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At least 379 records · Page 21

Comparative Performance Evaluation of High-performance Data Transfer Tools

Data transfer in wide-area networks has been long studied in different contexts, from data sharing among data centers to online access to scientific data. Many software tools and platforms have been developed to facilitate easy, reliable, fast, and secure data transfer over wide area networks, such as GridFTP, FDT, bbcp, mdtmFTP, and XDD. However, few studies have shown the full capabilities of existing data transfer tools from the perspective of whether such tools have fully adopted state-of-the-art techniques through meticulous comparative evaluations. In this paper, we evaluate the performance of the four highperformance data transfer tools (GridFTP, FDT, mdtmFTP, and XDD) in various environments. Our evaluation suggests that each tool has strengths and weaknesses. FDT and GridFTP perform consistently in diverse environments. XDD and mdtmFTP show improved performance in limited environments and datasets during our evaluation. Unlike other studies on data transfer tools, we also evaluate the predictability of the tools' performance, an important factor for scheduling different stages of science workflows. Performance predictability also helps in (auto)tuning the configurable parameters of the data transfer tool. We apply statistical learning techniques such as linear/polynomial regression, and k-nearest neighbors (kNN), to assess the performance predictability of each tool using its control parameters. Our results show that we can achieve good prediction performance for GridFTP and mdtmFTP using linear regression and kNN, respectively.

Nadig, Deepak↗

Planet Microbe: a platform for marine microbiology to discover and analyze interconnected ‘omics and environmental data

In recent years, large-scale oceanic sequencing efforts have provided a deeper understanding of marine microbial communities and their dynamics. These research endeavors require the acquisition of complex and varied datasets through large, interdisciplinary and collaborative efforts. However, no unifying framework currently exists for the marine science community to integrate sequencing data with physical, geological, and geochemical datasets. Planet Microbe is a web-based platform that enables data discovery from curated historical and on-going oceanographic sequencing efforts. In Planet Microbe, each ‘omics sample is linked with other biological and physiochemical measurements collected for the same water samples or during the same sample collection event, to provide a broader environmental context. This work highlights the need for curated aggregation efforts that can enable new insights into high-quality metagenomic datasets.

59 BASIC BIOLOGICAL SCIENCES↗

Local Weather Station Design and Development for Cost-Effective Environmental Monitoring and Real-Time Data Sharing

Current weather monitoring systems often remain out of reach for small-scale users and local communities due to their high costs and complexity. This paper addresses this significant issue by introducing a cost-effective, easy-to-use local weather station. Utilizing low-cost sensors, this weather station is a pivotal tool in making environmental monitoring more accessible and user-friendly, particularly for those with limited resources. It offers efficient in-site measurements of various environmental parameters, such as temperature, relative humidity, atmospheric pressure, carbon dioxide concentration, and particulate matter, including PM 1, PM 2.5, and PM 10. The findings demonstrate the station’s capability to monitor these variables remotely and provide forecasts with a high degree of accuracy, displaying an error margin of just 0.67%. Furthermore, the station’s use of the Autoregressive Integrated Moving Average (ARIMA) model enables short-term, reliable forecasts crucial for applications in agriculture, transportation, and air quality monitoring. Furthermore, the weather station’s open-source nature significantly enhances environmental monitoring accessibility for smaller users and encourages broader public data sharing. With this approach, crucial in addressing climate change challenges, the station empowers communities to make informed decisions based on real-time data. In designing and developing this low-cost, efficient monitoring system, this work provides a valuable blueprint for future advancements in environmental technologies, emphasizing sustainability. The proposed automatic weather station not only offers an economical solution for environmental monitoring but also features a user-friendly interface for seamless data communication between the sensor platform and end users. This system ensures the transmission of data through various web-based platforms, catering to users with diverse technical backgrounds. Furthermore, by leveraging historical data through the ARIMA model, the station enhances its utility in providing short-term forecasts and supporting critical decision-making processes across different sectors.

54 ENVIRONMENTAL SCIENCES↗

Efforts to enhance reproducibility in a human performance research project

Background: Ensuring the validity of results from funded programs is a critical concern for agencies that sponsor biological research. In recent years, the open science movement has sought to promote reproducibility by encouraging sharing not only of finished manuscripts but also of data and code supporting their findings. While these innovations have lent support to third-party efforts to replicate calculations underlying key results in the scientific literature, fields of inquiry where privacy considerations or other sensitivities preclude the broad distribution of raw data or analysis may require a more targeted approach to promote the quality of research output. Methods: We describe efforts oriented toward this goal that were implemented in one human performance research program, Measuring Biological Aptitude, organized by the Defense Advanced Research Project Agency's Biological Technologies Office. Our team implemented a four-pronged independent verification and validation (IV&V) strategy including 1) a centralized data storage and exchange platform, 2) quality assurance and quality control (QA/QC) of data collection, 3) test and evaluation of performer models, and 4) an archival software and data repository. Results: Our IV&V plan was carried out with assistance from both the funding agency and participating teams of researchers. QA/QC of data acquisition aided in process improvement and the flagging of experimental errors. Holdout validation set tests provided an independent gauge of model performance. Conclusions: In circumstances that do not support a fully open approach to scientific criticism, standing up independent teams to cross-check and validate the results generated by primary investigators can be an important tool to promote reproducibility of results.

59 BASIC BIOLOGICAL SCIENCES↗

Developing Southeast Asia Solar Resource Data to Support the Clean Energy Transition in the Region

This fact sheet describes the development and release of a high-fidelity solar time series data set for the entire Southeast Asia region, which can be used to drive energy sector investment, support enabling policies to support solar energy market expansion, and inform prospecting, renewable energy auctions, target-setting, grid integration and other high impact decisions, ranging from the micro to macro scale, to accelerate renewable energy deployment throughout SE Asia. This data is available on the enhanced and expanded RE Data Explorer (RE Explorer) platform.

Advanced Energy Partnership for Asia↗

VWC-BERT: Scaling Vulnerability–Weakness–Exploit Mapping on Modern AI Accelerators

Defending cybersystems needs accurate mapping of software and hardware vulnerabilities to generalized descriptions of weaknesses, and weaknesses to exploits. These mappings enable cyber defenders to build plans for effective defense and assessment of potential risks to a cybersystem. With close to 170k vulnerabilities, manual mapping is not a feasible option. However, automated mapping is challenging due to limited training data, computational intractability, and limitations in computational natural language processing. Tools based on breakthroughs in Transformer-based language models have been demonstrated to classify vulnerabilities with high accuracy. We make three key contributions in this paper: (1) We present a new framework, \VWCBERT, that augments the Transformer-based hierarchical multi-class classification framework of Das et al. (\textsc{V2W-BERT}) with the ability to map weaknesses to exploits. (2) We implement \VWCBERT~ on modern AI accelerator platforms using two data parallel techniques for the pre-training phase and demonstrate nearly linear speedups across NVIDIA and Graphcore accelerator platforms. We observe nearly linear speedups for up to 16 V100 and 8 A100 GPUs, and about 3.4$\times$ speedup for A100 relative to V100 GPUs. We also observe excellent speedups on Graphcore, with $5.7\times$ speedup on 128 IPUs relative to 16 IPUs. Enabled by scaling, we also demonstrate higher accuracy using a larger language model, RoBERTa-Large. We show up to 87\% accuracy for strict and up to 98\% accuracy for relaxed classification. (3) We develop a novel parallel link manager for the link prediction phase and demonstrate up to 21$\times$ speedup with 16 V100 GPUs relative to one V100 GPU, and thus reducing the runtime from 2.5 hours to 10 minutes. We believe that generalizability and scalability of \VWCBERT~ will benefit both the theoretical development and practical deployment of novel cyberdefense solutions and vulnerability classification.

Das, Siddhartha Shankar↗

Employing Technology to Enable Remote Research Charrettes as a Method for Engaging Industry and Uncovering Best Practices: A Novel Approach for a Post-COVID-19 World

Methods to collect data in construction engineering and management (CEM) research are evolving, informed by recent technological advancements. One such method is research charrettes that allow effective interactions and knowledge sharing between expert industry practitioners and academic researchers, all colocated in a single venue, enabling rich data collection and live communication. A pivot point in technological evolution occurred with the COVID-19 pandemic, forcing a global shift to remote work. Hence, planned in-person research charrettes had to shift to remote sessions, relying on virtual conferencing platforms and online data collection mechanisms. Technology-enabled charrettes have allowed the authors to collect significantly richer data sets and ensure a more diverse representation of participants, while saving tremendous amounts of time. With the continuing emergence of technological applications, the world might not go back to functioning fully in person. The authors believe remote research charrettes (RRCs) will still be used in a post-COVID-19 world because of their superior performance. This paper builds on a previous publication that described traditional research charrettes as a method to enhance CEM research a decade ago; it offers a significantly updated and improved RRC method based on the knowledge gained from transitioning a dozen in-person charrettes into RRCs. It also presents performance comparisons between RRCs and traditional charrettes by quantifying metrics indicating how RRCs are more time-efficient and cost-saving, harness more participants from more diverse locations, and enable the collection of richer data sets and four times more industry comments and expert feedback. This paper also provides guidance on the integration of technology with traditional research charrettes, hence contributing to the CEM body of knowledge.

42 ENGINEERING↗

Web-Based Tools for Data-Informed Remedy Optimization: Software Theory and User Guide

This report documents the development and application of two web-based decision-support tools for pump-and-treat (P&T) groundwater remediation systems: PTOLEMY (Pump-and-Treat Optimized Location Evaluation to Maximize Yields) and OPTIMA (Optimization for Pump-and-Treat Implementation, Management, & Assessment). These tools enhance remedy design and management by leveraging advanced computational methods – specifically deep learning and multi-objective optimization – within a user-friendly platform. By integrating data-driven models with established hydrogeological knowledge, PTOLEMY and OPTIMA enable more efficient evaluation of well placement and operational strategies, helping site managers balance multiple remediation objectives under complex conditions. Both tools are implemented as modules within the SOCRATES (Suite Of Comprehensive Rapid Analysis Tools for Environmental Sites) web platform, which provides data access, visualization, and analytics to support remedy optimization across sites in the U.S. Department of Energy Office of Environmental Management complex. PTOLEMY is a rapid screening module designed to identify promising locations for new extraction wells. It employs a multi-channel three-dimensional convolutional neural network (MC3D-CNN) trained on high-fidelity simulation data to predict the relative performance (in terms of contaminant mass recovery) of potential well sites. Through an interactive web interface, PTOLEMY visualizes the probability of high performance across a site, highlighting areas where an extraction well is likely to yield above-threshold contaminant removal over a multi-year period. PTOLEMY’s map-based displays and exportable results support transparent communication of screening analyses. By focusing attention on the most favorable candidate locations, the tool augments traditional engineering judgment and physics-based modeling, providing a data informed basis for subsequent detailed evaluations. OPTIMA is a multi objective optimization module designed to find wellfield layouts and operating schedules that meet various cleanup goals. It quickly evaluates thousands of candidate setups – combinations of well locations, timing, and rates – and returns a small set of best trade-off options for comparison. At its core, OPTIMA uses a U-Net-based surrogate model – a deep-learning emulator of a groundwater flow and transport simulator – to dramatically accelerate scenario evaluations. Coupling this fast surrogate with the NSGA-II (Non-dominated Sorting Genetic Algorithm II) evolutionary algorithm, OPTIMA explores a wide decision space of well locations and schedules to identify Pareto-optimal solutions that trade off key objectives (e.g., minimizing cleanup time, maximizing contaminant mass removal, and minimizing plume extent). The tool outputs a family of optimal configurations and visualizes their trade-offs (Pareto frontiers of cleanup metrics and maps of optimized well placements). Site managers can use these results to understand the range of viable strategies and to select candidate designs for more detailed verification. OPTIMA is currently under active development and not yet fully released; this guide provides early documentation to support planning and gather user feedback.

54 ENVIRONMENTAL SCIENCES↗

HyperKube: A Kubernetes Based System for the Automation of Processing and Analysis of Hyperspectral Data Obtained from Multiple Hyperspectral Imaging Systems

Hyperspectral imagery is an emerging field of technology that has enormous potential for remote and proximal sensing in numerous areas of research. The plant phenotyping community is applying this technology to advance the throughput and accuracy of plant phenotypes based on airborne and lab-based hyperspectral imaging technology. Here we report an automated processing and analysis pipeline for four different hyperspectral imaging platforms, discuss the data issues involved, and present a strategy for computing and data architecture to handle hyperspectral data.

47 OTHER INSTRUMENTATION↗

RNAseq analysis of Cellvibrio japonicus during starch utilization differentiates between genes encoding carbohydrate active enzymes controlled by substrate detection or growth rate

ABSTRACT Bacterial utilization of starch is increasingly of interest as the importance and contributions of animal gut microbiomes become more defined. Consequently, identifying and characterizing the bacterial enzymes responsible for the degradation, transport, and metabolism of starch will enable developments in pharmaceutical, biotechnological, and culinary industries searching for novel prebiotics, carrier molecules, and low glycemic index sweeteners. The current challenge is that bacteria proficient at starch utilization often have hundreds of carbohydrate active enzymes, and it is unclear which are essential for starch utilization using only homology-based bioinformatics or computational methods. Complementary experimental data are also needed, especially to understand the regulation of bacterial starch utilization. We have completed an RNAseq analysis of the Gram-negative bacterium Cellvibrio japonicus and found that it has sophisticated regulation that includes substrate sensing and growth rate components for genes that encode starch-degrading enzymes. Among the 22 genes predicted to encode starch-active enzymes, C. japonicus has 10 alpha-amylases, 4 alpha-glucosidases, 2 pullulnases, and 2 cyclomaltodextrin glucanotransferases, 15 of which were up-regulated during exponential growth on starch and 8 up-regulated in stationary phase. Growth analyses with an enzyme secretion deficient mutant of C. japonicus suggested that secreted amylases are essential for this bacterium to degrade starch. Our approach of coupling a physiological growth assay with transcriptomic data provides a platform to identify targets for further genetic or biochemical analysis that can be broadly applied to other starch-utilizing bacteria. IMPORTANCE Understanding the bacterial metabolism of starch is important as this polysaccharide is a ubiquitous ingredient in foods, supplements, and medicines, all of which influence gut microbiome composition and health. Our RNAseq and growth data set provides a valuable resource to those who want to better understand the regulation of starch utilization in Gram-negative bacteria. These data are also useful as they provide an example of how to approach studying a starch-utilizing bacterium that has many putative amylases by coupling transcriptomic data with growth assays to overcome the potential challenges of functional redundancy. The RNAseq data can also be used as a part of larger meta-analyses to compare how C. japonicus regulates carbohydrate active enzymes, or how this bacterium compares to gut microbiome constituents in terms of starch utilization potential.

59 BASIC BIOLOGICAL SCIENCES↗

Ecological Insights from Transferable Plant Biomass Mapping across the Arctic using High-resolution Structure-from-Motion and LiDAR Data

Warmer temperatures, permafrost thaw, and increased wildfire activity are driving rapid ecological change across the Arctic, significantly altering plant productivity and aboveground biomass (AGB). These rapid changes highlight the urgent need to improve monitoring of vegetation dynamics in the Earth’s northern ecosystems, where high spatiotemporal heterogeneity occurs at scales finer than those captured by traditional satellite observations. The growing use of Unoccupied Aerial Systems (UASs) presents an opportunity to overcome this limitation. Yet, the diversity of UAS platforms, sensors, and data collection and processing workflows presents challenges for developing standardized, generalizable approaches. To address this challenge, we compiled 672 AGB plots co-located with 183 UAS-based Structure-from-Motion (SfM) or Light Detection and Ranging (LiDAR) surveys collected across the Arctic. Here, we: (1) evaluated the generalizability of UAS-derived canopy structure derived from high-resolution SfM and LiDAR for estimating AGB, (2) assessed scaling errors and their sources in two recent satellite-based AGB products derived from Landsat and MODIS, and (3) demonstrated the use of high-resolution AGB maps to quantify biomass variation across tundra plant functional types (PFTs) and to monitor post-fire recovery. Our results show that both SfM and LiDAR accurately captured AGB and its variability across tundra PFTs using a Random Forest (RF) model (overall RMSE: 0.336 kg/m2), with mapping performance varying slightly by region and data source. Using UAS-derived AGB maps as a benchmark, we identified systematic biases in satellite-derived AGB products, largely attributable to the magnitude of AGB and structural heterogeneity within coarse-resolution pixels. Applying our model to repeat UAS surveys following a tundra fire on Seward Peninsula, we observed rapid AGB recovery in non-shrub patches, with biomass recovering to pre-fire levels within 2 years. In contrast, shrub patches recovered more slowly, with AGB gains continuing over 2–4 years through both in-patch growth and lateral expansion (via dispersal) into remaining burned areas. Overall, these findings demonstrate the generalizability of UAS-based SfM and LiDAR data for estimating tundra AGB and highlight the potential of our approach to be broadly applied to generate high-quality AGB data for ecological monitoring and model benchmarking across the Arctic.

Yang, Daryl [ORNL] (ORCID:0000000317057823)↗