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AmeriFlux BASE data pipeline to support network growth and data sharing
Abstract AmeriFlux is a network of research sites that measure carbon, water, and energy fluxes between ecosystems and the atmosphere using the eddy covariance technique to study a variety of Earth science questions. AmeriFlux’s diversity of ecosystems, instruments, and data-processing routines create challenges for data standardization, quality assurance, and sharing across the network. To address these challenges, the AmeriFlux Management Project (AMP) designed and implemented the BASE data-processing pipeline. The pipeline begins with data uploaded by the site teams, followed by the AMP team’s quality assurance and quality control (QA/QC), ingestion of site metadata, and publication of the BASE data product. The semi-automated pipeline enables us to keep pace with the rapid growth of the network. As of 2022, the AmeriFlux BASE data product contains 3,130 site years of data from 444 sites, with standardized units and variable names of more than 60 common variables, representing the largest long-term data repository for flux-met data in the world. The standardized, quality-ensured data product facilitates multisite comparisons, model evaluations, and data syntheses.
Particle Response of Antenna-Coupled TES Arrays: Results from SPIDER and the Laboratory
Future mm-wave and sub-mm space missions will employ large arrays of multiplexed transition-edge-sensor (TES) bolometers. Such instruments must contend with the high flux of cosmic rays beyond our atmosphere that induce ‘glitches’ in bolometer data, which posed a challenge to data analysis from the Planck bolometers. Future instruments will face the additional challenges of shared substrate wafers and multiplexed readout wiring. Here, we explore the susceptibility of modern TES arrays to the cosmic ray environment of space using two data sets: the 2015 long-duration balloon flight of the SPIDER cosmic microwave background polarimeter, and a laboratory exposure of SPIDER flight hardware to radioactive sources. We find manageable glitch rates and short glitch durations, leading to minimal effect on SPIDER analysis. We constrain energy propagation within the substrate through a study of multi-detector coincidences and give a preliminary look at pulse shapes in laboratory data.
Data Collection and Analysis Challenges and Mitigation Strategies for Quantitative Human Factors Research Studies in Nuclear Power Plant Modernization
The United States (U.S.) Department of Energy (DOE) Light Water Reactor Sustainability (LWRS) program Plant Modernization Pathway is conducting targeted research and development (R&D) to address aging and reliability concerns with the legacy instrumentation and control and related information systems of the U.S. LWR fleet. In this effort, the application of human factors engineering (HFE) provides an important role in ensuring new digital plant technologies enable broad innovation and business improvement with continued operational safety. Evaluation is a key activity in HFE, which often occurs iteratively through the system design lifecycle. While qualitative methods are important in collecting information of how users perform tasks through observations, quantitative methods are equally important in assessing system design based on performance. In collecting and analyzing this quantitative data, there are notable challenges in the nuclear HFE domain that may threaten the validity and reliability of the inferences made in these studies. Notable challenges include small sample size and limited resources, large error variance and small effect size, an “adding test features to losing degrees of freedom” dilemma, non-normal distribution, and heterogeneity of variance. The results in control room usability studies are often statistically non-significant, which makes it hard to interpret. This work discusses these challenges across different scientific viewpoints and provides real-world examples of these challenges in practice. Collectively, the objective of this work is to position these challenges to the larger data science community as a means of identifying future opportunities to address these issues.
Data Placement Optimization for ATLAS in a Multi-Tiered Storage System within a Data Center
Scientific experiments and computations, especially in High Energy Physics, are generating and accumulating data at an unprecedented rate. Effectively managing this vast volume of data while ensuring efficient data analysis poses a significant challenge for data centers, which must integrate various storage technologies. This paper proposes addressing this challenge by designing and developing a precise data popularity prediction model utilizing state-of-theart AI/ML techniques. This model is crafted from the analysis of ATLAS data and access patterns. It enables us to migrate infrequently accessed data to more economical storage media, such as tape drives, while storing frequently accessed data on faster yet costlier storage media like HDD or SSD. This strategic approach ensures data is placed optimally into the appropriate storage classes, thereby maximizing storage capacity while minimizing data access latency for end-users. Furthermore, the paper includes a performance evaluation of the prediction model using various key metrics such as F1 score, accuracy, precision and recall. Finally, we present a prototype use case, leveraging real-world file access data to assess the model’s impact on performance.
Evolution of standardization and dissemination of cryo-EM structures and data jointly by the community, PDB, and EMDB
Cryogenic electron microscopy (cryo-EM) methods began to be used in the mid-1970s to study thin and periodic arrays of proteins. Following a half-century of development in cryo-specimen preparation, instrumentation, data collection, data processing and modeling software, cryo-EM has become a routine method for solving structures from large biological assemblies to small biomolecules at near to true atomic resolution. This review explores the critical roles played by the Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB) in partnership with the community to develop the necessary infrastructure to archive cryo-EM maps and associated models. Public access to cryo-EM structure data has in turn facilitated better understanding of structure-function relationships and advancement of image processing and modeling tool development. The partnership between the global cryo-EM community and PDB and EMDB leadership has synergistically shaped the standards for metadata, one-stop deposition of maps and models, and validation metrics to assess the quality of cryo-EM structures. The advent of cryo-electron tomography (cryo-ET) for in situ molecular cell structures at a broad resolution range and their correlations with other imaging data introduces new data archival challenges in terms of data size and complexity in the years to come.
Performance Analysis of Data Processing in Distributed File Systems with Near Data Processing
In the era of big data, the escalating volume and velocity of data generation pose significant challenges in data processing. Traditional systems like Spark and Hadoop manage the increasing amount and velocity of data by improving data placement and processing speeds. However, they face inherent limitations due to the essential data movement required for processing. In this paper, we explore the Skyhook framework, a novel extension of the Ceph distributed system, which significantly reduces the need for data movement. We present an extensive case study using the Skyhook framework, applying it with the TPC-H and K-means clustering algorithms. More specifically, we leverage the TPC-H benchmark to distinguish between CPU-intensive and I/O-intensive tasks. We explore the integration of K-means clustering into SQL, coupled with a near-data processing system to offload the computational burden of the K-means clustering algorithm to storage nodes. We conduct a comprehensive performance evaluation of distributed data processing applications across three processing approaches: traditional layout (baseline), optimized layout, and near-data processing. Additionally, we introduce the use of the FIO tool to simulate real-world system workloads, enabling the measurement of performance metrics such as average latency and CPU utilization. Our research is a significant advance in understanding how to optimize data processing systems to meet the demands of the modern data landscape.
COVID-19 Data Curation Effort: An Initial Analysis of the Data
During the COVID-19 pandemic of 2020, major case reporting outlets quickly coalesced around two or three primary vendors. Johns Hopkins University and The New York Times were among the more prominent, and all were of great value to the nation, particularly during the uncertain early stages of the pandemic. They primarily focused on three major attributes: number of new cases, deaths, and recovery. Recognizing that many states were reporting very detailed data sets (e.g., hospital beds) at a county level or finer, the ORNL Pandemic Modeling team embarked on a major data curation effort from March to June 2020 for the purpose of capturing this wealth of detailed data. The challenge of curating this data was daunting. The number of attributes reported by the states grew on almost on a weekly basis. States were routinely shifting their web tool strategies away from easily parsable HTML-based formatting to new Tableau and ArcGIS content. This growth in the sheer number of attributes, combined with the unpredictable shifts in data format, meant an aggressive and agile combination of automated scripting and manual scraping was required to capture new daily streams. Further, the team had to scale up staff and widen its approach for capture and storage. As a result, the team collected more than 11 million data points. Following the close of this data collection effort on June 30 th , 2020, the team embarked on a major effort to appraise what had been collected, including an inventory list, spatial completeness, temporal completeness, scale and geographic characteristics, and a determination. A report on this matter was submitted on September 15 th , 2020, titled “DOE COVID-19 Data Curation Effort: Overview of Data Collection Coverage”. Over 2000 unique attributes had been netted over a wide range of spatial scales, including state, county, zip codes, health regions, and census blocks. Over 11 million individual data points were collected across these attributes, and spatial coverage (in total) included all 50 states and multiple territories. What became apparent in the process is that in the absence of any data standards, many states reported a wide variety of unique attributes that were not always compatible with attributes reported in other states. As time continued, states began adding new attributes and offering finer grain detail in some older attributes. This meant that not all data streams existed for the entire time period; in fact, the number tended to increase dramatically towards the end. Often, states would begin an attribute series and then stop altogether. These highly variable and uncertain conditions illuminated the need for harmonization approaches that would reconcile and conflate changing attribute names and detail over time. For example, grouping racial data reported as either Black or African American, depending on the state, into a single harmonized attribute. These choices would make a within-state analysis possible during the time period and lead to potential between-state analytics later on. This was almost entirely a manual decision process, requiring some subjective decision-making at times, to prevent a fragmented, short-lived collection of time series fragments that would offer few insights into trends, patterns, and correlates. This report imports harmonized data for state and county into the World Spatio-Temporal Analytics and Mapping Project (WSTAMP). WSTAMP is a major space-time analysis and visualization tool developed at ORNL for the National Geospatial-Intelligence Agency specifically for this kind of exploratory analysis. WSTAMP offers a rich analytical and graphical environment consisting of a wide range of analytics. These include time series plots, statistical summaries, data mining techniques, trend and pattern detection, and hypothesis generation.
DOE COVID-19 Data Curation Effort: Overview of Initial Data Collection Coverage (March - June 2020)
During the COVID-19 pandemic of 2020, major case reporting outlets quickly coalesced around two or three primary vendors. Johns Hopkins University and The New York Times were among the more prominent, and all were of great value to the nation, particularly during the uncertain early stages of the pandemic. They primarily focused on three major attributes: number of new cases, deaths, and recovery, but only at the state level. Recognizing that many states were reporting very detailed data sets (e.g., hospital beds) at a count level or finer, the ORNL Pandemic Modeling team embarked on a major data curation effort from March to June 2020 for the purpose of capturing this wealth of detailed data. The challenge of curating this data was daunting. The number of attributes reported by the states grew on almost on a weekly basis. States were routinely shifting their web tool strategies away from easily parsable HTML-based formatting to new Tableau and ArcGIS content. This growth in the sheer number of attributes combined with the unpredictable shifts in data format meant an aggressive and agile combination of automated scripting and manual scraping was required to capture new daily streams. To keep up, the team had to scale up staff and widen its approach for capture and storage. The DOE COVID-19 data collection effort resulted in over 11 million data points being collected, covering over 13,000 unique geographies and over 2,000 unique attributes that spanned predominantly from early March through the end of June 2020.
Challenges for monitoring and data analytics in a leadership public data repository
The availability and disposition of data has assumed increasing importance in large-scale computational science. Data repositories are evolving to meet new classes of requirements: compliance with government access guidelines, support for reproducibility of experimental results, and long-term availability of data products. The Constellation public data repository at the Oak Ridge Leadership Computing Facility faces these issues while being situated in one of the most productive data centers in the world. While monitoring and operational data analysis are ingrained in the operation of the OLCF’s large-scale high performance computing platforms, data repositories do not have this history of support. Problems faced by Constellation range from data size (over 7 petabytes in current holdings) to analytic complexity (detailed curation is both absolutely necessary for many data sets and absolutely impossible for humans to accomplish in any practical manner) to deployment environment (OLCF storage resources are oriented toward the needs of the compute platforms). In this paper we describe some of the challenges for collecting monitoring and analytic data from a leadership public data repository. We also discuss various strategies we are pursuing in order to address these challenges, from manual data collection to plans for introducing machine learning-based curatorial techniques.
Experimental data for damage mechanics simulation challenge
While there are many computational approaches for simulating damage in rock and other materials, few have been ground truth tested with either known experimental data or with blind data sets. Here, in this work, we present a bench-mark laboratory data set for a damage mechanics challenge to compare computational approaches on damage evolution in brittle-ductile materials. The samples were fabricated through additive manufacturing to produce repeatable specimens designed to fail in controlled ways. The failure was induced in the samples using a 3-point bending test to produce different Modes such as Mode I and mixed Modes including I-II, I-III and I-II-III Modes to generate a calibration data set and a blind challenge data set. Data collected included spatial and temporal measurements from traditional digital load–displacement sensors, 2D digital image correlation measurement to map surface deformations, 3D X-ray microscopy to ground-truth the crack-failure geometry, and laser profilometry to capture surface roughness. The data sets are available, on a data repository, to the community to advance computational models to improve our ability to predict damage in brittle-ductile materials.
A data integration framework of additive manufacturing based on FAIR principles
Abstract Laser-powder bed fusion (L-PBF) is a popular additive manufacturing (AM) process with rich data sets coming from both in situ and ex situ sources. Data derived from multiple measurement modalities in an AM process capture unique features but often have different encoding methods; the challenge of data registration is not directly intuitive. In this work, we address the challenge of data registration between multiple modalities. Large data spaces must be organized in a machine-compatible method to maximize scientific output. FAIR (findable, accessible, interoperable, and reusable) principles are required to overcome challenges associated with data at various scales. FAIRified data enables a standardized format allowing for opportunities to generate automated extraction methods and scalability. We establish a framework that captures and integrates data from a L-PBF study such as radiography and high-speed camera video, linking these data sets cohesively allowing for future exploration. Graphical abstract
Navigating Uncertainty: Challenges in Visualizing Ensemble Data and Surrogate Models for Decision Systems
Uncertainty visualization plays a critical role in transforming ensemble simulation data into actionable insights by effectively communicating various dimensions of uncertainty within a system. The emergence of artificial intelligence-driven surrogate models trained on multirun ensemble data offers a transformative opportunity to replace computationally intensive simulations with fast estimates, enabling users to explore data spaces with unprecedented depth and interactivity. However, integrating ensemble data and surrogate models into decision-making workflows and tools introduces novel challenges for uncertainty visualization. These include reconciling and clearly communicating the unique uncertainties associated with ensembles and their surrogate model estimates, and leveraging these approximations to inform actionable decisions. This work explores these challenges in the context of high-dimensional data visualization, bridging discrete datasets with their continuous representations and addressing the complexities of systems that support iterative navigation between input and output spaces. We evaluate the role of uncertainty visualization in fostering intuitive, actionable interactions and identify critical hurdles in advancing this frontier of computational simulation.
Novel approach for evaluating detector-related uncertainties in a LArTPC using MicroBooNE data
Primary challenges for current and future precision neutrino experiments using liquid argon time projection chambers (LArTPCs) include understanding detector effects and quantifying the associated systematic uncertainties. This paper presents a novel technique for assessing and propagating LArTPC detector-related systematic uncertainties. The technique makes modifications to simulation waveforms based on a parameterization of observed differences in ionization signals from the TPC between data and simulation, while remaining insensitive to the details of the detector model. The modifications are then used to quantify the systematic differences in low- and high-level reconstructed quantities. This approach could be applied to future LArTPC detectors, such as those used in SBN and DUNE.
A Case Study of Multimodal, Multi-institutional Data Management for the Combinatorial Materials Science Community
Although the convergence of high-performance computing, automation, and machine learning has significantly altered the materials design timeline, transformative advances in functional materials and acceleration of their design will require addressing the deficiencies that currently exist in materials informatics, particularly a lack of standardized experimental data management. The challenges associated with experimental data management are especially true for combinatorial materials science, where advancements in automation of experimental workflows have produced datasets that are often too large and too complex for human reasoning. The data management challenge is further compounded by the multimodal and multi-institutional nature of these datasets, as they tend to be distributed across multiple institutions and can vary substantially in format, size, and content. Furthermore, modern materials engineering requires the tuning of not only composition but also of phase and microstructure to elucidate processing–structure–property–performance relationships. To adequately map a materials design space from such datasets, an ideal materials data infrastructure would contain data and metadata describing (i) synthesis and processing conditions, (ii) characterization results, and (iii) property and performance measurements. In this work, we present a case study for the low-barrier development of such a dashboard that enables standardized organization, analysis, and visualization of a large data lake consisting of combinatorial datasets of synthesis and processing conditions, X-ray diffraction patterns, and materials property measurements generated at several different institutions. While this dashboard was developed specifically for data-driven thermoelectric materials discovery, we envision the adaptation of this prototype to other materials applications, and, more ambitiously, future integration into an all-encompassing materials data management infrastructure.
Nuclide Inventory Benchmark for BWR Spent Nuclear Fuel: Challenges in Evaluation of Modeling Data Assumptions and Uncertainties
This work discusses challenges and approaches to uncertainty analyses associated with the development of a nuclide inventory benchmark for fuel irradiated in a boiling water reactor. The benchmark under consideration is being developed based on experimental data from the SFCOMPO international database. The focus herein is on how to address missing data in fuel design and operating conditions that are important for adequately simulating the time-dependent changes in fuel during irradiation in the reactor. The effects of modeling assumptions and uncertainties in modeling parameters on the calculated nuclide inventory were analyzed and quantified through computational models developed using capabilities in the SCALE code system. Particular attention was given to the impact of the power history and water coolant density on the calculated nuclide inventory, as well as to the effect of geometry modeling considerations not usually addressed in a nuclide inventory benchmark. These considerations include gap closure, channel bow, and channel corner radius, which do not usually apply to regular reactor operation but are relevant for assessing impacts of potential anomalous operating scenarios.
Data Science Techniques, Assumptions, and Challenges in Alloy Clustering and Property Prediction
Data analytics methods have been increasingly applied to understanding materials chemistry, processing due to the manufacturing approach, and uni-axial and cyclic property relationships in the highly complex space of alloy design. There are several benefits to applying data analytics to this space, including the ability to manage non-linearities in the responses of the alloy attributes and the resulting mechanical properties. However, key difficulties in applying and understanding the results of data analytics include the often lack of reported assumptions and data processing steps necessary to improve interpretation and reproducibility in derived results. In this work, the methods used to generate clustering and correlation analyses for experimental 9% Cr ferritic-martensitic steel data were investigated and the resulting implications for mechanical property predictions were assessed. This work uses principal component analysis, partitioning around medoids, t-SNE, and k-means clustering to investigate trends in composition, processing and microstructure information with creep and tensile properties, building on work done previously using a smaller version of the same dataset. The initial assumptions, preprocessing steps and methods are investigated and outlined in order to depict the fine level of detail required to convey the steps taken to process data and produce analytical results. Here, the variations in the resulting analyses are explored due to the influence of new and more varied data.
Antarctic ice sheet model comparison with uncurated geological constraints shows that higher spatial resolution improves deglacial reconstructions
Accurately reconstructing past changes to the shape and volume of the Antarctic ice sheet relies on the use of physically based and thus internally consistent ice sheet modeling, benchmarked against spatially limited geologic data. The challenge in model benchmarking against geologic data is diagnosing whether model-data misfits are the result of an inadequate model, inherently noisy or biased geologic data, and/or incorrect association between modeled quantities and geologic observations. In this work we address this challenge by (i) the development and use of a new model-data evaluation framework applied to an uncurated data set of geologic constraints, and (ii) nested high-spatial-resolution modeling designed to test the hypothesis that model resolution is an important limitation in matching geologic data. While previous approaches to model benchmarking employed highly curated datasets, our approach applies an automated screening and quality control algorithm to an uncurated public dataset of geochronological observations (specifically, cosmogenic-nuclide exposure-age measurements from glacial deposits in ice-free areas). This optimizes data utilization by including more geological constraints, reduces potential interpretive bias, and allows unsupervised assimilation of new data as they are collected. We also incorporate a nested model framework in which high-resolution domains are downscaled from a continent-wide ice sheet model. We highlight the application of this framework by applying these methods to a small ensemble of deglacial ice-sheet model simulations, and demonstrate that the nested approach improves the ability of model simulations to match exposure age data collected from areas of complex topography and ice flow. We develop a range of diagnostic model-data comparison metrics to provide more insight into model performance than possible from a single-valued misfit statistic, showing that different metrics capture different aspects of ice sheet deflation.