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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Extraction and Analysis of Time Series Data from Building Automation Systems Using Large Language Models

Semantic schemas like Haystack 4, Brick and ASHRAE standard 223 enable the structured, standardized, and machine-readable representation of building data, facilitating interoperability, data integration, and advanced analytics. However, extracting information from these models requires specialized expertise in SPARQL and other programming languages, skills that are not commonly found among building professionals. Recent advancements in Large Language Models (LLMs), such as ChatGPT, enable the construction of queries using natural language, making it easier for individuals to interact with these systems in a manner that resembles everyday speech. However, these methods have not yet been tested on building semantic ontologies. This paper introduces a novel workflow and tool for enabling users to ask questions about a specific building's data, using natural language and receive answers automatically generated by GPT-4o. Our approach integrates semantic ontologies with advanced LLM capabilities to automate three critical steps: (1) generating SPARQL queries to retrieve time series references from ontological models, (2) extracting the corresponding time series data from the Building Automation System, and (3) performing computations and visualizations tailored to the user's query. The proposed method simplifies access to BAS data, allowing both domain experts and non-specialists to conduct sophisticated analyses without needing extensive technical knowledge of semantic web technologies. By demonstrating this pipeline, we facilitate more accessible and scalable data-driven decision-making in building operations and management.

Mulayim, Ozan Baris↗
DOE OSTI2023

Language-Theoretic Data Analysis to Support ICS Protocol Baselining

Critical infrastructure stakeholders need to baseline their systems to understand expected protocol communications. Baseline behaviors may vary based on operational context. Expected operations during a maintenance window, for example, may be different from normal operations. Furthermore, constructing system baselines for Industrial Control Systems (ICS) is difficult and time-consuming. ICS processes generate artifacts expressed across heterogeneous data sources such as network traffic and device logs. This paper explores the hypothesis that such ICS artifacts form a language in the language-theoretic sense. From a theoretical perspective, the variety of implementations of ICS protocols and constrained environment of OT networks provide a rich application domain for language-theoretic approaches. We present several use cases related to the practical construction of system baselines: grammars for data fusion, language dialects for device fingerprinting, and security automata for system baselining

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2025

LLM Benchmarking with LLaMA2: Evaluating Code Development Performance Across Multiple Programming Languages

The rapid evolution of large language models (LLMs) has opened new possibilities for automating various tasks in software development. This paper evaluates the capabilities of the LLaMA 2-70B model in automating these tasks for scientific applications written in commonly used programming languages. Using representative test problems, we assess the model's capacity to generate code, documentation, and unit tests, as well as its ability to translate existing code between commonly used programming languages. Our comprehensive analysis evaluates the compilation, runtime behavior, and correctness of the generated and translated code. Additionally, we assess the quality of automatically generated code, documentation, and unit tests. Here, our results indicate that while LLaMA 2-70B frequently generates syntactically correct and functional code for simpler numerical tasks, it encounters substantial difficulties with more complex, parallelized, or distributed computations, requiring considerable manual corrections. We identify key limitations and suggest areas for future improvements to better leverage AI-driven automation in scientific computing workflows.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Large language model evaluation for high–performance computing software development

We apply AI-assisted large language model (LLM) capabilities of GPT-3 targeting high-performance computing (HPC) kernels for (i) code generation, and (ii) auto-parallelization of serial code in C ++, Fortran, Python and Julia. Our scope includes the following fundamental numerical kernels: AXPY, GEMV, GEMM, SpMV, Jacobi Stencil, and CG, and language/programming models: (1) C++ (e.g., OpenMP [including offload], OpenACC, Kokkos, SyCL, CUDA, and HIP), (2) Fortran (e.g., OpenMP [including offload] and OpenACC), (3) Python (e.g., numpy, Numba, cuPy, and pyCUDA), and (4) Julia (e.g., Threads, CUDA.jl, AMDGPU.jl, and KernelAbstractions.jl). Kernel implementations are generated using GitHub Copilot capabilities powered by the GPT-based OpenAI Codex available in Visual Studio Code given simple + + prompt variants. To quantify and compare the generated results, we propose a proficiency metric around the initial 10 suggestions given for each prompt. For auto-parallelization, we use ChatGPT interactively giving simple prompts as in a dialogue with another human including simple “prompt engineering” follow ups. Results suggest that correct outputs for C++ correlate with the adoption and maturity of programming models. For example, OpenMP and CUDA score really high, whereas HIP is still lacking. We found that prompts from either a targeted language such as Fortran or the more general-purpose Python can benefit from adding language keywords, while Julia prompts perform acceptably well for its Threads and CUDA.jl programming models. Finally, we expect to provide an initial quantifiable point of reference for code generation in each programming model using a state-of-the-art LLM. Overall, understanding the convergence of LLMs, AI, and HPC is crucial due to its rapidly evolving nature and how it is redefining human-computer interactions.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

Automatic Determination of the Need for Intravenous Contrast in Musculoskeletal MRI Examinations Using IBM Watson’s Natural Language Processing Algorithm

Magnetic resonance imaging (MRI) protocoling can be time- and resource-intensive, and protocols can often be suboptimal dependent upon the expertise or preferences of the protocoling radiologist. Providing a best-practice recommendation for an MRI protocol has the potential to improve efficiency and decrease the likelihood of a suboptimal or erroneous study. The goal of this study was to develop and validate a machine learning-based natural language classifier that can automatically assign the use of intravenous contrast for musculoskeletal MRI protocols based upon the free-text clinical indication of the study, thereby improving efficiency of the protocoling radiologist and potentially decreasing errors. We utilized a deep learning-based natural language classification system from IBM Watson, a question-answering supercomputer that gained fame after challenging the best human players on Jeopardy! in 2011. We compared this solution to a series of traditional machine learning-based natural language processing techniques that utilize a term-document frequency matrix. Each classifier was trained with 1240 MRI protocols plus their respective clinical indications and validated with a test set of 280. Ground truth of contrast assignment was obtained from the clinical record. For evaluation of inter-reader agreement, a blinded second reader radiologist analyzed all cases and determined contrast assignment based on only the free-text clinical indication. In the test set, Watson demonstrated overall accuracy of 83.2% when compared to the original protocol. This was similar to the overall accuracy of 80.2% achieved by an ensemble of eight traditional machine learning algorithms based on a term-document matrix. When compared to the second reader’s contrast assignment, Watson achieved 88.6% agreement. When evaluating only the subset of cases where the original protocol and second reader were concordant (n = 251), agreement climbed further to 90.0%. The classifier was relatively robust to spelling and grammatical errors, which were frequent. Implementation of this automated MR contrast determination system as a clinical decision support tool may save considerable time and effort of the radiologist while potentially decreasing error rates, and require no change in order entry or workflow.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2026

Agentic framework for programmatic crystal structure generation using a fine-tuned worker–supervisor large language model

Platinum group metals (PGMs) underpin many catalytic technologies but face severe supply constraints, motivating the search for alternative materials and computational methods to accelerate discovery. While atomistic simulation tools such as Pymatgen and ASE have streamlined structure manipulation, they require detailed inputs, limiting accessibility for experimentalists and slowing early-stage exploration. Here, in this study, we present an AI-driven agentic framework that orchestrates worker–supervisor large language models (LLMs). The worker translates natural-language prompts of varying abstraction into valid crystallographic structures using a compact LLM fine-tuned with low-rank adaptation on a curated text–code–CIF dataset, emphasizing energy-efficient training. Benchmarking against the baseline CodeGen-350M-mono model shows that fine-tuning reduces hallucination rates from 100% to as low as 5% and improves structural match accuracy to up to 82% for fully specified inputs. Accuracy declines with decreasing prompt detail but remains nontrivial even when only stoichiometry and space group are provided, underscoring the LLM’s capacity for crystallographic inference. The supervisor Claude LLM evaluates the outputs and triggers iterative refinement through the worker’s built-in structure manipulation capabilities (e.g., supercell scaling, strain, vacancy, and substitution operations). We further demonstrate use cases for technologically relevant catalysts, including IrO 2 , pyrochlore Pb 2 Ir 2 O 7 , Ni 2 FeO 4 , and Ni 3 Mo, where the framework generates physically consistent structures that can be refined via geometry optimization. This work introduces a low-energy, language-driven pathway for integrating human and machine intelligence in materials design, paving the way for AI-assisted synthesis planning and high-throughput screening of complex oxides.

AI agent↗
DOE OSTI2021

Clinical Natural Language Processing for Radiation Oncology: A Review and Practical Primer

Natural language processing (NLP), which aims to convert human language into expressions that can be analyzed by computers, is one of the most rapidly developing and widely used technologies in the field of artificial intelligence. Natural language processing algorithms convert unstructured free text data into structured data that can be extracted and analyzed at scale. In medicine, this unlocking of the rich, expressive data within clinical free text in electronic medical records will help untap the full potential of big data for research and clinical purposes. Recent major NLP algorithmic advances have significantly improved the performance of these algorithms, leading to a surge in academic and industry interest in developing tools to automate information extraction and phenotyping from clinical texts. Thus, these technologies are poised to transform medical research and alter clinical practices in the future. Radiation oncology stands to benefit from NLP algorithms if they are appropriately developed and deployed, as they may enable advances such as automated inclusion of radiation therapy details into cancer registries, discovery of novel insights about cancer care, and improved patient data curation and presentation at the point of care. However, challenges remain before the full value of NLP is realized, such as the plethora of jargon specific to radiation oncology, nonstandard nomenclature, a lack of publicly available labeled data for model development, and interoperability limitations between radiation oncology data silos. Successful development and implementation of high quality and high value NLP models for radiation oncology will require close collaboration between computer scientists and the radiation oncology community. Here, we present a primer on artificial intelligence algorithms in general and NLP algorithms in particular; provide guidance on how to assess the performance of such algorithms; review prior research on NLP algorithms for oncology; and describe future avenues for NLP in radiation oncology research and clinics.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2023

KEBLM: Knowledge-Enhanced Biomedical Language Models

Pretrained language models (PLMs) have demonstrated strong performance on many natural language processing (NLP) tasks. Despite their great success, these PLMs are typically pretrained only on unstructured free texts without leveraging existing structured knowledge bases that are readily available for many domains, especially scientific domains. As a result, these PLMs may not achieve satisfactory performance on knowledge-intensive tasks such as biomedical NLP. Comprehending a complex biomedical document without domain-specific knowledge is challenging, even for humans. Inspired by this observation, we propose a general framework for incorporating various types of domain knowledge from multiple sources into biomedical PLMs. We encode domain knowledge using lightweight adapter modules, bottleneck feed-forward networks that are inserted into different locations of a backbone PLM. For each knowledge source of interest, we pretrain an adapter module to capture the knowledge in a self-supervised way. We design a wide range of self-supervised objectives to accommodate diverse types of knowledge, ranging from entity relations to description sentences. Once a set of pretrained adapters is available, we employ fusion layers to combine the knowledge encoded within these adapters for downstream tasks. Each fusion layer is a parameterized mixer of the available trained adapters that can identify and activate the most useful adapters for a given input. Our method diverges from prior work by including a knowledge consolidation phase, during which we teach the fusion layers to effectively combine knowledge from both the original PLM and newly-acquired external knowledge using a large collection of unannotated texts. After the consolidation phase, the complete knowledge-enhanced model can be fine-tuned for any downstream task of interest to achieve optimal performance. Extensive experiments on many biomedical NLP datasets show that our proposed framework consistently improves the performance of the underlying PLMs on various downstream tasks such as natural language inference, question answering, and entity linking. These results demonstrate the benefits of using multiple sources of external knowledge to enhance PLMs and the effectiveness of the framework for incorporating knowledge into PLMs. Finally, while primarily focused on the biomedical domain in this work, our framework is highly adaptable and can be easily applied to other domains, such as the bioenergy sector.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2015

Specifying structural constraints of architectural patterns in the ARCHERY language

ARCHERY is an architectural description language for modelling and reasoning about distributed, heterogeneous and dynamically reconfigurable systems in terms of architectural patterns. The language supports the specification of architectures and their reconfiguration. This paper introduces a language extension for precisely describing the structural design decisions that pattern instances must respect in their (re)configurations. The extension is a propositional modal logic with recursion and nominals referencing components, i.e., a hybrid µ-calculus. Its expressiveness allows specifying safety and liveness constraints, as well as paths and cycles over structures. Refinements of classic architectural patterns are specified.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

MetaText: Compositional Generalization in Deep Language Models

Compositional generalization, the ability to infer and reason using novel combinations of previously encountered entities and structures, is a trait of great utility across a variety of deep learning tasks; it implies a certain ability to reason using consistent and therefore interpretable rules, to understand the constituent parts of its input at multiple levels of granularity, to be robust to spurious differences between semantically equivalent inputs, and more. We seek to understand the degree to which existing natural language models achieve or fall short of compositional generalization across a variety of tasks, whether there are distinct types of compositional generalization in practice, and to identify avenues of intervention through which we can improve models’ compositional generalization ability. After exploring these questions using an array of models, tasks, and potential interventions we see that large, pretrained language models have encountered sufficient training data to account for a variety of fine-grained compositional behavior but still struggle to reason at the level of phrases or larger language structures. Non-intrusive, data-based interventions in the form of augmenting individual sequences with compressed versions of themselves or deriving new examples from induced grammars prove insufficient to encourage greater levels of compositional reasoning, indicating that future work might benefit most from focusing on changes to a model’s inductive bias at the architectural or loss level, or by integrating compositionality-boosting data interventions into the large-scale pretraining process itself.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Large Language Models (LLMs) for Energy Systems Research

The integration of Large Language Models (LLMs) in energy systems research promises transformative results, as demonstrated in this work, particularly in the realms of information retrieval and legal document analysis. We have developed a chat-based interface, specifically designed to query an extensive corpus of technical reports from the National Renewable Energy Laboratory (NREL). This interface capitalizes on the natural language processing capabilities of LLMs, providing future consumers of NREL research with a user-friendly platform to access and extract valuable information from technical documents, thus enhancing the dissemination of research to the public. In addition to information retrieval, we have employed LLMs to extract renewable energy siting ordinances from a variety of legal documents, a task traditionally driven by significant human labor. This automated extraction not only supports the ongoing development of the high-impact NREL siting ordinance database but also ensures the database's accuracy and comprehensiveness. Crucially, we have augmented the performance of LLMs through the integration of a decision tree framework, resulting in a substantial improvement in extraction accuracy. Comparative analysis with manual efforts has shown that this approach not only rivals but also significantly surpasses human accuracy, heralding increased reliability in legal document analysis for energy systems research. To democratize access to these advancements and foster collaborative research, we introduce the "Energy Language Model" (ELM), an open-source software package. ELM encapsulates the methodologies and tools developed in this work, providing researchers and practitioners with a robust toolkit to conduct similar analyses within their respective domains. Through these contributions, this work underscores the immense potential of LLMs in revolutionizing energy systems research, improving accuracy, efficiency, and accessibility in the field.

automation↗
DOE OSTI2018

Recurrent Neural Network Language Models for Open Vocabulary Event-Level Cyber Anomaly Detection

Automated analysis methods are crucial aids for monitoring and defending a network to protect the sensitive or confidential data it hosts. This work introduces a flexible, powerful, and unsupervised approach to detecting anomalous behavior in computer and network logs; one that largely eliminates domain-dependent feature engineering employed by existing methods. By treating system logs as threads of interleaved ``sentences'' (event log lines) to train online unsupervised neural network language models, our approach provides an adaptive model of normal network behavior. We compare the effectiveness of both standard and bidirectional recurrent neural network language models at detecting malicious activity within network log data. Extending these models, we introduce a tiered recurrent architecture, which provides context by modeling sequences of users' actions over time. Compared to isolation forests and Principal Components Analysis (PCA), two popular anomaly detection algorithms, we observe superior performance on the Los Alamos National Laboratory Cyber Security dataset. For log-line-level predictions, our best performing character-based model provides test set anomaly scores ranking red team events in the 98th percentile on average, and yields 0.97 area under the receiver operator characteristic curve, demonstrating the strong fine-grained anomaly detection performance of this approach on open vocabulary logging sources.

Cyber Analysis, Deep Learning, language analysis, ↗
DOE OSTI2023

Language model-accelerated deep symbolic optimization

Symbolic optimization methods have been used to solve varied challenging and relevant problems such as symbolic regression and neural architecture search. However, the current state of the art typically learns each problem from scratch and is unable to leverage pre-existing knowledge and datasets that are available for many applications. Here, inspired by the similarity between sequence representations learned in natural language processing and the formulation of symbolic optimization as a discrete sequence optimization problem, we propose language model-accelerated deep symbolic optimization (LA-DSO), a method that leverages language models to learn symbolic optimization solutions more efficiently. We demonstrate LA-DSO in two tasks: symbolic regression, which allows us to perform extensive experimentation due to its low computation requirements, and computational antibody optimization, which shows that our proposal accelerates learning in challenging real-world problems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

Retrospective Analysis of Clinical Performance of an Estonian Speech Recognition System for Radiology: Effects of Different Acoustic and Language Models

The aim of this study was to analyze retrospectively the influence of different acoustic and language models in order to determine the most important effects to the clinical performance of an Estonian language-based non-commercial radiology-oriented automatic speech recognition (ASR) system. An ASR system was developed for Estonian language in radiology domain by utilizing open-source software components (Kaldi toolkit, Thrax). The ASR system was trained with the real radiology text reports and dictations collected during development phases. The final version of the ASR system was tested by 11 radiologists who dictated 219 reports in total, in spontaneous manner in a real clinical environment. The audio files collected in the final phase were used to measure the performance of different versions of the ASR system retrospectively. ASR system versions were evaluated by word error rate (WER) for each speaker and modality and by WER difference for the first and the last version of the ASR system. Total average WER for the final version throughout all material was improved from 18.4% of the first version (v1) to 5.8% of the last (v8) version which corresponds to relative improvement of 68.5%. WER improvement was strongly related to modality and radiologist. In summary, the performance of the final ASR system version was close to optimal, delivering similar results to all modalities and being independent on user, the complexity of the radiology reports, user experience, and speech characteristics.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2016

Equation-based languages – A new paradigm for building energy modeling, simulation and optimization

Most of the state-of-the-art building simulation programs implement models in imperative programming languages. This complicates modeling and excludes the use of certain efficient methods for simulation and optimization. In contrast, equation-based modeling languages declare relations among variables, thereby allowing the use of computer algebra to enable much simpler schematic modeling and to generate efficient code for simulation and optimization. We contrast the two approaches in this paper. We explain how such manipulations support new use cases. In the first of two examples, we couple models of the electrical grid, multiple buildings, HVAC systems and controllers to test a controller that adjusts building room temperatures and PV inverter reactive power to maintain power quality. In the second example, we contrast the computing time for solving an optimal control problem for a room-level model predictive controller with and without symbolic manipulations. As a result, exploiting the equation-based language led to 2, 200 times faster solution

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2023

TransPolymer: a Transformer-based language model for polymer property predictions

Accurate and efficient prediction of polymer properties is of great significance in polymer design. Conventionally, expensive and time-consuming experiments or simulations are required to evaluate polymer functions. Recently, Transformer models, equipped with self-attention mechanisms, have exhibited superior performance in natural language processing. However, such methods have not been investigated in polymer sciences. Herein, we report TransPolymer, a Transformer-based language model for polymer property prediction. Our proposed polymer tokenizer with chemical awareness enables learning representations from polymer sequences. Rigorous experiments on ten polymer property prediction benchmarks demonstrate the superior performance of TransPolymer. Moreover, we show that TransPolymer benefits from pretraining on large unlabeled dataset via Masked Language Modeling. Experimental results further manifest the important role of self-attention in modeling polymer sequences. We highlight this model as a promising computational tool for promoting rational polymer design and understanding structure-property relationships from a data science view.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Large language models generate functional protein sequences across diverse families

Deep-learning language models have shown promise in various biotechnological applications, including protein design and engineering. Here, in this paper, we describe ProGen, a language model that can generate protein sequences with a predictable function across large protein families, akin to generating grammatically and semantically correct natural language sentences on diverse topics. The model was trained on 280 million protein sequences from >19,000 families and is augmented with control tags specifying protein properties. ProGen can be further fine-tuned to curated sequences and tags to improve controllable generation performance of proteins from families with sufficient homologous samples. Artificial proteins fine-tuned to five distinct lysozyme families showed similar catalytic efficiencies as natural lysozymes, with sequence identity to natural proteins as low as 31.4%. ProGen is readily adapted to diverse protein families, as we demonstrate with chorismate mutase and malate dehydrogenase.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Harnessing large language models’ zero-shot and few-shot learning capabilities for regulatory research

Abstract Large language models (LLMs) are sophisticated AI-driven models trained on vast sources of natural language data. They are adept at generating responses that closely mimic human conversational patterns. One of the most notable examples is OpenAI's ChatGPT, which has been extensively used across diverse sectors. Despite their flexibility, a significant challenge arises as most users must transmit their data to the servers of companies operating these models. Utilizing ChatGPT or similar models online may inadvertently expose sensitive information to the risk of data breaches. Therefore, implementing LLMs that are open source and smaller in scale within a secure local network becomes a crucial step for organizations where ensuring data privacy and protection has the highest priority, such as regulatory agencies. As a feasibility evaluation, we implemented a series of open-source LLMs within a regulatory agency’s local network and assessed their performance on specific tasks involving extracting relevant clinical pharmacology information from regulatory drug labels. Our research shows that some models work well in the context of few- or zero-shot learning, achieving performance comparable, or even better than, neural network models that needed thousands of training samples. One of the models was selected to address a real-world issue of finding intrinsic factors that affect drugs' clinical exposure without any training or fine-tuning. In a dataset of over 700 000 sentences, the model showed a 78.5% accuracy rate. Our work pointed to the possibility of implementing open-source LLMs within a secure local network and using these models to perform various natural language processing tasks when large numbers of training examples are unavailable.

Biochemistry & Molecular Biology↗