A Practical Application of Retrieval-Augmented Generation for Website-Based Chatbots: Combining Web Scraping, Vectorization, and Semantic Search

The paper introduces a Knowledge Retrieval-Based Intelligent Question and Answer Generation Framework for Education, leveraging Retrieval Augmented Generation (RAG) to enhance Large Language Models (LLMs) in producing high-quality, contextually relevant examination questions and answers across subjects. The framework addresses challenges in ensuring comprehensive subject coverage, educational standards, and evaluation metrics. Key components include Optical Character Recognition (OCR), data chunking, vectorization using multilingual BERT, and custom retrieval functions. The RAG system's effectiveness is evaluated using the RAGAs metric, covering metrics like faithfulness, answer relevancy, context recall, and context precision. Comparative results reveal OpenAI models surpassing Google's Gemini in coherence and context relevance due to differing architectures and training methods. Concluding, the paper highlights potential for both large and small language models in tailored educational applications, noting limitations such as hallucinations, high resource demands, and contextual drift.

Large language models (LLMs) are rapidly advancing natural language processing and driving increasing interest across biomedical research, clinical care, and healthcare operations. This systematic review synthesizes current empirical evidence on LLM applications in healthcare and biomedical informatics, focusing on their capabilities, evaluation practices, and reported outcomes. Existing studies highlight promising uses in research, where LLMs assist literature-informed genomic interpretation, functional annotation, and biological hypothesis generation, as well as support tasks related to protein and multiomics analysis. In clinical contexts, LLMs are primarily evaluated for natural language-driven tasks, including electronic health record summarization, clinical documentation support, medical question answering, and information extraction, rather than autonomous diagnostic or therapeutic decision-making. Early investigations also describe potential value in healthcare operations, patient communication, clinician education, and drug discovery workflows largely through knowledge retrieval, text generation, and semantic search. However, current evidence remains preliminary: most studies are retrospective, benchmark-based, simulation-driven, or limited to controlled research settings. Key challenges include hallucination and unreliable reasoning, bias and inequitable performance across populations, data privacy and security constraints, reproducibility limitations, and lack of prospective clinical validation and regulatory guidance. Emerging strategies, such as domain-specific pretraining, retrieval augmentation, multi-modal architectures, and privacy-preserving learning, aim to improve reliability, safety, and real-world applicability. This review concludes by outlining methodological, infrastructural, and governance requirements needed to responsibly integrate LLMs into biomedical workflows, emphasizing that clinical deployment remains exploratory and must be rigorously evaluated.

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.

On the role of the UMLS in supporting diagnosis generation proposed by Large Language Models

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.

Googling for Health Information

Serious Bacterial Infection (SBI) in neonates and young infants often exhibit nonspecific symptoms and clinical signs in the early stages of illness, making early diagnosis challenging. Timely recognition and appropriate treatment are essential to prevent adverse outcomes. While several clinical algorithms are widely used for SBI risk stratification, these tools have limitations, particularly low positive predictive value. This study evaluates the diagnostic accuracy of general-purpose large language models (LLMs) in detecting SBI in neonates and infants under 90 days of age admitted to the emergency department. Our objective is to improve diagnostic precision, reduce unnecessary interventions, and enhance patient outcomes. LLM performance was compared against traditional machine learning models, state-of-the-art rule-based methods, and an ensemble of physicians to assess their potential as clinical decision-support tools in scenarios of diagnostic uncertainty. On a dataset of 742 patients, LLMs demonstrated diagnostic accuracy comparable to traditional machine learning models and state-of-the-art rule-based methods. The optimized CatBoost (class-weighted) model achieved the best overall performance, with a PPV of 0.70, NPV of 0.90, sensitivity of 0.54, specificity of 0.95, F1-score of 0.60, and MCC of 0.54, outperforming the baseline CatBoost model and achieving results on par with large language models (LLMs) and physicians. When optimally prompted, LLMs performed on par with ensembles of experienced clinicians. Additionally, LLMs exhibited effective medical reasoning and provided credible diagnostic predictions, particularly valuable in cases of clinician uncertainty. The models achieved balanced performance across multiple evaluation metrics, including PPV, NPV, sensitivity, specificity, F1-score, and Matthew’s correlation coefficient (MCC). ChatGPT-4o achieved a sensitivity of 0.65 and specificity of 0.83, with an MCC of 0.41. Claude Sonnet 3.5 reached a sensitivity of 0.60 and specificity of 0.86, MCC 0.42 and Google Gemini 2.0 Flash had lower sensitivity (0.43) but the highest specificity (0.94), with an MCC of 0.43. In comparison, the best-performing individual pediatrician achieved a higher sensitivity (0.74) but lower specificity (0.68), with an MCC of 0.33, while the pediatricians’ majority vote yielded sensitivity of 0.69, specificity of 0.81, and MCC of 0.43 — comparable to the top-performing LLMs. These Artificial intelligence tools offer a promising direction for SBI risk prediction, achieving performance comparable to that of experienced pediatric specialists, while maintaining simplicity of use/data-preprocessing for potential real-world applications.

Introduction Advances in large language models (LLMs) have opened new avenues for healthcare applications. Recently, ChatGPT-4 successfully achieved the pass mark >80% in 5 of 10 sleep medicine examination domains, indicating a strong foundational knowledge of sleep medicine. However, the ability to answer USMLE-type multiple-choice questions may not equate to the capacity to offer accurate and comprehensive answers to clinical queries or real-world case scenarios. Current literature exhibits a significant gap in validation research examining the clinical utility of LLMs in evidence-based medicine practice. This investigation aims to evaluate the potential usefulness and reliability of LLMs as adjunctive clinical decision-support tools (namely, “curbside consultants”) in sleep medicine. Methods Six clinical sleep queries and six case scenarios were presented to 6 LLMs including 3 general-purpose LLMs (ChatGPT-4o, Gemini-1.5-Pro, and Llama-3.1-405B) and 3 medical-specialized LLMs (OpenEvidence, Clara AI, and MediGPT). Performance assessment was conducted independently utilizing two independently developed 5-point Likert scales evaluating two primary domains: answer content (accuracy, relevance, comprehensiveness/depth, clarity/coherence, and unique insightfulness) and reference quality (accuracy, relevance, currentness, comprehensiveness/depth, and searchability). Benchmark answers were established through consensus among four sleep medicine specialists. Analysis of variance was used to compare the performance of the LLMs. Results The medical LLMs demonstrated superior overall performance compared to the general LLMs (P< 0.001). The primary distinction was observed in reference quality metrics, where medical LLMs significantly outperformed general LLMs across all parameters: accuracy, relevance, and searchability (p< 0.001), currentness (p=0.001), and comprehensiveness/depth (p=0.010). Notably, Open Evidence achieved the highest reference quality (p< 0.001). In contrast, the answer content analysis revealed no significant overall differences between medical and general LLMs (p=0.659). Most answer content-related metrics, including accuracy, relevance, or unique insightfulness, did not differ significantly (p>0.050). An exception was clarify/coherence, where medical LLMs were superior to general LLMs (p=0.030). Furthermore, MediGPT and ChatGPT-4o displayed better content comprehensiveness/depth relative to other LLMs (p< 0.001). These two LLMs exhibited comparable performance in overall metrics (p=0.615), answer contents (p=0.922), and reference quality (p=0.621). Conclusion Both medical-specialized and general-purpose LLMs show promise as adjunctive decision-support tools in clinical practice. However, substantial improvements in reference quality are critically needed across most LLM platforms. Support (if any)

The growing interest in advanced large language models (LLMs) like ChatGPT has sparked debate about how best to use them in various human activities. However, a neglected issue in the debate concerning the applications of LLMs is whether they can reason logically and follow rules in novel contexts, which are critical for our understanding and applications of LLMs. To address this knowledge gap, this study investigates five LLMs (ChatGPT-4o, Claude, Gemini, Meta AI, and Mistral) using word ladder puzzles to assess their logical reasoning and rule-adherence capabilities. Our two-phase methodology involves (1) explicit instructions about word ladder puzzles and rules regarding how to solve the puzzles and then evaluate rule understanding, followed by (2) assessing LLMs’ ability to create and solve word ladder puzzles while adhering to rules. Additionally, we test their ability to implicitly recognize and avoid HIPAA privacy rule violations as an example of a real-world scenario. Our findings reveal that LLMs show a persistent lack of logical reasoning and systematically fail to follow puzzle rules. Furthermore, all LLMs except Claude prioritized task completion (text writing) over ethical considerations in the HIPAA test. Our findings expose critical flaws in LLMs’ reasoning and rule-following capabilities, raising concerns about their reliability in critical tasks requiring strict rule-following and logical reasoning. Therefore, we urge caution when integrating LLMs into critical fields and highlight the need for further research into their capabilities and limitations to ensure responsible AI development.

Large language models (LLMs) have shown impressive capabilities across various natural language tasks. However, evaluating their alignment with human preferences remains a challenge. To this end, we propose a comprehensive human evaluation framework to assess LLMs’ proficiency in following instructions on diverse real-world tasks. We construct a hierarchical task tree encompassing 7 major areas covering over 200 categories and over 800 tasks, which covers diverse capabilities such as question answering, reasoning, multiturn dialogue, and text generation, to evaluate LLMs in a comprehensive and in-depth manner. We also design detailed evaluation standards and processes to facilitate consistent, unbiased judgments from human evaluators. A test set of over 3,000 instances is released, spanning different difficulty levels and knowledge domains. Our work provides a standardized methodology to evaluate human alignment in LLMs for both English and Chinese. We also analyze the feasibility of automating parts of evaluation with a strong LLM (GPT-4). Our framework supports a thorough assessment of LLMs as they are integrated into real-world applications. We have made publicly available the task tree, TencentLLMEval dataset, and evaluation methodology which have been demonstrated as effective in assessing the performance of Tencent Hunyuan LLMs 1 . By doing so, we aim to facilitate the benchmarking of advances in the development of safe and human-aligned LLMs.

This paper investigates the impact of knowledge extraction methods on the effectiveness of RAG (Retrieval-Augmented Generation) systems that utilize knowledge graphs. It highlights that the quality of the knowledge graph, which is formed using various knowledge extraction methods, is crucial for overcoming limitations of large language models (LLMs), such as “hallucinations”. The paper analyzes the architectures of LightRAG and GraphRAG, emphasizing that the selection of an optimal knowledge extraction strategy depends on specific tasks and the subject area. LLMs have advanced significantly, but they have limitations, including generating factually incorrect information (“hallucinations”) and possessing “outdated knowledge”. RAG systems were proposed to address these issues by combining LLMs with external knowledge bases. This approach reduces hallucinations, ensures factual accuracy, solves the problem of outdated knowledge, and increases transparency. Knowledge graphs are powerful tools for structuring information, consisting of entities (nodes) and relations (edges). They enhance RAG systems by enabling more precise and contextually grounded retrieval compared to keyword-based searches. The quality of a knowledge graph depends on the knowledge extraction methods used, which include named entity recognition (NER), relation extraction (RE), entity linking (EL), and event extraction. Different methods, such as rule-based, classical machine learning, and deep learning approaches, have varying trade-offs in terms of accuracy, completeness, and scalability. Entity linking and knowledge graph completion are also crucial for accuracy and richness. LightRAG and GraphRAG are two main graph-based RAG systems. LightRAG uses the knowledge graph as a quick reference, requiring high precision in knowledge extraction to avoid noise degradation. GraphRAG uses the knowledge graph as a domain model, where completeness of extracted knowledge is more critical, though systematic errors are still harmful. Both systems rely on LLMs for knowledge extraction, which makes them dependent on the LLM’s quality and the size of document fragments processed. The theoretical analysis confirms that the effectiveness of RAG systems is critically dependent on knowledge extraction methods. The quality, completeness, and accuracy of the knowledge graph directly influence the RAG system’s ability to provide relevant, accurate, and truthful answers. Different RAG system architectures like LightRAG and GraphRAG have distinct requirements for knowledge graph characteristics, prioritizing either accuracy or completeness in knowledge extraction.

Brief hospital course (BHC) summaries are clinical documents that summarize a patient's hospital stay. While large language models (LLMs) depict remarkable capabilities in automating real-world tasks, their capabilities for healthcare applications such as synthesizing BHCs from clinical notes have not been shown. We introduce a novel preprocessed dataset, the MIMIC-IV-BHC, encapsulating clinical note and BHC pairs to adapt LLMs for BHC synthesis. Furthermore, we introduce a benchmark of the summarization performance of 2 general-purpose LLMs and 3 healthcare-adapted LLMs. Using clinical notes as input, we apply prompting-based (using in-context learning) and fine-tuning-based adaptation strategies to 3 open-source LLMs (Clinical-T5-Large, Llama2-13B, and FLAN-UL2) and 2 proprietary LLMs (Generative Pre-trained Transformer [GPT]-3.5 and GPT-4). We evaluate these LLMs across multiple context-length inputs using natural language similarity metrics. We further conduct a clinical study with 5 clinicians, comparing clinician-written and LLM-generated BHCs across 30 samples, focusing on their potential to enhance clinical decision-making through improved summary quality. We compare reader preferences for the original and LLM-generated summary using Wilcoxon signed-rank tests. We further request optional qualitative feedback from clinicians to gain deeper insights into their preferences, and we present the frequency of common themes arising from these comments. The Llama2-13B fine-tuned LLM outperforms other domain-adapted models given quantitative evaluation metrics of Bilingual Evaluation Understudy (BLEU) and Bidirectional Encoder Representations from Transformers (BERT)-Score. GPT-4 with in-context learning shows more robustness to increasing context lengths of clinical note inputs than fine-tuned Llama2-13B. Despite comparable quantitative metrics, the reader study depicts a significant preference for summaries generated by GPT-4 with in-context learning compared to both Llama2-13B fine-tuned summaries and the original summaries (P<.001), highlighting the need for qualitative clinical evaluation. We release a foundational clinically relevant dataset, the MIMIC-IV-BHC, and present an open-source benchmark of LLM performance in BHC synthesis from clinical notes. We observe high-quality summarization performance for both in-context proprietary and fine-tuned open-source LLMs using both quantitative metrics and a qualitative clinical reader study. Our research effectively integrates elements from the data assimilation pipeline: our methods use (1) clinical data sources to integrate, (2) data translation, and (3) knowledge creation, while our evaluation strategy paves the way for (4) deployment.

Custom Large Language Models Improve Accuracy: Comparing Retrieval Augmented Generation and Artificial Intelligence Agents to Non-Custom Models for Evidence-Based Medicine

Research Context: Nearest Neighbor Search (NNS) is a fundamental problem in computing, with applications in recommendation systems, semantic search, information retrieval, and Retrieval-Augmented Generation (RAG) in Large Language Models (LLMs). High-dimensional datasets with millions of vectors make exact search computationally intractable, demanding efficient approximations. Practical Problem: Approximate Nearest Neighbor Search (ANNS) has become the standard approach, with graph-based methods standing out. However, structures such as Hierarchical Navigable Small World (HNSW) graphs impose high construction and update costs, which limits their scalability in real-world scenarios. Proposed Solution: This paper proposes the integration of Canopy Clustering as a divide-and-conquer heuristic to mitigate the computational burden of HNSW graph construction under cosine similarity, enabling more cost-effective ANNS pipelines in information retrieval systems. Related IS Theory: The research aligns with Information Systems theories on efficiency of knowledge retrieval, and the optimization of data-intensive processes in decision-support environments. It builds upon principles of data organization and access structures in IS, particularly the trade-offs between accuracy and computational feasibility in large-scale information retrieval. Research Method: Controlled experiments were conducted to evaluate the applicability of divide-and-conquer and Canopy Clustering prior to HNSW construction. Comparative analyses measured build time, query latency, and recall performance. Summary of Results: Preliminary findings suggest that Canopy Clustering can reduce construction costs while sustaining recall levels adequate for IS applications. Contributions and Impact to IS area: The work introduces a novel heuristic combination to enhance the scalability of graph-based similarity search indexing, providing methodological advances that may extend to other high-dimensional data processing tasks. It offers actionable insights for designing more efficient and viable intelligent information systems.

In the current era of artificial intelligence, large language models such as ChatGPT and BARD are being increasingly used for various applications, such as language translation, text generation, and human-like conversation. The fact that these models consist of large amounts of data, including many different opinions and perspectives, could introduce the possibility of a new qualitative research approach: Due to the probabilistic character of their answers, “interviewing” these large language models could give insights into public opinions in a way that otherwise only interviews with large groups of subjects could deliver. However, it is not yet clear if qualitative content analysis research methods can be applied to interviews with these models. Evaluating the applicability of qualitative research methods to interviews with large language models could foster our understanding of their abilities and limitations. In this paper, we examine the applicability of qualitative content analysis research methods to interviews with ChatGPT in English, ChatGPT in German, and BARD in English on the relevance of computer science in K-12 education, which was used as an exemplary topic. We found that the answers produced by these models strongly depended on the provided context, and the same model could produce heavily differing results for the same questions. From these results and the insights throughout the process, we formulated guidelines for conducting and analyzing interviews with large language models. Our findings suggest that qualitative content analysis research methods can indeed be applied to interviews with large language models, but with careful consideration of contextual factors that may affect the responses produced by these models. The guidelines we provide can aid researchers and practitioners in conducting more nuanced and insightful interviews with large language models. From an overall view of our results, we generally do not recommend using interviews with large language models for research purposes, due to their highly unpredictable results. However, we suggest using these models as exploration tools for gaining different perspectives on research topics and for testing interview guidelines before conducting real-world interviews.