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At least 505 records · Page 28

On extending parallelism to serial simulators

This paper describes an approach to discrete event simulation modeling that appears to be effective for developing portable and efficient parallel execution of models of large distributed systems and communication networks. In this approach, the modeler develops submodels using an existing sequential simulation modeling tool, using the full expressive power of the tool. A set of modeling language extensions permit automatically synchronized communication between submodels; however, the automation requires that any such communication must take a nonzero amount off simulation time. Within this modeling paradigm, a variety of conservative synchronization protocols can transparently support conservative execution of submodels on potentially different processors. A specific implementation of this approach, U.P.S. (Utilitarian Parallel Simulator), is described, along with performance results on the Intel Paragon.

Nicol, David↗

An Ontology for State Analysis: Formalizing the Mapping to SysML

State Analysis is a methodology developed over the last decade for architecting, designing and documenting complex control systems. Although it was originally conceived for designing robotic spacecraft, recent applications include the design of control systems for large ground-based telescopes. The European Southern Observatory (ESO) began a project to design the European Extremely Large Telescope (E-ELT), which will require coordinated control of over a thousand articulated mirror segments. The designers are using State Analysis as a methodology and the Systems Modeling Language (SysML) as a modeling and documentation language in this task. To effectively apply the State Analysis methodology in this context it became necessary to provide ontological definitions of the concepts and relations in State Analysis and greater flexibility through a mapping of State Analysis into a practical extension of SysML. The ontology provides the formal basis for verifying compliance with State Analysis semantics including architectural constraints. The SysML extension provides the practical basis for applying the State Analysis methodology with SysML tools. This paper will discuss the method used to develop these formalisms (the ontology), the formalisms themselves, the mapping to SysML and approach to using these formalisms to specify a control system and enforce architectural constraints in a SysML model.

Wagner, David A.↗

NukeLM: Pre-Trained and Fine-Tuned Language Models for the Nuclear and Energy Domains

Natural language processing (NLP) tasks (text classification, named entity recognition, etc.) have seen amazing improvements over the last few years. This is due to models such as BERT that achieve deep knowledge transfer by using a large pre-trained model, then fine-tuning the model on specific tasks. The BERT architecture has shown even better performance on domain-specific tasks when the model is pre-trained using domain-relevant texts. Here, inspired by these recent advancements, we have developed NukeLM, a nuclear-domain BERT model pre-trained on 1.5 million abstracts from the DOE Office of Scientific and Technical Information (OSTI) database. This NukeLM model is then fine-tuned for the classification of research articles into either binary classes (related to the nuclear fuel cycle (NFC) or not) or multiple categories related to the subject of the article. We show that continued pre-training of a BERT-style architecture prior to fine-tuning results in greater performance in both article classification tasks. This information is critical for properly triaging manuscripts, a necessary task for better understanding citation networks that publish in the nuclear space and uncovering new areas of research in the nuclear (or nuclear relevant) domain.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Mitigating Satellite-Based Fire Sampling Limitations in Deriving Biomass Burning Emission Rates: Application to WRF-Chem Model over the Northern sub-Saharan African Region

Largely used in several independent estimates of fire emissions, fire products based on MODIS sensors aboard the Terra and Aqua polar-orbiting satellites have a number of inherent limitations, including (a) inability to detect fires below clouds, (b) significant decrease of detection sensitivity at the edge of scan where pixel sizes are much larger than at nadir, and (c) gaps between adjacent swaths in tropical regions. To remedy these limitations, an empirical method is developed here and applied to correct fire emission estimates based on MODIS pixel level fire radiative power measurements and emission coefficients from the Fire Energetics and Emissions Research (FEER) biomass burning emission inventory. The analysis was performed for January 2010 over the northern sub-Saharan African region. Simulations from WRF-Chem model using original and adjusted emissions are compared with the aerosol optical depth (AOD) products from MODIS and AERONET as well as aerosol vertical profile from CALIOP data. The comparison confirmed an 30-50% improvement in the model simulation performance (in terms of correlation, bias, and spatial pattern of AOD with respect to observations) by the adjusted emissions that not only increases the original emission amount by a factor of two but also results in the spatially continuous estimates of instantaneous fire emissions at daily time scales. Such improvement cannot be achieved by simply scaling the original emission across the study domain. Even with this improvement, a factor of two underestimations still exists in the modeled AOD, which is within the current global fire emissions uncertainty envelope. Plain Language Summary Polar-orbiting satellites sensors, such as MODIS, have limitations in detecting fires under clouds or when viewing angles are large or in the gaps among satellites' different ground swaths. Here we developed an empirical method to mitigate the effect of these limitations in fire emission estimate. The method is applied to a fire emission inventory (FEER) based on MODIS. We show that, with our method, the adjusted emission inventory improves WRF-Chem simulation of smoke transport and distribution.

emissions properties↗

Assessing the evolution of research topics in a biological field using plant science as an example

Scientific advances due to conceptual or technological innovations can be revealed by examining how research topics have evolved. But such topical evolution is difficult to uncover and quantify because of the large body of literature and the need for expert knowledge in a wide range of areas in a field. Using plant biology as an example, we used machine learning and language models to classify plant science citations into topics representing interconnected, evolving subfields. The changes in prevalence of topical records over the last 50 years reflect shifts in major research trends and recent radiation of new topics, as well as turnover of model species and vastly different plant science research trajectories among countries. Our approaches readily summarize the topical diversity and evolution of a scientific field with hundreds of thousands of relevant papers, and they can be applied broadly to other fields.

60 APPLIED LIFE SCIENCES↗

Online Tools for Astronomy and Cosmochemistry

Over the past year, the Webnucleo Group at Clemson University has been developing a web site with a number of interactive online tools for astronomy and cosmochemistry applications. The site uses SHP (Simplified Hypertext Preprocessor), which, because of its flexibility, allows us to embed almost any computer language into our web pages. For a description of SHP, please see http://www.joeldenny.com/ At our web site, an internet user may mine large and complex data sets, such as our stellar evolution models, and make graphs or tables of the results. The user may also run some of our detailed nuclear physics and astrophysics codes, such as our nuclear statistical equilibrium code, which is written in fortran and C. Again, the user may make graphs and tables and download the results.

Meyer, B. S.↗

Implementing Access to Data Distributed on Many Processors

A reference architecture is defined for an object-oriented implementation of domains, arrays, and distributions written in the programming language Chapel. This technology primarily addresses domains that contain arrays that have regular index sets with the low-level implementation details being beyond the scope of this discussion. What is defined is a complete set of object-oriented operators that allows one to perform data distributions for domain arrays involving regular arithmetic index sets. What is unique is that these operators allow for the arbitrary regions of the arrays to be fragmented and distributed across multiple processors with a single point of access giving the programmer the illusion that all the elements are collocated on a single processor. Today's massively parallel High Productivity Computing Systems (HPCS) are characterized by a modular structure, with a large number of processing and memory units connected by a high-speed network. Locality of access as well as load balancing are primary concerns in these systems that are typically used for high-performance scientific computation. Data distributions address these issues by providing a range of methods for spreading large data sets across the components of a system. Over the past two decades, many languages, systems, tools, and libraries have been developed for the support of distributions. Since the performance of data parallel applications is directly influenced by the distribution strategy, users often resort to low-level programming models that allow fine-tuning of the distribution aspects affecting performance, but, at the same time, are tedious and error-prone. This technology presents a reusable design of a data-distribution framework for data parallel high-performance applications. Distributions are a means to express locality in systems composed of large numbers of processor and memory components connected by a network. Since distributions have a great effect on the performance of applications, it is important that the distribution strategy is flexible, so its behavior can change depending on the needs of the application. At the same time, high productivity concerns require that the user be shielded from error-prone, tedious details such as communication and synchronization.

James, Mark↗

Data Centers and Digital Assurance Workshop 3 – Mitigations for Digital Assurance Risks

The third session of the TADA (Technical Assistance for Digital Assurance) Data Centers Cohort, held on November 18, 2025, focused on developing mitigation strategies for digital assurance risks identified in previous workshops. Hosted by Idaho National Laboratory (INL) and ScottMadden, the session emphasized the application of Cyber-Informed Engineering (CIE) to data center infrastructure, particularly at the utility–data center interface. Participants revisited and ranked key digital assurance risks, including architecture and interface weaknesses, governance gaps, and AI-enabled threats. The workshop introduced the 12 principles of CIE, advocating for consequence-focused design, engineered controls, and secure information architecture to proactively reduce cyber-physical vulnerabilities. These principles were applied to critical data center systems such as power distribution, UPS, cooling, SCADA/BMS, and grid-forming batteries. The session also addressed governance challenges at the interconnection boundary, highlighting the need for clear roles in telemetry sharing, firmware management, and trip settings. Special attention was given to emerging risks from behind-the-meter (BTM) generation, including reverse-power flow and the integration of small modular reactors (SMRs), which shift data centers from large loads to complex generation nodes. Participants explored how interconnection agreements can serve as enforceable instruments for digital assurance, and reviewed gaps in current standards such as NERC CIP, IEC 62443, and IEEE 1547. The workshop concluded with pathways to standardization, including model agreement language, state-level programs, and expanded NERC guidance. INL also presented tools and frameworks for secure procurement and supplier risk management, reinforcing the need for integrated engineering and policy solutions to secure the evolving data center–grid ecosystem. Session 3 of 3.

24 - POWER TRANSMISSION AND DISTRIBUTION↗

EpitopeVec: linear epitope prediction using deep protein sequence embeddings

Motivation: B-cell epitopes (BCEs) play a pivotal role in the development of peptide vaccines, immuno-diagnostic reagents and antibody production, and thus in infectious disease prevention and diagnostics in general. Experimental methods used to determine BCEs are costly and time-consuming. Therefore, it is essential to develop computational methods for the rapid identification of BCEs. Although several computational methods have been developed for this task, generalizability is still a major concern, where cross-testing of the classifiers trained and tested on different datasets has revealed accuracies of 51–53%. Results: We describe a new method called EpitopeVec, which uses a combination of residue properties, modified antigenicity scales, and protein language model-based representations (protein vectors) as features of peptides for linear BCE predictions. Extensive benchmarking of EpitopeVec and other state-of-the-art methods for linear BCE prediction on several large and small datasets, as well as cross-testing, demonstrated an improvement in the performance of EpitopeVec over other methods in terms of accuracy and area under the curve. As the predictive performance depended on the species origin of the respective antigens (viral, bacterial and eukaryotic), we also trained our method on a large viral dataset to create a dedicated linear viral BCE predictor with improved cross-testing performance.

59 BASIC BIOLOGICAL SCIENCES↗

Difference-Equation/Flow-Graph Circuit Analysis

Numerical technique enables rapid, approximate analyses of electronic circuits containing linear and nonlinear elements. Practiced in variety of computer languages on large and small computers; for circuits simple enough, programmable hand calculators used. Although some combinations of circuit elements make numerical solutions diverge, enables quick identification of divergence and correction of circuit models to make solutions converge.

Mcvey, I. M.↗

BERT-Based Topic Modeling and Information Retrieval to Support Fishbone Diagramming for Safe Integration of Unmanned Aircraft Systems in Wildfire Response

Recent concepts for emerging wildfire response operations have included unmanned aircraft systems (UAS) due to their increasing accessibility and capabilities. To integrate UAS into wildfire response safely, researchers have studied the use of large repositories of historic incident reports to improve the scope of root cause analysis. Recent work has emphasized applying state-of-the-art natural language processing techniques to extract useful information from these repositories. However, it has not yet been studied how these results can be interpreted and integrated into the systems engineering process. In this work, we propose a process in which Bidirectional Encoder Representations from Transformers (BERT)-based topic modeling and information retrieval are applied to a relevant set of documents in order to support the development of a fishbone diagram in a semiautomated process. High-level themes in the document set are identified using topic modeling, which are then refined and interpreted by a human analyst. Then, the themes are used to guide a finer search using information retrieval, which returns specific incident reports of relevance. This provides traceability to specific incidents as well as broader categorizations that comprise the fishbone branches. We apply the proposed process to relevant documents from NASA’s Aviation Safety Reporting System (ASRS). The proposed process is widely applicable when relevant documents are available, and the results from this study will be useful to identifying potential causes of wildfire response UAS incidents.

Hazard analysis↗

BERT-based Topic Modeling and Information Retrieval to Support Fishbone Diagramming for Safe Integration of Unmanned Aircraft Systems in Wildfire Response

Recent concepts for emerging wildfire response operations have included unmanned aircraft systems (UAS) due to their increasing accessibility and capabilities. To integrate UAS into wildfire response safely, researchers have studied the use of large repositories of historic incident reports to improve the scope of root cause analysis. Recent work has emphasized applying state-of-the-art natural language processing techniques to extract useful information from these repositories. However, it has not yet been studied how these results can be interpreted and integrated into the systems engineering process. In this work, we propose a process in which Bidirectional Encoder Representations from Transformers (BERT)-based topic modeling and information retrieval are applied to a relevant set of documents in order to support the development of a fishbone diagram in a semiautomated process. High-level themes in the document set are identified using topic modeling, which are then refined and interpreted by a human analyst. Then, the themes are used to guide a finer search using information retrieval, which returns specific incident reports of relevance. This provides traceability to specific incidents as well as broader categorizations that comprise the fishbone branches. We apply the proposed process to relevant documents from NASA’s Aviation Safety Reporting System (ASRS). The proposed process is widely applicable when relevant documents are available, and the results from this study will be useful to identifying potential causes of wildfire response UAS incidents.

hazard analysis↗

BERT-based Topic Modeling and Information Retrieval to Support Fishbone Diagramming for Safe Integration of Unmanned Aircraft Systems in Wildfire Response

Recent concepts for emerging wildfire response operations have included unmanned aircraft systems (UAS) due to their increasing accessibility and capabilities. To integrate UAS into wildfire response safely, researchers have studied the use of large repositories of historic incident reports to improve the scope of root cause analysis. Recent work has emphasized applying state-of-the-art natural language processing techniques to extract useful information from these repositories. However, it has not yet been studied how these results can be interpreted and integrated into the systems engineering process. In this work, we propose a process in which Bidirectional Encoder Representations from Transformers (BERT)-based topic modeling and information retrieval are applied to a relevant set of documents in order to support the development of a fishbone diagram in a semiautomated process. High-level themes in the document set are identified using topic modeling, which are then refined and interpreted by a human analyst. Then, the themes are used to guide a finer search using information retrieval, which returns specific incident reports of relevance. This provides traceability to specific incidents as well as broader categorizations that comprise the fishbone branches. We apply the proposed process to relevant documents from NASA’s Aviation Safety Reporting System (ASRS). The proposed process is widely applicable when relevant documents are available, and the results from this study will be useful to identifying potential causes of wildfire response UAS incidents.

hazard analysis↗

Pile-up mitigation using attention

Abstract Particle production from secondary proton-proton collisions, commonly referred to as pile-up, impair the sensitivity of both new physics searches and precision measurements at large hadron collider (LHC) experiments. We propose a novel algorithm, Puma , for modeling pile-up with the help of deep neural networks based on sparse transformers. These attention mechanisms were developed for natural language processing but have become popular in other applications. In a realistic detector simulation, our method outperforms classical benchmark algorithms for pile-up mitigation in key observables. It provides a perspective for mitigating the effects of pile-up in the high luminosity era of the LHC, where up to 200 proton-proton collisions are expected to occur simultaneously.

47 OTHER INSTRUMENTATION↗

W2VPCA: A Machine Learning Method for Measuring Attitudes With Natural Language

Company strategy influences many decisions in freight transportation. Behavioral models of company decision-making therefore could benefit from including strategy variables. However, strategy is difficult to observe and quantify. Attitudinal surveys of company executives can be used to collect measurements of latent strategy to use in quantitative models. However, surveys are costly and burdensome. Text mining methods to collect measurements overcome these issues somewhat, but typically require manual intervention and ignore the context of words, which can be problematic. This study introduces a new machine learning method to generate strategy measurement data from existing big text data. The new method, called W2VPCA, combines Natural Language Processing and Principal Components Analysis. W2VPCA produces measurement data that serve as quantitative indicators of latent strategy in behavioral models. W2VPCA is unsupervised, data-driven, and uses information on word context. We apply W2VPCA to generate measurements of latent strategies using readily available, large-scale text data: annual company reports. The empirical measurements are used successfully to associate two latent strategies, one focusing on distribution and the other on products, with truck fleet and distribution center outsourcing decisions. The main empirical outcome is that the W2VPCA measurements outperform Bag-of-Words measurements in a psychometric analysis of latent firm strategies. While this study focuses on freight behavioral models, W2VPCA may also have applications in behavioral modeling in other domains.

97 MATHEMATICS AND COMPUTING↗

A Fine-grained Asynchronous Bulk Synchronous parallelism model for PGAS applications

The Partitioned Global Address Space (PGAS) model is well suited for executing irregular applications on cluster-based systems, due to its efficient support for short, one-sided messages. Separately, the actor model has been gaining popularity as a productive asynchronous message-passing approach for distributed objects in enterprise and cloud computing platforms, typically implemented in languages such as Erlang, Scala or Rust. To the best of our knowledge, there has been no past work on using the actor model to deliver both productivity and scalability to irregular PGAS applications with large number of small messages. In this paper, we introduce a new programming system for PGAS applications, in which point-to-point remote operations can be expressed as fine-grained asynchronous actor messages. In our approach, the programmer does not need to worry about programming complexities related to message aggregation and termination detection. Our approach can be viewed as extending the classical Bulk Synchronous Parallelism model with fine-grained asynchronous communications within a phase or superstep. Here, we believe that our approach offers a desirable point in the productivity-performance space for PGAS applications, with more scalable performance and higher productivity relative to past approaches. Specifically, for seven irregular mini-applications from the Bale Kernels and three graph kernels executed using 2048 cores in the NERSC Cori system, our approach shows geometric mean performance improvements of ≥ 20X relative to standard PGAS versions (UPC and OpenSHMEM) while maintaining comparable productivity to those versions.

97 MATHEMATICS AND COMPUTING↗

A large-scale, agent-based simulation of metropolitan freight movements with passenger and freight market interactions

This study summarizes the first stage in the implementation of an agent-based freight modeling system that has a global representation of agents and detailed modeling of a large-scale transportation network. The model is used to evaluate the transportation and energy impacts of goods movement across urban and national scales. The framework is implemented within POLARIS, a C++-based Planning and Operations Language for Agent-based Regional Integrated Simulation, which consists of an activity-based modeling (ABM) and dynamic traffic assignment (DTA) system that has robust features for passenger travel. This platform provides a tool to model interactions among consumers, producers, and the transportation system. The main objective of this initial implementation is to implement a freight model within POLARIS following an agent-based paradigm with behavioral and simulation methods. This paper presents the initial framework and illustrates the application of the model. Building upon earlier works, a parcel location assignment algorithm for business establishments in the population is documented, along with a method for estimating establishment production and consumption volumes. In addition to population generation, other features of the model include push-pull supply chains, multimodal path choice, choice of transportation logistics node, and dynamic traffic assignment. A module with e-commerce supply and demand was also developed to analyze the effects of e-commerce delivery on last-mile energy use and congestion.

agent-based freight↗

Experimental Applications of Automatic Test Markup Language (ATML)

The authors describe challenging use-cases for Automatic Test Markup Language (ATML), and evaluate solutions. The first case uses ATML Test Results to deliver active features to support test procedure development and test flow, and bridging mixed software development environments. The second case examines adding attributes to Systems Modelling Language (SysML) to create a linkage for deriving information from a model to fill in an ATML document set. Both cases are outside the original concept of operations for ATML but are typical when integrating large heterogeneous systems with modular contributions from multiple disciplines.

Lansdowne, Chatwin A.↗