bims-arines Biomed News
on AI in evidence synthesis
Issue of 2026–11–01
twenty-one papers selected by
Farhad Shokraneh, Systematic Review Consultants LTD



  1. Phenomics. 2026 Aug;6(4): 372-390
      Systematic literature reviews are widely acknowledged to be at the top of most evidence hierarchies but are very time-consuming and labour-intensive. The advent of artificial intelligence (AI) offers possibilities to accelerate the review process. We propose a systematic literature review protocol that incorporates AI and evaluate the accuracy of AI against a human-constructed gold standard. Human researchers performed a systematic literature review on the PubMed metabolomic literature investigating Long COVID. OpenAI model o3-mini was then used via the application programming interface to carry out the three key stages of a systematic literature review: 1) screening articles for inclusion criteria, 2) evaluating articles' risk of bias (RoB) using a customised metabolomics tool based on well-established quality criteria, and 3) extracting data from articles. The performance of AI was evaluated against a manually created reference by the assessment of accuracy, negative predictive value, precision, sensitivity, specificity, F1 score, and Cohen's kappa. Out of the 320 identified articles, 33 met all inclusion criteria. AI performed screening, RoB assessment, and data extraction with mean accuracies of 92.7% ± 4.9%, 91.9% ± 5.9%, and 92.0% ± 9.2%, respectively, in ~ 10 h and at a cost of ~ 15.35 USD, while human reviewers took ~ 116 h, equivalent to ~ 2000 USD at minimum wages, to complete these steps in duplicate. OpenAI model o3-mini can independently complete the three main stages of systematic literature reviews in the metabolomics domain, thus considerably reducing the time to complete such reviews, at minimal cost. Nonetheless, human reviewers should always verify the AI-generated output to ensure robustness.
    Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1007/s43657-026-00336-y.
    Keywords:  Artificial Intelligence; Long COVID; Metabolomics; Systematic Literature Reviews
    DOI:  https://doi.org/10.1007/s43657-026-00336-y
  2. Orthop Traumatol Surg Res. 2026 Oct 29. pii: S1877-0568(26)00400-7. [Epub ahead of print] 104979
       BACKGROUND: There is increasing interest in artificial intelligence (AI) to accelerate selected steps of evidence synthesis. However, AI-generated syntheses should not be confused with systematic reviews (SRs) conducted according to rigorous, exhaustive, and reproducible methodology. The reliability of specialized extractive AI tools for reproducing selected SR-related tasks remains insufficiently validated. The purpose of this study was to evaluate the ability of AI tools to assist selected tasks derived from published orthopedic systematic reviews: (1) answering review-derived research questions, (2) summarizing conclusions, (3) retrieving and citing references concordant with the source SRs, organize accurately reference the scientific literature, (4) generating a PICO framework from a study title alone, and (5) extracting PICO elements from full-texts SRs.
    HYPOTHESIS: We hypothesized that AI tools would be able to assist selected synthesis tasks, including answering review-derived questions and structuring PICO elements, but would show important limitations for bibliographic exhaustiveness, methodological reproducibility, and source concordance.
    MATERIAL AND METHODS: Ten peer-reviewed systematic reviews (SRs) published between 2020 and 2022 were selected as the human reference corpus. They were used as a pragmatic benchmark for comparison. Human reviewers independently extracted the main research questions and conclusions. Consensus and SciSpace were evaluated for extractive synthesis and bibliographic concordance; ChatGPT-5.1 was evaluated for PICO generation from titles and PICO extraction from full texts. Standardized prompts, scoring procedures, and he dates of AI querying were recorded.
    RESULTS: A total of 126 AI-generated responses per tool were evaluated. Consensus achieved higher Likert scores than SciSpace (22.06 ± 2.12 vs 21.04 ± 2.76 (p = 0.001)), particularly for clarity/coherence (p = 0.003) and readability (p < 0.001), with no differences in scientific accuracy, originality, or writing efficiency. Multivariate analyses confirmed significant effects of tool, question type, cognitive level, and evaluator (all p < 0.001). Interobserver agreement was excellent (ICC (1,k) = 0.990, 95% CI: 0.989-0.992). Objective quality scores were similar between Consensus and human texts (70.52 ± 10.14 vs 69.95 ± 10.75 (p = 0.804)), whereas SciSpace scored lower (65.62 ± 8.30 (p = 0.042)) and produced shorter texts with fewer sentences (p < 0.05). SciSpace retrieved more references than Consensus (296/1,126; 26.3% vs 204/1,126; 18.1%) and showed higher concordance with gold-standard reviews (41/947; 4.3% vs 14/882; 1.6%), although overall accuracy remained low. PICO generation showed strong reliability for identifying the main objective, intervention, primary outcome, and population. PICO extraction was most reliable for population, outcomes, and main objective, but less accurate for comparator, study design, and especially inclusion period.
    CONCLUSION: Specialized AI tools can assist rapid synthesis of selected questions derived from orthopedic systematic reviews, but they cannot currently replace a full systematic review or meta-analysis. Their bibliographic concordance with human SRs remained very low, confirming that narrative plausibility and true source retrieval are distinct capabilities.
    LEVEL OF EVIDENCE: IV; Methodological comparative study.
    Keywords:  Artificial intelligence; Extractive AI; Generative AI; Orthopedics; PICO framework; Systematic review
    DOI:  https://doi.org/10.1016/j.otsr.2026.104979
  3. JMIR AI. 2026 Oct 28. 5 e103273
       BACKGROUND: Clinical practice guidelines (CPGs) translate research evidence into actionable recommendations, but their development faces mounting challenges. With dozens of trials and systematic reviews published daily, the traditional 18- to 24-month development cycle struggles to incorporate emerging evidence, and manual screening, synthesis, and quality assessment consume thousands of person-hours per guideline. The resulting knowledge translation pipeline is slow, inconsistent, and quickly outdated.
    OBJECTIVE: This review aimed to chart the computational methods empirically tested for automating CPG development, the tasks they address, and their evaluation measures, and to map where that evidence is concentrated and where it is absent for living guidelines.
    METHODS: The review followed the Joanna Briggs Institute scoping review framework and PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews) guidance. We searched PubMed and Scopus for studies published between January 2001 and December 2025, supplemented by backward and forward citation searching. Eligible studies used automated methods for a guideline development task, reported original research with empirical testing, and gave sufficient methodological detail. Two reviewers independently screened records and extracted data. Findings were charted across 4 pillars: retrieval, extraction, encoding, and evaluation.
    RESULTS: A total of 47 studies met eligibility criteria, spanning 2001 to 2025, with a marked increase after 2015 and a surge in large language model (LLM) work in 2024-2025. Pillar counts (nonexclusive) were as follows: retrieval, 6; extraction, 15; encoding, 26; and evaluation, 17. In retrieval pillar, query expansion achieved 80% recall, while semantic search tools traded recall for specificity (98%). In extraction, rule-based natural language processing achieved an F-measure of 81.96% for structured clinical actions and 71.75% for patient states, and hybrid ontology methods covered 86% of eligibility criteria; LLMs performed well on structured fields but degraded on interpretive content. In encoding, approaches progressed from formalisms such as Guideline Interchange Format version 3 (GLIF3) and guideline elements model toward Fast Healthcare Interoperability Resources (FHIR)-based representation; semiautomated tools assisted guideline encoding, and logic verification detected inconsistencies and coverage gaps missed by human reviewers. In evaluation, LLM appraisers assigned higher Appraisal of Guidelines for Research and Evaluation II (AGREE II) scores than human appraisers, by a mean difference of 12.5% in one study (95% limits of agreement -30.6% to 55.5%; intraclass correlation coefficient 0.753) and by 22 to 60 percentage points across domains in another.
    CONCLUSIONS: Automation shows promise for bounded, well-structured guideline development tasks, while robust evidence for end-to-end, production-scale living guideline pipelines remains limited. No included study demonstrated a validated pipeline connecting all 4 pillars in an operating guideline program, and evidence on clinical safety, workflow integration, and cost-effectiveness is largely absent. Realizing living guidelines will require interoperability standards such as FHIR, and evaluation in real guideline production rather than retrospective benchmarks.
    Keywords:  AGREE II; Appraisal of Guidelines for Research and Evaluation II; GRADE; Grading of Recommendations Assessment, Development and Evaluation; artificial intelligence; automation; clinical practice guidelines; computer-interpretable guidelines; decision support systems; evidence-based medicine; living guideline; machine learning; natural language processing
    DOI:  https://doi.org/10.2196/103273
  4. NEJM AI. 2026 Jul;3(7): AIe2600680
      AbstractClinical guidelines are outdated. Improving upon them by using large language models would be advantageous were it not for the significant potential dangers. There is a better way of applying AI to synthesize guidelines: Focus on errors of omission and generate a bias-free summary of key messages from the AI output.
    DOI:  https://doi.org/10.1056/AIe2600680
  5. JBRA Assist Reprod. 2026 Oct 26.
       OBJECTIVE: To assess whether the TRUST-MA framework produces reproducible methodological and clinical reliability judgments when independently applied by two large language models.
    METHODS: In this pilot calibration study, 51 reproductive-medicine meta-analyses published in 2025- 2026 were randomly selected from PubMed. ChatGPT (AI-X) and Claude (AI-Y) independently received the same full articles and available supplements and applied TRUSTMA in July 2026, without access to each other's outputs. Practice Change Confidence (PCC) was introduced during the sequence and was available for a consecutive nested subgroup of 24 cases (cases 27-50). Agreement was evaluated using paired comparisons, intraclass correlation coefficients (ICC), Lin's concordance correlation coefficient, Bland-Altman analysis, and weighted Cohen's kappa.
    RESULTS: Mean TRUST-MA scores were 56.21±19.90 for ChatGPT and 64.28±18.22 for Claude. Claude scored 8.07 points higher on average (95% confidence interval [CI], 5.33-10.82; p<0.001). Absolute-agreement ICC was 0.800 (bootstrap 95% CI, 0.698-0.868). Exact A/B/C agreement was 68.6%, with linear weighted κ=0.451. PCC means were identical (3.54 for both models; Wilcoxon p=0.794), with ICC=0.844 (bootstrap 95% CI, 0.541-0.955), exact fivetier agreement of 66.7%, and linear weighted κ=0.653. TRUST-MA and PCC scores were correlated for each evaluator (Spearman ρ=0.677 and 0.631; both p<0.001).
    CONCLUSION: TRUST-MA and PCC showed good scorelevel reproducibility across independent AI evaluators. However, systematic calibration differences in TRUST-MA scores and only moderate categorical agreement preclude treating the models as interchangeable. Standardized version reporting, threshold rules, and human adjudication remain necessary.
    Keywords:  artificial intelligence; evidence-based medicine; meta-analysis; reproducibility; risk assessment; systematic review
    DOI:  https://doi.org/10.5935/1518-0557.20260148
  6. Int Endod J. 2026 Oct 28.
       OBJECTIVE: To evaluate the level of agreement between ChatGPT-5.5 and human assessments when appraising the methodological quality and overall confidence of the results of systematic reviews (SRs) with meta-analysis (MA) in endodontology.
    METHODS: SRs with MA related to endodontology and published in English between 2021 and 2024 were included. The methodological quality of the SRs was appraised by three human experts using AMSTAR 2, and a consensus dataset was generated. ChatGPT-5.5 was applied to generate AMSTAR 2 item-level ratings and overall confidence classifications for each SR through three newly created accounts. Agreement between consolidated ChatGPT-5.5 ratings and human consensus was assessed for both overall confidence and each AMSTAR 2 item. Overall-confidence agreement was evaluated under the primary criterion (Partial Yes = Yes) and an alternative sensitivity criterion (Partial Yes = No). Direct agreement and linearly weighted Cohen's kappa were calculated, and complete 3/3 agreement was used to assess consistency across ChatGPT-5.5 accounts.
    RESULTS: One hundred SRs were included. Human consensus and ChatGPT-5.5 classified 47 and 85 SRs, respectively, as critically low. Under the primary criterion (Partial Yes = Yes), overall confidence matched in 52/100 SRs (52%; weighted κ = 0.182). Under the alternative criterion (Partial Yes = No), agreement increased to 83%, while weighted κ remained similar (κ = 0.173), indicating that direct agreement was sensitive to the handling of Partial Yes. Item-level agreement varied substantially. Overall confidence was identical across the three ChatGPT-5.5 accounts in 85 SRs, and global item-level 3/3 agreement was 86.12%. In the 100 sampled SRs, 15% met the criterion for reporting primary-study funding and 21% for justifying study designs.
    CONCLUSION: Overall-confidence direct agreement was sensitive to the handling of Partial Yes ratings, whereas chance-corrected agreement remained similar under both criteria. ChatGPT-5.5 assigned lower overall confidence classifications more frequently than human consensus, and agreement varied across AMSTAR 2 domains. Although outputs were frequently consistent across the three ChatGPT-5.5 accounts, between-account consistency did not ensure concordance with human judgements. The findings do not support the use of ChatGPT-5.5 as an independent AMSTAR 2 assessor; any exploratory application requires item-by-item verification by reviewers with methodological expertise.
    Keywords:  artificial intelligence; endodontics; meta‐analysis; methodological quality; systematic reviews
    DOI:  https://doi.org/10.1111/iej.70297
  7. Ecol Evol. 2026 Nov;16(11): e74626
      The contemporary ecological crisis calls for integration and synthesis of vast amounts of mostly scattered and often hard-to-extract ecological information that is dispersed across hundreds of thousands of scientific papers. Recent advancements in natural language processing (NLP) and the emergence of large language models (LLMs) offer a novel and promising approach to this persistent challenge. Here, we present a replicable and adaptable workflow that automates the extraction of a broad range of biological interactions among species from scientific literature using LLMs. We provide a demonstration of this workflow by performing a large-scale data extraction directly from a corpus of 83,910 scientific articles using OpenAI GPT-4o. Our approach successfully extracted a network of 144,402 interactions between 36,471 taxa. Performance analysis shows that the model exhibits a precision of 89.5% with a recall of 70.0%, demonstrating that a general-purpose LLM can perform complex ecological information extraction at scale for analysis and synthesis. Results depend on quality filtering choices and inherit biases present in the underlying literature, emphasizing the need for validation and quality control. Standardized outputs can be browsed, queried, or joined with existing interaction repositories and taxonomic backbones, facilitating downstream reuse and interoperability. Our case study shows that LLMs are capable of carrying out complex extraction tasks on key ecological data on a very large scale, paving the way for a multitude of potential applications in ecology and beyond.
    Keywords:  biological interactions; large language models; prompt engineering; relation extraction; structured data extraction; taxonomic entity linking; taxonomic named entity recognition; text mining
    DOI:  https://doi.org/10.1002/ece3.74626
  8. NEJM AI. 2025 Jun;2(6): AIp2401106
      AbstractLarge language models (LLMs) have advanced artificial intelligence research in medicine, especially in natural language processing tasks. However, the nascent evolution of LLM practices presents challenges to the transparency, reproducibility, and rigor of research methods. Standardized reporting in research is critical to ensure reliable scientific communication and evaluation. This article introduces the Development, Evaluation, and Assessment of Large Language Models (DEAL) checklist, designed to guide authors and reviewers in reporting LLM studies. The checklist comprises two pathways: DEAL-A, tailored for advanced model development and fine-tuning, and DEAL-B, suited to applied research using pretrained models with minimal modifications. Each pathway addresses critical elements such as model specifications, data-handling practices, training procedures, evaluation metrics, and transparency standards. The DEAL checklist provides a comprehensive structure for documenting LLM research with the aim of making it accessible and reproducible. This structured approach aims to set a standard for future research, facilitating peer review and encouraging best practices. The DEAL checklist will serve as a valuable tool for enhancing the quality and reproducibility of LLM research. By offering clear guidelines on critical reporting elements, the DEAL checklist promotes robust and transparent scientific reporting, ultimately supporting the reliable advancement of LLM technologies.
    DOI:  https://doi.org/10.1056/AIp2401106
  9. BMC Bioinformatics. 2026 Aug 03. pii: 251. [Epub ahead of print]27(1):
       BACKGROUND: Persistent clinical failures in drug development arise from multiple factors, including imbalanced molecular properties, underscoring the need for systematic structure-activity relationship analysis to link structural modifications with optimized efficacy, selectivity, and safety of small-molecule drugs. Compared with academic literature, drug-related patent documents contain earlier and richer structure-activity relationship information that can support preclinical decision making. However, extracting structure-activity relationship information from patents is technically challenging due to ambiguous terminology, fragmented tables, dispersed compound descriptions, and the need to correctly link compound identities with activity endpoints. To address these issues, we developed PatSAR, a prompt-engineering-centered LLM workflow implemented through the ChatGPT web interface, in which finalized task-specific prompts guide document-by-document extraction of SAR information from patent PDF documents.
    RESULTS: When evaluated on 214 PARP-related patents containing 8226 expert-annotated SAR entities, PatSAR achieved a recall of 79.05%, a precision of 99.65%, and an F1 score of 88.16%. In a multi-target generalization test set of 200 recent patents across ten non-PARP small-molecule targets, PatSAR achieved a recall of 85.25%, a precision of 98.97%, and an F1 score of 91.60%. In an external comparison on DocSAR-Patent-96, PatSAR achieved a Table Recall of 81.86%, compared with the reported Doc2SAR result of 74.09% on the patent subset.
    CONCLUSIONS: These results support the potential of large language models for patent information extraction and highlight the role of prompt engineering in improving task-specific extraction performance. The proposed PatSAR framework illustrates the promise of hybrid human-AI workflows for SAR curation and patent analysis.
    Keywords:  Large language models; Lead optimization; Pharmaceutical patent; Prompt engineering; Structure–activity relationships
    DOI:  https://doi.org/10.1186/s12859-026-06587-w
  10. J Chem Inf Model. 2026 Oct 26. 66(20): 13383-13396
      Force field models are one of the central pillars of molecular simulations. A large number of molecular force field models has been developed in the past decades─mostly published in scientific papers. Building machine-readable force field input files for simulation engines is a tedious and error-prone task. We developed a method for extracting and building force field files from publications using large language models (LLMs). We have tested the new method by extracting 114 force field models from 21 scientific publications. The studied force fields comprise 6-74 parameters that were automatically extracted, identified, annotated, and allocated. We have compared the performance of different LLMs, namely Gemini 2.5 Pro, Claude 4 Sonnet, Claude 3.7 Sonnet, Gemini 2.5 Flash, and GPT-4o. Overall, they yield similar performance─yet there are important differences in individual cases. The overall best performance was obtained by the Gemini 2.5 Pro LLM. The force field parameters were extracted and identified with an accuracy of 94.0% using the Gemini 2.5 Pro LLM. The new LLM-assisted extraction method drastically reduces the time required for building force field files. Nevertheless, human-in-the-loop verification is still indispensable.
    DOI:  https://doi.org/10.1021/acs.jcim.6c02128
  11. Methods Mol Biol. 2027 ;3079 29-45
      The rapid growth of biomedical publications has created a critical need for tools that can extract meaningful insights from RNA-RNA interaction (RRI) literature. This study presents RRI-Senti, a literature-driven framework that applies sentiment analysis to scientific publications to infer potential disease relevance and emerging research trends in RRIs. By leveraging Transformer-based models-including RIScoper, BioBERT, SciBERT, and PubMedBERT-RRI-Senti encodes contextual semantic representations of RNA entities and their interactions, enabling automatic extraction of sentiment signals related to experimental findings, therapeutic strategies, and research consensus. We provide a systematic comparison of these models, discuss their practical applications in literature curation and hypothesis generation, and highlight how sentiment-aware NLP can enhance understanding of RNA biology. This framework represents one of the first efforts to integrate sentiment analysis specifically with RNA-RNA interaction literature, offering a novel approach to guide future research priorities and knowledge synthesis in the field.
    Keywords:  BioBERT; Biomedical literature mining; Biomedical text mining; Domain adaptation; Healthcare informatics; NLP; PubMedBERT; RIScoper; RRI analysis; SciBERT; Sentiment analysis; Transformer models
    DOI:  https://doi.org/10.1007/978-1-0716-5567-2_3
  12. Health Educ Behav. 2026 Oct 25. 10901981261497634
      The rapid integration of artificial intelligence into research has raised urgent questions about whether generative models can contribute meaningfully to qualitative inquiry, particularly in health contexts where cultural nuance and contextual interpretation are essential. This study evaluates ChatGPT's capacity to support ethnographic analysis by comparing AI-assisted outputs with a previously conducted human-led analysis of 20 interviews with college students managing Type 1 diabetes. Guided by Spradley's four-phase ethnographic interview method, it examines ChatGPT-4o's ability to identify cultural domains, construct taxonomies, articulate contrastive dimensions, and synthesize higher-order themes. While ChatGPT efficiently generated surface-level summaries and facilitated early data organization, its analytic contributions remained largely descriptive. The model struggled to identify symbolic tensions, contextual meanings, and culturally embedded interpretations that human analysts derived through iterative reading, reflexivity, and familiarity with the lived experience of chronic illness. AI-generated taxonomies lacked internal structure, and thematic interpretations failed to account for the institutional, relational, and identity-based dynamics shaping students' experiences. These findings suggest that although generative AI can serve as a useful assistive tool for preliminary coding and pattern recognition, it cannot replicate the interpretive depth central to qualitative health research. The study highlights the methodological implications of incorporating AI into qualitative inquiry, underscoring the need for critical oversight and researcher reflexivity when integrating AI-assisted approaches. As the use of AI expands in health education and behavior research, understanding its limitations is essential for ensuring that culturally grounded, meaning-rich insights remain at the center of qualitative analysis.
    Keywords:  AI-assisted research; ChatGPT; artificial intelligence; health; qualitative analysis
    DOI:  https://doi.org/10.1177/10901981261497634
  13. Hand (N Y). 2026 Oct 27. 15589447261495072
       BACKGROUND: Large language models (LLMs) such as ChatGPT, Gemini, Claude, and Mistral are increasingly used to obtain medical information, but their accuracy in carpal tunnel syndrome (CTS) management is uncertain. This study evaluated whether LLM-generated recommendations align with American Academy of Orthopaedic Surgeons (AAOS) clinical practice guidelines (CPGs).
    METHODS: Four LLMs (ChatGPT-4, Gemini, Claude-3, Mistral-7B) were queried with standardized prompts derived from AAOS CTS CPGs. Each prompt was asked 3 times per model, and responses were synthesized. Two blinded reviewers graded outputs as concordant, discordant, or indeterminate, with disagreements resolved by consensus. Concordance distributions were compared using χ2 testing with Bonferroni correction. Inter-rater reliability was measured with Cohen's κ.
    RESULTS: Across 252 recommendations, 72.6% were concordant, 11.5% discordant, and 15.9% indeterminate. ChatGPT achieved the highest concordance (92.1%) and lowest discordance (1.6%), while Mistral performed poorest (52.4% concordance, 17.5% discordance). Reviewer agreement was excellent (κ = 0.91).
    CONCLUSIONS: Over 1 in 4 LLM-generated CTS recommendations were not concordant with AAOS CPGs. ChatGPT outperformed other models, though variable performance underscores the need for clinician oversight and careful validation before clinical use.
    Keywords:  artificial intelligence; carpal tunnel syndrome; clinical practice guidelines; concordance; decision support; large language models; orthopedic surgery
    DOI:  https://doi.org/10.1177/15589447261495072
  14. J Exp Orthop. 2026 Oct;13(4): e70964
       Purpose: This study aimed to evaluate the interpretive and applicative performance of three conditions applied to the formal EU-US, ESSKA-AOSSM-AASPT consensus on meniscus rehabilitation: (1) single-pass prompting, (2) sequential chain-of-thought prompting and (3) human expert-written output.
    Methods: This exploratory comparative study evaluated three conditions applied to two parts of the formal EU-US ESSKA-AOSSM-AASPT meniscus rehabilitation consensus: (1) single-pass prompting, (2) sequential chain-of-thought prompting using ChatGPT (GPT-5.1), Claude (Sonnet 4.5), and Gemini (3.0), and (3) human expert-written output from three collaborating human experts. For each part, three tasks were assessed: generation of summaries, application of summaries to three predefined clinical scenarios, and resistance to three predefined misinterpretation queries. Three blinded senior sports physiotherapists evaluated summary quality using five QUEST categories and rated the clinical application and misinterpretation resistance responses. Median ratings were compared using Friedman and post-hoc Wilcoxon signed-rank tests. Gwet's AC2 coefficient with quadratic weights was used to assess inter-rater agreement for each QUEST category and for the clinical application and misinterpretation resistance items.
    Results: Across consensus parts, no statistically significant differences were identified between large language model prompting strategies and human expert outputs for QUEST categories, clinical application, and misinterpretation resistance queries. Sequential chain-of-thought prompting received higher numerical reviewer ratings than single-pass prompting for ChatGPT and Gemini, particularly for quality of information and trust and confidence, although differences were not statistically significant. Inter-rater agreement ranged from substantial to almost perfect (Gwet's AC2 = 0.79-0.99).
    Conclusion: No statistically significant differences in reviewer ratings were observed between ChatGPT, Claude, Gemini and human expert output, with generally high ratings for summaries and responses to clinical scenarios. Large language models may therefore represent a potential adjunct for summarisation and interpretation of sports medicine consensus recommendations to inform rehabilitation decision-making.
    Level of Evidence: Level V.
    Keywords:  LLM; artificial intelligence; clinical decision support; machine learning; prompt engineering; rehabilitation
    DOI:  https://doi.org/10.1002/jeo2.70964
  15. Cureus. 2026 Sep;18(9): e116893
       OBJECTIVE: This study aimed to evaluate the bibliographic accuracy of the references that ChatGPT-5.3 (OpenAI, San Francisco, CA) presented as PubMed-indexed sources for open fracture management and determine whether the verifiable references were relevant to the topics they were meant to support.
    METHODOLOGY: In a single session in March 2026, ChatGPT-5.3 (Plus subscription), with the web search function enabled, was asked to systematically describe the management of open fractures. The model was then prompted to provide three PubMed-indexed references for each topic it had generated. ChatGPT-5.3 structured open fracture management into 15 topic categories and produced a total of 45 references. Two independent reviewers assessed each reference for bibliographic accuracy and content relevance. Bibliographic accuracy was scored from 0 to 2, and content relevance from 0 to 1. Final scores were determined by consensus. Inter-rater agreement was assessed using Cohen's kappa coefficient.
    RESULTS: Of the 45 references, 11 (24.4%) were fully bibliographically accurate. Nineteen references (42.2%) existed but contained errors in the PMID, year, journal, title, or other bibliographic details. Fifteen references (33.3%) could not be verified as valid PubMed-indexed articles. The overall bibliographic accuracy rate was 11 (45.6%), the content relevance rate was 30 (66.7%), and the overall performance score was 52.6%. All bibliographically verifiable references were content-relevant to their assigned open fracture management topics, with 30 (66.7%) references being content-relevant. The 45 references corresponded to only 36 unique sources; a single review article was reproduced under 8 (53.3%) of the 15 topic categories and accounted for 8 (72.7%) of the 11 fully accurate references. In a sensitivity analysis restricted to unique sources, the bibliographic accuracy rate decreased to 13 (37.5%). Inter-rater agreement was high, with Cohen's kappa values of 0.966 for bibliographic accuracy and 0.951 for content relevance.
    CONCLUSIONS: Although ChatGPT-5.3 generated a clinically reasonable and systematic framework for open fracture management, the references provided to support this response showed substantial bibliographic reliability problems. Because all verifiable references were content-relevant, the model's principal limitation appeared to lie not in the selection of irrelevant sources, but in the presentation of seemingly appropriate sources with inaccurate or unverifiable bibliographic information. References generated by ChatGPT should not be used for academic or clinical purposes without independent verification.
    Keywords:  artificial intelligence; bibliographic accuracy; chatgpt; open fracture; orthopedic trauma; reference accuracy
    DOI:  https://doi.org/10.7759/cureus.116893
  16. Proc Natl Acad Sci U S A. 2026 Nov 03. 123(44): e2623869123
      References to nonexistent studies are well documented in biomedical research, but evidence outside biomedicine is limited. We analyzed a stratified random sample of 500,000 peer-reviewed journal papers in chemistry, physics, materials science, engineering, and computer science published from January 2023 through March 31, 2026, using OpenAlex, a large open index of scholarly works and citations. Our automated pipeline classified 1,135 references across 619 papers as fabricated, with 85.8% precision on masked expert review; fabricated is an operational label for a claimed title that could not be located in any of seven bibliographic and open-web sources. Affected-paper prevalence rose from 1 in 1,600 (6.3 per 10,000) in 2023 to 1 in 435 (23.0 per 10,000) in the first quarter of 2026, and full-period rates differed roughly sixfold across fields, from 25.6 per 10,000 papers in physics to 4.3 in chemistry. Most affected papers contained one or two fabricated references, but the 27 papers containing five or more accounted for more than a third of all fabricated references identified. Applying each field's rate to the approximately 7 million OpenAlex papers indexed in these fields gives an estimated 8,500 papers carrying at least one fabricated reference. Routine automated reference verification at submission, together with retrospective screening of the published literature, can detect fabricated references before and after they enter the scientific record.
    Keywords:  citation errors; citation verification; fabricated references; research integrity; scientific publishing
    DOI:  https://doi.org/10.1073/pnas.2623869123
  17. JAMIA Open. 2026 Oct;9(5): ooag197
       Objectives: We sought to evaluate the accuracy and suitability of a transformer-based model (TM) for indexing clinical study designs, in comparison to National Library of Medicine (NLM) indexing.
    Materials and methods: For 2016 (manual NLM) and 2025 (automated NLM) published articles, we conducted a limited evaluation of the TM model, with articles that received the most confident predictions, with which NLM assignments disagreed. Ground truth was established through independent dual annotation for 4 prominent study designs: cohort, case-control, cross-sectional, and case report.
    Results: For 3 designs (case-control, case report, and cross-sectional), the articles having the top 100 predictive TM scores (when NLM failed to assign that design) were judged to exhibit that design in the great majority (86%-100%) of cases. Conversely, the articles having the lowest 100 predictive TM scores (when NLM did assign the study design) exhibited the design only in relatively few (0%-21%) of cases. The most confident predictions of the TM model were highly accurate and not redundant with automated NLM indexing; the exception was cohort studies articles, in which both TM and NLM labels showed high error rates of both omission and commission.
    Discussion: TM may have value for identifying articles exhibiting study designs, which is important for clinical decision-making and evidence syntheses.
    Conclusion: NLM's cohort studies indexing is unreliable as a gold standard for building automated systems, warranting efforts to create a new manually annotated corpus.
    Keywords:  National Library of Medicine (US); bibliographic; databases; evidence-based medicine; indexing; study characteristics; study design
    DOI:  https://doi.org/10.1093/jamiaopen/ooag197
  18. Bioengineering (Basel). 2026 Sep 22. pii: 1097. [Epub ahead of print]13(10):
       BACKGROUND: Reliable access to postoperative guidance between clinic visits remains inconsistent, and the usefulness of large language models depends on how clinical knowledge is structured and retrieved. Knowledge graph-only (KG-only), vector retrieval-augmented generation (RAG-only), and hybrid graph-retrieval (GraphRAG) architectures have not been directly compared under controlled conditions for postoperative care.
    OBJECTIVE: It was to compare these three pipelines on a curated postoperative question-answering benchmark using automated grounding metrics and blinded clinician review.
    METHODS: A benchmark of 250 expert-authored questions (200 in-scope, 20 emergency-intent, 30 out-of-scope) was evaluated on an identical knowledge corpus using Gemini 2.5 Flash for generation and Gemini Embedding-001 for retrieval. Three blinded clinicians rated all 750 outputs; the primary outcome was majority-consensus accuracy across all 250 questions. GraphRAG is a multi-component pipeline that also includes query expansion, a second retrieval stage, evidence fusion, and a monotonic RAG fallback, and is therefore evaluated as a complete hybrid system rather than as graph retrieval in isolation.
    RESULTS: Overall accuracy was 96.8% (95% CI: 93.8-98.4) for GraphRAG, 94.8% (95% CI: 91.3-96.9) for RAG-only, and 56.0% (95% CI: 49.8-62.0) for KG-only. Both retrieval-augmented systems outperformed KG-only (adjusted p < 0.001). The GraphRAG versus RAG-only difference was 2.0 percentage points, arose from five discordant question pairs and did not reach the Bonferroni-adjusted threshold (exact McNemar p = 0.062; adjusted p = 0.188). The monotonic RAG fallback determined 44.8% of GraphRAG outputs (112 of 250 queries). GraphRAG showed higher context recall (0.851 versus 0.796; adjusted p < 0.001), whereas RAG-only showed higher context precision. Estimated hallucination risk, derived from an LLM-as-a-judge procedure using Gemini 2.5 Flash rather than independent clinical adjudication, was 0.108, 0.132, and 0.436, respectively; the GraphRAG versus RAG-only difference was not significant (adjusted p = 0.771). Inter-rater agreement was high (Fleiss' kappa = 0.854).
    CONCLUSIONS: Retrieval augmentation, rather than the choice of retrieval architecture, accounted for most of the difference observed. The incremental advantage of GraphRAG over a well-implemented RAG-only system was small, was not statistically significant after correction and reflects the complete hybrid system rather than graph augmentation alone. Emergency-intent accuracy was 75.0% for both retrieval-augmented systems; the architecture is therefore suited to supervised clinical workflows with clinician review, not autonomous patient-facing triage. Prospective validation on authentic patient messages and formal component ablations are required.
    Keywords:  GraphRAG; clinical AI; faithfulness; hallucination; knowledge graph; large language models; patient communication; postoperative care; retrieval-augmented generation; surgical informatics
    DOI:  https://doi.org/10.3390/bioengineering13101097
  19. Bioinformatics. 2026 Oct 24. pii: btag794. [Epub ahead of print]
       MOTIVATION: The exponential growth of biomedical literature has made automatic indexing essential for advancing biomedical research. While automatic indexing has made strides in English biomedical literature, there has been limited research on non-English biomedical texts due to insufficient high-quality training data.
    RESULTS: We propose BERTDeCS, a novel deep learning framework for automatically indexing Spanish biomedical literature using contrastive transfer learning. BERTDeCS utilizes a multilingual BERT (M-BERT) to generate multi-language representations and adapts M-BERT for Spanish biomedical literature domain through contrastive learning. Additionally, BERTDeCS enhances its semantic indexing capabilities on Spanish biomedical literature by leveraging enriched English annotated literature in MEDLINE through transfer learning. Experimental results on Spanish datasets demonstrate that BERTDeCS outperforms state-of-the-art indexing methods, achieving top performance in the MESINESP and MESINESP2 Tasks on medical semantic indexing in Spanish within the BioASQ challenge. Additional experiments on Portuguese provide preliminary evidence that BERTDeCS can transfer to a closely related language sharing substantial lexical and biomedical terminology with Spanish.
    AVAILABILITY: The source code is available at https://github.com/yourh/BERTDeCS and at https://doi.org/10.5281/zenodo.23212468.
    DOI:  https://doi.org/10.1093/bioinformatics/btag794
  20. R Soc Open Sci. 2026 Oct 07. 13(10): 261365
      Patent codes may lack granularity when carbon capture, utilization and storage (CCUS) inventions combine climate and chemical engineering concepts. We evaluate term presence models on 10 603 English patent abstracts through document completion, calibration and cooperative patent classification (CPC) prefix retrieval. We compare two variational autoencoders (VAEs), a product of the experts latent Dirichlet allocation model, a unigram prior, term frequency-inverse document frequency (TF-IDF), PatentSBERTa and PaECTER. With a target masking rate of 50 per cent for positive terms, TF-IDF nearest neighbours give the best ranked completion. The direct Bernoulli VAE ranks slightly above the negative binomial to Bernoulli VAE (NB VAE), while the latter has lower expected calibration error (ECE). Conditional posterior predictive draws retain positive rank associations for document and term counts, but the NB VAE and direct Bernoulli VAE predict 1.47 and 1.63 times the observed positive count, respectively. PaECTER and the TF-IDF representation after singular value decomposition (SVD) give the strongest CPC prefix retrieval, while VAE probabilities could support inspectable term screening.
    Keywords:  carbon capture; cooperative patent classification; patent retrieval; patent text mining; probability calibration; utilization and storage; variational autoencoder
    DOI:  https://doi.org/10.1098/rsos.261365
  21. NEJM AI. 2025 Jan;2(1): AIe2401073
      AbstractIn this edition of NEJM AI, Ifargan and colleagues present data-to-paper, an autonomous platform designed to mimic human scientific practice by guiding a large language model through a stepwise research process to produce complete research papers. While the platform shows promise, significant errors frequently occur with complex datasets, requiring human intervention for correction. Here, we explore the risks of over-reliance on such automated tools, echoing potential threats to scientific integrity and a surge in low-quality publications, while also considering their potential role in the reproduction and verification of scientific findings. To address these challenges, we recommend the development of clearer guidelines and ethical standards for the use of artificial intelligence (AI) in research, fostering human-AI collaboration to enhance research quality while preserving human oversight, and integrating the innovative "data-chaining" transparency mechanisms more broadly to support reproducibility and traceability.
    DOI:  https://doi.org/10.1056/AIe2401073