Genolator: A Multimodal Large Language Model Fusing Natural Language, Genomic, and Structural Tokens for Protein Function Interpretation

This study aimed to evaluate the diagnostic accuracy of multimodal large language models in classifying superior labial frenulum attachments from intraoral photographs using expert consensus as the reference standard. Five experts (two periodontists and three orthodontists) established the consensus standard by classifying frenulum attachments in 117 intraoral images as mucosal, gingival, papillary, and papilla penetrating. The same photographs were then presented to three multimodal large language models (ChatGPT 4o, Gemini 2.5 Pro, and Microsoft Copilot GPT-4), and their diagnostic performance was evaluated using accuracy, sensitivity, specificity, and F1 score. Reliability was assessed using Fleiss' and Cohen's Kappa, and diagnostic performances were compared using Cochran's Q test. Human raters demonstrated almost perfect agreement (κ = 0.838, p < 0.001), whereas large language models showed poor inter-model agreement (κ = -0.124, p < 0.001). ChatGPT achieved slight significant agreement with the consensus (κ = 0.114, p = 0.019), although its clinical relevance was negligible. Gemini (κ = 0.099) and Copilot (κ = 0.027) showed no significant agreement (p > 0.05). Copilot yielded the highest overall accuracy (46.2%), followed by Gemini (44.5%) and ChatGPT (35.0%). The performance of the large language models varied across frenulum types. Current multimodal large language models demonstrate inconsistent and clinically insufficient accuracy in the classification of superior labial frenulum attachments from photographs. Domain-specific training is essential before large language models can be considered reliable diagnostic tools in dentistry.

AI-enabled language models (LMs) to large language models (LLMs) and multimodal large language models (MLLMs) in drug discovery and development

In recent years, generative artificial intelligence (AI), particularly large language models (LLMs) and their multimodal counterparts, multimodal large language models, including vision language models, have generated considerable interest in the global AI discourse. LLMs, or pre-trained language models (such as ChatGPT, Med-PaLM, LLaMA), are neural network architectures trained on extensive text data, excelling in language comprehension and generation. Multimodal LLMs, a subset of foundation models, are trained on multimodal data sets, integrating text with another modality, such as images, to learn universal representations akin to human cognition better. This versatility enables them to excel in tasks like chatbots, translation, and creative writing while facilitating knowledge sharing through transfer learning, federated learning, and synthetic data creation. Several of these models can have potentially appealing applications in the medical domain, including, but not limited to, enhancing patient care by processing patient data; summarizing reports and relevant literature; providing diagnostic, treatment, and follow-up recommendations; and ancillary tasks like coding and billing. As radiologists enter this promising but uncharted territory, it is imperative for them to be familiar with the basic terminology and processes of LLMs. Herein, we present an overview of the LLMs and their potential applications and challenges in the imaging domain.

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.

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.

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.

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

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

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.

Recent advances in Multimodal Large Language Models (MLLMs) have achieved remarkable progress in general domains and demonstrated promise in multimodal mathematical reasoning. However, applying MLLMs to geometry problem solving (GPS) remains challenging due to lack of accurate step-by-step solution data and severe hallucinations during reasoning. In this paper, we propose GeoGen, a pipeline that can automatically generates step-wise reasoning paths for geometry diagrams. By leveraging the precise symbolic reasoning, GeoGen produces large-scale, high-quality question-answer pairs. To further enhance the logical reasoning ability of MLLMs, we train GeoLogic, a Large Language Model (LLM) using synthetic data generated by GeoGen. Serving as a bridge between natural language and symbolic systems, GeoLogic enables symbolic tools to help verifying MLLM outputs, making the reasoning process more rigorous and alleviating hallucinations. Experimental results show that our approach consistently improves the performance of MLLMs, achieving remarkable results on benchmarks for geometric reasoning tasks. This improvement stems from our integration of the strengths of LLMs and symbolic systems, which enables a more reliable and interpretable approach for the GPS task. Codes are available at https://github.com/ycpNotFound/GeoGen.

Recently, Large Language Models (LLMs) and Multimodal Large Language Models (MLLMs) have shown promise in instruction following and image understanding. While these models are powerful, they have not yet been developed to comprehend the more challenging 3D geometric and physical scenes, especially when it comes to the sparse outdoor LiDAR data. In this paper, we introduce LiDAR-LLM, which takes raw LiDAR data as input and harnesses the remarkable reasoning capabilities of LLMs to gain a comprehensive understanding of outdoor 3D scenes. The central insight of our LiDAR-LLM is the reformulation of 3D outdoor scene cognition as a language modeling problem, encompassing tasks such as 3D captioning, 3D grounding, 3D question answering, etc. Specifically, due to the scarcity of 3D LiDAR-text pairing data, we introduce a three-stage training strategy and generate relevant datasets, progressively aligning the 3D modality with the language embedding of LLM. Furthermore, we design a Position-Aware Transformer (PAT) to connect the 3D encoder with the LLM, which effectively bridges the modality gap and enhances the LLM's spatial orientation comprehension of visual features. Our experiments demonstrate that LiDAR-LLM effectively comprehends a wide range of instructions related to 3D scenes, achieving a 40.9 BLEU-1 score on the 3D captioning dataset, a Grounded Captioning accuracy of 63.1%, and a BEV mIoU of 14.3%.

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.

BackgroundNIAGADS is a national data repository that offers qualified investigators access to genomic data for Alzheimer’s disease (AD) and related dementia. In addition, NIAGADS has made substantial effort to curate, harmonize, standardize, and disseminate AD‐relevant variant, gene, and sequence annotations from publications, functional genomics datasets, and summary statistics deposited at NIAGADS. These results are made available to the public in a collection of interactive knowledgebases (AD Variant Portal, FILER Functional Genomics Repository, VariXam, Alzheimer’s GenomicsDB & Genome Browser), all of which are accessible programmatically via the NIAGADS API. However, as these offerings grow, navigating them can be challenging. Here, we introduce AI‐based enhancements to NIAGADS sites to help guide researchers and facilitate data discovery.MethodWe leverage OpenAI’s generative AI to build and train three large language models (LLMs) based on NIAGADS documentation, step‐by‐step recipes for data‐access requests, subject‐specific vocabularies, and the OpenAPI specification defining the NIAGADS API that allows programmatic access to the NIAGADS knowledgebases. For users of the API and to enhance search interfaces, we build on the LLMs to construct a framework for handling complex natural language instructions that decomposes an inquiry into tasks and subtasks and then plans, selects, and optionally executes API calls and parses the results.ResultDeveloping these LLMs allows NIAGADS to improve user experiences by integrating topic‐specific chatbots and generative AI search tools into NIAGADS sites. Rule‐based chatbots that leverage conversational AI on the NIAGADS portal and Data Sharing Service will respond to inquiries with answers inferred from the LLMs, with responses improving with user feedback. These bots will also supplement help requests, suggesting solutions to common inquiries. Planner‐enhanced generative AI based on the API‐specification trained LLMs will be tied to knowledgebase searches and filters in resources such as the GenomicsDB and FILER to allow users to leverage natural language processing to ask sophisticated questions that require multiple API calls to resolve the answer.ConclusionIntroducing AI‐enhanced search creates an interactive opportunity for NIAGADS users to learn new information or discover resources and tools they can use to supplement their research, which, in turn, improves NIAGADS ability to support AD genetics research.

The Ministry of Food and Drug Safety (MFDS) of the Republic of Korea, similar to the United States Food and Drug Administration and the United Kingdom's Medicines and Healthcare products Regulatory Agency, issued specific regulatory guidelines on January 24, 2025, for approving generative artificial intelligence (AI) technologies as medical devices [1].Although these guidelines use the term 'generative AI,' they predominantly focus on the approval of AI software tools based on large language models (LLMs) and large multimodal models (LMMs) [2], the latter of which can process various types of input data, such as texts, images, videos, audio, and bio-signals.Unlike the broader guidelines for approving AI models as medical devices, specific regulatory guidelines for LLMs/LMMs have arguably not yet been proposed in other countries.

DocuMind AI is an advanced document-based question answering system developed using Retrieval-Augmented Generation (RAG) to address challenges in extracting meaningful information from unstructured data. Organizations often struggle to extract useful information from large volumes of unstructured documents. Traditional keyword-based search methods often fail to capture semantic context, resulting in irrelevant outputs. To overcome this limitation, the proposed system integrates semantic search with large language models (LLMs) to generate accurate and context-aware responses. The system utilizes vector embeddings to represent document content and retrieve relevant information efficiently. It is implemented using a Java Spring Boot backend integrated with LangChain4j, which manages document ingestion, text chunking, embedding generation, and retrieval processes. Users interact with the system through a React.js-based interface, allowing them to upload documents and query in natural language. The system supports multiple document formats such as PDF and DOCX, ensuring flexibility in real-world applications. Additionally, JWTbased authentication is implemented to provide secure access to the system. The modular and scalable architecture makes DocuMind suitable for enterprise-level deployment, bridging the gap between traditional information retrieval systems and modern AI-driven solutions. Keywords: Retrieval-Augmented Generation, Natural Language Processing, Large Language Models, Vector Database, Java Spring Boot, LangChain4j, PostgreSQL pgvector, Cosine Similarity.