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At least 37 records · Page 2

Expert evaluation of LLM world models: A high-T c superconductivity case study

Large Language Models (LLMs) show great promise as a powerful tool for scientific literature exploration. However, their effectiveness in providing scientifically accurate and comprehensive answers to complex questions within specialized domains remains an active area of research. Using the field of high-temperature cuprates as an exemplar, we evaluate the ability of LLM systems to understand the literature at the level of an expert. We construct an expert-curated database of 1,726 scientific papers that covers the history of the field, and a set of 67 expert-formulated questions that probe deep understanding of the literature. We then evaluate six different LLM-based systems for answering these questions, including both commercially available closed models and a custom retrieval-augmented generation (RAG) system capable of retrieving images alongside text. Experts then evaluate the answers of these systems against a rubric that assesses balanced perspectives, factual comprehensiveness, succinctness, and evidentiary support. Among the six systems, two using RAG on curated literature outperformed existing closed models across key metrics, particularly in providing comprehensive and well-supported answers. We discuss promising aspects of LLM performances as well as critical short-comings of all the models. The set of expert-formulated questions and the rubric will be valuable for assessing expert level performance of LLM based reasoning systems.

36 MATERIALS SCIENCE

brag

Basic RAG-A python application for retrieval augmented generation (RAG).

Lui, Arthur

ARCS: Agentic Retrieval-Augmented Code Synthesis with Iterative Refinement

Agentic Retrieval-Augmented Code Synthesis with Iterative RefinementIn supercomputing, efficient and optimized code generation is essential to leverage high-performance systems effectively. We have developed Agentic Retrieval-Augmented Code Synthesis (ARCS), an advanced framework for accurate, robust, and efficient code generation, completion, and translation. ARCS integrates Retrieval-Augmented Generation (RAG) with Chain-of-Thought (CoT) reasoning to systematically break down and iteratively refine complex programming tasks. An agent-based RAG mechanism retrieves relevant code snippets, while real-time execution feedback drives the synthesis of candidate solutions. This process is formalized as a state-action search tree optimization, balancing code correctness with editing efficiency. Evaluations on the Geeks4Geeks and HumanEval benchmarks demonstrate that ARCS significantly outperforms traditional prompting methods in translation and generation quality. By enabling scalable and precise code synthesis, ARCS offers transformative potential for automating and optimizing code development in supercomputing applications, enhancing computational resource utilization

Bhattarai, Manish [Los Alamos National Labs]

Towards Unlocking Insights from Logbooks Using AI

Electronic logbooks contain valuable information about activities and events concerning their associated particle accelerator facilities. However, the highly technical nature of logbook entries can hinder their usability and automation. As natural language processing (NLP) continues advancing, it offers opportunities to address various challenges that logbooks present. This work explores jointly testing a tailored Retrieval Augmented Generation (RAG) model for enhancing the usability of particle accelerator logbooks at institutes like DESY, BESSY, Fermilab, BNL, SLAC, LBNL and CERN. The RAG model uses a corpus built on logbook contributions and aims to unlock insights from these logbooks by leveraging retrieval over facility datasets, including discussion about potential multimodal sources. Our goals are to increase the FAIR-ness (findability, accessibility, interoperability, and reusability) of logbooks by exploiting their information content to streamline everyday use, to enable macro-analysis for root cause analysis, and to facilitate problem-solving automation.

43 PARTICLE ACCELERATORS

Retrieval-Augmented Generation and LLM Agents for Biomimicry Design Solutions

We present BIDARA, a Bio-Inspired Design And Research Assistant, to address the complexity of biomimicry – the practice of designing modern-day engineering solutions inspired by biological phenomena. Large Language Models (LLMs) have been shown to act as sufficient general purpose task solvers, but they often hallucinate and fail in regimes that require domain-specific and up-to-date knowledge. We integrate Retrieval-Augmented Generation (RAG) and Reasoning-and-Action agents to aid LLMs in avoiding hallucination and utilizing updated knowledge during generation of biomimetic design solutions. We find that incorporating RAG increases the feasibility of the design solutions in both prompting and agent settings, and we use these findings to guide our ongoing work. To the extent of our knowledge, this is the first work that integrates and evaluates Retrieval-Augmented Generation within LLM-generated biomimetic design solutions.

biomimicry

Retrieval-Augmented Generation and LLM Agents for Biomimicry Design Solutions

We present BIDARA, a Bio-Inspired Design And Research Assistant, to address the complexity of biomimicry – the practice of designing modern-day engineering solutions inspired by biological phenomena. Large Language Models (LLMs) have been shown to act as sufficient general purpose task solvers, but they often hallucinate and fail in regimes that require domain-specific and up-to-date knowledge. We integrate Retrieval-Augmented Generation (RAG) and Reasoning-and-Action agents to aid LLMs in avoiding hallucination and utilizing updated knowledge during generation of biomimetic design solutions. We find that incorporating RAG increases the feasibility of the design solutions in both prompting and agent settings, and we use these findings to guide our ongoing work. To the extent of our knowledge, this is the first work that integrates and evaluates Retrieval-Augmented Generation within LLM-generated biomimetic design solutions.

biomimicry

Towards Unlocking Insights from Logbooks Using AI

Electronic logbooks contain valuable information about activities and events concerning their associated particle accelerator facilities. However, the highly technical nature of logbook entries can hinder their usability and automation. As natural language processing (NLP) continues advancing, it offers opportunities to address various challenges that logbooks present. This work explores jointly testing a tailored Retrieval Augmented Generation (RAG) model for enhancing the usability of particle accelerator logbooks at institutes like DESY, BESSY, Fermilab, BNL, SLAC, LBNL, and CERN. The RAG model uses a corpus built on logbook contributions and aims to unlock insights from these logbooks by leveraging retrieval over facility datasets, including discussion about potential multimodal sources. Our goals are to increase the FAIR-ness (findability, accessibility, interoperability, and reusability) of logbooks by exploiting their information content to streamline everyday use, enable macro-analysis for root cause analysis, and facilitate problem-solving automation.

43 PARTICLE ACCELERATORS

Generative large language models for predictive maintenance planning

Maintenance planning and the generation of necessary components for tasks can prove time-consuming and complex. Automating the creation of recurring or similar tasks by leveraging previous planning packages and data, while uncovering insights to automate planning package generation, presents an opportunity to conserve valuable time and resources. This work aims to harness the textual and probabilistic capabilities of large language models (LLMs) to automate the generation of planning packages. Utilizing diverse data sources ranging from raw data to handwritten text, both singular and collaborative LLMs are trained and tested. Results demonstrate their capability to generate essential planning package components, effectively replicating the statistical patterns in the data. This demonstrates the use of these tools inside a digital asset for automated planning. This work outlines a methodology for constructing datasets, a training suite, and evaluation methods for LLM-based textual and conversational planning tools utilized in an asset digital twin. Results indicate that the fine-tuned models generate estimated planning information within the statistical ranges observed in real maintenance data. The models achieve high accuracy (>90%) in document question-answering and instruction generation tasks. Furthermore, the conversational retrieval-augmented generation (RAG) assistant system achieves 100% document retrieval accuracy, while conversational information capture exceeds 98% across the majority of work-package assistant modules.

97 MATHEMATICS AND COMPUTING

ESAC (EQ-SANS Assisting Chatbot): Application of large language models and retrieval-augmented generation for enhanced user experience at EQ-SANS

Neutron scattering experiments have played vital roles in exploring materials properties in the past decades. While user interfaces have been improved over time, neutron scattering experiments still require specific knowledge or training by an expert due to the complexity of such advanced instrumentation and the limited number of experiments each person may perform each year. This paper introduces an innovative chatbot application that leverages Large Language Models(LLM) and Retrieval-Augmented Generation (RAG) technologies to significantly enhance the user experience at the EQ-SANS, a small-angle neutron scattering instrument at the Spallation Neutron Source of Oak Ridge National Laboratory. Through a user-centric design approach, the EQ-SANS Assisting Chatbot (ESAC) serves as an interactive reference for users, thereby facilitating the use of the instrument by visiting scientists. By bridging the gap between the users of EQ-SANS and the control systems required to perform their experiments, the ESAC sets a new standard for interactive learning and support for the scientific community using large-scale scientific facilities.

97 MATHEMATICS AND COMPUTING

GraphAide: Advanced Graph-Assisted Query and Reasoning System

Curating knowledge from multiple siloed sources that contain both structured and unstructured data is a major challenge in many real-world applications. Pattern matching and querying represent fundamental tasks in modern data analytics that leverage this curated knowledge. The development of such applications necessitates overcoming several research challenges, including data extraction, named entity recognition, data modeling, and designing query interfaces. Moreover, the explainability of these functionalities is critical for their broader adoption. The emergence of Large Language Models (LLMs) has accelerated the development lifecycle of new capabilities. Nonetheless, there is an ongoing need for domain-specific tools tailored to user activities. The creation of digital assistants has gained considerable traction in recent years, with LLMs offering a promising avenue to develop such assistants utilizing domain-specific knowledge and assumptions. In this context, we introduce an advanced query and reasoning system, GraphAide, which constructs a knowledge graph (KG) from diverse sources and allows to query and reason over the resulting KG. GraphAide harnesses both the KG and LLMs to rapidly develop domain-specific digital assistants. It integrates design patterns from retrieval augmented generation (RAG) and the semantic web to create an agentic LLM application. GraphAide underscores the potential for streamlined and efficient development of specialized digital assistants, thereby enhancing their applicability across various domains.

Purohit, Sumit [BATTELLE (PACIFIC NW LAB)] (ORCID:

From Rules to Reasoning: A Survey of Large Language Model-Based Approaches to Scientific Hypothesis and Idea Generation

Scientific hypothesis generation represents a fundamental challenge in contemporary research due to exponentially expanding literature volumes and increasing disciplinary specialization. Large language models (LLMs) have emerged as transformative tools for automated scientific discovery, moving beyond traditional rule-based and literature-mining approaches. Four paradigmatic approaches define current LLM-driven hypothesis generation: direct prompting and fine-tuning methods, knowledge-enhanced frameworks integrating retrieval-augmented generation (RAG), multi-agent collaborative systems simulating research teams, and reasoning-focused approaches implementing cognitive architectures. Domain-specific applications demonstrate statistical equivalence to human expert performance in social psychology, experimental validation in biomedical research, and near-expert quality in astronomy. Evaluation methodologies encompass human expert assessment, LLM-as-judge frameworks, and comprehensive benchmarking systems. Technical challenges include hallucination management, knowledge integration limitations, and balancing novelty with feasibility. Future directions emphasize hybrid neural-symbolic architectures and sophisticated human-AI collaboration models for responsible scientific discovery acceleration.

AI-driven discovery

LLaMP v0.1.0

Reducing hallucination of Large Language Models (LLMs) is imperative for use in the sciences, where reliability and reproducibility are crucial. However, LLMs inherently lack long-term memory, making it a nontrivial, ad hoc, and inevitably biased task to fine-tune them on domain-specific literature and data. LLaMP is a multimodal retrieval-augmented generation (RAG) framework of hierarchical reasoning and acting (ReAct) agents that can dynamically and recursively interact with Materials Project to ground large language models on high-fidelity materials informatics.

Riebesell, Janosh [Lawrence Berkeley National Labo

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

Lost in OCR Translation? Vision-Based Approaches to Robust Document Retrieval

Code for ‘Lost in OCR Translation?’: robust document retrieval under degradation. Compares OCR-based, vision-only, and hybrid pipelines; includes SambaNova LLaMA Vision OCR, Nougat, and ViDoRe baselines. Provides QA data generation, RAG evaluation, and metrics (Levenshtein, nDCG@k, Recall@k, EM/F1) with reproducible scripts. Includes dataset guides

Bhattarai, Manish [Los Alamos National Labs]

Atlas-UI-3

SAND2025-14754O Atlas-UI-3 is the third iteration of the LLM chat user interface called Atlas. The tool does not share code with previous versions. It supports chat with large language models (LLMs), connects to retrieval-augmented generation (RAG) servers, features a marketplace/store for model and content providers (MCP), and enables tool calling. 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.

Melander, Darryl [Sandia National Lab. (SNL-CA), L

An Open-source Llm Enhanced-tool Specialized In Helping Moose Related Problems And Tasks

MOOSEenger is an open-source, terminal-first chat application for the MOOSE ecosystem that couples specialized parsing of MOOSE documentation and “.i” input files with retrieval-augmented generation to deliver grounded answers about multiphysics modeling and workflows. It includes dedicated readers for MOOSE-style HTML and a pyhit-based parser that uses the MOOSE syntax tree to preserve block structure and attach retrieval metadata. A data-ingestion pipeline performs semantic chunking into atomic facts and stores them hierarchically in a local Chroma vector database that maintains parent–child relationships across documents; the system can ingest directories, individual files, and single-page web content, and it provides CRUD operations (insert, update, delete) to manage the corpus. At query time, relevant chunks are embedded, retrieved, and fused into the model context, with interactive features such as token streaming, persistent chat history, and dynamic RAG (retrieval triggered by user input or intermediate model output). Deployment is flexible: MOOSEenger runs with local Ollama models or remote Hugging Face/OpenAI backends—typically coordinating generation, lightweight tagging/summarization, and embeddings across three models—and it also supports a server mode and integration with the VS Code Continue interface.

Li, Mengnan [Idaho National Laboratory (INL), Idah

AstraAI v1

AstraAI is an open-source, structure-aware AI coding agent designed for large scientific and DOE-HPC codebases such as AMReX-based applications. Unlike general-purpose coding assistants, AstraAI combines retrieval-augmented generation (RAG) with compiler-level Abstract Syntax Tree (AST) analysis to perform precise, scope-constrained code modifications. It identifies exact function spans, enforces locality of edits, and maintains cross-file invariants, enabling deterministic and build-safe transformations in complex C++/GPU environments. AstraAI is intended for developers working on large, evolving HPC frameworks where correctness, reproducibility, and structural integrity are critical. Typical use cases include modifying physics kernels, updating GPU device lambdas, and performing multi-file refactors without breaking compilation or runtime semantics. Compared to conventional LLM-based coding agents - even those with repository access - AstraAI provides structural guarantees rather than free-form text patches. It minimizes unintended diffs, prevents scope drift, preserves formatting and build stability, and reduces structural hallucinations. By integrating compiler tooling directly into the generation loop, AstraAI transforms AI-assisted coding from probabilistic text editing into deterministic, structure-preserving program transformation suitable for mission-critical scientific software.

Natarajan, Mahesh [Lawrence Berkeley National Labo