Mirror: A Natural Language Interface for Data Querying, Summarization, and Visualization

JupyterLab is a web-based interactive development platform that is widely used in the Earth science community. Using Jupyter Notebooks, it is possible to perform data analysis tasks, annotate and visualize results in a way that is easy to reproduce, present and share with others. JupyterLab allows the use of “extensions”, which add functionality to the platform. One of these is Jupyter-AI [1], which allows the use of Large Language Models (LLMs), such as ChatGPT, Claude Sonnet and Ollama, within the JupyterLab environment, through  a chat interface or directly within notebooks. By integrating LLMs into JupyterLab, it is possible to leverage their code generation capabilities to assist a user to translate their analysis tasks from an idea to actual executable code in an efficient manner. One drawback of using these LLMs in tasks involving spatio–temporal data is that the models typically do not have access to the data necessary for the analysis task and will often resort to generating fictional data or using placeholders in the code that they create. This requires the user to adapt the provided code to their data, which removes some of the utility provided by the LLM.In this context we make use of FrevaGPT, an approach for using LLMs in climate data analysis that allows for quick, complex and reproducible analyses of data sets, such as decadal climate model forecasts. Leveraging LLM’s capability to write code and using few-shot prompting (in-context learning) allows the LLM to utilize Freva [2,3] (Free Evaluation Framework), a data search and analysis platform, which provides a standardised interface to spatio-temporal datasets hosted on an HPC cluster [4].  FrevaGPT integrates seamlessly into Jupyter-AI and, by making use of the Freva library, combines the code-generating capabilities of LLMs with contextual understanding of how to access relevant datasets on the HPC cluster. This in addition with FrevaGPT’s ability to execute generated code in an isolated environment on an HPC node, annotating and explaining any intermediate results, as well as automatically correcting errors encountered along the way, could serve as a starting ramp for researchers to efficiently produce new analysis products based on spatio-temporal climate data. This PICO will include examples of using FrevaGPT within JupyterLab to analyse spatio-temporal datasets from the climate of the past, as well seasonal to decadal climate predictions.  

Large language models (LLMs) have the potential to transform how climate scientists interact with data by lowering technical barriers and enabling more intuitive analysis workflows. Building on previous demonstrations of LLM-assisted climate analysis, we present how FrevaGPT, an LLM-powered scientific assistant integrated into Freva - a climate data search and analysis platform- , supports climate scientists in their day-to-day data exploration and analysis. FrevaGPT interprets natural language queries and automatically generates traceable, editable, and reusable analysis scripts that can be executed within established scientific environments. It retrieves relevant datasets and literature, performs analyses, and visualises results, therefore allowing researchers to focus on scientific interpretation rather than coding intricacies. By leveraging a broad repository of climate observations and model output, FrevaGPT ensures transparent and reproducible workflows that adhere to best practices in climate research. It also integrates seamlessly into Jupyter-AI and, by making use of the Freva library, combines the code-generating capabilities of LLMs with contextual understanding of how to access relevant datasets on the HPC cluster. As a “co-pilot” for geoscientists, the system not only responds to explicit requests but also proactively suggests relevant climate modes, events, and next analytical steps, helping to uncover insights that might otherwise be overlooked. Practical use cases demonstrate how FrevaGPT assists with interactive exploratory analysis and hypothesis refinement across climate datasets of varying complexity. By embedding LLM-assisted natural language interaction into real-world climate research workflows, this work highlights methodological considerations and opportunities for enhancing scientific productivity, promoting broader adoption of NLP and AI tools among Earth system scientists. We provide scientific evaluation of FrevaGPT’s capability through a benchmark suite. A live demo will be presented and can be used by the audience to do real climate analysis on a high-performance computer with access to petabytes of Earth system data - starting with a simple prompt.

Evaluating gpt-4 for zero-shot classification of bleeding and clotting events: Can large language models serve as second reviewers?

Generative large language models (LLMs) are a subset of transformers-based neural network architecture models. LLMs have successfully leveraged a combination of an increased number of parameters, improvements in computational efficiency, and large pre-training datasets to perform a wide spectrum of natural language processing (NLP) tasks. Using a few examples (few-shot) or no examples (zero-shot) for prompt-tuning has enabled LLMs to achieve state-of-the-art performance in a broad range of NLP applications. This article by the American Medical Informatics Association (AMIA) NLP Working Group characterizes the opportunities, challenges, and best practices for our community to leverage and advance the integration of LLMs in downstream NLP applications effectively. This can be accomplished through a variety of approaches, including augmented prompting, instruction prompt tuning, and reinforcement learning from human feedback (RLHF). Our focus is on making LLMs accessible to the broader biomedical informatics community, including clinicians and researchers who may be unfamiliar with NLP. Additionally, NLP practitioners may gain insight from the described best practices. We focus on 3 broad categories of NLP tasks, namely natural language understanding, natural language inferencing, and natural language generation. We review the emerging trends in prompt tuning, instruction fine-tuning, and evaluation metrics used for LLMs while drawing attention to several issues that impact biomedical NLP applications, including falsehoods in generated text (confabulation/hallucinations), toxicity, and dataset contamination leading to overfitting. We also review potential approaches to address some of these current challenges in LLMs, such as chain of thought prompting, and the phenomena of emergent capabilities observed in LLMs that can be leveraged to address complex NLP challenge in biomedical applications.

Aim/Purpose: The study investigates the factors influencing the acceptance and utilisation of large language models (LLMs) (predictor variables of LLM usage), such as ChatGPT, in Learning design by instructional designers and university-teaching academics from various countries. Background: Large language models (LLMs) have exploded onto the scene, transforming the landscape of learning design. Instructional designers and university teaching academics have been overburdened with content creation for their teaching programmes, and the arrival of LLM models will help in this regard by developing more interactive content that drives student engagement and, in turn, contributes to student success. Since LLMs are a relatively new phenomenon, little is known about the factors influencing their acceptance in learning design; therefore, this research is needed, as learning design principles are the bedrock of student engagement and success. Methodology: A cross-sectional correlational quantitative study was employed. Data was collected using an online questionnaire posted on social media, including LinkedIn, from 203 instructional designers and university teaching academics. Purposive and snowball sampling methods were used to target instructional designers and university teaching academics at colleges and universities worldwide. Participants were asked to share the survey link with fellow instructional designers and university-teaching academics in their communities. The factor structure of the data was determined using exploratory factor analysis. Nonetheless, the factor structure derived from the LLMs did not entirely reflect the original configuration of the Unified Theory of Acceptance and Use of Technology (UTAUT3), as certain predictors appeared to coalesce, indicating LLMs’ unique nature in learning design. Confirmatory factor analysis was used to verify the fit of the data on the measurement model. First-order and second-order structural modelling were used to identify the structural relationships among the variables. Contribution: The study determines significant factors for the acceptance of LLMs by instructional designers and academic teaching staff in learning design, enabling possible opportunities for best practices in the field through interventions to optimize LLM usage. The study applies the technology acceptance model to the emerging LLM technology and extends the technology acceptance model by adding the trust construct as a predictor variable. Findings: The structural analysis results indicated that the ingrained LLM practices, LLM peer-driven expectations, innovative propensity towards LLM adoption, reliability and provider trust in LLMs, and ease of use and support influenced perceived LLM benefits and usage, but community standards and infrastructure had no influence. The second-order structural equation modelling indicated that perceived LLM benefits and usage and ingrained LLM habits contributed most to the learning design. Recommendations for Practitioners: Teaching academics and instructional designers must use LLMs in designing content, assessments, and interactive learning activities, and attend LLM training workshops on prompting and best practices in integrating LLMs into learning and teaching to see their benefits; hence, regular use of LLMs will then lead to trust and innovation in LLMs usage, enhancing learning design and improving student learning outcomes. Recommendation for Researchers: Researchers must use mixed methods approaches to have a deeper understanding of the factors influencing LLMs. Since habit and perceived LLM benefits and usage contributed the most variance to learning design, researchers must investigate strategies that optimise these factors in learning design, such as effective intervention strategies that can help form positive LLM habits. In addition, the findings provide researchers with a starting point for future research. Further researchers must investigate interventions that optimise the influence of personal innovativeness and trust that contributed the least variance to learning design, hence unlocking the potential of LLMs in learning design through innovation, responsible, and ethical use. Impact on Society: The use of LLMs in learning design has a high possibility of transforming education, specifically the learning design landscape. Using LLMs will free up more time for teaching academics and instructional designers so that they spend more time on higher-order thinking skill demands. Consequently, the students will be exposed to more engaging and interactive content, resulting in improved learning outcomes. Future Research: Future research must include context-derived external variables in technology acceptance models, such as levels of prompting competencies, to provide a deeper understanding of LLMs. In addition, future research must be based on the application and impact of LLMs on student engagement and success, and their attainment of 21st-century skills.

Background and Aims Large language models (LLMs) have gained significant attention in the field of natural language processing (NLP), marking a shift from traditional techniques like Term Frequency-Inverse Document Frequency (TF-IDF). We developed a traditional NLP model to predict arteriovenous fistula (AVF) failure within next 30 days using clinical notes. The goal of this analysis was to investigate whether LLMs would outperform traditional NLP techniques, specifically in the context of predicting AVF failure within the next 30 days using clinical notes. Method We defined AVF failure as the change in status from active to permanently unusable status or temporarily unusable status. We used data from a large kidney care network from January 2021 to December 2021. Two models were created using LLMs and traditional TF-IDF technique. We used “distilbert-base-uncased”, a distilled version of BERT base model [1], and compared its performance with traditional TF-IDF-based NLP techniques. The dataset was randomly divided into 60% training, 20% validation and 20% test dataset. The test data, comprising of unseen patients’ data was used to evaluate the performance of the model. Both models were evaluated using metrics such as area under the receiver operating curve (AUROC), accuracy, sensitivity, and specificity. Results The incidence of 30 days AVF failure rate was 2.3% in the population. Both LLMs and traditional showed similar overall performance as summarized in Table 1. Notably, LLMs showed marginally better performance in certain evaluation metrics. Both models had same AUROC of 0.64 on test data. The accuracy and balanced accuracy for LLMs were 72.9% and 59.7%, respectively, compared to 70.9% and 59.6% for the traditional TF-IDF approach. In terms of specificity, LLMs scored 73.2%, slightly higher than the 71.2% observed for traditional NLP methods. However, LLMs had a lower sensitivity of 46.1% compared to 48% for traditional NLP. However, it is worth noting that training on LLMs took considerably longer than TF-IDF. Moreover, it also used higher computational resources such as utilization of graphics processing units (GPU) instances in cloud-based services, leading to higher cost. Conclusion In our study, we discovered that advanced LLMs perform comparably to traditional TF-IDF modeling techniques in predicting the failure of AVF. Both models demonstrated identical AUROC. While specificity was higher in LLMs compared to traditional NLP, sensitivity was higher in traditional NLP compared to LLMs. LLM was fine-tuned with a limited dataset, which could have influenced its performance to be similar to that of traditional NLP methods. This finding suggests that while LLMs may excel in certain scenarios, such as performing in-depth sentiment analysis of patient data for complex tasks, their effectiveness is highly dependent on the specific use case. It is crucial to weigh the benefits against the resources required for LLMs, as they can be significantly more resource-intensive and costly compared to traditional TF-IDF methods. This highlights the importance of a use-case-driven approach in selecting the appropriate NLP technique for healthcare applications.

Large language models (LLMs) are increasingly adopted in educational contexts to provide personalized support to students and teachers. The unprecedented capacity of LLM‐based applications to understand and generate natural language can potentially improve instructional effectiveness and learning outcomes, but the integration of LLMs in education technology has renewed concerns over algorithmic bias, which may exacerbate educational inequalities. Building on prior work that mapped the traditional machine learning life cycle, we provide a framework of the LLM life cycle from the initial development of LLMs to customizing pre‐trained models for various applications in educational settings. We explain each step in the LLM life cycle and identify potential sources of bias that may arise in the context of education. We discuss why current measures of bias from traditional machine learning fail to transfer to LLM‐generated text (eg, tutoring conversations) because text encodings are high‐dimensional, there can be multiple correct responses, and tailoring responses may be pedagogically desirable rather than unfair. The proposed framework clarifies the complex nature of bias in LLM applications and provides practical guidance for their evaluation to promote educational equity. Practitioner notes What is already known about this topic The life cycle of traditional machine learning (ML) applications which focus on predicting labels is well understood. Biases are known to enter in traditional ML applications at various points in the life cycle, and methods to measure and mitigate these biases have been developed and tested. Large language models (LLMs) and other forms of generative artificial intelligence (GenAI) are increasingly adopted in education technologies (EdTech), but current evaluation approaches are not specific to the domain of education. What this paper adds A holistic perspective of the LLM life cycle with domain‐specific examples in education to highlight opportunities and challenges for incorporating natural language understanding (NLU) and natural language generation (NLG) into EdTech. Potential sources of bias are identified in each step of the LLM life cycle and discussed in the context of education. A framework for understanding where to expect potential harms of LLMs for students, teachers, and other users of GenAI technology in education, which can guide approaches to bias measurement and mitigation. Implications for practice and/or policy Education practitioners and policymakers should be aware that biases can originate from a multitude of steps in the LLM life cycle, and the life cycle perspective offers them a heuristic for asking technology developers to explain each step to assess the risk of bias. Measuring the biases of systems that use LLMs in education is more complex than with traditional ML, in large part because the evaluation of natural language generation is highly context‐dependent (eg, what counts as good feedback on an assignment varies). EdTech developers can play an important role in collecting and curating datasets for the evaluation and benchmarking of LLM applications moving forward.

Purpose This study aims to explore the integration of large language models (LLMs) and vision-language models (VLMs) in robotics, highlighting their potential benefits and the safety challenges they introduce, including robustness issues, adversarial vulnerabilities, privacy concerns and ethical implications. Design/methodology/approach This survey conducts a comprehensive analysis of the safety risks associated with LLM- and VLM-powered robotic systems. The authors review existing literature, analyze key challenges, evaluate current mitigation strategies and propose future research directions. Findings The study identifies that ensuring the safety of LLM-/VLM-driven robots requires a multi-faceted approach. While current mitigation strategies address certain risks, gaps remain in real-time monitoring, adversarial robustness and ethical safeguards. Originality/value This study offers a structured and comprehensive overview of the safety challenges in LLM-/VLM-driven robotics. It contributes to ongoing discussions by integrating technical, ethical and regulatory perspectives to guide future advancements in safe and responsible artificial intelligence-driven robotics.

Interacting with Large Language Models (LLMs) via declarative queries is increasingly popular for tasks like question answering and data extraction, thanks to their ability to process vast unstructured data. However, LLMs often struggle with answering complex factual questions, exhibiting low precision and recall in the returned data. This challenge highlights that executing queries on LLMs remains a largely unexplored domain, where traditional data processing assumptions often fall short. Conventional query optimization, typically cost-driven, overlooks LLM-specific quality challenges such as contextual understanding. Just as new physical operators are designed to address the unique characteristics of LLMs, optimization must consider these quality challenges. Our results highlight that adhering strictly to conventional query optimization principles fails to generate the best plans in terms of result quality. To tackle this challenge, we present a novel approach to enhance SQL results by applying query optimization techniques specifically adapted for LLMs. We introduce a database system, GALOIS, that sits between the query and the LLM, effectively using the latter as a storage layer. We design alternative physical operators tailored for LLM-based query execution and adapt traditional optimization strategies to this novel context. For example, while pushing down operators in the query plan reduces execution cost (fewer calls to the model), it might complicate the call to the LLM and deteriorate result quality. Additionally, these models lack a traditional catalog for optimization, leading us to develop methods to dynamically gather such metadata during query execution. Our solution is compatible with any LLM and balances the trade-off between query result quality and execution cost. Experiments show up to 144% quality improvement over questions in Natural Language and 29% over direct SQL execution, highlighting the advantages of integrating database solutions with LLMs.

Designing preference elicitation (PE) methodologies that can quickly ascertain a user’s top item preferences in a cold-start setting is a key challenge for building effective and personalized conversational recommendation (ConvRec) systems. While large language models (LLMs) enable fully natural language (NL) PE dialogues, we hypothesize that monolithic LLM NL-PE approaches lack the multi-turn, decision-theoretic reasoning required to effectively balance the exploration and exploitation of user preferences towards an arbitrary item set. In contrast, traditional Bayesian optimization PE methods define theoretically optimal PE strategies, but cannot generate arbitrary NL queries or reason over content in NL item descriptions – requiring users to express preferences via ratings or comparisons of unfamiliar items. To overcome the limitations of both approaches, we formulate NL-PE in a Bayesian Optimization (BO) framework that seeks to actively elicit NL feedback to identify the best recommendation. Key challenges in generalizing BO to deal with natural language feedback include determining: (a) how to leverage LLMs to model the likelihood of NL preference feedback as a function of item utilities, and (b) how to design an acquisition function for NL BO that can elicit preferences in the infinite space of language. We demonstrate our framework in a novel NL-PE algorithm, PEBOL, which uses: 1) Natural Language Inference (NLI) between user preference utterances and NL item descriptions to maintain Bayesian preference beliefs, and 2) BO strategies such as Thompson Sampling (TS) and Upper Confidence Bound (UCB) to guide LLM query generation. We numerically evaluate our methods in controlled simulations, finding that after 10 turns of dialogue, PEBOL can achieve an MRR@10 of up to 0.27 compared to the best monolithic LLM baseline’s MRR@10 of 0.17, despite relying on earlier and smaller LLMs.1

The paper studies the problem of software code migration during the transition from the old version of the SAP ERP 6.0 system to modern ERP platforms, in particular SAP S/4HANA. The necessity of automation of the migration process using artificial intelligence methods and tools is substantiated. A comprehensive analysis of existing academic and industrial case studies confirmed the feasibility of using large language models for code migration. A number of advantages of the approach based on large language models are revealed, in particular, the ability to handle various migration scenarios. The key risks and limitations common in the enterprise environment are highlighted, including data security, privacy, high cost of API calls and limited knowledge of models regarding the subject area. A method is developed for selecting a large open source language model that can be safely used in the enterprise landscape, thereby mitigating the risks associated with cloud solutions. The method is based on the developed system of criteria, including: model size, context window size, license type, support for fine-tuning training, focus on code quality (measured using a reference dataset), support for model quantization and community support. The hybrid AHP-TOPSIS method is proposed for systematic ranking of candidate models. The AHP method was used to check the weights of the criteria, while TOPSIS was used to rank the models based on their proximity to the ideal solution. Based on the developed method, three large language models were selected: Qwen 2.5 Coder 14B, DeepSeek-Coder-V2 16B and Llama 3.1 8B. A comprehensive testing plan for the selected models was developed for further experimental studies. The scientific novelty of the work lies in the development of a method for selecting large language models for custom code migration tasks, which differs from the existing system of model selection criteria and the use of a hybrid AHP-TOPSIS approach for ranking candidate models. The practical value of the work is that the developed method allows you to select a model taking into account the constraints of the corporate environment and information security requirements, which will increase the level of automation in the migration of AVAP when switching to new versions of ERP systems from SAP SE. The developed method can be applied to the selection of large language models when upgrading any large computer systems developed in both open source and proprietary programming languages.

Introduction Game theory has long served as a foundational tool in cybersecurity to test, predict, and design strategic interactions between attackers and defenders. The recent advent of Large Language Models (LLMs) offers new tools and challenges for the security of computer systems. In this work, we investigate whether classical game-theoretic frameworks can effectively capture the behaviors of LLM-driven actors and bots. Methods Using a reproducible framework for game-theoretic LLM agents, we investigate two canonical scenarios—the one-shot zero-sum game and the dynamic Prisoner's Dilemma—and we test whether LLMs converge to expected outcomes or exhibit deviations due to embedded biases. We experiments on four state-of-the-art LLMs and five natural languages (English, French, Arabic, Vietnamese, and Mandarin Chinese) to assess linguistic sensitivity. Results For both games, we observe that the final payoffs are influenced by agents characteristics such as personality traits or knowledge of repeated rounds. We also uncover an unexpected sensitivity of the final payoffs to the choice of languages, which should warn against indiscriminate application of LLMs in cybersecurity applications and call for in-depth studies, as LLMs may behave differently when deployed in different countries. We also employ quantitative metrics to evaluate the internal consistency and cross-language stability of LLM agents. Discussion In addition to uncovering unexpected behaviors requiring attention by scholars and practitioners, our work can help guide the selection of the most stable LLMs and optimizing models for secure applications.

Readability & quality of large language model responses in CAR-T patient education

Abstract. Large language models (LLMs) have revolutionized the field of natural language processing (NLP), demonstrating remarkable capabilities in understanding, generating, and manipulating human language. This comprehensive review explores the development, applications, optimizations, and challenges of LLMs. This paper begin by tracing the evolution of these models and their foundational architectures, such as the Transformer, GPT, and BERT. We then delve into the applications of LLMs in natural language understanding tasks, including sentiment analysis, named entity recognition, question answering, and text summarization, highlighting real-world use cases. Next, we examine the role of LLMs in natural language generation, covering areas such as content creation, language translation, personalized recommendations, and automated responses. We further discuss LLM applications in other NLP tasks like text style transfer, text correction, and language model pre-training. Subsequently, we explore techniques for optimizing and improving LLMs, including model compression, explainability, robustness, and security. Finally, we address the challenges posed by the significant computational requirements, sample inefficiency, and ethical considerations surrounding LLMs. We conclude by discussing potential future research directions, such as efficient architectures, few-shot learning, bias mitigation, and privacy-preserving techniques, which will shape the ongoing development and responsible deployment of LLMs in NLP.

e23161 Background: Data retrieval is challenging in clinical research and traditional methods for data collection are often time-consuming and may be error-prone. Large Language Models (LLMs) have shown zero-shot capabilities in converting unstructured clinical text into structured data. These technologies could support the retrieval stage of clinical trials by leveraging the information reported in Electronic Health Records (EHRs) without relying any longer on manual curation. APOLLO 11 Consortium (NCT05550961) is a multicentric Italian trial which leverages a federated infrastructure for the analysis of advanced lung cancer patient data across Italy. Methods: We conducted a pilot study using Llama 3.1 8B on 358 Non-Small Cell Lung Cancer patients from the IRCCS Istituto Nazionale dei Tumori, leader of the APOLLO 11 Consortium. Anonymized EHRs have been analyzed within the LLM pipeline for feature extraction by Wiest et al. A combination of zero/few shot prompting techniques both in English and Italian languages was used. We selected smoking, histology, PD-L1 and staging as multiclass variables and bone/brain/liver metastases as binary variables. The ground truth collection involved a first Manual Data Entry (1-MDE) and a final full-revised MDE (2-MDE). The LLM accuracy was calculated only for the comparison LLM vs 2-MDE. In addition, we calculated the percentage of Missing Information (% MI) in 1-MDE, 2-MDE and LLM extraction. Results: Compared to 2-MDE, LLM achieved feature-specific accuracies of 0.78 for PD-L1, 0.85 for BONE METASTASIS, 0.83 for BRAIN METASTASIS, 0.89 for LIVER METASTASIS and 0.96 for TUMOUR STAGING. For smoking and staging, LLM extraction also reduced % MI relative to 1-MDE (Table 1). Only for PD-L1, we further analyzed the 12.8% of MI and found that 91.3% resulted from hallucinations (i.e., PD-L1 was misclassified as missing). Evaluations using English prompts confirmed the pipeline’s adaptability and high tasks accuracy. Conclusions: This study confirms the feasibility of LLMs for data retrieval in clinical trials demonstrating strong performance across diverse clinical features with minimal prompt optimization. LLMs could assist clinicians and data entry personnel in the 1-MDE process, streamlining initial data structuring and saving time. The 2-MDE step can remain as a quality check to address any discrepancies. Further improvements could focus on prompt optimization and integrating human feedback to reduce hallucination rates. Clinical trial information: NCT05550961 . %MI in 1-MDE, 2-MDE and LLM extraction. Accuracy refers only to LLM vs 2-MDE. Histology and metastasis sites were collected only in 2-MDE. NA = not available. Smoking PD-L1 Histology Bone Met Brain Met Liver Met T N M Stage % MI 1-MDE 6.4 8.9 NA NA NA NA 22.5 22.5 23.11 98.3 % MI 2-MDE 6.6 3 0 0 0 0 0 0 0 0 % MI LLM 2.7 12.8 10.3 0 0 0 0 0 0 6.9 % accuracy (LLM vs 2-MDE) 67 78 91 85 83 89 39 52 70 96