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At least 55 records · Page 3

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↗

A change language for ontologies and knowledge graphs

Ontologies and knowledge graphs (KGs) are general-purpose computable representations of some domain, such as human anatomy, and are frequently a crucial part of modern information systems. Most of these structures change over time, incorporating new knowledge or information that was previously missing. Managing these changes is a challenge, both in terms of communicating changes to users and providing mechanisms to make it easier for multiple stakeholders to contribute. To fill that need, we have created KGCL, the Knowledge Graph Change Language (https://github.com/INCATools/kgcl), a standard data model for describing changes to KGs and ontologies at a high level, and an accompanying human-readable Controlled Natural Language (CNL). This language serves two purposes: a curator can use it to request desired changes, and it can also be used to describe changes that have already happened, corresponding to the concepts of “apply patch” and “diff” commonly used for managing changes in text documents and computer programs. Another key feature of KGCL is that descriptions are at a high enough level to be useful and understood by a variety of stakeholders—e.g. ontology edits can be specified by commands like “add synonym ‘arm’ to ‘forelimb’” or “move ‘Parkinson disease’ under ‘neurodegenerative disease’.” We have also built a suite of tools for managing ontology changes. These include an automated agent that integrates with and monitors GitHub ontology repositories and applies any requested changes and a new component in the BioPortal ontology resource that allows users to make change requests directly from within the BioPortal user interface. Overall, the KGCL data model, its CNL, and associated tooling allow for easier management and processing of changes associated with the development of ontologies and KGs.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

ChatGrid: Power Grid Visualization Empowered by Large Language Model

This paper presents a novel open framework, ChatGrid, for easy, intuitive, and interactive geospatial visualization of large-scale transmission networks. ChatGrid uses state-of-the-art techniques for geospatial visualization of large networks including 2.5D views, animated flows, hierarchical and level-based filtering, and aggregation to provide visual information in an easy, cognitive manner. The highlight of ChatGrid is a natural language query based interface powered by large language model (ChatGPT) that offers an enhanced interactive experience whereby the user asks a question and ChatGrid provides the information both in text and visual. We discuss the architecture, implementation, design decisions, and usage of large language model for ChatGrid.

Jin, Sichen↗

Using a Large Language Model as a Building Block to Generate Usable Validation and Verification Suite for OpenMP

In the HPC area, both hardware and software move quickly. Often new hardware is developed and deployed, the corresponding software stack, including compilers and other tools, are under active development while leading edge software developers are working to port and tune their applications, all at the same time. While the software ecosystem is in flux, one of the key challenges for users is obtaining insight into the state of implementation of key features in the programming languages and models their applications are using – whether they have been implemented, and whether the implementation conforms to the specification, especially for newly implemented features (less tested by widespread use). OpenMP is one of the most prominent shared memory programming models used for on-node programming in HPC. With the shift towards accelerators (such as GPUs and FPGAs) and heterogeneous programming OpenMP features are getting more complex. It is natural to ask whether generative AI approaches, and large language models (LLMs) in particular, can help in producing validation and verification test suites to allow users better and faster insights into the availability and correctness of OpenMP features of interest. In this work, we explore the use of ChatGPT-4 to generate a suite of tests for OpenMP features. We have chosen a set of directives and clauses, a total of 78 combinations, which first appeared in OpenMP 3.0 (released in May 2008) but are also relevant for accelerators. We prompted ChatGPT to generate tests in the C and Fortran languages, for both host (CPU) and device (accelerator). On the Summit super-computer using the GNU implementation, we found that, of the 78 generated tests 67 C tests and 43 Fortran tests compiled successfully and fewer than those executed to completion. On further analysis we show that not all generated tests are valid. We document the process, results, and provide detailed analysis regarding the quality of tests generated. With the aim of providing input to a production quality validation and verification suite, we manually implement the corrections required to make the tests valid according to the current OpenMP specification. We quantify this effort as small, medium, or large, and record the lines of code changed to correct the invalid tests. With the corrected tests we validate recent implementations from HPE, AMD, and GNU on the Frontier supercomputer. Our experiment and subsequent analysis show that although LLMs are capable of producing HPC specific codes, they are limited by their understanding of the deeper semantics and restrictions of programming models such as OpenMP. Unsurprisingly more commonly used features have better support, while some OpenMP 3.0 directives such as sections and tasking are not universally supported on accelerators. We demonstrate that successful compilation and execution to completion are inadequate metrics for evaluating generated code and that, at this time, commodity LLMs require expert intervention for code verification. This points to gaps in the training data that is currently available for HPC. We demonstrate that with "small" effort 37% of generated invalid C tests and 63% of generated invalid Fortran tests could be corrected. This improves productivity of test generation as we circumvent writing from scratch and the common programming errors associated with it.

Pophale, Swaroop [ORNL] (ORCID:0000000185446367)↗

BuildingQA: A Benchmark for Natural Language Question Answering over Building Knowledge Graphs

Graph-based representations of building metadata using ontologies like Brick are vital for smart building applications, but querying them remains a challenge for practitioners. Knowledge Graph Question Answering (KGQA) systems, meant to retrieve answers from natural language questions, traditionally require large-scale training data, making them ill-suited for the specialized and data-scarce building domain. The advent of Large Language Models (LLMs) offers a paradigm shift, enabling zero-shot natural language querying without building/domain-specific training. Yet, there is no standardized benchmark for building-specific KGQA which can guide and validate research in this area. To address this gap, our work makes three primary contributions. First, we introduce the BuildingQA Benchmark Dataset, constructed through a multi-stage process of collecting practitioner data, augmenting it with LLMs for linguistic diversity, and curating a final set of 188 questions across 4 buildings. Second, we characterize the benchmark's complexity and ambiguity, introducing a novel method to quantify its "lexical gap" and providing a four-stage diagnostic framework for analyzing how systems fail. Third, we benchmark zero-shot LLM-powered KGQA systems to establish baseline performance and analyze their failure modes. Our evaluation reveals that top-performing systems achieve a maximum F1 score of only 0.38. This result does not indicate a failure of these powerful systems, but rather underscores the unique challenges posed by our benchmark. It demonstrates a critical performance gap, showing that current methods successful on general KGs struggle with the specific lexical and structural nuances of the building domain. BuildingQA1 thus provides the benchmark dataset and foundational analysis needed to drive the development of novel, domain-aware methods required to unlock the use of semantic data in buildings.

Mulayim, Ozan Baris↗

EV-ELM (Electric Vehicle Policies with the Energy Language Model) [SWR-25-156]

Electric Vehicle Policies with the Energy Language Model (EV-ELM) leverages previous work using Large Language Models (LLMs) to find, download, and parse policy information related to energy infrastructure. In this application, we use LLMs to find policy documents related to the permitting and installation of electric vehicle charging infrastructure. This software contains the code to find, download, and parse these documents, while a related data record in the Open Energy Data Initiative (OEDI) will include the resulting output dataset that can be used for downstream analysis. The EV-ELM repository contains code for the EV-ELM project, which focuses on retrieving and processing EV permitting processes using large language models. The project is composed of two pipelines: (1) a web scraping pipeline for discovering and downloading EV permitting documents, and (2) a document parsing and extraction pipeline that processes the downloaded files to produce structured data. The web scraping pipeline is designed to extract relevant information from various websites, while the document parsing pipeline processes and analyzes the extracted documents to derive meaningful insights. Both pipelines depend on the NLR elm repository, which provides essential tools and functionalities for handling and processing the data. The web scraping pipeline is a modified version of the ordinance_gpt example within the elm repository. It has been adapted to fit the specific requirements of the EV-ELM project, ensuring that it effectively captures and processes the necessary information related to EV permitting.

Olson, Reid [National Laboratory of the Rockies (N↗

Genomic Language model for Annotation of Repetitive Elements (GLARE) v1.0

GLARE (Genomic Language model for Annotation of Repetitive Elements) is a tool that classifies transposable elements (TEs)—the mobile, repetitive DNA sequences that make up large fractions of eukaryotic genomes. GLARE fine-tunes the NTv3-650M genomic language model on a harmonized collection of curated TE sequences from the PanTEon and Repbase reference databases, assigning each input sequence to one of 11 orders and 32 superfamilies in a Wicker-compatible taxonomy. Features. From nucleotide FASTA input, GLARE outputs per-sequence predictions, class summaries, composition figures, and an annotated FASTA. It provides calibrated confidence scores with optional abstention and runs on CPU or GPU. Uses. GLARE serves as a classification component in genome-annotation pipelines, downstream of TE discovery, supporting genome annotation and comparative and evolutionary genomics. Advantages. GLARE is the first repeat-element classifier to leverage a pretrained genomic language model. Combined with multi-database training, this approach outperformed all nine classifiers in the PanTEon benchmark, generalized better to unseen taxonomic clades, and remained robust to sequence orientation—a common failure mode of existing tools.

Bruna, Tomas [Lawrence Berkeley National Laborator↗

Examining Perceptions of Spanish Language Health Information Among Hispanics Living in the United States: A Qualitative Study Assessing Videos, Brochures, and Websites

Background Nationally, Hispanics experience health disparities manifested as a higher prevalence of chronic diseases in comparison to non-Hispanic Whites. Factors that influence health disparities in this population include inadequate dissemination of culturally and linguistically appropriate health information. Method Our qualitative analysis is based on data obtained from three focus groups with Spanish-speaking Hispanic adults conducted at a clinic in Nebraska. Participants were asked about their perceptions of health information in the form of videos, brochures, and websites. We followed the consolidated criteria for reporting qualitative research and used the theoretical framework of content analysis. Results For videos, attributes associated with higher levels of trust included a friendly health professional, the logo or name of a health care institute, and a reference specifying “se habla Español.” For brochures, attributes associated with trust included use of visual aids, use of numerous colors and big font sizes, the year of printing, and a health care agency logo. For websites, characteristics associated with trust were inclusion of plain language, use of pictures and videos, and date of last update. In all focus groups, participants perceived the use of mixed English/Spanish language in health information from pamphlets and websites as unprofessional. The use of unknown governmental logos in health promotional videos and websites was perceived as untrustworthy information. Conclusions Spanish-speaking Hispanics prefer health information supported by a health care agency or delivered by a health care professional. Health communication strategies should avoid the use of mixed English/Spanish language in sensitive information especially when combined with governmental logos.

De Alba Rosales, Armando↗

Physiological Characterization of Language Comprehension

In this project, our goal was to develop methods that would allow us to make accurate predictions about individual differences in human cognition. Understanding such differences is important for maximizing human and human-system performance. There is a large body of research on individual differences in the academic literature. Unfortunately, it is often difficult to connect this literature to applied problems, where we must predict how specific people will perform or process information. In an effort to bridge this gap, we set out to answer the question: can we train a model to make predictions about which people understand which languages? We chose language processing as our domain of interest because of the well- characterized differences in neural processing that occur when people are presented with linguistic stimuli that they do or do not understand. Although our original plan to conduct several electroencephalography (EEG) studies was disrupted by the COVID-19 pandemic, we were able to collect data from one EEG study and a series of behavioral experiments in which data were collected online. The results of this project indicate that machine learning tools can make reasonably accurate predictions about an individual?s proficiency in different languages, using EEG data or behavioral data alone.

42 ENGINEERING↗

Unified Language Frontend for Physic-Informed AI/ML

Artificial intelligence and machine learning (AI/ML) are becoming important tools for scientific modeling and simulation as in several other fields such as image analysis and natural language processing. ML techniques can leverage the computing power available in modern systems and reduce the human effort needed to configure experiments, interpret and visualize results, draw conclusions from huge quantities of raw data, and build surrogates for physics based models. Domain scientists in fields like fluid dynamics, microelectronics and chemistry can automate many of their most difficult and repetitive tasks or improve the design times by use of the faster ML-surrogates. However, modern ML and traditional scientific highperformance computing (HPC) tend to use completely different software ecosystems. While ML frameworks like PyTorch and TensorFlow provide Python APIs, most HPC applications and libraries are written in C++. Direct interoperability between the two languages is possible but is tedious and error-prone. In this work, we show that a compiler-based approach can bridge the gap between ML frameworks and scientific software with less developer effort and better efficiency. We use the MLIR (multi-level intermediate representation) ecosystem to compile a pre-trained convolutional neural network (CNN) in PyTorch to freestanding C++ source code in the Kokkos programming model. Kokkos is a programming model widely used in HPC to write portable, shared-memory parallel code that can natively target a variety of CPU and GPU architectures. Our compiler-generated source code can be directly integrated into any Kokkosbased application with no dependencies on Python or cross-language interfaces.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Identifying Disinformation Using Rhetorical Devices in Natural Language Models

Foreign disinformation campaigns are strategically organized, extended efforts using disinformation – false or misleading information deliberately placed by an adversary – to achieve some goal. Disinformation campaigns pose severe threats to our nation’s security by misinforming decision makers and negatively influencing their actions when they are operating on limited amounts of evidence. Current efforts rely on subject matter experts to manually identify disinformation, or on computers and traditional natural language processing algorithms to identify patterns in data to calculate the probability that something is disinformation or not. While both have their merits and successes, subject matter experts are unable to keep up with the high volumes of global information and traditional natural language algorithms do not do well in identifying “why” something is disinformation or not. Our hypothesis is that we can identify disinformation by looking at the way someone speaks, in the rhetorical devices they use. We have curated and annotated a dataset designed for multiple natural language processing tasks, but specifically useful for disinformation detection algorithms.

97 MATHEMATICS AND COMPUTING↗

Emergent Behaviors and the Limits of Large Language Model Generalization

Over the past couple years, large language models (LLMs) have rapidly grown in size and performance across wide numbers of tasks, leading some to herald them as machine learning models with truly “general” capabilities. We address some of the ways that the language used to describe these models can be both deceptive and a poor framing for making progress towards understanding their capabilities, and also review arguments on to what extent these models can represent and interact with the meaning of language. Emergent behaviors in these highly complex models are unpredictable and research into understanding them is still in early phases, which limits the strength of claims of generality about them. Moreover, while these models demonstrate surprising emergent reasoning capabilities on many tasks, there are still many limitations in generalization that overall high benchmark performance can hide. We review the literature showcasing limitations of LLMs as well as techniques to mitigate or overcome these challenges, while also highlighting how fundamental problems in model evaluation may prevent true claims of generality. We conclude with a practical section on using LLMs on real world problems while appropriately evaluating and validating these tasks to prevent or mitigate the downstream impacts of incorrect results.

97 MATHEMATICS AND COMPUTING↗

Demystifying the Resilience of Large Language Models: An End-to-End Perspective

Deep neural networks are known to be resilient to random bit-wise faults in their parameters. However, this resilience has primarily been established through evaluations of classification models. The extent to which this claim holds for large-language models remains underexplored. In this work, we conduct an extensive measurement study on the impact of random bitwise faults in commercial-scale language models. We perform an in-depth analysis of the resulting generation outputs. We first expose that these language models are not truly resilient to random bit-flips. While aggregate metrics such as accuracy may suggest resilience, an in-depth inspection of the generated outputs shows significant degradation in text quality. Our analysis also shows that tasks requiring more complex reasoning suffer more from performance and quality degradation. Moreover, we extend our analysis to models with augmented reasoning capabilities, such as Chain-of-Thought or Mixture of Experts architectures, and characterize their failure scenarios under random bit-flips.

Sun, Yu↗

HARMONY: Large-Scale Architecture Search for Efficient Hybrid Language Models

As large language models scale to trillions of parameters, their computational and memory requirements present critical challenges for efficient training and deployment. While Mixture of Experts (MoE) architectures enable efficient scaling through sparse parameter activation, and state-space models like Mamba offer linear-time complexity, principled methods for combining these paradigms remain undeveloped. We introduce HARMONY (Hybrid Architecture Research for Mamba, Optimized with Neural efficiencY), a multi-objective evolutionary neural architecture search framework for discovering efficient hybrid language models that integrate Transformer attention mechanisms, Mixture-of-Experts routing, and Mamba state-space components. Through large-scale distributed search using 16,384 MI250X GPUs on the Frontier supercomputer, HARMONY explores a comprehensive design space encompassing six attention variants (MHA, MQA, GQA, MLA, SWA, and Mamba-2), variable MoE configurations with both routed and shared experts, and extensive Mamba hyperparameters. Our framework discovers heterogeneous architectures that balance training performance with computational efficiency through multi-objective optimization incorporating latency penalties and fitness-based selection. Analysis of discovered architectures reveals that optimal hybrid designs favor heterogeneous component mixing rather than homogeneous patterns, with Mamba-2 and Multi-Head Latent Attention (MLA) emerging as preferred mechanisms. Discovered architectures demonstrate superior training efficiency: our best configuration achieves a final perplexity of 1.0874 with 2.38B parameters while processing 4,320 tokens/second, outperforming significantly larger manually designed models. Full-scale evaluation shows HARMONY's top architectures achieve better loss trajectories than equivalently-sized models using state-of-the-art configurations including Mixtral, Jamba, and Samba. Additionally, we demonstrate 91% weak scaling efficiency when training discovered 36B-parameter models across 1,024 GPUs. HARMONY is released as an open framework with comprehensive tools for building and training hybrid models using expert-data-pipeline parallelism, democratizing access to automated architecture design for next-generation language models.

Herron, Emily [ORNL] (ORCID:0000000273008172)↗

AI-based language models powering drug discovery and development

The discovery and development of new medicines is expensive, time-consuming, and often inefficient, with many failures along the way. Powered by artificial intelligence (AI), language models (LMs) have changed the landscape of natural language processing (NLP), offering possibilities to transform treatment development more effectively. Here, we summarize advances in AI-powered LMs and their potential to aid drug discovery and development. We highlight opportunities for AI-powered LMs in target identification, clinical design, regulatory decision-making, and pharmacovigilance. We specifically emphasize the potential role of AI-powered LMs for developing new treatments for Coronavirus 2019 (COVID-19) strategies, including drug repurposing, which can be extrapolated to other infectious diseases that have the potential to cause pandemics. Finally, we set out the remaining challenges and propose possible solutions for improvement.

60 APPLIED LIFE SCIENCES↗

Large language models for batteries

Large Language Models (LLMs) are advanced artificial intelligence systems capable of solving diverse tasks using language, reasoning, and external tools. Despite their growing deployment in academia and industry, their potential remains underexplored in battery research. This review presents a comprehensive overview of existing and emerging applications of LLMs in batterie field, addressing two critical questions: What can LLMs offer to support battery-related tasks, and how to develop more effective models for this purpose. We begin by outlining the principles of LLMs and criteria for selecting appropriate models and tools for battery research and development. We then explore their roles in text-mining, data interpretation, and the development of intelligent battery systems. In parallel, we discuss technical challenges, such as data standardizing and sharing, model evaluation, and tool integration. Lastly, we propose future research directions with short-, medium-, and long-term goals and highlight more broad perspectives for connecting experts and cross-disciplinary collaborations.

SoC↗

Language models for materials discovery and sustainability: Progress, challenges, and opportunities

Significant advancements have been made in one of the most critical branches of artificial intelligence: natural language processing (NLP). These advancements are exemplified by the remarkable success of OpenAI’s GPT-3.5/4 and the recent release of GPT-4.5, which have sparked a global surge of interest akin to an NLP gold rush. Here, in this article, we offer our perspective on the development and application of NLP and large language models (LLMs) in materials science. We begin by presenting an overview of recent advancements in NLP within the broader scientific landscape, with a particular focus on their relevance to materials science. Next, we examine how NLP can facilitate the understanding and design of novel materials and its potential integration with other methodologies. To highlight key challenges and opportunities, we delve into three specific topics: (i) the limitations of LLMs and their implications for materials science applications, (ii) the creation of a fully automated materials discovery pipeline, and (iii) the potential of GPT-like tools to synthesize existing knowledge and aid in the design of sustainable materials.

36 MATERIALS SCIENCE↗

Protein–Protein Interaction Networks Derived from Classical and Machine Learning-Based Natural Language Processing Tools

The study of protein-protein interactions (PPIs) provides insight into various biological mechanisms, including the binding of antibodies to antigens, enzymes to inhibitors or promoters, and receptors to ligands. Recent studies of PPIs have led to significant biological breakthroughs. For example, the study of PPIs involved in the human:SARS-CoV-2 viral infection mechanism aided in the development of the SARS-CoV-2 vaccines. Though several databases exist for the manual curation of PPI networks, text mining methods have been routinely demonstrated as useful alternatives for newly studied or understudied species where databases are incomplete. Here, the relationship extraction (RE) performance of several open-source classical text processing, machine learning (ML)-based natural language processing (NLP), and large language model (LLM)-based NLP tools were compared. Overall, our results indicated that networks derived from classical methods tend to have high true positive rates at the expense of having overconnected-networks, ML-based NLP methods have lower true positive rates but networks with the closest structures to the target network, and LLM-based NLP methods tend to exist in-between the two other approaches, with variable performances. Finally, the selection of a specific NLP approach should be tied to the needs of a study and text availability, as models varied in performance due to the amount of text provided.

59 BASIC BIOLOGICAL SCIENCES↗