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CALMS: CONTEXT-AWARE LANGUAGE MODEL FOR SCIENCE

Context-Aware Language Model for Science (CALMS) is designed to assist scientists with instrument operations and complex experimentation. CALMS consists of a large-language model (LLM) augmented with context and tool use abilities. With the ability to retrieve relevant information from facility documentation, CALMS can answer simple questions on scientific capabilities and other operational procedures. With the ability to interface with software tools and experimental hardware, CALMS can operate scientific instruments in a conversational manner.

CHERUKARA, MATTHEW↗

Coreii - Scout

COREII Scout employs React, Vite, TypeScript, Tailwind, and Daisy UI for its graphical user interface (GUI), offering both dark and light modes. The code is modular, with components and reusable wrappers to enhance efficiency. The primary goal of COREII Scout is to aid analysts in collecting and analyzing various sources related to cyber attacks, utilizing models to automate the report writing process. It uses Named Entity Recognition (NER), a type of Natural Language Processing (NLP), to extract key entities from each source. Analysts review and classify these entities using the COREII Attack Chain Estimator (ACE), adding their comments. Ultimately, a Large Language Model (LLM) generates a detailed report with user guidance. This setup ensures a streamlined and effective approach to cyber attack analysis and reporting.

Pluth, Adam [Idaho National Laboratory (INL), Idah↗

FAIR to WISE (F2W) v1.0.0

FAIR to WISE (F2W) is an iterative, large-language model (LLM) driven pipeline that turns unstructured research PDFs into structured, queryable knowledge graphs (KGs). Core features include schema-driven extraction to a LinkML model; full provenance capture; ontology-grounded enrichment (e.g., chemical validation and ChEBI lookup); graph construction to JSON-LD with stable IDs; and KG-RAG question answering with evidence-aware retrieval. The system is engineered for reproducibility and accessibility (open-source Ollama models, temperature=0, NVTX/Nsight profiling) with robust QA (relation verification, deduplication, and deterministic outputs). Primary uses are literature-to-KG automation, knowledge-grounded Q&A, and experimental steering support. We demonstrate the approach in organic photovoltaics, where the pipeline ingests papers, builds a domain KG, and evaluates answers against expert competency questions to guide experimental planning and interpretation. Compared with off-the-shelf LLMs and ad-hoc NLP tools, F2W addresses ontology gaps and reduces hallucination risk by grounding responses in extracted evidence and enforcing schema constraints; it also offers deterministic, provenance-linked outputs and open, cost-aware deployment. Evidence-aware ranking further improves answer quality over pure vector search.

Abramov, David [Lawrence Berkeley National Laborat↗

TalkPipe Writing Assistant

SAND2025-14316O TalkPipe Writing Assistant offers AI assistance, providing help on a point-by-point basis. Authors can start with their own ideas—whether bullet points, partial paragraphs, or phrases—and specify the document type, desired tone, audience, and any other relevant context. As they write, the assistant provides tailored suggestions for each paragraph. They can request high-level concepts, draft a paragraph, or proofread existing text. The large language model (LLM) considers both preceding and following paragraphs to ensure coherence and flow. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Bauer, Travis [Sandia National Lab. (SNL-CA), Live↗

MADA: Multi-Agent Design Assistant

MADA (Multi-Agent Design Assistant) is a Large Language Model (LLM) powered multi-agent framework that coordinates specialized agents for complex design workflows. The system was designed for HPC workflows with the following agents in mind: 1) A Job Management Agent (JMA) launches and manages ensemble simulations on HPC systems, 2) a Geometry Agent (GA) generates meshes, and 3) an Inverse Design Agent (IDA) proposes new designs informed by simulation outcomes. Our framework reduces cumbersome manual workflow setup, and enables automated design exploration at scale. However, the software also enables users to rapidly create new multi-agent systems. Simply define new agents in a configuration file, giving each their own set of tools (via MCP), and then chat and prompt your new multi-agent system. Is

Gunnarson, BrianS [Lawrence Livermore National Lab↗

Monte Carlo Thought Search: Large Language Model Querying for Complex Scientific Reasoning in Catalyst Design

Discovering novel catalysts requires complex reasoning involving multiple chemical properties and resultant trade-offs, leading to a combinatorial growth in the search space. While large language models (LLM) have demonstrated novel capabilities for chemistry through complex instruction following capabilities and high quality reasoning, a goal-driven combinatorial search using LLMs has not been explored in detail. In this work, we present a Monte Carlo Tree Search-based approach that improves beyond state-of-the-art chain-of-thought prompting variants to augment scientific reasoning. We introduce two new reasoning datasets: 1) a curation of computational chemistry simulations, and 2) diverse questions written by catalysis researchers for reasoning about novel chemical conversion processes. We improve over the best baseline by 25.8\% and find that our approach can augment scientist's reasoning and discovery process with novel insights.\footnote{All resources will be publicly available upon publication.

Sprueill, Henry W.↗

Evaluating the Effectiveness of Retrieval-Augmented Large Language Models in Scientific Document Reasoning

Despite the dramatic progress in Large Language Model (LLM) development, LLMs often provide seemingly plausible but not factual information, often referred as hallucinations. Retrieval-augmented LLMs provide a non-parametric approach to solve these issues by retrieving relevant information from external data sources and augment the training process. These models helps to trace evidence from an externally provided knowledge base allowing the model predictions to be better interpreted and verified. In this work, we critically evaluate these models in their ability to perform in scientific document reasoning tasks. To this end, we tuned multiple such model variants with science-focused instructions and evaluated them on a scientific document reasoning benchmark for the usefulness of the retrieved document passages. Our findings suggest that models justify predictions in science tasks with fabricated evidence and leveraging scientific corpus as pretraining data does not alleviate the risk of evidence fabrication.

• Artificial intelligence (AI) / machine learning ↗

PRIMED for the Future: Purposing Raw Intake for Machine Learning-Enabled Detection (Final Report)

The COVID-19 pandemic demonstrated how a novel, elusive, and diffuse biological threat can engender uncertainty and misinformation, and it underscored the need for flexible analytical modalities agnostic to the identity of biological material. Yet even before the pandemic, recognition of the limitations of the current, list-based approach, which focuses on known pathogens and biotoxins, and of the importance of agent-agnostic biodetection was growing within the biosecurity community. In a 2018 report on “Biodefense in the Age of Synthetic Biology,” for example, the National Academy of Sciences stated that “an overreliance on the Select Agent List is a systematic weakness affecting many aspects of the United States’ current biodefense mitigation capability”. More recently, a group of biodefense researchers proposed the identification and adoption of “bioagent-agnostic signatures (BASs)” as a way of detecting and characterizing not only existing agents but also novel ones, an approach they believe will “enable a more flexible and resilient biodefense posture”. Indeed, the future of biodetection requires us to begin developing novel analytics that can identify anomalies and/or characteristics that indicate a potential threat, whether known or unknown, without looking for a specific signature that has been identified previously. To assess potential threats more rapidly, it is critical to develop agnostic artificial intelligence (AI)/machine learning (ML) systems that can be employed for real-time assessment of the nature and source of a perturbation. Such systems should be multi scale and multi-dimensional, integrating sensor data from a range of biological, chemical, and physical application spaces. Emerging deep learning (DL) models demonstrate exceptional promise for identification of discriminatory features within multi-dimensional datasets. DL models have the capacity to recognize and encode highly complex patterns in a wide range of input data modalities, including images, text, and biological/chemical/physical spectra. As such, they can execute a wide range of assessments and determinations that have traditionally required a human operator. The promise of advances in DL is apparent in the realm of human health and medicine. DL models have been validated for evaluating a variety of clinical threats to human health in a range of contexts, including infection and cancer, and they demonstrated improved performance in predicting stroke relative to human neurologists in some categories of data. Continuously evolving advances in AI/ML are expected to support more efficient evaluation of raw sequence, spectroscopy, and spectrometry data. For instance, recent advances and deployment of large language models (LLM) such as Generative Pre training Transformer (GPT) and Bidirectional Encoder Representations from Transformers (BERT) have already motivated application of these models for biological function prediction. As frameworks such as LLMs become larger and more complex in their representations, their capacity to serve as pre-trained models that can be fine-tuned for biological/biodetection purposes will similarly be amplified. While existing and emerging AI/ML have found broad applicability and use cases in the clinical sciences, development for environmental evaluation and biodetection has been limited. Functionalizing such capabilities for this purpose requires an understanding of the existing technical landscape and how the respective tools and algorithms are currently being employed. This landscape awareness then allows an assessment of the current practical capabilities of existing models and the anticipated requirements and development efforts that will be needed to adapt available algorithms for biodetection applications relevant to DHS. Leveraging expertise in biodetection, ML, and operational biodetection, the effort described in this report is comprised of a systematic landscape assessment (Subtask 2.1), comparative evaluation (Subtask 2.2), and formulation of a value proposition (Subtask 2.3) for the prospect of ML-enabled, agnostic biodetection from raw, or minimally-processed, datasets.

59 BASIC BIOLOGICAL SCIENCES↗

Assurance of Reasoning Enabled Systems (ARES)

ARES was in part motivated by the determination of President’s Council of Advisors on Science and Technology (PCAST) on May 13th, 2023 that published a set of inquiries: In an era in which convincing images, audio, and text can be generated with ease on a massive scale, how can we ensure reliable access to verifiable, trustworthy information? How can we be certain that a particular piece of media is genuinely from the claimed source? What technologies, policies, and infrastructure can be developed to detect and counter AI-generated disinformation? In an effort to automatically analyze and patch/optimize code the work in this report describes various neural Machine Learning (ML) analysis engine implementations to assist in situations where source code is deficient or completely lacking to decompile (lift) binary code to ’C’. The goal is to gradually reduce human intervention. To this end, two Large Language Model (LLM) variants (Code LLama 2, LLama 3.1 and Starcoder1, Starcoder 2) where finetuned with ’before/after’ code pairs on the OpenBLAS library. LLama trained on the lowering process, Starcoder trained on the lifting process with National Security Agency’s (NSA) open-source Ghidra decompiler assist. The inferencing test results indicate correctness for only very short sequences for Starcoder 2. Moving forward, the experiments conclude with a set of recommendations of required resources and technologies

97 MATHEMATICS AND COMPUTING↗

Automating the Analysis of Large Language Models Responses through Zero-Shot Question Answering

Recent advancements in Large Language Models (LLMs) have shown significant potential in various applications, yet their evaluation, particularly in zero-shot question answering scenarios, remains a challenging task. In this study, our objective was to explore precision metrics for Large Language Models (LLM) and design and implement a software pipeline to automatically evaluate LLMs' outputs under zero-shot question answering. Zero-shot question answering involves a model providing answers to questions about topics it hasn't seen during training. It leverages the principles of zero-shot learning by relying on semantic understanding and generalization from related knowledge. The data used was metadata from medical databases on congenital heart disease. We explored eleven LLM metrics and selected three for our evaluation: BLEU, BERTScore, and MoverScore. BLEU calculates a score based on the overlap of n-grams (contiguous sequences of n items, typically words) between the machine-generated translation and the reference translations. Higher BLEU scores indicate better correspondence between the machine-generated and human-generated translations. BERTScore is a metric used to evaluate the quality of machine-generated text by measuring the similarity of token embeddings produced by BERT (Bidirectional Encoder Representations from Transformers) between the generated text and reference text. MoverScore is a metric that quantifies the dissimilarity between the distributions of word embeddings from machine-generated text and reference text, emphasizing semantic similarity over exact token overlap. We also introduced HBKI, a composite metric summarizing these approaches. We tested five models —GPT-3, Llama-2, Gemini 1.5 Pro, Solar 10.7B, and Mixtral-8x7b. Our software pipeline, designed and implemented using Object-Oriented Programming principles, allows users to customize the selection and extraction of features for topics of interest in their own research. Our results show that MoverScore delivered the most precise evaluation of the LLM's outputs, while Mixtral-8x7b achieved the best overall performance in extracting metadata from the databases.

97 MATHEMATICS AND COMPUTING↗

Solar and Battery Storage Permitting and Siting Requirements - Solar Prize Round 7 (CRADA Final Report)

The purpose of this project is to identify local zoning ordinances, state permitting requirements, federal regulatory bottlenecks throughout the development process, and the potential to use Large Language Models (LLM) and aggregate permitting and interconnection data for commercial and industrial (C&I), community, and utility-scale solar photovoltaic (PV) and battery storage projects.

14 SOLAR ENERGY↗

Mini Report: LLMs on Code Translation

The goal of this mini report is to give opinions on the current state of the art in large language model (LLM) assisted code translation, which aims to replicate the behavior of a program written in one programming language to another. The first section provides our overall sense of literature and suggested directions of research, and the second section summarizes a few of the most relevant papers in greater depth.

97 MATHEMATICS AND COMPUTING↗

Exploring Large Language Model Agents in Cybersecurity: A Literature Review with Experiments

The accelerated development and integration of large language model (LLM) agents have led researchers and developers to explore their effectiveness in cybersecurity, specifically with penetration testing (pentesting). Recent research efforts have attempted to use LLM agents to automate the process of pentesting because of the cost and time requirements that are required to perform a manual review. However, not all of the tools perform as expected. This paper reviews some of the newest and most popular autonomous pentesting frameworks, highlighting the capabilities and limitations of each one with the goal of providing the components needed to successfully and effectively build an autonomous pentesting agent in the future.

97 MATHEMATICS AND COMPUTING↗

Finch: Toxicity Dose Response Curve Prediction of Chemical Compounds and Mixtures

A paradigm shift in chemical risk assessment is emphasizing mixture testing over single compound analysis, eliminating animal testing, and adopting advanced modeling approaches to understand mixture activity profiles. However, existing computational models largely focus on single chemicals, with few effective solutions for modeling complex mixtures that account for synergistic or antagonistic effects and multiple Modes of Action (MoA). Conventional methods like concentration addition (CA) and independent action (IA) are insufficient for this task as they are designed for simplistic interactions and struggle to account for the dynamic and multifaceted nature of chemical mixtures, such as overlapping MoA and non-linear interactions. Finch offers a novel approach utilizing deep learning (DL) embeddings and multi-task quantitative structure-activity relationship (QSAR) models to improve chemical exposure prediction. By leveraging molecular descriptors, physiochemical properties, and large language model (LLM) embeddings from SMILES inputs, Finch preserves critical information in a latent space thereby enhancing predictive accuracy. The multi-task learning aspect of Finch is highly advantageous, as it simultaneously optimizes multiple loss functions, leveraging all available data across tasks to develop generalized representations that effectively capture complex ingredient interactions within mixtures.

59 BASIC BIOLOGICAL SCIENCES↗

Large Language Model for Validation, Optical Calibration, and Learning (VOCAL) Distributed Temperature Sensing Interface

Distributed temperature sensing (DTS) using fiber optic sensors (FOS) offers a promising method for temperature measurements in advanced reactors, such as sodium fast reactors and molten salt cooled reactors. To support the calibration and validation of DTS measurements, Argonne National Laboratory developed the Validation, Optical Calibration, and Learning (VOCAL) software package. This report describes the integration of a local large language model (LLM) with a retrieval-augmented generation (RAG) system into the VOCAL interface to serve as an interactive user assistant. The LLM framework enhances the VOCAL platform’s accessibility to users by explaining interface components, clarifying inputs and outputs, and answering user queries dynamically in real-time. The accuracy of the LLM assistant performance was evaluated with 20 queries regarding the interface and its parameters using experimental data from the Thermal Hydraulic Experimental Test Article (THETA) facility. Results demonstrate that the LLM achieved a 95% accuracy rate, with a BERTScore of 0.8816 and SBERT value of 0.7417. Furthermore, validation of the RAG system within the LLM framework showed optimal accuracy with k-values between 1 and 2 using the k-refinement convergence test. The prompt perturbation analysis demonstrated good initial consistency for the RAG system, exhibiting the highest accuracy under punctuation variations and the greatest sensitivity under query reordering. Notably, the model’s errors were limited to data retrieval failures rather than factual hallucinations, reinforcing its baseline reliability. The integration of LLM provides a highly accurate, userfriendly enhancement to the VOCAL platform without disrupting its core computational capabilities for FOS calibration and validation.

Hong, Evan↗

Harnessing Artificial Intelligence for Medical Diagnosis and Treatment During Space Exploration Missions

From May 8th to June 9th, 2023, I had the opportunity to participate in an experiential learning experience at Johnson Space Center in Houston, TX with Exploration Medical Capability (ExMC), an element of the NASA Human Research Program. During this research experience, I was not only able to work on the above titled research project, but also gain an immense exposure to the field of aerospace medicine, make numerous connections within the field, tour NASA facilities, as well as travel to the Aerospace Medical Association Annual Conference (AsMA) in New Orleans. To briefly introduce my project, it is well understood that the medical capabilities available to crew medical officers (CMOs) on the International Space Station will be different than the capabilities available and needed during deep space exploration missions to the Moon, Mars, and beyond. Ground support is particularly limited due to distance, communication delays (or lack of communication), and lack of resupply. Therefore, to support medical care by CMOs on these missions, robust clinical decision support systems (CDSSs) must be designed. The recent publication and public launch of generative artificial intelligence (AI) tools based upon large language models (LLM) such as ChatGPT provides the opportunity to create a smart assistant for onboard triage, diagnosis, and treatment of medical conditions. Ultimately, the overall purpose of the project was to research what AI tools currently exist or are in development, and to see how they might be implemented onboard during exploration class spaceflights of the future. The ExMC element is actively developing several tools to be used in preparation for and during deep space exploration missions. One of those tools, known as IMPACT, is a probabilistic risk assessment model which can be used to propose a desired medical system (based on mass and volume) and suggest the clinical outcomes likely to occur for a design reference mission (DRM). The group recently presented the IMPACT model and a DRM of interest titled “Modified Long Duration Lunar Orbital and Lunar Surface” (mLDLOLS) at the recent AsMA conference. The mLDLOLS mock mission is a 9 month and 6-day deep space exploration mission consisting of time in Moon’s orbit (3 months on the Gateway space station), on the lunar surface (3 months within habitat), and another 3 months on Gateway before return to Earth. For this DRM, IMPACT ultimately outlined a preferred medical system that was then associated with medical conditions considered to be most likely based on frequency, most likely to cause astronaut task time loss (TTL), most likely to cause return to definitive care (RTDC), and most likely cause loss of crew life (LOCL). IMPACT also highlighted the medical capabilities/skills that would be required to care for those medical conditions, such as performing a history of present illness or musculoskeletal exam with ultrasound. The primary objective of the project was to perform a survey of the AI tools and systems applicable to the conditions outlined for the proposed mLDLOLS mission. Using PubMed (including most relevant MeSH terms) and Google Scholar, we then created a robust annotated bibliography organized by condition. The 56-page and over 500 reference annotated bibliography was subsequently used to create a review outline that would become the basis for drafting of a future publication. For the review outline, we took those medical conditions researched within the annotated bibliography (condition-based approach) and deployed a systems-based approach, combining those medical conditions and related tools into ten categories. These categories included general/all-purpose CDSSs, tools to diagnose or manage respiratory, dermatologic, neurologic, auditory and vestibular, ophthalmic, musculoskeletal, infection-associated, and gynecologic conditions, as well as tools that could be deployed in the setting of trauma/emergency. With the completion of the 30-page outline, we then began drafting the review paper. To conclude the research experience, I presented the findings from our survey to the ExMC Clinical and Science team. With these objectives, I ultimately learned about the number of AI tools that exist today to assist medical professionals with the triage, diagnosis, and management of several medical conditions. These tools can span from chatbot assistants to help triage knee pain to vision transformer models that can identify ophthalmic conditions based on ocular surface images captured with a cell phone. We also highlighted the current gaps that exist in the literature alongside the advancements that are needed to make the desired CDSS for deep space exploration missions. With this experience, I certainly confirmed an existing career goal and identified several additional skills needed to become an aerospace medical doctor including knowledge of critical care in an extreme medicine setting, aerospace engineering and human integration systems, artificial intelligence, machine learning, and risk models. I also identified numerous transferable skills for this career goal including the basic knowledge of medicine (MD), deployment of the scientific method for critical thought about new scientific questions (PhD), review of published literature, including creating an annotated bibliography (PhD), as well as detailed scientific writing (PhD). The results of my research will likely guide the design of an all-encompassing onboard medical assistant for use during deep space exploration missions of the future. I plan on sharing the outcomes from this experience with my peers at a student seminar in the Fall semester on August 30th. During the seminar, I will detail the project, my experience at NASA and AsMA, as well as offer best practice guidelines for students entertaining similar experiences or careers. In conclusion, I would like to thank the WVU School of Medicine, Research and Graduate Education office, as well as NASA ExMC for the unwavering support of this life-changing experience.

Ryan A. Lacinski↗

Harnessing Artificial Intelligence for Medical Diagnosis and Treatment During Space Exploration Missions

BACKGROUND The medical capabilities necessary for long-duration exploration missions (LDEMs) will differ tremendously from those currently available to crew medical officers (CMOs) on the International Space Station (ISS). Ground support will be more challenging due to distance-related communication delays and data transmission, and resource utilization must be optimized given limited ability for resupply. Clinical decision support systems (CDSSs) can help mitigate these limitations. The recent launch of generative artificial intelligence (AI) tools based upon large language models (LLM) support the creation of a smart assistant for onboard triage, diagnosis, and guided treatment of medical conditions during these missions. The Informing Mission Planning via Analysis of Complex Tradespaces (IMPACT) tool can help predict which clinical problems and outcomes are likely to occur for a design reference mission (DRM) and assist Medical Operations and systems engineering teams in creating a medical system that may optimally mitigate the predicted risks. The purpose of this study was to identify AI tools currently available or in development for the assistive diagnosis and care of medical conditions predicted for an extended duration Lunar mission. METHODS The 119 medical conditions currently built into the IMPACT suite were categorized into systems, and these diagnoses were used as keywords for our literature search. Using PubMed and Google Scholar, we performed a literature survey of AI tools applicable to these conditions. Article inclusion criteria included publication between the years 2017-2023, as the sentinel paper discussing the “selective attention” driving ChatGPT and other generative transformer models was published in June 2017. Where applicable, we reviewed only the top 1000 research articles (based on relevance) for each of the keywords/phrases. AI tools whose training sets were exclusive to a pediatric patient population were excluded. We also excluded any medical diagnostic tools (such as CT, MRI, mass spectrometry) or procedures (such as endoscopy, surgery) that are unlikely to be available during LDEMs due to mass and volume constraints, CMO knowledge, skills, and abilities, and/or inherent procedural risks. RESULTS Our survey highlighted several AI-driven tools for the triage, diagnosis, and management of those medical conditions highlighted by IMPACT. Selected publications for each medical condition were then screened for inclusion within ten systems-based categories including: general diagnostic tools (25), tools to diagnose and manage respiratory (40), dermatologic (34), neurologic (28), auditory and vestibular (30), ophthalmic (34), musculoskeletal (104), infection-associated (92), and gynecologic (19) conditions, as well as tools that could be deployed in the setting of trauma and emergency (34). CONCLUSIONS Numerous AI-driven tools were highlighted within this literature survey, ranging from chatbot assistants that triage knee pain to vision transformer models for diagnosis of ophthalmic conditions using ocular surface images captured with a mobile phone. Remaining challenges include optimizing connectivity and integration of existing and developing systems into the vehicles or habitats. Notably, findings from this survey could help guide the initial design of an all-encompassing, onboard medical AI assistant for use during future LDEMs.

R A Lacinski↗

Analyzing EOSDIS Dataset Research Outputs using Knowledge Graphs and Large Language Models

Datasets, unlike publications, can be updated over time, with each new version receiving a DOI but not always being linked to previous ones. This complicates tracking citations across a dataset’s lifecycle. We address this by integrating dataset versions and citations into a knowledge graph (KG), which helps trace dataset citations and analyze dataset usage in applied research. To categorize publications from various journals, we fine-tuned NASA IMPACT INDUS Large Language Model (LLM) on a labeled publication set, assigning publications to one of twenty applied research areas. By linking datasets to these research areas, we improved dataset searchability and discovery through these domains.

open-source↗