MedSumGraph: enhancing GraphRAG for medical QA with summarization and optimized prompts.

Large Language Models (LLMs) hold the potential for clinical task-shifting by processing unstructured clinical text, enabling tasks such as clinical concept extraction and medical question answering from electronic health records. If implemented reliably, such approaches may benefit over-burdened healthcare systems, particularly in resource-limited settings and for traditionally overlooked populations, provided that local fine-tuning is supported by appropriate clinical and technical expertise. However, this powerful technology remains largely understudied in real-world contexts, particularly in the Global South. This study aims to assess whether openly available LLMs can be used reliably for processing medical notes in real-world settings in South Asia. We used publicly available LLMs to parse de-identified clinical notes from a large electronic health records (EHR) database in Pakistan, containing hospital records for 8.2 million patients. ChatGPT (GPT-3.5) as a general-purpose LLM, and GatorTron (base), BioMegatron, BioBert and ClinicalBERT as medical LLMs were evaluated when applied to these data, after fine-tuning them with (a) publicly available clinical datasets namely Informatics for Integrating Biology & the Bedside (I2B2) and National NLP Clinical Challenges (N2C2) for medical concept extraction (MCE) and emrQA for medical question answering (MQA), and (b) the local Pakistani de-identified EHR dataset, which includes inpatient Discharge Summaries (DS) and Subjective, Objective, Assessment, and Plan (SOAP) notes, as detailed in this paper. MCE models were applied to these clinical notes using both 3-label and 9-label formats, while MQA models were applied to medical questions. Internal and external validation performance was measured for (a) and (b) using F1 score, precision, recall, and accuracy for MCE and BLEU and ROUGE-L, which measure lexical and sequence similarity, for MQA. When clinical LLMs were not fine-tuned on the local EHR dataset, their performance during external validation on local data was notably poorer compared to internal validation on the dataset used for fine-tuning, with reductions of at least 15% in F1 scores for MCE and 35% in ROUGE-L and BLEU scores for MQA tasks. This suggests potential bias and highlights the inability of the medical LLMs to reliably handle the data distribution of the local population without further fine-tuning and adaptation. This trend persisted across two distinct natural language processing tasks: concept extraction and question answering, spanning a spectrum of task complexities. However, fine-tuning the LLMs with local EHR data significantly improved model performance across both tasks, yielding a 7.5% to 15% increase in the F1 score for MCE and a 27% to 53% increase in ROUGE-L and BLEU scores for MQA. Notably, ChatGPT, as a general-purpose LLM, stood out as an exception, demonstrating superior performance across all measured metrics on the local dataset compared to the publicly available dataset, with improvements ranging from 3% to 17% on the local EHR dataset, even without fine-tuning on the local data. Publicly available LLMs, predominantly trained on data from high-income regions, were found to be unreliable when applied in a real-world clinical setting in Pakistan. Fine-tuning them with local EHR data and regional clinical contexts improved their reliability, demonstrating a feasible adaptation strategy that is substantially less resource-intensive than training large language models from scratch. Close collaboration between local clinical and technical experts to curate and leverage more representative, inclusive, and unbiased medical datasets, can play a crucial role in further ensuring reliability of LLMs for resource-limited, overburdened settings, to be used in ways that are safe, fair, and beneficial for all.

Large language models (LLMs) are increasingly adopted in medical question answering (QA) scenarios. However, LLMs have been proven to generate hallucinations and nonfactual information, undermining their trustworthiness in high-stakes medical tasks. Conformal Prediction (CP) is now recognized as a robust framework within the broader domain of machine learning, offering statistically rigorous guarantees of marginal (average) coverage for prediction sets. However, the applicability of CP in medical QA remains to be explored. To address this limitation, this study proposes an enhanced CP framework for medical multiple-choice question answering (MCQA) tasks. The enhanced CP framework associates the non-conformance score with the frequency score of the correct option. The framework generates multiple outputs for the same medical query by leveraging self-consistency theory. The proposed framework calculates the frequency score of each option to address the issue of limited access to the model’s internal information. Furthermore, a risk control framework is incorporated into the enhanced CP framework to manage task-specific metrics through a monotonically decreasing loss function. The enhanced CP framework is evaluated on three popular MCQA datasets using off-the-shelf LLMs. Empirical results demonstrate that the enhanced CP framework achieves user-specified average (or marginal) error rates on the test set. Moreover, the results show that the test set’s average prediction set size (APSS) decreases as the risk level increases. It is concluded that it is a promising evaluation metric for the uncertainty of LLMs.

Although large language models (LLMs) have been assessed for general medical knowledge using licensing exams, their ability to support clinical decision-making, such as selecting medical calculators, remains uncertain. We assessed nine LLMs, including open-source, proprietary, and domain-specific models, with 1,009 multiple-choice question-answer pairs across 35 clinical calculators and compared LLMs to humans on a subset of questions. While the highest-performing LLM, OpenAI's o1, provided an answer accuracy of 66.0% (CI: 56.7-75.3%) on the subset of 100 questions, two human annotators nominally outperformed LLMs with an average answer accuracy of 79.5% (CI: 73.5-85.0%). Ultimately, we evaluated medical trainees and LLMs in recommending medical calculators across clinical scenarios like risk stratification and diagnosis. With error analysis showing that the highest -performing LLMs continue to make mistakes in comprehension (49.3% of errors) and calculator knowledge (7.1% of errors), our findings highlight that LLMs are not superior to humans in calculator recommendation.

Large Language Models (LLMs) have the potential of facilitating the development of Artificial Intelligence technology to assist medical experts for interactive decision support. This potential has been illustrated by the state-of-the-art performance obtained by LLMs in Medical Question Answering, with striking results such as passing marks in licensing medical exams. However, while impressive, the required quality bar for medical applications remains far from being achieved. Currently, LLMs remain challenged by outdated knowledge and by their tendency to generate hallucinated content. Furthermore, most benchmarks to assess medical knowledge lack reference gold explanations which means that it is not possible to evaluate the reasoning of LLMs predictions. Finally, the situation is particularly grim if we consider benchmarking LLMs for languages other than English which remains, as far as we know, a totally neglected topic. In order to address these shortcomings, in this paper we present MedExpQA, the first multilingual benchmark based on medical exams to evaluate LLMs in Medical Question Answering. To the best of our knowledge, MedExpQA includes for the first time reference gold explanations, written by medical doctors, of the correct and incorrect options in the exams. Comprehensive multilingual experimentation using both the gold reference explanations and Retrieval Augmented Generation (RAG) approaches show that performance of LLMs, with best results around 75 accuracy for English, still has large room for improvement, especially for languages other than English, for which accuracy drops 10 points. Therefore, despite using state-of-the-art RAG methods, our results also demonstrate the difficulty of obtaining and integrating readily available medical knowledge that may positively impact results on downstream evaluations for Medical Question Answering. Data, code, and fine-tuned models will be made publicly available.11https://huggingface.co/datasets/HiTZ/MedExpQA.

Over the past five years, medical question answering (QA) has witnessed rapid advancements, driven by the evolution of large language models (LLMs), explainability techniques, and the growing emphasis on human-centered AI in healthcare. In clinical settings, where decisions directly impact patient outcomes, the need for transparency, interpretability, and trust in AI-generated answers is not merely beneficial but essential..Traditional QA systems, although reasonably accurate, often lack explainability, thus continuing to function as black boxes. This opacity raises fundamental concerns about accountability, safety in high-stakes medical domains. We introduce ExplainMed++, a novel system designed to generate human-centered medical QA summaries with intelligible explanations. Our approach enhances the interpretability and reliability of QA outputs by fine-tuning state-of-the-art LLMs using domain-specific datasets such as MedQA. This design is influenced by cognitive models of physician decision-making and recent progress in self-rationale LLMs. This literature increasingly highlights the limitations of accuracy-centric but also provides evidence-based and clinically aligned explanations.We incorporate an explanation module that leverages retrieval-augmented generation and reflective reasoning to align model outputs with clinical reasoning patterns. This literature review synthesizes findings from 70 influential studies published between 2020 and 2025,spanning foundational work in biomedical NLP, explainable AI(XAI), highlighting key technological advances, unresolved challenges, and promising future directions in explainable medical QA. These works collectively illuminate both the promise and limitations of current methodologies, including prompt-based reasoning and counterfactual generation. ExplainMed++ contributes to this landscape by bridging the gap between model performance and clinical usability and also, advancing both the performance and the trust-worthiness of QA systems in healthcare.

Large Language Models (LLMs) have garnered increasing attention in neurosurgery and possess significant potential to improve the field. However, the breadth and performance of LLMs across diverse neurosurgical tasks have not been systematically examined, and LLMs come with their own challenges and unique terminology. We seek to identify key models, establish reporting guidelines for replicability, and highlight progress in key application areas of LLM use in the neurosurgical literature. We searched PubMed and Google Scholar using terms related to LLMs and neurosurgery ("large language model" OR "LLM" OR "ChatGPT" OR "GPT-3" OR "GPT3" OR "GPT-3.5" OR "GPT3.5" OR "GPT-4" OR "GPT4" OR "LLAMA" OR "MISTRAL" OR "BARD") AND "neurosurgery". The final set of articles was reviewed for publication year, application area, specific LLM(s) used, control/comparison groups used to evaluate LLM performance, whether the article reported specific LLM prompts, prompting strategy types used, whether the LLM query could be reproduced in its entirety (including both the prompt used and any adjoining data), measures of hallucination, and reported performance measures. Fifty-one articles met inclusion criteria, and were categorized into six application areas, with the most common being Generation of Text for Direct Clinical Use (n = 14, 27.5%), Answering Standardized Exam Questions (n = 12, 23.5%), and Clinical Judgement and Decision-Making Support (n = 11, 21.6%). The most frequently used LLMs were GPT-3.5 (n = 30, 58.8%), GPT-4 (n = 20, 39.2%), Bard (n = 9, 17.6%), and Bing (n = 6, 11.8%). Most studies (n = 43, 84.3%) used LLMs directly out-of-the-box, while 8 studies (15.7%) conducted advanced pre-training or fine-tuning. Large language models show advanced capabilities in complex tasks and hold potential to transform neurosurgery. However, research typically addresses basic applications and overlooks enhancing LLM performance, facing reproducibility issues. Standardizing detailed reporting, considering LLM stochasticity, and using advanced methods beyond basic validation are essential for progress.

The integration of large language models (LLMs) into medical diagnostics has garnered substantial attention due to their potential to enhance diagnostic accuracy, streamline clinical workflows, and address health care disparities. However, the rapid evolution of LLM research necessitates a comprehensive synthesis of their applications, challenges, and future directions. This scoping review aimed to provide an overview of the current state of research regarding the use of LLMs in medical diagnostics. The study sought to answer four primary subquestions, as follows: (1) Which LLMs are commonly used? (2) How are LLMs assessed in diagnosis? (3) What is the current performance of LLMs in diagnosing diseases? (4) Which medical domains are investigating the application of LLMs? This scoping review was conducted according to the Joanna Briggs Institute Manual for Evidence Synthesis and adheres to the PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews). Relevant literature was searched from the Web of Science, PubMed, Embase, IEEE Xplore, and ACM Digital Library databases from 2022 to 2025. Articles were screened and selected based on predefined inclusion and exclusion criteria. Bibliometric analysis was performed using VOSviewer to identify major research clusters and trends. Data extraction included details on LLM types, application domains, and performance metrics. The field is rapidly expanding, with a surge in publications after 2023. GPT-4 and its variants dominated research (70/95, 74% of studies), followed by GPT-3.5 (34/95, 36%). Key applications included disease classification (text or image-based), medical question answering, and diagnostic content generation. LLMs demonstrated high accuracy in specialties like radiology, psychiatry, and neurology but exhibited biases in race, gender, and cost predictions. Ethical concerns, including privacy risks and model hallucination, alongside regulatory fragmentation, were critical barriers to clinical adoption. LLMs hold transformative potential for medical diagnostics but require rigorous validation, bias mitigation, and multimodal integration to address real-world complexities. Future research should prioritize explainable artificial intelligence frameworks, specialty-specific optimization, and international regulatory harmonization to ensure equitable and safe clinical deployment.

The rapid growth of biomedical literature poses challenges for manual knowledge curation and synthesis. Biomedical Natural Language Processing (BioNLP) automates the process. While Large Language Models (LLMs) have shown promise in general domains, their effectiveness in BioNLP tasks remains unclear due to limited benchmarks and practical guidelines. We perform a systematic evaluation of four LLMs—GPT and LLaMA representatives—on 12 BioNLP benchmarks across six applications. We compare their zero-shot, few-shot, and fine-tuning performance with the traditional fine-tuning of BERT or BART models. We examine inconsistencies, missing information, hallucinations, and perform cost analysis. Here, we show that traditional fine-tuning outperforms zero- or few-shot LLMs in most tasks. However, closed-source LLMs like GPT-4 excel in reasoning-related tasks such as medical question answering. Open-source LLMs still require fine-tuning to close performance gaps. We find issues like missing information and hallucinations in LLM outputs. These results offer practical insights for applying LLMs in BioNLP.

e13609 Background: Precision oncology revolutionized cancer treatment by identifying molecular biomarkers to guide personalized care. The ever-growing body of medical literature presents a challenge for oncologists researching targeted therapies. While recent studies investigated large language models (LLMs) to streamline this process, LLM reliance on general rather than medical knowledge limits clinical relevance and trustworthiness. To address these limitations, we developed a retrieval augmented generation (RAG) system that integrates PubMed clinical studies, trial databases and oncological guidelines with LLMs to support targeted treatment recommendations. The Molecular Tumor Board (MTB) at the Center of Personalized Medicine (ZPMTUM) guided and evaluated treatment options proposed by the LLM to assess their applicability for clinical decision support. Methods: We used 10 publicly accessible fictional patient cases with 7 tumor types and 59 distinct molecular alterations. Our LLM system MEREDITH (Medical Evidence Retrieval and Data Integration for Tailored Healthcare) consists of Google's Gemini Pro, enhanced with RAG and Chain-of-Thought (CoT) prompting. To establish a benchmark, clinical experts at ZPMTUM manually annotated the cases. Informed by MTB expert feedback, we iteratively improved our LLM system from a draft system relying on PubMed-indexed data to an enhanced system, which replicated expert annotation processes by incorporating oncology guidelines, drug availability and trial databases (ClinicalTrials.gov, QuickQueck.de). ZPMTUM assessed credibility and clinical relevance of manually annotated and LLM-generated recommendations. Patient-level data on (likely) pathogenic molecular alterations and recommended treatment options were summarized using median and interquartile range (IQR). Semantic similarity between LLM and clinician responses was assessed using cosine similarity of text vector embeddings; paired t-test evaluated significance. Results: The median of (likely) pathogenic molecular alterations per patient was 2.5 (IQR: 2-3). ZPMTUM identified a median of 2 treatment options per patient (IQR: 1-3), while the enhanced LLM identified a median of 4 (IQR: 3-5). MEREDITH proposed multiple relevant treatment suggestions, including therapies based on preclinical studies, and molecular interactions, for further assessment by the MTB. ZPMTUM prioritized the most suitable clinical option. The mean semantic textual similarity of LLM responses increased significantly from 0.69 in the draft system to 0.76 in the enhanced system (p <0.001). Thus, feedback from ZPMTUM enhanced the model's ability to align its responses with clinician thought processes. Conclusions: Leveraging expert thought processes to instruct LLMs holds promise as a novel decision support tool for precision oncology.

Cardiovascular disease (CVD) remains the leading cause of morbidity and mortality worldwide. Large language models (LLMs) offer potential solutions for enhancing patient education and supporting clinical decision-making. This study aimed to evaluate LLMs' applications in CVD and explore their current implementation, from prevention to treatment. Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines, this systematic review assessed LLM applications in CVD. A comprehensive PubMed search identified relevant studies. The review prioritized pragmatic and practical applications of LLMs. Key applications, benefits, and limitations of LLMs in CVD prevention were summarized. Thirty-five observational studies met the eligibility criteria. Of these, 54% addressed primary prevention and risk factor management, while 46% focused on established CVD. Commercial LLMs were evaluated in all but one study, with 91% (32 studies) assessing ChatGPT. The LLM applications were categorized as follows: 72% addressed patient education, 17% clinical decision support, and 11% both. In 68% of studies, the primary objective was to evaluate LLMs' performance in answering frequently asked patient questions, with results indicating accurate, comprehensive, and generally safe responses. However, occasional misinformation and hallucinated references were noted. Additional applications included patient guidance on CVD, first aid, and lifestyle recommendations. Large language models were assessed for medical questions, diagnostic support, and treatment recommendations in clinical decision support. Large language models hold significant potential in CVD prevention and treatment. Evidence supports their potential as an alternative source of information for addressing patients' questions about common CVD. However, further validation is needed for their application in individualized care, from diagnosis to treatment.

The aim of this study was to examine the application of artificial intelligence (AI) and generative AI (GAI) in dental education through a comprehensive bibliometric analysis, with the goal of identifying potential future research areas in this field. Data were obtained from the Web of Science and Scopus databases, with no date restrictions. The inclusion criteria encompassed research articles, reviews and proceedings papers focused on the use of AI in dental education. The Bibliometrix R package was used for data analysis. A total of 54 documents were analysed, revealing a significant increase in publications from 2021 to 2024. The Journal of Dental Education was identified as the most prolific source, with the United States leading in terms of contributions. The findings showed a growing interest in AI's potential to transform dental education, with significant contributions from a diverse set of global authors and institutions. Several key themes were identified, including 'large language models', 'chatbots' and 'clinical decision support systems'. The citation analysis highlighted influential papers, including those by Thurzo etal. (2023) and Yüzbaşıoğlu (2021). There is a growing interest in the use of AI and GAI in dental education. However, further research, particularly experimental studies, is essential to fully understand their impact on educational outcomes in dentistry. Key areas for exploration include the application of AI for personalised learning, the integration of chatbots as educational tools to support students, and the use of AI for training and assessing practical skills.

Named entity recognition (NER) plays a vital role in extracting critical medical entities from health care records, facilitating applications such as clinical decision support and data mining. Developing robust NER models for low-resource languages, such as Estonian, remains a challenge due to the scarcity of annotated data and domain-specific pretrained models. Large language models (LLMs) have proven to be promising in understanding text from any language or domain. This study addresses the development of medical NER models for low-resource languages, specifically Estonian. We propose a novel approach by generating synthetic health care data and using LLMs to annotate them. These synthetic data are then used to train a high-performing NER model, which is applied to real-world medical texts, preserving patient data privacy. Our approach to overcoming the shortage of annotated Estonian health care texts involves a three-step pipeline: (1) synthetic health care data are generated using a locally trained GPT-2 model on Estonian medical records, (2) the synthetic data are annotated with LLMs, specifically GPT-3.5-Turbo and GPT-4, and (3) the annotated synthetic data are then used to fine-tune an NER model, which is later tested on real-world medical data. This paper compares the performance of different prompts; assesses the impact of GPT-3.5-Turbo, GPT-4, and a local LLM; and explores the relationship between the amount of annotated synthetic data and model performance. The proposed methodology demonstrates significant potential in extracting named entities from real-world medical texts. Our top-performing setup achieved an F1-score of 0.69 for drug extraction and 0.38 for procedure extraction. These results indicate a strong performance in recognizing certain entity types while highlighting the complexity of extracting procedures. This paper demonstrates a successful approach to leveraging LLMs for training NER models using synthetic data, effectively preserving patient privacy. By avoiding reliance on human-annotated data, our method shows promise in developing models for low-resource languages, such as Estonian. Future work will focus on refining the synthetic data generation and expanding the method's applicability to other domains and languages.

Large language models for electronic health records in pediatric and surgical care: A systematic review.

PurposeCurrent benchmarks evaluating large language models (LLMs) in ophthalmology are narrow and disproportionately prioritize accuracy. We introduce BEnchmarking LLMs for Ophthalmology (BELO), a standardized evaluation benchmark developed through multiple rounds of expert checking by 13 ophthalmologists. BEnchmarking LLMs for Ophthalmology assesses ophthalmology-related knowledge and reasoning quality.SubjectsThis study did not involve human participation.DesignCross-sectional study.MethodsUsing keyword matching and a fine-tuned PubMed Bidirectional Encoder Representations from Transformers model, we curated ophthalmology-specific multiple-choice questions (MCQs) from diverse medical data sets (Basic and Clinical Science Course [BCSC], Multi-Subject Multi-Choice Dataset for Medical domain [MedMCQA], Medical Question Answering [MedQA], Biomedical Semantic Indexing and Question Answering [BioASQ], and PubMed Question Answering [PubMedQA]). The data set underwent multiple rounds of expert checking. Duplicate and substandard questions were systematically removed. Ten ophthalmologists refined the explanations of each MCQ's correct answer. This was further adjudicated by 3 senior ophthalmologists. To illustrate BELO's utility, we evaluated 8 LLMs (OpenAI o1, o3-mini, GPT-5, GPT-4o, DeepSeek-R1, MedGemma-4B, Llama-3-8B, and Gemini 1.5 Pro).Main Outcome MeasuresThe 8 LLMs were evaluated in terms using accuracy, macro-F1, and 5 text-generation metrics (Recall-Oriented Understudy for Gisting Evaluation, BERTScore, BARTScore, Metric for Evaluation of Translation with Explicit Ordering, and AlignScore). In a further evaluation involving human experts, 2 ophthalmologists qualitatively reviewed 50 randomly selected outputs for accuracy, comprehensiveness, and completeness.ResultsBEnchmarking LLMs for Ophthalmology consists of 900 high-quality, expert-reviewed questions aggregated from 5 sources: BCSC (260), BioASQ (10), MedMCQA (572), MedQA (40), and PubMedQA (18). To demonstrate BELO's utility, we conducted a series of benchmarking exercises. In the quantitative evaluation, GPT-5 achieved the highest accuracy (0.90, 95% confidence interval [CI]: 0.89–0.92) and macro-F1 score (0.91, 95% CI: 0.89–0.93). On the other hand, the models' performance on text-generation metrics varied and were generally suboptimal, with scores ranging from 20.4 to 72.0 (out of 100, excluding the BARTScore metric), indicating room for improvement in clinical reasoning. In expert evaluations, GPT-4o was rated highest for accuracy and readability, while Gemini 1.5 Pro scored highest for completeness. A public leaderboard has been established to promote transparent evaluation and reporting. Importantly, the BELO data set will remain a hold-out, evaluation-only benchmark to ensure fair and reproducible comparisons of future models.ConclusionsBEnchmarking LLMs for Ophthalmology provides a robust clinically relevant benchmark for evaluating both the accuracy and reasoning capabilities of current and emerging LLMs in ophthalmology. Future BELO benchmarking efforts will expand to include vision-based question answering and clinical scenario management tasks.Financial Disclosure(s)The authors have no proprietary or commercial interest in any materials discussed in this article.

A survey for large language models in biomedicine.