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At least 127 records · Page 7

Discovering Research Areas in Dataset Applications Through Knowledge Graphs and Large Language Models

Scientific datasets are increasingly cited in peer-reviewed journal publications, facilitating easy access to research utilizing those datasets. Datasets undergo a life cycle where older versions of datasets are replaced by newer versions often due to improvements in data resolution, algorithms, and other factors. Unlike peer reviewed documents registered with a single Digital Unique Identifier (DOI), datasets can be updated over time and the newer version of the datasets are registered with a new DOI which is not necessarily linked to the previous version of the dataset. It is challenging when publications citing a dataset need to be traced over the entire life cycle of that dataset. We provide an innovative approach to link the dataset versions and publications using a knowledge graph (KG). KG can help to trace the dataset cited in publications over the entire dataset life cycle and shed light into dataset usage in various applied research areas. We fine-tuned the pretrained NASA IMPACTINDUS Large Language Model (LLM) on a set of labeled publications abstracts. Our results showed that 87% of the publications were classified into one of twenty applied research areas, while the remaining 13% were classified into non-applied research areas. By linking datasets to applied research areas through the KG and employing Global Change Master Directory(GCMD), a well-established controlled vocabulary of scientific keywords describing Earth science datasets, we contribute to a transparent and advanced search and discovery mechanism for datasets across the Earth data ecosystem. The integrated KG and LLM approach is now incorporated and operational in dataset publication management at one of NASA’s Earth science data archival centers.

data provenance↗

Toward particle accelerator machine state embeddings as a modality for large language models

Understanding and diagnosing the state of a particle accelerator requires navigating high-dimensional control system data, often involving hundreds of interdependent parameters. We propose a novel multimodal embedding framework that jointly learns representations of machine states from both numerical control system readouts and natural language descriptions. This enables the translation of complex machine conditions into human-readable summaries while maintaining fidelity to the underlying physical system. The obtained embeddings are subsequently adapted to an open-weights large language model via cross-attention conditioning. We demonstrate a first implementation trained on European XFEL machine state data. This work covers the embedding model architecture, training methodology, and presents initial examples demonstrating the model's capabilities in action. Due to the general concept of machine state, the model can be easily adapted to other facilities and control system environments.

Accelerator Physics↗

Decoding substance use disorder severity from clinical notes using a large language model

Substance use disorder (SUD) poses a major concern due to its detrimental effects on health and society. SUD identification and treatment depend on a variety of factors such as severity, co-determinants (e.g., withdrawal symptoms), and social determinants of health. Existing diagnostic coding systems used by insurance providers, like the International Classification of Diseases (ICD-10), lack granularity for certain diagnoses, but American clinicians will add this granularity (as that found within the Diagnostic and Statistical Manual of Mental Disorders classification or DSM-5) as supplemental unstructured text in clinical notes. Traditional natural language processing (NLP) methods face limitations in accurately parsing such diverse clinical language. Large language models (LLMs) offer promise in overcoming these challenges by adapting to diverse language patterns. This study investigates the application of LLMs for extracting severity-related information for various SUD diagnoses from clinical notes. We propose a workflow employing zero-shot learning of LLMs with carefully crafted prompts and post-processing techniques. Through experimentation with Flan-T5, an open-source LLM, we demonstrate its superior recall compared to the rule-based approach. Focusing on 11 categories of SUD diagnoses, we show the effectiveness of LLMs in extracting severity information, contributing to improved risk assessment and treatment planning for SUD patients.

60 APPLIED LIFE SCIENCES↗

Assessing the nature of large language models: A caution against anthropocentrism.

Generative AI models garnered a large amount of public attention and speculation with the release of OpenAI’s chatbot, ChatGPT in November of 2022. At least two opinion camps exist – one that is excited about the possibilities these models offer for fundamental changes to human tasks, and another that is highly concerned about the power these models seem to have – especially since the release of GPT-4, which was trained on multimodal data and has ~1.7 trillion (T) parameters. We evaluated some concerns regarding these models’ power by assessing GPT-3.5 using standard, normed, and validated cognitive and personality measures. These measures come from the tradition of psychometrics in experimental psychology and have a long history of providing valuable insights and predictive distinctions in humans. For this seedling project, we developed a battery of tests that allowed us to estimate the boundaries of some of these models’ capabilities, how stable those capabilities are over a short period of time, and how they compare to humans.

97 MATHEMATICS AND COMPUTING↗

Assessing the nature of large language models: A caution against anthropocentrism

Generative AI models garnered a large amount of public attention and speculation with the release of OpenAI’s chatbot, ChatGPT in November of 2022. At least two opinion camps exist – one that is excited about the possibilities these models offer for fundamental changes to human tasks, and another that is highly concerned about the power these models seem to have – especially since the release of GPT-4, which was trained on multimodal data and has ~1.7 trillion (T) parameters. We evaluated some concerns regarding these models’ power by assessing GPT 3.5 using standard, normed, and validated cognitive and personality measures. These measures come from the tradition of psychometrics in experimental psychology and have a long history of providing valuable insights and predictive distinctions in humans. For this seedling project, we developed a battery of tests that allowed us to estimate the boundaries of some of these models’ capabilities, how stable those capabilities are over a short period of time, and how they compare to humans.

97 MATHEMATICS AND COMPUTING↗

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↗

Debiasing Watermarks for Large Language Models via Maximal Coupling

Watermarking language models is essential for distinguishing between human and machine-generated text and thus maintaining the integrity and trustworthiness of digital communication. Here, we present a novel green/red list watermarking approach that partitions the token set into “green” and “red” lists, subtly increasing the generation probability for green tokens. To correct token distribution bias, our method employs maximal coupling, using a uniform coin flip to decide whether to apply bias correction, with the result embedded as a pseudorandom watermark signal. Theoretical analysis confirms this approach’s unbiased nature and robust detection capabilities. Experimental results show that it outperforms prior techniques by preserving text quality while maintaining high detectability, and it demonstrates resilience to targeted modifications aimed at improving text quality. This research provides a promising watermarking solution for language models, balancing effective detection with minimal impact on text quality.

97 MATHEMATICS AND COMPUTING↗

Achieving GPT-4o level performance in astronomy with a specialized 8B-parameter large language model

AstroSage-Llama-3.1-8B is a domain-specialized natural-language AI assistant tailored for research in astronomy, astrophysics, cosmology, and astronomical instrumentation. Trained on the complete collection of astronomy-related arXiv papers from 2007 to 2024 along with millions of synthetically-generated question-answer pairs and other astronomical literature, AstroSage-Llama-3.1-8B demonstrates remarkable proficiency on a wide range of questions. AstroSage-Llama-3.1-8B scores 80.9% on the AstroMLab-1 benchmark, greatly outperforming all models—proprietary and open-weight—in the 8-billion parameter class, and performing on par with GPT-4o. This achievement demonstrates the potential of domain specialization in AI, suggesting that focused training can yield capabilities exceeding those of much larger, general-purpose models. AstroSage-Llama-3.1-8B is freely available, enabling widespread access to advanced AI capabilities for astronomical education and research.

AI assistant↗

Solving tricky quantum optics problems with assistance from large language models

The capabilities of modern artificial intelligence (AI) as a “scientific collaborator” are explored by engaging it with three nuanced problems in quantum optics: state populations in optical pumping, resonant transitions between decaying states (the Burshtein effect), and degenerate mirrorless lasing. Through iterative dialogue, the authors observe that AI models–when prompted and corrected–can reason through complex scenarios, refine their answers, and provide expert-level guidance, closely resembling the interaction with an adept colleague. The findings highlight that AI can democratize access to sophisticated modeling and analysis, shifting the focus in scientific practice from technical mastery to the generation and testing of ideas, and reducing the time for completing research tasks from days to minutes.

74 ATOMIC AND MOLECULAR PHYSICS↗