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At least 793 records · Page 44

Architecture for time or transform domain decoding of reed-solomon codes

Two pipeline (255,233) RS decoders, one a time domain decoder and the other a transform domain decoder, use the same first part to develop an errata locator polynomial .tau.(x), and an errata evaluator polynominal A(x). Both the time domain decoder and transform domain decoder have a modified GCD that uses an input multiplexer and an output demultiplexer to reduce the number of GCD cells required. The time domain decoder uses a Chien search and polynomial evaluator on the GCD outputs .tau.(x) and A(x), for the final decoding steps, while the transform domain decoder uses a transform error pattern algorithm operating on .tau.(x) and the initial syndrome computation S(x), followed by an inverse transform algorithm in sequence for the final decoding steps prior to adding the received RS coded message to produce a decoded output message.

Shao, Howard M.↗

SnowPac : a multiscale cubic B-spline wavelet compressor for astronomical images

ABSTRACT As more advanced and complex survey telescopes are developed, the size and scale of data being captured grows at increasing rates. Across various domains, data compression through wavelets has enabled the reduction of data size and increase in computation efficiency. In this paper, we provide qualitative and quantitative tests of a new wavelet-based image compression method compared against the current standard for astronomical images. The analysis is improved by making use of state-of-the-art object detection systems to accurately measure the impact of the compression. We find that a combination of lossy wavelet-based methods, efficient quantization, and lossless dictionary compressors can preserve up to 98 per cent of astronomical objects at a 10:1 compression ratio. This significant reduction in file size also preserves astronomical object properties better than existing methods. These methods help further reduce future workloads for image-heavy processing pipelines.

Pulido, Jesus↗

PFLOTRAN modeling data and scripts associated with “Refining the Hydrogeologic Framework of a Large River Corridor Model Using Waterborne Transient Electromagnetics”

NOTE: The manuscript associated with this data package is currently in review. The data may be revised based on reviewer feedback. Upon manuscript acceptance, this data package will be updated with the final dataset and additional metadata. This data package is associated with the publication “Refining the Hydrogeologic Framework of a Large River Corridor Model Using Waterborne Transient Electromagnetics” submitted to Water Resources Research (Terry et al. 2025). The data package contains the groundwater modeling dataset from PFLOTRAN software. It includes the python script for mesh generation, boundary condition setting, PFLOTRAN input deck formation and postprocessing. It couples groundwater flow and species transport for Hanford Reach river corridor and pipelines the model generation and processing. This model can be used to easily generate the model and analysis for Hanford site. It can also be adjusted to other hydrologic area with ease. For details on how to navigate data packages generated by this project, see https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA/About. The data package consists of 6 folders: (1) “data” contains all necessary data as input and intermediate data for processing; (2) “mesh” contains all mesh related files to generate mesh in Hanford Reach river corridor; (3) “model_run” contains the generated script for PFLOTRAN modeling; (4) “notebooks” contains all the Python script to generate the model; (5) “output” contains all the output from the computation; (6) “postprocessing” contains the Python script to generate scientific figure for manuscript. All files are .csv (comma-separated values), .h5 (HDF5 format), .in (input files), .ipynb (Jupyter notebooks), .p (Python pickle), .png (images), .PNG (images), .py (Python scripts), .pyc (Python bytecode), .r (R scripts), .sh (shell scripts), .txt (text files), .vtu (3D mesh/visualization format), .xz (compressed archive), or .zip (compressed archive).

54 ENVIRONMENTAL SCIENCES↗

Opportunities in AI/ML for the Rubin LSST Dark Energy Science Collaboration

The Vera C. Rubin Observatory's Legacy Survey of Space and Time (LSST) will produce unprecedented volumes of heterogeneous astronomical data (images, catalogs, and alerts) that challenge traditional analysis pipelines. The LSST Dark Energy Science Collaboration (DESC) aims to derive robust constraints on dark energy and dark matter from these data, requiring methods that are statistically powerful, scalable, and operationally reliable. Artificial intelligence and machine learning (AI/ML) are already embedded across DESC science workflows, from photometric redshifts and transient classification to weak lensing inference and cosmological simulations. Yet their utility for precision cosmology hinges on trustworthy uncertainty quantification, robustness to covariate shift and model misspecification, and reproducible integration within scientific pipelines. This white paper surveys the current landscape of AI/ML across DESC's primary cosmological probes and cross-cutting analyses, revealing that the same core methodologies and fundamental challenges recur across disparate science cases. Since progress on these cross-cutting challenges would benefit multiple probes simultaneously, we identify key methodological research priorities, including Bayesian inference at scale, physics-informed methods, validation frameworks, and active learning for discovery. With an eye on emerging techniques, we also explore the potential of the latest foundation model methodologies and LLM-driven agentic AI systems to reshape DESC workflows, provided their deployment is coupled with rigorous evaluation and governance. Finally, we discuss critical software, computing, data infrastructure, and human capital requirements for the successful deployment of these new methodologies, and consider associated risks and opportunities for broader coordination with external actors.

Aubourg, Eric [APC, Paris] (ORCID:000000025592023X↗

py4DSTEM: A Software Package for Four-Dimensional Scanning Transmission Electron Microscopy Data Analysis

Scanning transmission electron microscopy (STEM) allows for imaging, diffraction, and spectroscopy of materials on length scales ranging from microns to atoms. By using a high-speed, direct electron detector, it is now possible to record a full two-dimensional (2D) image of the diffracted electron beam at each probe position, typically a 2D grid of probe positions. These 4D-STEM datasets are rich in information, including signatures of the local structure, orientation, deformation, electromagnetic fields, and other sample-dependent properties. However, extracting this information requires complex analysis pipelines that include data wrangling, calibration, analysis, and visualization, all while maintaining robustness against imaging distortions and artifacts. In this paper, we present py4DSTEM, an analysis toolkit for measuring material properties from 4D-STEM datasets, written in the Python language and released with an open-source license. We describe the algorithmic steps for dataset calibration and various 4D-STEM property measurements in detail and present results from several experimental datasets. We also implement a simple and universal file format appropriate for electron microscopy data in py4DSTEM, which uses the open-source HDF5 standard. We hope this tool will benefit the research community and help improve the standards for data and computational methods in electron microscopy, and we invite the community to contribute to this ongoing project.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Automated Model for Improved Mapping of Country-Scale High-Resolution Coastal Bathymetry

Accurate and up-to-date maps of coastal bathymetry are critical for a variety of sectors from vessel navigation to port construction and are increasingly vital to inform coastal infrastructure management amid accelerating sea-level rise and more frequent and severe storm-surge events. The primary challenges to accurate and efficient bathymetric mapping from optical remote sensing are: accurately modeling light attenuation in both the atmosphere and water column; and inefficient data processing pipelines for highresolution satellite imagery. To address the effects of light attenuation within the water-column we have developed a novel physics-based bathymetry model that accounts for variations in water-column inherent optical properties on a pixel-by-pixel basis in optically-shallow aquatic environments, which represents a major advancement. For applications to satellite imagery, we have developed a software package that automatically applies the robust 6S atmospheric correction algorithm, estimates the bottom depth from the physics-based bathymetry model, which corrects for attenuation by suspended particulate matter and colored dissolved organic matter in the water column on a pixel-by-pixel basis, and leverages highperformance computing for rapid application to region-scale (e.g., CONUS) 2-meter resolution imagery datasets. Our approach is tailored to sensors that collect data at two-meter resolution with high return times for frequent updates. We mapped 591 WorldView satellite images for Florida, North Carolina, and Alaska and validated the maps against LiDAR-derived bathymetry data. Results show median RMSE of 1.75, 1.59, and 2.67 meters, respectively. By combining the strengths of Oak Ridge National Laboratory in high-performance computing and remote-sensing science with the water-column modeling expertise of Scripps Institution of Oceanography we advance the state of bathymetric mapping capability.

54 ENVIRONMENTAL SCIENCES↗

HELPR Version 1.1.0 User Guide

Hydrogen Extremely Low Probability of Rupture (HELPR) is a modular probabilistic fracture mechanics modeling platform developed to assess structural integrity of pipelines for transmission and distribution of hydrogen. HELPR couples fatigue and fracture engineering models with probabilistic methods to generate fast predictions and enables quantification of prediction uncertainty and sensitivity. This user manual serves as a guide through the various analysis features HELPR contains.

08 HYDROGEN↗

Benchmarking Computational Tools for Calling SNPs and Indels in Complex Microbial Populations

The NASA BioNutrients missions seek to understand the suitability of microorganisms for bioproduction during space flight. One topic of interest is the stability of microbial genomes during long-term ambient storage and subsequent rehydration and growth. To address these questions, samples from 8 species were flown to ISS for 5 years of desiccated storage at ambient temperature (Stasis Packs) and 2 species were packaged along with powdered media inside a bioreactor system to allow hydration and growth in microgravity (Production Packs). For both systems, Whole Genome Sequencing (WGS) of the DNA extracted from the returned samples and paired ground controls will be conducted to identify changes in genome stability due to time, storage conditions and growth in space. Across the technical replicates, ground controls, 10 timepoints, and multiple experimental conditions, ~300 samples have been selected for initial analysis with WGS sequencing to 100x coverage. A flexible and resource efficient mutation calling pipeline is needed to process this large dataset and allow for comparisons between species. Many bioinformatics tools for calling Indels and Single Nucleotide Variants (SNVs) are designed for use with pure isolates, where true variations from the reference genome are expected to dominate the reads aligning to the location of mutation. In contrast, DNA from the Stasis Pack (SP) samples was collected directly after recovery from desiccated storage and the Production Pack (PP) samples were collected after fermentation. In this context, reads with mutations are expected to be less frequent than reads that align with the reference genome, as each sample will include multiple lines of cells. Thus, BioNutrients samples are expected to be similar to samples from cancer cell or “pooled” sequencing approaches. In preparation for the analysis of the BioNutrients samples, we have tested three mutation calling tools (GATK for Microbes, BreSeq and DiscoSNP) designed for complex samples. A challenge of validating mutation identification pipelines is a lack of “Ground Truth” datasets, especially for complex samples. To compare these three tools, we sought to identify mutations in pre-existing WGS data collected from populations of Chlamydomonas reinhardtii that were exposed to UV mutagenesis and growth in LEO as part of the Space Algae-1 mission. Here we present a summary of these tools against the analysis originally conducted using the CRISP tool. Critical metrics are compared such as runtime, the number of SNPs, the number and size of Indels, and patterns of transversion and transitions identified by each tool are reported. By sharing these benchmarking results collected in support of the BioNutrients mission, we aim to guide others seeking to identify SNVs in similarly complex microbial samples.

Biology↗

Flux REaction TArget Prioritization (Flux RETAP) v1

Metabolic engineering is evolving rapidly as a result of new advances in synthetic biology and automation, as well as the irruption of machine learning (ML). ML has been shown to provide the predictive power synthetic biology lacked and needed, and to be able to effectively guide the metabolic engineering process. However, current technical limitations prevent the independent application of ML approaches to metabolic engineering without the use of previous biological knowledge in the form of a prioritized list of desirable engineering targets. Here, we present FluxRETAP, a simple and computationally inexpensive method that leverages the prior mechanistic knowledge embedded in genome-scale metabolic models (GSMs) for suggesting targets for genetic overexpression, downregulation or deletion, with the final goal of increasing metabolite production. FluxRETAP captured 100% of reaction targets experimentally verified to improve Escherichia coli isoprenol production in the literature accessible to us, 50% of targets that experimentally improved taxadiene production in E. coli and ~60% of genetic targets from a verified minimal constrained cut-set in Pseudomonas putida while providing additional high priority targets that could be tested. Overall, FluxRETAP is an efficient algorithm for identifying a prioritized list of testable genetic and reaction targets which can also be utilized in ML pipelines.

Czajka, Jeffrey [Battelle Memorial Institute, Paci↗

Multi-modal Energy-optimal Trip Scheduling in Real-time (METS-R) for Transportation Hubs (Final Report)

This report summarizes the work performed under the award number EE0008524. The project develops the Multi-modal Energy-optimal Trip Scheduling in Real-time (METS-R) platform as the next-generation transportation solution based on autonomous electric vehicles (AEV) serving passenger trips from and to urban transportation hubs, to substantially reduce transportation energy consumption. Extensive data collection and analyses were first conducted to understand the demand patterns and energy consumption of hub-based on-road trips. Then, a data-driven framework that consists of an analytical module and a simulation module was proposed. For the analytical module, five planning + operation tools were developed to support the planning and energy-efficient operations of urban AEV services: the charging station planning that robotically allocates charging supplies based on the stationary charging demand distribution; the transit planning and demand adaptive scheduling model that efficiently generates\ candidate transit routes from hubs to other places and dynamically adjusts the transit time table to fit the current demand; the online energy-efficient routing that learns the energy-optimal paths from observations of link-level energy consumption in real-time; the hub-based ridesharing that matches trip requests together with account for the uncertainty of future trip demand and vehicle supply; and finally, the integrated demand prediction and anomaly detection pipeline that leverages the flight/train time table and support other planning/operation tools. To demonstrate the performance of these tools, a scalable high-performance agent-based simulator was built. We divided the urban space into multiple service zones where each zone was considered as an agent for passenger generation and vehicle charging. Two types of AEV agents were coded to model two types of mobility services: AEV taxi and AEV transit. For the AEV taxi, the team implemented the functions of pickup/drop-off passengers, energy-efficient routing, ridesharing, fleet rebalancing, and recharging. For the AEV bus, the team implemented the functions of demand-adaptive route scheduling, passenger boarding, and recharging. A high-performance computing framework was introduced to receive various profiling information (such as link energy updates, vehicle speed) from the simulator instances and communicate the operational commands back to the instances. The numerical experiments show that each of the proposed operational algorithms can reduce energy consumption and improve system efficiency. Furthermore, there exists the need to collectively consider multiple planning + operational strategies as multiple strategies can influence each other in terms of performance impacts. Recommendations for future work related to AEV planning and simulation are discussed.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Highly parallel computer architecture for robotic computation

In a computer having a large number of single instruction multiple data (SIMD) processors, each of the SIMD processors has two sets of three individual processor elements controlled by a master control unit and interconnected among a plurality of register file units where data is stored. The register files input and output data in synchronism with a minor cycle clock under control of two slave control units controlling the register file units connected to respective ones of the two sets of processor elements. Depending upon which ones of the register file units are enabled to store or transmit data during a particular minor clock cycle, the processor elements within an SIMD processor are connected in rings or in pipeline arrays, and may exchange data with the internal bus or with neighboring SIMD processors through interface units controlled by respective ones of the two slave control units.

Fijany, Amir↗

The throughput calibration of the VERITAS telescopes

Context. The response of imaging atmospheric Cherenkov telescopes to incident γ -ray-initiated showers in the atmosphere changes as the telescopes age due to exposure to light and weather. These aging processes affect the reconstructed energies of the events and γ -ray fluxes. Aims. This work discusses the implementation of signal calibration methods for the Very Energetic Radiation Imaging Telescope Array System (VERITAS) to account for changes in the optical throughput and detector performance over time. Methods. The total throughput of a Cherenkov telescope is the product of camera-dependent factors, such as the photomultiplier tube gains and their quantum efficiencies, and the mirror reflectivity and Winston cone response to incoming radiation. This document summarizes different methods to determine how the camera gains and mirror reflectivity have evolved over time and how we can calibrate this changing throughput in reconstruction pipelines for imaging atmospheric Cherenkov telescopes. The implementation is validated against seven years of observations with the VERITAS telescopes of the Crab Nebula, which is a reference object in very-high-energy astronomy. Results. Regular optical throughput monitoring and the corresponding signal calibrations are found to be critical for the reconstruction of extensive air shower images. The proposed implementation is applied as a correction to the signals of the photomultiplier tubes in the telescope simulation to produce fine-tuned instrument response functions. This method is shown to be effective for calibrating the acquired γ -ray data and for recovering the correct energy of the events and photon fluxes. At the same time, it keeps the computational effort of generating Monte Carlo simulations for instrument response functions affordably low.

79 ASTRONOMY AND ASTROPHYSICS↗

End-to-end learning of multiple sequence alignments with differentiable Smith–Waterman

Abstract Motivation Multiple sequence alignments (MSAs) of homologous sequences contain information on structural and functional constraints and their evolutionary histories. Despite their importance for many downstream tasks, such as structure prediction, MSA generation is often treated as a separate pre-processing step, without any guidance from the application it will be used for. Results Here, we implement a smooth and differentiable version of the Smith–Waterman pairwise alignment algorithm that enables jointly learning an MSA and a downstream machine learning system in an end-to-end fashion. To demonstrate its utility, we introduce SMURF (Smooth Markov Unaligned Random Field), a new method that jointly learns an alignment and the parameters of a Markov Random Field for unsupervised contact prediction. We find that SMURF learns MSAs that mildly improve contact prediction on a diverse set of protein and RNA families. As a proof of concept, we demonstrate that by connecting our differentiable alignment module to AlphaFold2 and maximizing predicted confidence, we can learn MSAs that improve structure predictions over the initial MSAs. Interestingly, the alignments that improve AlphaFold predictions are self-inconsistent and can be viewed as adversarial. This work highlights the potential of differentiable dynamic programming to improve neural network pipelines that rely on an alignment and the potential dangers of optimizing predictions of protein sequences with methods that are not fully understood. Availability and implementation Our code and examples are available at: https://github.com/spetti/SMURF. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

A Data Processing Pipeline for Socio-Technical Network Analysis [Slides]

With the rapid adoption of emerging technologies, there is a need to catalog and model sociotechnical interdependencies that have been historically used to influence the operation of Critical Infrastructure networks including the impacts of mergers and acquisitions, hostile takeovers, and foreign investment. Our research intends to address this need with two primary contributions. First, we have developed a data curation and processing pipeline to generate sociotechnical networks extracted from a variety of data sources including SEC filings and infrastructure asset databases. The pipeline, implemented in Apache Airflow, extracts and normalizes the representation of entities and relations, specified within ontologies. Second, networks produced by our pipeline enable the development of graph-theoretic metrics that consider the properties of network components in addition to its topology. Measures of network complexity, such as degree distribution, reachability analyses, temporal analysis, and community detection may be adapted to indicate adversarial organizational influence. Our intent is to provide an extensible, machine-actionable approach to quickly communicate such models, reproduce previous results, and adapt them to new, unanticipated situations.

97 MATHEMATICS AND COMPUTING↗

Highly parallel reconfigurable computer architecture for robotic computation having plural processor cells each having right and left ensembles of plural processors

In a computer having a large number of single-instruction multiple data (SIMD) processors, each of the SIMD processors has two sets of three individual processor elements controlled by a master control unit and interconnected among a plurality of register file units where data is stored. The register files input and output data in synchronism with a minor cycle clock under control of two slave control units controlling the register file units connected to respective ones of the two sets of processor elements. Depending upon which ones of the register file units are enabled to store or transmit data during a particular minor clock cycle, the processor elements within an SIMD processor are connected in rings or in pipeline arrays, and may exchange data with the internal bus or with neighboring SIMD processors through interface units controlled by respective ones of the two slave control units.

Fijany, Amir↗

Describing Point Defect Topology in 2D Energy Materials Through Computer Vision

Point defects such as vacancies and impurity atoms strongly impact the performance of 2D materials. Traditional efforts often rely on manual detection, a process that is time-intensive, prone to human error, and challenging to scale. Here we leverage machine learning (ML) methods to identify and quantify vacancies within 2D transition metal carbides (Ti3C2, MXenes), aiming to expedite detection while improving accuracy. MXenes exhibit valuable defect-defined electrochemical properties, but we currently lack statistical understanding of defect topology needed to fully harness these materials. Here we employ a convolutional neural network for semantic segmentation of experimental MXene images, opening an opportunity to conduct a rigorous statistical study on defect hierarchy while investigating local relaxation in the lattice. We show how the integration of ML can yield fundamental insight into point defects, providing a powerful tool that will play an increasingly crucial role in the future of materials science. ML is often not just a matter of straightforward application, and pretrained models proved ineffective in this case. Instead, we trained our own neural network (NN) and applied data augmentation techniques and fine-tuning to the training dataset. Since labeled microscopy data is often scarce, we developed training data from a previously published wide-frame MXene image, using customized Gaussian fitting to locate atomic positions. Our trained model was then applied to a large dataset of experimental images, enabling a statistical study of defect configurations across three samples prepared with different HF etchant concentrations (5%, 9.1%, and 12.5%), as shown in Fig. 1. This also allowed us to investigate local strain around vacancies, though we find that we are limited by the precision of measurements using high-angle annular dark field (HAADF) images, as shown in Fig. 2. This study demonstrates how ML enables large-scale, quantitative analysis of atomic defects - an otherwise infeasible task with traditional methods. While our NN was specialized for Ti3C2 MXenes, the pipeline we developed provides a foundation for future ML models tailored to other materials. Ultimately, we envision embedding the NN onto the microscope to give real-time feedback to the user. To make this a reality, continued work is necessary to fully understand the NN's capabilities and limitations. This study gets one step closer to our goals of automated experimentation moving away from traditional methods of manual labeling. As ML capabilities advance, we hope to continue adapting and applying these techniques in microscopy.

2D materials↗

Design of a Novel Information System for Semi-Automated Management of Cybersecurity in Industrial Control Systems

There is an urgent need in many critical infrastructure sectors, including the energy sector, for attaining detailed insights into cybersecurity features and compliance with cybersecurity requirements related to their Operational Technology (OT) deployments. Frequent feature changes of OT devices interfere with this need, posing a great risk to customers. One effective way to address this challenge is via a semi-automated cyber-physical security assurance approach, which enables verification and validation of the OT device cybersecurity claims against actual capabilities, both pre- and post-deployment. To realize this approach, this paper presents new methodology and algorithms to automatically identify cybersecurity-related claims expressed in natural language form in ICS device documents. Here, we developed an identification process that employs natural language processing (NLP) techniques with the goal of semi-automated vetting of detected claims against their device implementation. We also present our novel NLP components for verifying feature claims against relevant cybersecurity requirements. The verification pipeline includes components such as automated vendor identification, device document curation, feature claim identification utilizing sentiment analysis for conflict resolution, and reporting of features that are claimed to be supported or indicated as unsupported. Our novel matching engine represents the first automated information system available in the cybersecurity domain that directly aids the generation of ICS compliance reports.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Final technical report for DE-SC0022255: Discovering Physically Meaningful Structures from Climate Extreme Data

The past two decades have witnessed natural disasters and extreme weather events that affect millions of people. At the same time, the data volume from high-resolution climate models, satellite, in-situ and ground-based measurements have substantially increased to petabyte scales. These new and readily accessible datasets create the previously missing pipeline required for scientific machine learning (ML) and therefore new opportunities for improved understanding and prediction capability of climate extreme events. This project developed a deep latent variable model framework to discover physically meaningful hidden structures from high-dimensional, spatiotemporal climate extreme data.

97 MATHEMATICS AND COMPUTING↗