show roughly how long the operators would have to respond to an attack, given a specific set of spoofing signals within the issue space analyzed. Furthermore, we have generated a simple surface by fitting a combination of exponential functions to the data obtained from the GPWR Simulator. In general, trips on a low level have been observed to occur faster than those on a high level.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Active learning of reactive Bayesian force fields applied to heterogeneous catalysis dynamics of H/Pt

Abstract Atomistic modeling of chemically reactive systems has so far relied on either expensive ab initio methods or bond-order force fields requiring arduous parametrization. Here, we describe a Bayesian active learning framework for autonomous “on-the-fly” training of fast and accurate reactive many-body force fields during molecular dynamics simulations. At each time-step, predictive uncertainties of a sparse Gaussian process are evaluated to automatically determine whether additional ab initio training data are needed. We introduce a general method for mapping trained kernel models onto equivalent polynomial models whose prediction cost is much lower and independent of the training set size. As a demonstration, we perform direct two-phase simulations of heterogeneous H 2 turnover on the Pt(111) catalyst surface at chemical accuracy. The model trains itself in three days and performs at twice the speed of a ReaxFF model, while maintaining much higher fidelity to DFT and excellent agreement with experiment.

42 ENGINEERING↗

Processing system of jaws tomograms for pathology identification and surgical guide modeling

The aim of the study is to create an image processing system, which allows dentists to find pathological resorption and to build surgical guide surface automatically. X-rays images of jaws from cone beam tomography or spiral computed tomography are the initial data for processing. One patient’s examination always includes up to 600 images (or tomograms), that’s why the development of processing system for fast automation search of pathologies is necessary. X-rays images can be useful not for only illness diagnostic but for treatment planning too. We have studied the case of dental implantation – for successful surgical manipulations surgical guides are used. We have created a processing system that automatically builds jaw and teeth boundaries on the x-ray image. After this step, obtained teeth boundaries used for surgical guide surface modeling and jaw boundaries limit the area for further pathologies search. Criterion for the presence of pathological resorption zones inside the limited area is based on statistical investigation. After described actions, it is possible to manufacture surgical guide using 3D printer and apply it in surgical operation.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Automatic optical detection and classification of marine animals around MHK converters using machine vision

Optical systems provide valuable information for evaluating interactions and associations between organisms and MHK energy converters and for capturing potentially rare encounters between marine organisms and MHK device. The deluge of optical data from cabled monitoring packages makes expert review time-consuming and expensive. We propose algorithms and a processing framework to automatically extract events of interest from underwater video. The open-source software framework consists of background subtraction, filtering, feature extraction and hierarchical classification algorithms. This principle classification pipeline was validated on real-world data collected with an experimental underwater monitoring package. An event detection rate of 100% was achieved using robust principal components analysis (RPCA), Fourier feature extraction and a support vector machine (SVM) binary classifier. The detected events were then further classified into more complex classes – algae | invertebrate | vertebrate, one species | multiple species of fish, and interest rank. Greater than 80% accuracy was achieved using a combination of machine learning techniques.

16 TIDAL AND WAVE POWER↗

Real-time data-intensive computing

Today users visit synchrotrons as sources of understanding and discovery—not as sources of just light, and not as sources of data. To achieve this, the synchrotron facilities frequently provide not just light but often the entire end station and increasingly, advanced computational facilities that can reduce terabytes of data into a form that can reveal a new key insight. The Advanced Light Source (ALS) has partnered with high performance computing, fast networking, and applied mathematics groups to create a “super-facility”, giving users simultaneous access to the experimental, computational, and algorithmic resources to make this possible. This combination forms an efficient closed loop, where data—despite its high rate and volume—is transferred and processed immediately and automatically on appropriate computing resources, and results are extracted, visualized, and presented to users or to the experimental control system, both to provide immediate insight and to guide decisions about subsequent experiments during beamtime. We will describe our work at the ALS ptychography, scattering, micro-diffraction, and micro-tomography beamlines.

43 PARTICLE ACCELERATORS↗

Feature-Based Analysis of Plasma-Based Particle Acceleration Data

Plasma-based particle accelerators can produce and sustain thousands of times stronger acceleration fields than conventional particle accelerators, providing a potential solution to the problem of the growing size and cost of conventional particle accelerators. To facilitate scientific knowledge discovery from the ever growing collections of accelerator simulation data generated by accelerator physicists to investigate next-generation plasma-based particle accelerator designs, we describe a novel approach for automatic detection and classification of particle beams and beam substructures due to temporal differences in the acceleration process, here called acceleration features. The automatic feature detection in combination with a novel visualization tool for fast, intuitive, query-based exploration of acceleration features enables an effective top-down data exploration process, starting from a high-level, feature-based view down to the level of individual particles. We describe the application of our analysis in practice to analyze simulations of single pulse and dual and triple colliding pulse accelerator designs, and to study the formation and evolution of particle beams, to compare substructures of a beam and to investigate transverse particle loss.

43 PARTICLE ACCELERATORS↗

Mapping Benthic Habitat Conditions and Seafloor Deposits using Sediment Profile Imaging and a Semiautomated Image Processing System

Objectives/Scope: Sediment profile imaging (SPI) technology characterizes in situ physical, geochemical, and biological seafloor features. SPI was required by Mexico’s Agency for Safety, Energy, and Environment in 2017 for environmental baseline surveys (EBS) of oil lease blocks in the southern Gulf of Mexico. Because of its ability to provide information on benthic community health and the distribution of very thin (down to the centimeter scale) layers of deposited materials, SPI technology is highly effective for mapping drill cuttings or drilling muds released around wellheads during exploration or production and documenting their ecological impacts. SPI technology has not been widely used in the oil and gas industry for EBS or other monitoring activities. A primary objective of this work is to improve the transparency and consistency of the SPI data generation and data management process. Methods, Procedures, Process: The SPI camera works like an inverted periscope and obtains an undisturbed 21x15-cm cross-sectional image of the upper sediment column. The camera is internally powered and can be deployed rapidly from a standard winch in depths to 4,000 m. Many stations can be sampled in a single day by “pogo-sticking” across a survey area. Sediment grain size, penetration depth, surface boundary roughness, natural and anthropogenic depositional layers, depth of the oxidized surface sediment layer, maximum biogenic mixing depth, and infaunal successional stage can be directly measured at sea or immediately following the cruise. Final SPI data sets can be provided within a few weeks of the survey. Results, Observations, Conclusions: Details on the features measured in SPI images and the underlying interpretive paradigms are presented. To standardize the SPI data generation process, Integral Consulting Inc. has developed 1) a semiautomated image analysis platform, and 2) a SPI data-specific database architecture that allows both numerical and non-numerical metrics to be incorporated into a standard database structure. An integrated, software-based SPI analysis platform has been developed that imports image files and metadata and provides a graphical user interface. The software automatically stores the data, which can then be reviewed for quality assurance, plotted, statistically analyzed, and mapped or exported to other platforms (e.g., Esri ArcGIS©) for further evaluation. Image processing algorithms have been developed using a combination of open-source and commercially available software packages (e.g., MATLAB® and OpenCV) to automatically quantify key parameters. Novel/Additive Information: SPI technology’s underutilization in the oil and gas industry may be in part due to a lack of standardization in the measurement of basic features in SPI images. A primary objective of this work is to develop a streamlined, standardized, and transparent process for generating and managing SPI data.

02 PETROLEUM↗

Model America - Arizona extract from ORNL's AutoBEM v1.1

Oak Ridge National Laboratory (ORNL) has developed the Automatic Building Energy Modeling (AutoBEM) software suite to process multiple types of data, extract building-specific descriptors, generate building energy models, and simulate them on High Performance Computing (HPC) resources. For more information, see AutoBEM-related publications (bit.ly/AutoBEM).Two sets of sample data are provided for 2,555,152 buildings located within the boundary of Arizona in the United States:Data (846.3MB *.csv) - minimalist list of each building (rows) for the following fields (columns) • ID - unique building ID • Centroid - building center location in latitude/longitude (from Footprint2D) • Footprint2D - building polygon of 2D footprint (lat1/lon1_lat2/lon2_...) • State_abbr - state name • Area - estimate of total conditioned floor area (ft2) • Area2D - footprint area (ft2) • Height - building height (ft) • NumFloors - number of floors (above-grade) • WWR_surfaces - percent of each facade (pair of points from Footprint2D) covered by fenestration/windows (average 14.5% for residential, 40% for commercial buildings) • CZ - ASHRAE Climate Zone designation • BuildingType - DOE prototype building designation (IECC=residential) as implemented by OpenStudio-standards • Standard - building vintage • Sample Models (114GB*.zip by county) - OpenStudio and EnergyPlus building energy models named according to IDThis data is made free and openly available in hopes of stimulating any simulation-informed use case. Data is provided as-is with no warranties, express or implied, regarding fitness for a particular purpose. We wish to thank our sponsors which include Oak Ridge National Laboratory (ORNL), U.S. Dept. of Energy’s (DOE) Building Technologies Office (BTO), Office of Electricity (OE), and Biological and Environmental Research (BER).

54 ENVIRONMENTAL SCIENCES↗

Physics-Guided Machine Learning (PGML) for Improved Aerostructure Manufacturing

The Physics-Guided Machine Learning (PGML) for Improved Aerostructure Manufacturing project objective is to automatically tune machining parameter predictions from physics-based models using process data and Bayesian machine learning. The intent is to enable a step change in aerospace manufacturing by combining machine learning, physics-based process models, and sensors/data in a comprehensive digital environment that simultaneously considers the computer numerically controlled (CNC) machining center capabilities, the workpiece material and geometry, and the workpiece support (fixturing). The project hypothesis is that this combination will enable improved performance in machining operations.

42 ENGINEERING↗

FastProNGS: fast preprocessing of next-generation sequencing reads

Background Next-generation sequencing technology is developing rapidly and the vast amount of data that is generated needs to be preprocessed for downstream analyses. Yet, until now, software that can efficiently make all the quality assessments and filtration of raw data is still lacking. Results We developed FastProNGS to integrate the quality control process with automatic adapter removal. Parallel processing was implemented to speed up the process by allocating multiple threads. Compared with similar up-to-date preprocessing tools, FastProNGS is by far the fastest. Read information before and after filtration can be output in plain-text, JSON, or HTML formats with user-friendly visualization. Conclusions FastProNGS is a rapid, standardized, and user-friendly tool for preprocessing next-generation sequencing data within minutes. It is an all-in-one software that is convenient for bulk data analysis. It is additionally very flexible and can implement different functions using different user-set parameter combinations.

97 MATHEMATICS AND COMPUTING↗

GNET2: an R package for constructing gene regulatory networks from transcriptomic data

Abstract Motivation The Gene Network Estimation Tool (GNET) is designed to build gene regulatory networks (GRNs) from transcriptomic gene expression data with a probabilistic graphical model. The data preprocessing, model construction and visualization modules of the original GNET software were developed on different programming platforms, which were inconvenient for users to deploy and use. Results Here, we present GNET2, an improved implementation of GNET as an integrated R package. GNET2 provides more flexibility for parameter initialization and regulatory module construction based on the core iterative modeling process of the original algorithm. The data exchange interface of GNET2 is handled within an R session automatically. Given the growing demand for regulatory network reconstruction from transcriptomic data, GNET2 offers a convenient option for GRN inference on large datasets. Availability and implementation The source code of GNET2 is available at https://github.com/jianlin-cheng/GNET2. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

Sparse modeling of space- and time-varying diffraction response of a progressively loaded aluminum alloy

Highlights: • Plasticity induces crystal orientation and lattice spacing heterogeneity. • High energy x-ray diffraction spot broadening typically accompanies plasticity. • Method quantifies spot broadening in difficult, mixed microstructure data. • Algorithm finds sparse combination of entries from dictionary of peak functions. • Approach showed asymmetric plastic response in preprocessed AA7075 T651 sample. - Abstract: High energy X-ray diffraction data collected in situ during loading experiments permits probing of the crystal structure of a plastically deforming material sample. An elastoplastic deformation is associated with heterogeneity in both crystal orientation and lattice spacing—each manifesting as azimuthal broadening and radial broadening of diffraction peaks respectively. Quantifying the spreading effect is challenging, especially in cases where the sample has a granularity between that of a single crystal and fine grain or powder material. The approach developed in this paper begins by modeling the intensity signal in the vicinity of a Debye-Scherrer ring as a sparse, nonnegative superposition of Gaussian basis functions drawn from an over-complete dictionary. Processing automatically selects from the dictionary basis functions whose widths and amplitudes are representative of the data. The chosen basis functions are used to compute scalar measures of radial and azimuthal broadening for the set of diffraction peaks composing a Debye-Scherrer ring. To demonstrate the utility of the approach, we show that analysis of diffraction peak shape information from an aluminum alloy 7075 T651 (AA7075 T651) sample provides insight into the origin of material state that would have otherwise have been difficult if not impossible to extract using conventional methods. Furthermore, the extracted information revealed a deformation response linked to the processing history of the sample.

36 MATERIALS SCIENCE↗

Automated Work Package: Initial Wireless Communication Platform Design, Development, and Evaluation

The Department of Energy's Light Water Reactor Sustainability Program is developing the scientific basis to ensure long-term reliability, productivity, safety, and security of the nuclear power industry in the United States. The Instrumentation, Information, and Control (II and C) pathway of the program aims to increase the role of advanced II and C technologies to achieve this objective. One of the pathway efforts at Idaho National Laboratory (INL) is to improve the work packages execution process by replacing the expensive, inefficient, bulky, complex, and error-prone paper-based work orders with automated work packages (AWPs). An AWP is an automated and dynamic presentation of the work package designed to guide the user through the work process. It is loaded on a mobile device, such as a tablet, and is capable of communicating with plant equipment and systems to acquire plant and procedure states. The AWP replaces those functions where a computer is more efficient and reliable than a human. To enable the automatic acquisition of plant data, it is necessary to design and develop a prototype platform for data exchange between the field instruments and the AWP mobile devices. The development of the platform aims to reveal issues and solutions generalizable to large-scale implementation of a similar system. Topics such as bandwidth, robustness, response time, interference, and security are usually associated with wireless communication. These concerns, along with other requirements, are listed in an earlier INL report. Specifically, the targeted issues and performance aspects in this work are relevant to the communication infrastructure from the perspective of promptness, robustness, expandability, and interoperability with different technologies. The development of a prompt system entailed significant performance optimization, including the use of parallel processing, parallel communication, modularity, noise filtering, and frequency tuning. A robust system was achieved by enforcing a persistent continuous data exchange that automatically detects and conveys a failure of any link or component in any part of the system, and that automatically restores the communication once the link or component is restored. An expandable topology was enabled by modularity and load sharing. The number of servers, mobile devices, and field instruments is not limited from a system structure point of view. The system interoperability was achieved by enforcing the independence of the field communication application from the mobile device application. (authors)

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Towards Auto-Generated Data Systems

After decades of progress, database management systems (DBMSs) are now the backbones of many data applications that we interact with on a daily basis. Yet, with the emergence of new data types and hardware, building and optimizing new data systems remain as difficult as the heyday of relational databases. In this paper, we summarize our work towards automating the building and optimization of data systems. Drawing from our own experience, we further argue that any automation technique must address three aspects: user specification, code generation, and result validation. We conclude by discussing a case study using videos data processing, along with opportunities for future research towards designing data systems that are automatically generated.

Computer Science↗

SU-D-BRD-07: Automatic Patient Data Audit and Plan Quality Check to Support ARIA and Eclipse

Purpose: To ensure patient safety and treatment quality in RT departments that use Varian ARIA and Eclipse, we developed a computer software system and interface functions that allow previously developed electron chart checking (EcCk) methodologies to support these Varian systems. Methods: ARIA and Eclipse store most patient information in its MSSQL database. We studied the contents in the hundreds database tables and identified the data elements used for patient treatment management and treatment planning. Interface functions were developed in both c-sharp and MATLAB to support data access from ARIA and Eclipse servers using SQL queries. These functions and additional data processing functions allowed the existing rules and logics from EcCk to support ARIA and Eclipse. Dose and structure information are important for plan quality check, however they are not stored in the MSSQL database but as files in Varian private formats, and cannot be processed by external programs. We have therefore implemented a service program, which uses the DB Daemon and File Daemon services on ARIA server to automatically and seamlessly retrieve dose and structure data as DICOM files. This service was designed to 1) consistently monitor the data access requests from EcCk programs, 2) translate the requests for ARIA daemon services to obtain dose and structure DICOM files, and 3) monitor the process and return the obtained DICOM files back to EcCk programs for plan quality check purposes. Results: EcCk, which was previously designed to only support MOSAIQ TMS and Pinnacle TPS, can now support Varian ARIA and Eclipse. The new EcCk software has been tested and worked well in physics new start plan check, IMRT plan integrity and plan quality checks. Conclusion: Methods and computer programs have been implemented to allow EcCk to support Varian ARIA and Eclipse systems. This project was supported by a research grant from Varian Medical System.

60 APPLIED LIFE SCIENCES↗