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Evaluation of large language models for clinical sign-based oral assessment in dogs compared with veterinary practitioners.

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Evaluation of large language models for clinical sign-based oral assessment in dogs compared with veterinary practitioners.

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  • Research Article
  • 10.2196/86630
Evaluation of GPT-5 for Esophageal Cancer Staging Using Fluorodeoxyglucose Positron Emission Tomography Maximum-Intensity Projection Images: Comparative Pilot Study.
  • Feb 23, 2026
  • JMIR cancer
  • Hiroki Maruyama + 7 more

Accurate esophageal cancer staging relies on 18F fluorodeoxyglucose positron emission tomography (18F FDG-PET), but its interpretation is complex and time-intensive. This diagnostic burden is exacerbated by significant workforce shortages in both radiology and surgery, thus necessitating automated support systems. The emergence of advanced large language models (LLMs) has raised expectations for their potential to fulfill this role in complex medical tasks. We evaluated the diagnostic accuracy of LLMs for staging esophageal cancer using 18F FDG-PET images, with a focus on their ability to assess lymph nodes (LNs; clinical N [cN]) and distant metastases (clinical M [cM]) for automated radiology reporting. This retrospective study included 120 consecutive adult patients who were diagnosed with esophageal squamous cell carcinoma and underwent 18F FDG-PET/computed tomography at Tohoku University Hospital between January 2019 and December 2021. Patients with prior treatment, nonsquamous cell carcinoma histology, or blood glucose levels ≥200 mg/dL were excluded. Frontal maximum-intensity projection positron emission tomography images were extracted, standardized, and analyzed along with information regarding the tumor location. Six LLMs (GPT-5, GPT-4.5, GPT-4.1, OpenAI-o3, -o1, and GPT-4 Turbo) and 4 blinded human evaluators (a nuclear medicine specialist, a gastrointestinal surgeon, and 2 radiology residents) assessed the presence of thoracic and abdominal LN metastases on a region-level basis and determined cN and cM staging on a patient-level basis. The model analyses were performed using the application programming interface in a zero-shot setting. Radiology reports served as the reference standard. Diagnostic agreement and accuracy were evaluated using Cohen κ and the Cochran Q test. Additionally, to account for the class imbalance in the dataset, the Matthews Correlation Coefficient was calculated as a robust metric for binary classification performance. Post hoc McNemar tests were performed with Bonferroni correction; statistical significance for pairwise comparisons was set at P<.0083 (adjusted from P<.05) using JMP Pro (version 18.0; SAS Institute Inc). The average accuracy was 41/120 (34%) to 94/120 (78%) for LLMs and 72/120 (60%) to 102/120 (85%) for physicians, with significantly higher accuracy for physicians (P<.05) in the thoracic LN, abdominal LN, and cN stages. Interrater reliability was slight to fair for LLMs (κ: -0.07 to 0.25) and fair to substantial for physicians (κ: 0.27 to 0.74). Matthews Correlation Coefficient scores were consistently higher for physicians (0.28 to 0.75) than for LLMs (-0.07 to 0.32). Among the LLMs, GPT-5 demonstrated the highest overall accuracy, with newer LLMs showing improved diagnostic accuracy when compared with previous models in identifying abdominal LN metastases and cM staging, though they showed weaker consistency for cN staging. For example, in thoracic LN detection, GPT-5 achieved 76/120 (63%) accuracy, whereas other LLMs achieved 72/120 (60%) or lower accuracy. Although current LLMs have not yet reached physician-level accuracy in comprehensive staging, recent models show promise in assisting with specific diagnostic tasks.

  • Research Article
  • Cite Count Icon 119
  • 10.1001/jamanetworkopen.2023.46721
Performance of Large Language Models on a Neurology Board–Style Examination
  • Dec 7, 2023
  • JAMA network open
  • Marc Cicero Schubert + 2 more

Recent advancements in large language models (LLMs) have shown potential in a wide array of applications, including health care. While LLMs showed heterogeneous results across specialized medical board examinations, the performance of these models in neurology board examinations remains unexplored. To assess the performance of LLMs on neurology board-style examinations. This cross-sectional study was conducted between May 17 and May 31, 2023. The evaluation utilized a question bank approved by the American Board of Psychiatry and Neurology and was validated with a small question cohort by the European Board for Neurology. All questions were categorized into lower-order (recall, understanding) and higher-order (apply, analyze, synthesize) questions based on the Bloom taxonomy for learning and assessment. Performance by LLM ChatGPT versions 3.5 (LLM 1) and 4 (LLM 2) was assessed in relation to overall scores, question type, and topics, along with the confidence level and reproducibility of answers. Overall percentage scores of 2 LLMs. LLM 2 significantly outperformed LLM 1 by correctly answering 1662 of 1956 questions (85.0%) vs 1306 questions (66.8%) for LLM 1. Notably, LLM 2's performance was greater than the mean human score of 73.8%, effectively achieving near-passing and passing grades in the neurology board examination. LLM 2 outperformed human users in behavioral, cognitive, and psychological-related questions and demonstrated superior performance to LLM 1 in 6 categories. Both LLMs performed better on lower-order than higher-order questions, with LLM 2 excelling in both lower-order and higher-order questions. Both models consistently used confident language, even when providing incorrect answers. Reproducible answers of both LLMs were associated with a higher percentage of correct answers than inconsistent answers. Despite the absence of neurology-specific training, LLM 2 demonstrated commendable performance, whereas LLM 1 performed slightly below the human average. While higher-order cognitive tasks were more challenging for both models, LLM 2's results were equivalent to passing grades in specialized neurology examinations. These findings suggest that LLMs could have significant applications in clinical neurology and health care with further refinements.

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  • Cite Count Icon 4
  • 10.1038/s41698-025-00916-7
Evaluating the performance of large language & visual-language models in cervical cytology screening
  • May 23, 2025
  • npj Precision Oncology
  • Qi Hong + 15 more

Large language models (LLMs) and large visual-language models (LVLMs) have exhibited near-human levels of knowledge, image comprehension, and reasoning abilities, and their performance has undergone evaluation in some healthcare domains. However, a systematic evaluation of their capabilities in cervical cytology screening has yet to be conducted. Here, we constructed CCBench, a benchmark dataset dedicated to the evaluation of LLMs and LVLMs in cervical cytology screening, and developed a GPT-based semi-automatic evaluation pipeline to assess the performance of six LLMs (GPT-4, Bard, Claude-2.0, LLaMa-2, Qwen-Max, and ERNIE-Bot-4.0) and five LVLMs (GPT-4V, Gemini, LLaVA, Qwen-VL, and ViLT) on this dataset. CCBench comprises 773 question-answer (QA) pairs and 420 visual-question-answer (VQA) triplets, making it the first dataset in cervical cytology to include both QA and VQA data. We found that LLMs and LVLMs demonstrate promising accuracy and specialization in cervical cytology screening. GPT-4 achieved the best performance on the QA dataset, with an accuracy of 70.5% for close-ended questions and average expert evaluation score of 6.9/10 for open-ended questions. On the VQA dataset, Gemini achieved the highest accuracy for close-ended questions at 67.8%, while GPT-4V attained the highest expert evaluation score of 6.1/10 for open-ended questions. Besides, LLMs and LVLMs revealed varying abilities in answering questions across different topics and difficulty levels. However, their performance remains inferior to the expertise exhibited by cytopathology professionals, and the risk of generating misinformation could lead to potential harm. Therefore, substantial improvements are required before these models can be reliably deployed in clinical practice.

  • Research Article
  • Cite Count Icon 10
  • 10.1016/j.csbj.2024.12.019
Visual-textual integration in LLMs for medical diagnosis: A preliminary quantitative analysis.
  • Jan 1, 2025
  • Computational and structural biotechnology journal
  • Reem Agbareia + 5 more

Visual data from images is essential for many medical diagnoses. This study evaluates the performance of multimodal Large Language Models (LLMs) in integrating textual and visual information for diagnostic purposes. We tested GPT-4o and Claude Sonnet 3.5 on 120 clinical vignettes with and without accompanying images. Each vignette included patient demographics, a chief concern, and relevant medical history. Vignettes were paired with either clinical or radiological images from two sources: 100 images from the OPENi database and 20 images from recent NEJM challenges, ensuring they were not in the LLMs' training sets. Three primary care physicians served as a human benchmark. We analyzed diagnostic accuracy and the models' explanations for a subset of cases. LLMs outperformed physicians in text-only scenarios (GPT-4o: 70.8 %, Claude Sonnet 3.5: 59.5 %, Physicians: 39.5 %, p < 0.001, Bonferroni-adjusted). With image integration, all improved, but physicians showed the largest gain (GPT-4o: 84.5 %, p < 0.001; Claude Sonnet 3.5: 67.3 %, p = 0.060; Physicians: 78.8 %, p < 0.001, all Bonferroni-adjusted). LLMs altered their explanatory reasoning in 45-60 % of cases when images were provided. Multimodal LLMs showed higher diagnostic accuracy than physicians in text-only scenarios, even in cases designed to require visual interpretation, suggesting that while images can enhance diagnostic accuracy, they may not be essential in every instance. Although adding images further improved LLM performance, the magnitude of this improvement was smaller than that observed in physicians. These findings suggest that enhanced visual data processing may be needed for LLMs to achieve the degree of image-related performance gains seen in human examiners.

  • Research Article
  • Cite Count Icon 5
  • 10.1016/j.sleep.2025.106677
Diagnostic performance of Large Language Models (LLMs) compared with physicians in sleep medicine.
  • Oct 1, 2025
  • Sleep medicine
  • Anshum Patel + 5 more

Diagnostic performance of Large Language Models (LLMs) compared with physicians in sleep medicine.

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  • Cite Count Icon 3
  • 10.1182/blood-2023-185854
Evaluating the Performance of Large Language Models in Hematopoietic Stem Cell Transplantation Decision Making
  • Nov 2, 2023
  • Blood
  • Ivan Civettini + 14 more

Evaluating the Performance of Large Language Models in Hematopoietic Stem Cell Transplantation Decision Making

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  • Cite Count Icon 12
  • 10.1097/rti.0000000000000805
The Diagnostic Performance of Large Language Models and General Radiologists in Thoracic Radiology Cases: A Comparative Study.
  • May 1, 2025
  • Journal of thoracic imaging
  • Yasin Celal Gunes + 1 more

To investigate and compare the diagnostic performance of 10 different large language models (LLMs) and 2 board-certified general radiologists in thoracic radiology cases published by The Society of Thoracic Radiology. We collected publicly available 124 "Case of the Month" from the Society of Thoracic Radiology website between March 2012 and December 2023. Medical history and imaging findings were input into LLMs for diagnosis and differential diagnosis, while radiologists independently visually provided their assessments. Cases were categorized anatomically (parenchyma, airways, mediastinum-pleura-chest wall, and vascular) and further classified as specific or nonspecific for radiologic diagnosis. Diagnostic accuracy and differential diagnosis scores (DDxScore) were analyzed using the χ 2 , Kruskal-Wallis, Wilcoxon, McNemar, and Mann-Whitney U tests. Among the 124 cases, Claude 3 Opus showed the highest diagnostic accuracy (70.29%), followed by ChatGPT 4/Google Gemini 1.5 Pro (59.75%), Meta Llama 3 70b (57.3%), ChatGPT 3.5 (53.2%), outperforming radiologists (52.4% and 41.1%) and other LLMs ( P <0.05). Claude 3 Opus DDxScore was significantly better than other LLMs and radiologists, except ChatGPT 3.5 ( P <0.05). All LLMs and radiologists showed greater accuracy in specific cases ( P <0.05), with no DDxScore difference for Perplexity and Google Bard based on specificity ( P >0.05). There were no significant differences between LLMs and radiologists in the diagnostic accuracy of anatomic subgroups ( P >0.05), except for Meta Llama 3 70b in the vascular cases ( P =0.040). Claude 3 Opus outperformed other LLMs and radiologists in text-based thoracic radiology cases. LLMs hold great promise for clinical decision systems under proper medical supervision.

  • Research Article
  • Cite Count Icon 2
  • 10.1016/j.jclinepi.2026.112221
Large language models show promising performance for some systematic review tasks but call for cautious implementation: a systematic review.
  • Jun 1, 2026
  • Journal of clinical epidemiology
  • Florian Laignelot + 9 more

With the exponential growth of biomedical literature, the challenge of conducting systematic reviews is becoming increasingly burdensome. We aimed to evaluate the performance of large language models (LLMs) in the automation of some or all steps of systematic reviews and meta-analyses. In this systematic review, we searched PubMed, Embase, the Cochrane Library and preprint platforms up to January 14, 2025. We included any studies assessing the performance of LLMs (eg, generative pre-trained transformer [GPT], Claude, Mistral) in any step of the systematic review process. Pairs of reviewers independently extracted data and assessed risk of bias. We conducted analyses using median (interquartile range [IQR]) for positive (PPA) and negative percent agreements (NPA), respectively, analogous to sensitivity and specificity, between LLMs and human reviewers. From 3889 unique references, we included 63 studies of which 52 reporting performance metrics for a total of 148 LLM performance assessments. Most assessments concerned GPT models (n = 114, 77%). The most frequently evaluated tasks were title and abstract screening (n = 78, 53%), data extraction (n = 23, 16%), and full-text screening (n = 20, 14%). For title and abstract screening, overall median PPA was 0.92 (IQR 0.69-0.98) and median NPA was 0.89 (0.72-0.95). For full-text screening, the overall median PPA was 0.93 (0.87-1.00) and median NPA was 0.92 (0.78-0.97). Late-generation LLMs released after GPT-4 seemed to provide higher performance than earlier models. For other tasks, authors reported overall good performances, but variability of performance metrics precluded complete quantitative synthesis. Global accuracy for data extraction tasks ranged from 0.36 to 1.00, with a median accuracy of 0.95 (IQR 0.91-0.97, n = 11). For the "risk of bias assessment" task, accuracy ranged from 0.44 to 0.90 (median = 0.62, IQR 0.53-0.76, n = 6). The performance of LLMs, particularly newer generations, shows promise in automating some repetitive steps of systematic reviews such as screening. However, their successful integration will require appropriate safeguards and careful implementation. Systematic reviews are one of the most reliable ways to answer medical and public health questions. They bring together all available studies on a topic and help clinicians and policymakers make informed decisions. However, producing a high-quality systematic review takes a lot of time and effort. Whole teams of researchers spend months screening thousands of articles, extracting data, and double-checking results. With little more than a million of new publications every year, keeping reviews up to date is becoming increasingly difficult. LLMs, such as ChatGPT, may help reduce this workload. These tools can read and summarize text and might assist with repetitive tasks like selecting relevant studies or extracting information from articles. But it is still unclear how reliable these tools are for research purposes. This is the first systematic review to assess LLMs' performance to facilitate systematic reviews. We sought to review all studies that tested LLMs in the different steps of systematic reviews and found 63 studies evaluating how well these tools performed compared with human reviewers. Overall, LLMs showed good agreement with humans for tasks such as screening titles and abstracts, and full-text articles. Newer models seemed to perform better than older ones. However, performance was more variable for complex tasks that require interpretation, such as extracting detailed data or assessing methodological quality. Our findings suggest that LLMs could help researchers work faster and make systematic reviews more efficient. However, they are not ready to replace human judgment. These tools can make mistakes, produce inconsistent results, or generate inaccurate information if not carefully supervised. In practice, LLMs should be used as assistants rather than substitutes. With proper safeguards, transparent reporting, and human oversight, they may become valuable tools to support evidence-based healthcare and help keep research up to date.

  • Research Article
  • 10.1007/s00330-025-12211-x
Predicting molecular types of adult-type diffuse gliomas based on MRI reports with large language models.
  • Dec 22, 2025
  • European radiology
  • Pae Sun Suh + 18 more

To evaluate the performance of large language models (LLMs) in predicting molecular types of adult-type diffuse gliomas according to the 2021 WHO classification using MRI radiology reports. This retrospective study included 2169 patients diagnosed with adult-type diffuse gliomas (294 oligodendrogliomas, 295 IDH-mutant astrocytomas, and 1580 IDH-wildtype glioblastomas) between July 2005 and March 2024 from four hospitals in Asia and Europe. Seven proprietary and open-source LLMs were assessed: GPT-4o-mini, GPT-4.1-mini, Llama 3.1 8B, Llama 3.1 70B, Qwen2.5 7B, Deepseek-r1 8B, and Mistal 7B. The performance of LLMs in classifying molecular types was compared based on the provision of relevant knowledge of glioma imaging findings (knowledge-based vs. naïve prompt). The impact of radiologists' subspecialization in neuro-oncology, report quality, and reporting language on LLMs' performance was also evaluated. LLMs achieved significantly higher (naïve vs. knowledge-based; GPT-4o-mini, 77.0% vs. 79.1%, p < 0.001; Qwen2.5 7B, 75.9% vs. 79.5%, p < 0.001; Deepseek-r1 8B, 66.0% vs. 73.2%, p < 0.001) or comparable accuracy (GPT-4.1-mini, 78.7% vs. 78.6%; Llama 3.1 70B, 78.0% vs. 78.1%; Mistral 7B, 58.4% vs. 57.4%) using knowledge-based prompt compared to naïve prompt, except for Llama 3.1 8B (65.4% vs. 44.6%, p < 0.001). Differences in accuracy were more pronounced in smaller-sized LLMs. Additionally, the accuracy was significantly higher with reports by neuro-oncology specialists and high-quality reports in all LLMs (p < 0.001). LLMs may provide preoperative information on the tumor types of adult-type diffuse gliomas from MRI reports by providing relevant knowledge in the prompt. Informative and descriptive reports could further enhance LLMs' performance. Question Our study aimed to evaluate large language models' (LLMs) ability to efficiently predict molecular types of adult-type diffuse gliomas according to the 2021 WHO classification. Findings Larger models generally showed better accuracy and were less sensitive to domain-specific knowledge. Their performance improved when using high-quality, longer reports or reports by neuro-oncology specialists. Clinical relevance These findings highlight the potential role of LLMs in predicting glioma molecular types, underscoring the importance of informative and descriptive reports in enhancing their performance.

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  • Cite Count Icon 3
  • 10.3389/froh.2026.1748450
Multimodal large language models for oral lesion diagnosis: a systematic review of diagnostic performance and clinical utility
  • Feb 24, 2026
  • Frontiers in Oral Health
  • Fatma E A Hassanein + 5 more

BackgroundDiagnosing oral lesions from benign conditions to oral cancer remains challenging due to overlapping visual features and reliance on histopathology. Large language models (LLMs) can integrate textual and visual cues, but their diagnostic accuracy and clinical utility in real decision-making contexts remain uncertain. To systematically evaluate the diagnostic performance, clinical usefulness, and limitations of LLMs in identifying oral lesions.MethodsPubMed, CINAHL, Embase, Web of Science, and Google Scholar were searched to 20 July 2025. Eligible studies applied LLMs (e.g., ChatGPT, Gemini, DeepSeek, Copilot, Claude) for diagnosis or differential diagnosis of oral lesions using text, images, or multimodal inputs. Outcomes included diagnostic accuracy, agreement metrics, and qualitative assessments of explanation quality and clinical applicability. Risk of bias was assessed using an adapted QUADAS-2. Narrative synthesis was performed due to heterogeneity.ResultsSeventeen studies (>1,200 cases) were included. Diagnostic accuracy ranged from 25%–96%, varying by model version, input modality, and lesion complexity. Multimodal inputs consistently improved performance, with Cohen's κ up to 0.85–0.90. Advanced models (GPT-4o, DeepSeek-R1, o1-preview) outperformed earlier versions and approached expert performance in some tasks, although specialists generally retained superior Top-1 accuracy. Clinical utility was highest when LLMs were used to structure differential reasoning, highlight red-flag features, and support communication, but limited in tasks requiring fine morphological interpretation or severity grading. Overall risk of bias was low to moderate.ConclusionsLLMs demonstrate variable diagnostic performance and context-dependent supportive utility as adjunctive tools in oral lesion assessment, particularly in multimodal settings. They should complement, rather than replace, expert clinical judgment. Future research should prioritize real-world workflow evaluation, standardized prompting strategies, and prospective clinical validation.Systematic Review Registrationhttps://www.crd.york.ac.uk/PROSPERO/view/CRD420251090315, identifier CRD420251090315.

  • Research Article
  • Cite Count Icon 5
  • 10.1093/dmfr/twaf060
The performance of large language models in dentomaxillofacial radiology: a systematic review
  • Aug 12, 2025
  • Dentomaxillofacial Radiology
  • Zekai Liu + 6 more

ObjectivesThis study aimed to systematically review the current performance of large language models (LLMs) in dento-maxillofacial radiology (DMFR).MethodsFive electronic databases were used to identify studies that developed, fine-tuned, or evaluated LLMs for DMFR-related tasks. Data extracted included study purpose, LLM type, images/text source, applied language, dataset characteristics, input and output, performance outcomes, evaluation methods, and reference standards. Customized assessment criteria adapted from the TRIPOD-LLM reporting guideline were used to evaluate the risk-of-bias in the included studies specifically regarding the clarity of dataset origin, the robustness of performance evaluation methods, and the validity of the reference standards.ResultsThe initial search yielded 1621 titles, and 19 studies were included. These studies investigated the use of LLMs for tasks including the production and answering of DMFR-related qualification exams and educational questions (n = 8), diagnosis and treatment recommendations (n = 7), and radiology report generation and patient communication (n = 4). LLMs demonstrated varied performance in diagnosing dental conditions, with accuracy ranging from 37% to 92.5% and expert ratings for differential diagnosis and treatment planning between 3.6 and 4.7 on a 5-point scale. For DMFR-related qualification exams and board-style questions, LLMs achieved correctness rates between 33.3% and 86.1%. Automated radiology report generation showed moderate performance with accuracy ranging from 70.4% to 81.3%.ConclusionsLLMs demonstrate promising potential in DMFR, particularly for diagnostic, educational, and report generation tasks. However, their current accuracy, completeness, and consistency remain variable. Further development, validation, and standardization are needed before LLMs can be reliably integrated as supportive tools in clinical workflows and educational settings.

  • Research Article
  • Cite Count Icon 1
  • 10.3389/fonc.2025.1613818
Performance of large language models in the differential diagnosis of benign and malignant biliary stricture.
  • Jul 3, 2025
  • Frontiers in oncology
  • Chenxi Kang + 19 more

Distinguishing benign from malignant biliary strictures remains challenging. Large Language Models (LLMs) show promise in enhancing diagnostic accuracy. This study aimed to evaluate the performances of ten LLMs in the differential diagnosis of benign and malignant biliary strictures. Consecutive patients with biliary strictures undergoing endoscopic retrograde cholangiopancreatography (ERCP) at Xijing Hospital between January and December 2024 were retrospectively analyzed. Ten LLMs were systematically prompted with standardized clinical, laboratory, and imaging data. Performance was compared against tumor markers (CA19-9, CEA), a new multivariable clinical model, and ten independent pancreaticobiliary exoerienced physicians. Subgroup analyses assessed hilar (n=29) versus non-hilar strictures. Gold-standard diagnosis relied on histopathology and ≥3-month follow-up. Among the 159 included patients (83 benign, 76 malignant), four LLMs (Kimi, Deepseek-R1, Claude-3.5S, Llama-3.1), the clinical model (AUC:0.83), and six physicians achieved >80% accuracy. Kimi demonstrated superior accuracy (87%), significantly outperforming 70% of physicians (7/10, p<0.01). Three other LLMs (Deepseek-R1:83%, Claude-3.5S:82%, Llama-3.1:81%) and the clinical model performed comparably to physicians (78-84%, p>0.05), collectively surpassing tumor markers (CA19-9 accuracy:66%, CEA:71%). Physicians demonstrated higher accuracy for hilar strictures (87% vs. 79% for non-hilar, p<0.001). LLMs showed similar performance across stricture locations (hilar:64-95%; non-hilar:62-88%, p>0.05). For hilar strictures, 7/10 physicians achieved significantly higher accuracy (87-90%) than 8/10 LLMs (64-84%, p<0.05). Using clinical, lab, and imaging data, some LLMs achieved diagnostic accuracy comparable to or exceeding clinical models and experienced physicians for differentiating benign versus malignant strictures. However, for hilar strictures, LLM performance was inferior to over half of the physicians.

  • Research Article
  • 10.1177/20552076251349616
To take a different approach: Can large language models provide knowledge related to respiratory aspiration?
  • May 1, 2025
  • DIGITAL HEALTH
  • Yirou Niu + 7 more

Objective To investigate the performance (accuracy, comprehensiveness, consistency, and the necessary information ratio) of large language models (LLMs) in providing knowledge related to respiratory aspiration, and to explore the potential of using LLMs as training tools. Methods This study was a non-human-subject evaluative research. Two LLMs (GPT-3.5 and GPT-4) were asked 36 questions (32 objective questions and four subjective questions) about respiratory aspiration in English and Chinese. Responses were scored by two experts against gold standards derived from authoritative books. The accuracy of the two LLMs’ responses of objective questions were compared by chi-square test or Fisher exact probability method. For subjective questions, the t-test or Mann–Whitney U test was used to compare the differences between two LLMs. Results There was no significant difference in the ratings provided by the two experts. The accuracy scores of objective questions of two LLMs were high. LLMs also performed well on subjective questions, showing high levels of accuracy, comprehensiveness, consistency, and necessary information ratio. And no significant differences were found in the accuracy of the English and Chinese responses to subjective questions between the two LLMs (z = 0.331, p = 0.886; z = 1.703, p = 0.114). There was no significant difference in the comprehensiveness of the English and Chinese responses between the two LLMs (t = 0.787, p = 0.461; t = 1.175, p = 0.285). Conclusions LLMs demonstrated promising performance in delivering respiratory aspiration-related knowledge and showed promise as supportive tools in training, particularly when their limitations were well understood.

  • Research Article
  • Cite Count Icon 10
  • 10.1186/s12859-025-06081-9
Comparative Assessment of Protein Large Language Models for Enzyme Commission Number Prediction
  • Feb 27, 2025
  • BMC Bioinformatics
  • João Capela + 5 more

Background: Protein large language models (LLM) have been used to extract representations of enzyme sequences to predict their function, which is encoded by enzyme commission (EC) numbers. However, a comprehensive comparison of different LLMs for this task is still lacking, leaving questions about their relative performance. Moreover, protein sequence alignments (e.g. BLASTp or DIAMOND) are often combined with machine learning models to assign EC numbers from homologous enzymes, thus compensating for the shortcomings of these models’ predictions. In this context, LLMs and sequence alignment methods have not been extensively compared as individual predictors, raising unaddressed questions about LLMs’ performance and limitations relative to the alignment methods. In this study, we set out to assess the performance of ESM2, ESM1b, and ProtBERT language models in their ability to predict EC numbers, comparing them with BLASTp, against each other and against models that rely on one-hot encodings of amino acid sequences.Results: Our findings reveal that combining these LLMs with fully connected neural networks surpasses the performance of deep learning models that rely on one-hot encodings. Moreover, although BLASTp provided marginally better results overall, DL models provide results that complement BLASTp’s, revealing that LLMs better predict certain EC numbers while BLASTp excels in predicting others. The ESM2 stood out as the best model among the LLMs tested, providing more accurate predictions on difficult annotation tasks and for enzymes without homologs.Conclusions: Crucially, this study demonstrates that LLMs still have to be improved to become the gold standard tool over BLASTp in mainstream enzyme annotation routines. On the other hand, LLMs can provide good predictions for more difficult-to-annotate enzymes, particularly when the identity between the query sequence and the reference database falls below 25%. Our results reinforce the claim that BLASTp and LLM models complement each other and can be more effective when used together.

  • Discussion
  • Cite Count Icon 1
  • 10.1002/pros.24748
Responses to queries concerning "Performance of large language models on benign prostatic hyperplasia frequently asked questions".
  • May 16, 2024
  • The Prostate
  • Yuning Zhang + 1 more

We thank Hinpetch Daungsupawong and Viroj Wiwanitkit for their interest in our work.1 Our study categorized the responses generated by the three different Large language model (LLMs) into four grades based on correctness and comprehensiveness. With this definition, we use the accuracy rate as the main indicator for LLMs' performance. However, as they mentioned, relying solely on the accuracy rate to assess LLMs' performance is limited and incomplete. Other indicators, such as specificity and the depth of responses generated by LLMs, are also important for evaluating their performance. Therefore, in subsequent related studies, we will consider incorporating specificity and depth into the criteria for grading answers or using them as additional indicators for assessing LLMs' performance. We agree with their opinions that any biases or restrictions in the training data that the LLMs were developed using could have an impact on the replies' accuracy and dependability, however, due to the inaccessibility of the data sets that the LLMs were trained on, an assessment in this regard is difficult to do at this time. In addition, their comments on the future direction of LLMs research, such as evaluating the efficacy of LLMs in answering more complex questions, how to improve the reproducibility of LLMs, and developing standards to make LLM-generated content more ethical and transparent, are all very valuable and worth thinking about. Not limited to us, we feel that all researchers interested in the application of LLMs in medicine should fully consider their valuable opinions in future research.

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