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Applications in Data-Intensive Computing

This book chapter, to be published in Advances in Computers, Volume 78, in 2010 describes applications of data intensive computing (DIC). This is an invited chapter resulting from a previous publication on DIC. This work summarizes efforts coming out of the PNNL's Data Intensive Computing Initiative. Advances in technology have empowered individuals with the ability to generate digital content with mouse clicks and voice commands. Digital pictures, emails, text messages, home videos, audio, and webpages are common examples of digital content that are generated on a regular basis. Data intensive computing facilitates human understanding of complex problems. Data-intensive applications provide timely and meaningful analytical results in response to exponentially growing data complexity and associated analysis requirements through the development of new classes of software, algorithms, and hardware.

99 GENERAL AND MISCELLANEOUS↗

Search for dark matter produced in association with heavy-flavor quark pairs in proton-proton collisions at $\sqrt{s}=13$ TeV

A search is presented for an excess of events with heavy-flavor quark pairs ( ${t}\overline{{t}} $ and ${b} \overline{{b}} $ ) and a large imbalance in transverse momentum in data from proton–proton collisions at a center-of-mass energy of 13 $\,\text{TeV}$ . The data correspond to an integrated luminosity of 2.2 $\,\text{fb}^{-1}$ collected with the CMS detector at the CERN LHC. No deviations are observed with respect to standard model predictions. The results are used in the first interpretation of dark matter production in ${t}\overline{{t}} $ and ${b} \overline{{b}} $ final states in a simplified model. This analysis is also the first to perform a statistical combination of searches for dark matter produced with different heavy-flavor final states. The combination provides exclusions that are stronger than those achieved with individual heavy-flavor final states.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

PylotDB - A Database Management, Graphing, and Analysis Tool Written in Python

PylotDB, written completely in Python, provides a user interface (UI) with which to interact with, analyze, graph data from, and manage open source databases such as MySQL. The UI mitigates the user having to know in-depth knowledge of the database application programming interface (API). PylotDB allows the user to generate various kinds of plots from user-selected data; generate statistical information on text as well as numerical fields; backup and restore databases; compare database tables across different databases as well as across different servers; extract information from any field to create new fields; generate, edit, and delete databases, tables, and fields; generate or read into a table CSV data; and similar operations. Since much of the database information is brought under control of the Python computer language, PylotDB is not intended for huge databases for which MySQL and Oracle, for example, are better suited. PylotDB is better suited for smaller databases that might be typically needed in a small research group situation. PylotDB can also be used as a learning tool for database applications in general.

Barnette, DanielW.↗

A meta-analysis of semantic classification of citations

The aim of this literature review is to examine the current state of the art in the area of citation classification. In particular, we investigate the approaches for characterizing citations based on their semantic type. We conduct this literature review as a meta-analysis covering 60 scholarly articles in this domain. Although we included some of the manual pioneering works in this review, more emphasis is placed on the later automated methods, which use Machine Learning and Natural Language Processing (NLP) for analyzing the fine-grained linguistic features in the surrounding text of citations. The sections are organized based on the steps involved in the pipeline for citation classification. Specifically, we explore the existing classification schemes, data sets, pre-processing methods, extraction of contextual and non-contextual features, and the different types of classifiers and evaluation approaches. The review highlights the importance of identifying the citation types for research evaluation, the challenges faced by the researchers in the process, and the existing research gaps in this field.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Spin-glass behavior and vacancy order in van der Waals layered β - MoCl 4

Two-dimensional ${\beta}\text{-}{\mathrm{MoCl}}_{4}$ is an attractive material from the perspectives of magnetism in $4d$ transition metal compounds, geometrically frustrated lattices, and magnetic van der Waals layered materials, but the magnetism in this compound has not been particularly well studied to date. In this paper the magnetic properties and crystal structure of ${\mathrm{MoCl}}_{4}$ are revisited, and results of ac and dc magnetic measurements and single crystal x-ray diffraction are reported. Crystals grow as well-formed and easily cleaved hexagonal plates that are unstable in air. The revised structural model comprises ${\mathrm{CdCl}}_{2}$-type layers with 50% Mo vacancies distributed over the sites of the triangular cation net. Interestingly, a structural ambiguity regarding the vacancy distribution is identified in the analysis of the diffraction data. The orbital moment is not expected to be quenched in this $4{d}^{2}$ compound. Accordingly, magnetization measurements indicate an effective moment that is about 20% lower than the spin-only value. The magnetic data reveal an anomaly near 5 K, below which a divergence of field-cooled and zero-field-cooled dc magnetization, a slow relaxation of thermoremanent magnetization, and enhanced frequency dependence of ac magnetization are observed. Finally and thus, ${\beta}\text{-}{\mathrm{MoCl}}_{4}$ represents an uncommon example of a cleavable spin-glass system.

36 MATERIALS SCIENCE↗

GIDEP Batching Tool

This software provides internal, automated search mechanics of GIDEP (Government- Industry Data Exchange Program) Alert data imported from the GIDEP government Web site. The batching tool allows the import of a single parts list in tab-delimited text format into the local JPL GIDEP database. Delimiters from every part number are removed. The original part numbers with delimiters are compared, as well as the newly generated list without the delimiters. The two lists run against the GIDEP imports, and output any matches. This feature only works with Netscape 2.0 or greater, or Internet Explorer 4.0 or greater. The user selects the browser button to choose a text file to import. When the submit button is pressed, this script will import alerts from the text file into the local JPL GIDEP database. This batch tool provides complete in-house control over exported material and data for automated batch match abilities. The batching tool has the ability to match capabilities of the parts list to tables, and yields results that aid further research and analysis. This provides more control over GIDEP information for metrics and reports information not provided by the government site. This software yields results quickly and gives more control over external data from the government site in order to generate other reports not available from the external source. There is enough space to store years of data. The program relates to risk identification and management with regard to projects and GIDEP alert information encompassing flight parts for space exploration.

Fong, Danny↗

Photoproduction of the f 1 ( 1285 ) meson

The f 1 (1285) meson with mass 1281.0 ± 0.8 MeV/c 2 and width 18.4 ± 1.4 MeV (full width at half maximum) was measured for the first time in photoproduction from a proton target using CLAS at Jefferson Lab. Differential cross sections were obtained via the ηπ + π - , K + K 0 π - , and K - K 0 π + decay channels from threshold up to a center-of-mass energy of 2.8 GeV. The mass, width, and an amplitude analysis of the ηπ + π - final-state Dalitz distribution are consistent with the axial-vector J P = 1 + f 1 (1285) identity, rather than the pseudoscalar 0-η (1295). The production mechanism is more consistent with s -channel decay of a high-mass N * state and not with t -channel meson exchange. Decays to η π π go dominantly via the intermediate a$^±_0$ (980) π ∓ states, with the branching ratio Γ [a 0 π (no $\overline{K}K$) ] / Γ [ηππ (all) ] = 0.74 ± 0.09 . The branching ratios Γ ($\overline{K}K$ π )/ Γ (ηππ) = 0.216 ± 0.033 and Γ (γρ 0 ) / Γ (ηππ) = 0.047 ± 0.018 were also obtained. The first is in agreement with previous data for the f 1 (1285), while the latter is lower than the world average.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Unified Medical Language System resources improve sieve-based generation and Bidirectional Encoder Representations from Transformers (BERT)–based ranking for concept normalization

Concept normalization, the task of linking phrases in text to concepts in an ontology, is useful for many downstream tasks including relation extraction, information retrieval, etc. We present a generate-and-rank concept normalization system based on our participation in the 2019 National NLP Clinical Challenges Shared Task Track 3 Concept Normalization. The shared task provided 13 609 concept mentions drawn from 100 discharge summaries. We first design a sieve-based system that uses Lucene indices over the training data, Unified Medical Language System (UMLS) preferred terms, and UMLS synonyms to generate a list of possible concepts for each mention. We then design a listwise classifier based on the BERT (Bidirectional Encoder Representations from Transformers) neural network to rank the candidate concepts, integrating UMLS semantic types through a regularizer. Our generate-and-rank system was third of 33 in the competition, outperforming the candidate generator alone (81.66% vs 79.44%) and the previous state of the art (76.35%). During postevaluation, the model’s accuracy was increased to 83.56% via improvements to how training data are generated from UMLS and incorporation of our UMLS semantic type regularizer. Analysis of the model shows that prioritizing UMLS preferred terms yields better performance, that the UMLS semantic type regularizer results in qualitatively better concept predictions, and that the model performs well even on concepts not seen during training. Our generate-and-rank framework for UMLS concept normalization integrates key UMLS features like preferred terms and semantic types with a neural network–based ranking model to accurately link phrases in text to UMLS concepts.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

SAPHIRE 8 Volume 7 - Data Loading

The Systems Analysis Programs for Hands-on Integrated Reliability Evaluations (SAPHIRE) is a software application developed for performing a complete probabilistic risk assessment (PRA) using a personal computer. SAPHIRE Version 8 is funded by the U.S. Nuclear Regulatory Commission and developed by the Idaho National Laboratory. This report is intended to assist the user to enter PRA data into the SAPHIRE program using the built-in MAR-D ASCII-text file data transfer process. Towards this end, a small sample database is constructed and utilized for demonstration. Where applicable, the discussion includes how the data processes for loading the sample database relate to the actual processes used to load a larger PRA models. The procedures described herein were developed for use with SAPHIRE Version 8. The guidance specified in this document will allow a user to have sufficient knowledge to both understand the data format used by SAPHIRE and to carry out the transfer of data between different PRA projects.

97 MATHEMATICS AND COMPUTING↗

What Went Wrong: A Survey of Wildfire UAS Mishaps through Named Entity Recognition

Increasingly, unmanned aircraft systems (UAS) are being applied to wildfire incidents for tasks such as mapping, aerial ignition, and delivery. As a result, incident reporting systems for wildfires are beginning to accumulate data related to UAS mishaps in wildfire response. In this research, we apply state-of-the-art natural language processing (NLP) techniques to develop a custom Named Entity Recognition (NER) model which extracts a Failure Modes and Effects Analysis (FMEA)-style survey of wildfire UAS mishaps reported in SAFECOM. The custom NER model is built by fine-tuning an existing (BERT) model, resulting in a generalizable NER model that can extract engineering relevant entities including failure modes, causes, effects, control processes, and recommendations from any failure-relevant text. Similar mishaps are clustered and reported as single rows within the FMEA. For each cluster, frequency, severity, and overall risk are computed. The methodology can be applied as part of a broader safety management system to track trends in mishaps and discover knowledge that can be utilized to improve safety outcomes and system performance.

Machine Learning↗

What Went Wrong: A Survey of Wildfire UAS Mishaps through Named Entity Recognition

Increasingly, unmanned aircraft systems (UAS) are being applied to wildfire incidents for tasks such as mapping, aerial ignition, and delivery. As a result, incident reporting systems for wildfires are beginning to accumulate data related to UAS mishaps in wildfire response. In this research, we apply state-of-the-art natural language processing (NLP) techniques to develop a custom Named Entity Recognition (NER) model which extracts a Failure Modes and Effects Analysis (FMEA)-style survey of wildfire UAS mishaps reported in SAFECOM. The custom NER model is built by fine-tuning an existing (BERT) model, resulting in a generalizable NER model that can extract engineering relevant entities including failure modes, causes, effects, control processes, and recommendations from any failure-relevant text. Similar mishaps are clustered and reported as single rows within the FMEA. For each cluster, frequency, severity, and overall risk are computed. The methodology can be applied as part of a broader safety management system to track trends in mishaps and discover knowledge that can be utilized to improve safety outcomes and system performance.

Machine Learning↗

ICARTT File Format Enhancements: Supporting FAIRness of Airborne and Field Campaign Data

The ICARTT (International Consortium for Atmospheric Research on Transport and Transformation) standards were developed to fulfill data management needs for the ICARTT campaign in 2004. The ICARTT file format is text-based and composed of a header with important data description information and the data section. The ICARTT format, built on the NASA Ames and GTE data formats, was created to facilitate data exchange and promote collaborations among the science teams for achieving the ICARTT campaign goals. Due to the success of the ICARTT campaign, the ICARTT file format was exposed to a broad range of airborne researchers and was adopted for use in many other field campaigns sponsored by NASA and other partner agencies. The ICARTT format standards became a NASA standard in 2010 and was amended in January 2017 providing many enhancements, including the requirement for variable standard names. Primarily designed for airborne field studies, ICARTT has been further utilized for ground-based studies. The ICARTT format can host metadata that is critical for proper use of the data, especially for in-situ measurements. However, the information that needs to be included is often in free text, meaning the information are human readable, but not machine interpretable. Furthermore, the amount and type of information provided can vary substantially between principal investigators and campaigns. To support interoperability and FAIR principles, further enhancements to the ICARTT standards are recommended. Possible recommendations include standardizing timestamps for easier data comparisons and analysis; potential use of controlled and consistent vocabulary for variable short name and certain common metadata elements; and providing guidance on variable measurement units and how they are reported.

Megan Buzanowicz↗

Final Report for Transmission of Information by Acoustic Communication along Metal Pathways in Nuclear Facilities

Transmission of information using elastic waves on existing metallic pipes provides an alternative communication option for a nuclear facility. The advantages of this approach consist of transmitting information through barriers, such as the containment building wall. A viable candidate for acoustic communication channel is a chemical volume control system (CVCS) stainless steel pipe, which penetrates through the containment building wall. A laboratory bench-scale system consisting of a nuclear grade CVCS-like pipe and ultrasonic transducers was assembled for a preliminary communication system analysis. Because of low bandwidth and spectral dispersion of ultrasonic transducers, on off keying (OOK) protocol was chosen for data communication. Operation of the acoustic communication during normal and post-accident conditions involves data transmission on the CVCS pipe, which according to literature guidelines, will be at 50°C and 150°C, respectively. Preliminary communication system development was performed using paintbrush PZT transducers capable of continuous operation at temperatures up to 80°C. Next, high-temperature LiNbO 3 acoustic transducers, originally developed for flow metering applications of EBRII reactor at Argonne, were utilized to develop a high-temperature acoustic communication system. A Gaussian pulse shape filter was introduced to suppress ringing and thus reduce inter-symbol interference. This resulted in enhancement of data transmission bitrate. Heating tapes, temperature controllers, and thermal insulation were installed on the laboratory pipe to study acoustic communication at elevated temperature. This included development of custom insertion heating elements for controlling temperature at pipe ends. Demonstrations of communication at high temperature included transmission of images and text files. Main achievements thus far include demonstration of transmission of 90KB image at the bitrate of 10Kbps with bit error rate smaller than 10 -3 across the pipe heated to 50°C and 150°C. Final phase of project development involved investigating strategies for deployment of the ultrasonic communication system in a representative environment. Mechanisms Engineering Test Loop (METL) facility at ANL was chosen as a viable candidate for communication system demonstration. Analysis of piping manifolds at METL has shown that in a typical scenario, ultrasonic signals have to be transmitted over straight and bent piping sections. This report describes preliminary studies on transmission of information with ultrasonic shear waves across bent piping sections. A test article consisting of a stainless steel pipe bent at 90° was developed for laboratory analysis of ultrasonic signal transmission. The bent piping test article developed by welding two straight pipes to an elbow. For consistency, the diameter and wall thickness of the bent pipe is the same as that of the straight pipe utilized in prior studies. COMSOL computer simulations were performed to study ultrasonic refracted shear wave coupling and transmission across bent piping. Preliminary evaluations of ultrasonic shear wave transmission were conducted with piezoelectric (PZT) and LiNbO 3 transducers, with the signals recorded with previously developed LabView interface. Preliminary results have shown significant dispersion of transmitted signals, most likely due to reflections and scattering by piping welds. Signal distortion compensation algorithm based on time reversal modulation (TRM) was initially investigated for transmission through solids, and demonstrated for signals transmitted over the bent pipe. Using TRM, it was shown that communication bitrates of 100Kbps were achievable, in principle.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Mountain Basin Controls on the Snow-to-Streamflow Signal: An AIC-Weighted Multiple Linear Regression Framework

A regression-based analysis quantifies how basin characteristics modulate the snow-to-streamflow signal. First, we use the ERA5-Land reanalysis gridded product (European Centre for Medium Range Weather Forecasts reanalysis 5 -Land component) for 4,655 hydrologic unit code - 10 (HUC10) mountain basins across the western United States (US) for water years 1987–2024. Linear regressions are performed for peak snow water equivalent (SWE) and annual streamflow for each mountain basin. Models use ordinary least squares in Python’s statsmodels package. After which, an Akaike Information Criterion (AIC)–weighted ensemble multiple linear regression (MLR) framework with 47 watershed traits is used to predict the linear regression coefficient of determination (r-squared) defining the ability of peak SWE to predict annual streamflow across all mountain basin. Predictor sets are constrained to avoid multicollinearity by excluding models with variance inflation factors (VIF) greater than 5. Mountain basin traits included in the MLR include seasonal climate, topography, vegetation type and structure, and bedrock geology. Accepted models are considered if their AIC is within 2.0 of the model with the minimum AIC, or best model. To compare predictor influence across acceptable models, we computed standardized regression coefficients. To evaluate structural redundancy among models, we constructed binary inclusion vectors for each acceptable model, denoting whether a predictor was present (1) or absent (0). Core predictor variables are defined as occurring in at least 67% of the acceptable models. For this regional analysis, only one model was found acceptable, with higher snow-to-streamflow translation (higher r-squared) occurring in colder mountain basins with higher relative winter precipitation, more snow accumulation and a lower fraction of annual precipitation that falls in the spring and summer. The second component of the data package uses previously published, high-resolution output from an integrated hydrological model of the East River watershed using the U.S. Geological Survey Groundwater and Surface water Flow model (GSFLOW, doi:10.15485/1998576). East River MLR expands upon the approach described above to explore the response of five streamflow metrics—annual streamflow, runoff efficiency, 7-day minimum flow, low-flow duration, and non-perennial stream fraction to snow system indicators including peak SWE, snow-covered area, snow disappearance date, and the fraction of basin area characterized by low-to-no snow, as well as seasonal precipitation and temperature, and annual hydrologic variables representing soil moisture, evapotranspiration (ET), the partitioning of incoming precipitation to evapotranspiration (ET/P), groundwater storage, and groundwater inflow to streams. MLR was done on all water years (P0: 1987-2024) and for each period as determined in the split analysis using pooled regression techniques (P1: 1987-2011 and P2: 2012-2024) to evaluate shifting predictor variable emphasis on streamflow generation. Results indicate that since 2012, peak SWE has lost statistical strength in its prediction of annual streamflow and runoff efficiency, and the indirect influence of spring temperature has emerged as critically important. Low-flow metrics remain largely influenced by soil moisture, vegetation water use and groundwater inflows with summer precipitation becoming a direct influence on minimum summer flow. Together, these data and Python-based analysis tools provide a framework for identifying the key watershed characteristics that control how streamflow responds to snow from year to year. The package also helps quantify uncertainty in statistical models and assess how snow–streamflow relationships vary across regions and over time. This dataset contains comma-separated values files (.csv), text files (.txt), python code files (.py), figure files (.png), and shapefiles (.cpg, .dbf, .prj, .sbn, .sbx, .shp, .xml). Further details on file contents and MLR execution can be found in the readme file and the FLMD files. Work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231.

54 ENVIRONMENTAL SCIENCES↗

Measurement of the top quark mass in the $t\bar{t}\rightarrow\text{ lepton+jets }$→ and $t\bar{t}\rightarrow\text{dilepton}$ → channels using $\sqrt{s}=7$TeV ATLAS data

The top quark mass was measured in the channels $t\bar{t}$→ lepton+jets and $t\bar{t}$→ dilepton (lepton = e,μ) based on ATLAS data recorded in 2011. The data were taken at the LHC with a proton–proton centre-of-mass energy of √s = 7 TeV and correspond to an integrated luminosity of 4.6 fb –1 . The $t\bar{t}$→ lepton+jets analysis uses a three-dimensional template technique which determines the top quark mass together with a global jet energy scale factor (JSF), and a relative b-to-light-jet energy scale factor (bJSF), where the terms b-jets and light-jets refer to jets originating from b-quarks and u, d, c, s-quarks or gluons, respectively. The analysis of the $t\bar{t}$→ dilepton channel exploits a one-dimensional template method using the m ℓb observable, defined as the average invariant mass of the two lepton+b-jet pairs in each event. The top quark mass is measured to be 172.33 ± 0.75 (stat + JSF + bJSF) ± 1.02(syst) GeV, and 173.79 ± 0.54(stat) ± 1.30(syst) GeV in the $t\bar{t}$→ lepton+jets and $t\bar{t}$→ dilepton channels, respectively. Thus, the combination of the two results yields m top = 172.99 ± 0.48(stat) ± 0.78(syst) GeV, with a total uncertainty of 0.91 GeV.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Interface design of VSOP'94 computer code for safety analysis

Today, most software applications, also in the nuclear field, come with a graphical user interface. VSOP'94 (Very Superior Old Program), was designed to simplify the process of performing reactor simulation. VSOP is a integrated code system to simulate the life history of a nuclear reactor that is devoted in education and research. One advantage of VSOP program is its ability to calculate the neutron spectrum estimation, fuel cycle, 2-D diffusion, resonance integral, estimation of reactors fuel costs, and integrated thermal hydraulics. VSOP also can be used to comparative studies and simulation of reactor safety. However, existing VSOP is a conventional program, which was developed using Fortran 65 and have several problems in using it, for example, it is only operated on Dec Alpha mainframe platforms and provide text-based output, difficult to use, especially in data preparation and interpretation of results. We develop a GUI-VSOP, which is an interface program to facilitate the preparation of data, run the VSOP code and read the results in a more user friendly way and useable on the Personal 'Computer (PC). Modifications include the development of interfaces on preprocessing, processing and postprocessing. GUI-based interface for preprocessing aims to provide a convenience way in preparing data. Processing interface is intended to provide convenience in configuring input files and libraries and do compiling VSOP code. Postprocessing interface designed to visualized the VSOP output in table and graphic forms. GUI-VSOP expected to be useful to simplify and speed up the process and analysis of safety aspects.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

PlasmoData.jl — A Julia framework for modeling and analyzing complex data as graphs

Datasets encountered in scientific and engineering applications appear in complex formats (e.g., images, multivariate time series, molecules, video, text strings, networks). Graph theory provides a unifying framework to model such datasets and enables the use of powerful tools that can help analyze, visualize, and extract value from data. In this work, we present PlasmoData.jl, an open-source, Julia framework that uses concepts of graph theory to facilitate the modeling and analysis of complex datasets. The core of our framework is a general data modeling abstraction, which we call a DataGraph. We show how the abstraction and software implementation can be used to represent diverse data objects as graphs and to enable the use of tools from topology, graph theory, and machine learning (e.g., graph neural networks) to conduct a variety of tasks. We illustrate the versatility of the framework by using real datasets: (i) an image classification problem using topological data analysis to extract features from the graph model to train machine learning models; (ii) a disease outbreak problem where we model multivariate time series as graphs to detect abnormal events; and (iii) a technology pathway analysis problem where we highlight how we can use graphs to navigate connectivity. Further, our discussion also highlights how PlasmoData.jl leverages native Julia capabilities to enable compact syntax, scalable computations, and interfaces with diverse packages. Overall, we show that the DataGraph abstraction and PlasmoData.jl Julia package are able to model data within graphs and enable useful analysis.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Global differential geometry: An introduction for control engineers

The basic concepts and terminology of modern global differential geometry are discussed as an introduction to the Lie theory of differential equations and to the role of Grassmannians in control systems analysis. To reach these topics, the fundamental notions of manifolds, tangent spaces, vector fields, and Lie algebras are discussed and exemplified. An appendix reviews such concepts needed for vector calculus as open and closed sets, compactness, continuity, and derivative. Although the content is mathematical, this is not a mathematical treatise but rather a text for engineers to understand geometric and nonlinear control.

Doolin, B. F.↗