bims-arines Biomed News
on AI in evidence synthesis
Issue of 2026–08–02
eleven papers selected by
Farhad Shokraneh, Systematic Review Consultants LTD



  1. J Biomed Inform. 2026 Jul 25. pii: S1532-0464(26)00110-3. [Epub ahead of print]181 105086
       OBJECTIVE: Data extraction is among the most resource-intensive and error-prone stages of systematic review production. Large language models (LLMs) offer potential for automating or semi-automating this process, yet their performance characteristics remain incompletely characterised. This systematic review aimed to comprehensively evaluate LLM accuracy, reliability, and efficiency for data extraction in evidence synthesis, and to identify optimal implementation strategies.
    METHODS: We searched PubMed, Embase, Web of Science, and preprint servers (medRxiv, arXiv) through December 2025. Studies were eligible if they evaluated one or more LLMs for data extraction against a human reference standard and reported quantitative performance metrics. Two reviewers independently extracted data and assessed methodological quality using PROBAST + AI and reporting completeness using TRIPOD-LLM. Narrative synthesis was performed due to substantial heterogeneity precluding meta-analysis.
    RESULTS: Twenty-seven studies met inclusion criteria, evaluating models including GPT-4/4o (n = 15), Claude versions 2-3.5 (n = 10), Gemini (n = 3), and open-source alternatives including Llama, Mistral, Qwen, and DeepSeek. Overall accuracy ranged from 47% to 99.9%, with substantial heterogeneity by task type and data granularity. Categorical and string variables were extracted more reliably (74-96%) than numerical data (47-88%). Claude 3.5 Sonnet achieved high accuracy in an assistive workflow (91.0%; 95% CI: 90.4-91.6%), exceeding human-only extraction (89.0%). Claude models outperformed GPT in head-to-head comparisons (OR 1.70 for event counts). Omissions were the dominant error type (60-74%), with hallucination rates of only 0.08-6%, challenging widespread fabrication concerns. Time savings of 33% to 87% were reported, although most included studies did not quantitatively assess efficiency. Methodological quality was generally robust, with 74.1% of studies rated low risk of bias under PROBAST + AI. Mean TRIPOD-LLM compliance was 88.5%, though gaps in inference settings and model version documentation were common.
    CONCLUSION: LLMs demonstrate promising but variable performance for data extraction in evidence synthesis. Current evidence supports their integration as assistive tools within dual-extraction workflows requiring human verification, rather than as autonomous extractors. Categorical data is extracted more reliably than numerical outcomes, and few-shot prompting with structured output formats consistently improves performance. Standardised benchmarks and prospective comparative studies remain priorities for future research.
    Keywords:  Artificial intelligence; ChatGPT; Data extraction; Evidence synthesis; Large language models; Meta-analysis
    DOI:  https://doi.org/10.1016/j.jbi.2026.105086
  2. Pharmacoeconomics. 2026 Jul 29.
       BACKGROUND: Systematic literature reviews offer high potential for efficiency gains from artificial intelligence (AI), now integrated into several systematic literature review software platforms. Validation studies show acceptable sensitivity, specificity, and accuracy for AI-assisted systematic literature reviews of clinical trial publications. Unlike trials, economic model publications lack consistency in content, terminology, and structure.
    OBJECTIVE: We aimed to test the efficiency and accuracy of AI-assisted search, screening, and data extraction when applied to a systematic literature review of economic evaluations.
    METHODS: A previously conducted manual systematic literature review of economic evaluations for chronic rhinosinusitis with nasal polyps was replicated using a machine learning-based inclusion prediction model (Robot Screener) and a large language model-based criteria screener (Smart Screener) within Nested Knowledge software, with performance benchmarked against the original human-conducted systematic literature review.
    RESULTS: The AI-generated search retrieved 22/43 (51%) PubMed articles from the original systematic literature review. Accuracy exceeded 95% for title/abstract screening but fell below 80% for full-text screening. Extraction was reliable for high-level model descriptors and general study characteristics, but less so for model structures, health states, outcomes, and distinguishing sensitivity from scenario analyses and complex modeling assumptions for duration of response, discontinuation, surgery, and mortality. Estimated time savings ranged from ~20% (data extraction) to 60% (title/abstract screening and searches), varying by task human validation requirement.
    CONCLUSIONS: Artificial intelligence-driven tools performed well for title/abstract screening and general data extraction but were less accurate for full-text screening and interpretation of modeling choices. They can increase systematic literature review efficiency for economic evaluations but fall below the reliability seen for systematic literature reviews of clinical trials.
    DOI:  https://doi.org/10.1007/s40273-026-01648-7
  3. MethodsX. 2026 Dec;17 104041
      This methods article presents a reproducible workflow for optimising and testing improving large language models (LLMs) prompts in evidence-synthesis tasks with defined inputs and outputs. The method separates the fixed rules that define the scientific task from the editable prompt instructions that frame and apply them. It optimises those instructions against labelled or reference examples and an explicit task metric, then saves the final workflow with its specification, metric, settings, and evaluation traces so others can inspect and reuse it. The example code uses DSPy and GEPA tools, but the same logic can transfer to other prompt-optimisation frameworks that support structured task definitions, metric-guided search, and reusable outputs. Title and abstract screening is the illustrative validation case here as it provides labelled benchmark data and clear evaluation metrics. The demonstrated workflow uses a smaller student LLM for the scientific task and a larger reflection LLM to steer prompt optimisation during calibration. This work shows compilation, saving and reloading, and how optimisation budget affects a smaller student model.•Separate what the model must decide (the fixed rules), from how it is prompted to decide (the mutable prompt instructions).•Optimise the prompt automatically against labelled examples and a declared scoring function, rather than iterating manually.•Package the calibrated prompt with its rules, metric, settings, traces, and evaluation logs for inspection and reuse.
    Keywords:  Declarative programming; Evidence synthesis automation; Language model calibration; Prompt optimisation; Reproducible workflows; Systematic reviews
    DOI:  https://doi.org/10.1016/j.mex.2026.104041
  4. PLoS One. 2026 ;21(7): e0347081
      Although bar charts are widely used in scientific publications, their rasterized format within Portable Document Format (PDF) files complicates automated data extraction, hindering large-scale evidence synthesis and meta-analysis. To address this, we developed and evaluated an automated pipeline for extracting quantitative data from bar charts embedded in the biomedical literature. The four-stage pipeline comprises (1) image extraction and panel segmentation, (2) optical character recognition (OCR)-based text detection, (3) image disassembly to identify chart components, and (4) data reconstruction using numeric parsing and axis-based interpolation. The system combines edge detection, morphological operations, and convolutional neural network (CNN)-based figure classification using a transfer-learned Inception v3 model. Performance was validated on randomized controlled trials in age-related macular degeneration, with manually annotated values from a semi-automated labeling tool as the reference standard, and agreement was assessed using Bland-Altman analysis. Across 28 bar charts from ten publications, the pipeline correctly recognized 92.9% (95% confidence interval [CI], 77.4-98.0) of figure types, 96.0% (95% CI, 94.2-97.3) of text blocks, and 79.1% (95% CI, 74.7-83.0) of bars. For numerical reconstruction, 81.2% (95% CI, 76.3-85.2) of bar values fell within ±5% of the reference standard, 63.0% (95% CI, 57.3-68.3) within ±2%, and 48.6% (95% CI, 43.0-54.3) within ±1%. Bland-Altman analysis showed a small negative bias of -0.18 (95% CI, -0.34 to -0.02), with 94.9% of differences within the limits of agreement. Most outliers arose from OCR digit misclassification or ambiguous bar boundaries. This proof-of-concept study demonstrates the feasibility of automated data extraction from bar charts using a hybrid approach that combines image-processing heuristics with CNN-based classification. Although currently limited to bar charts and a single clinical domain, the pipeline represents a step toward scalable, end-to-end systems for automated evidence extraction to support meta-analyses across the biomedical literature.
    DOI:  https://doi.org/10.1371/journal.pone.0347081
  5. Bioengineering (Basel). 2026 Jul 02. pii: 773. [Epub ahead of print]13(7):
      (1) Background: Clinical trial data extraction from registries such as ClinicalTrials.gov remains labor-intensive and error-prone, often missing critical details hidden in unstructured protocol descriptions. Large Language Models (LLMs) offer potential to automate this process, yet systematic multi-model comparisons on real clinical trial data remain scarce. (2) Methods: Four LLMs (OpenAI o4-mini-high, Anthropic Claude-Sonnet-4, Google Gemini 2.5-Pro, and Meta Llama-4-Maverick) extracted brain stimulation parameters from 67 transcranial direct current stimulation (tDCS) trials in Parkinson's disease via a structured JSON schema. Pairwise inter-model agreement was quantified with Cohen's Kappa and percentage agreement across binary, categorical, and multi-component task tiers. (3) Results: Under exact-string matching, agreement was near-perfect for binary classifications (non-invasive classification: 100%; brain stimulation presence: 99.3%, κ = 0.50) and substantial for categorical extractions (primary stimulation type: 96.4%, κ = 0.70), but fell to 48.6% (κ = 0.43) for complex anatomical targets. Numeric parameters revealed model-specific strengths: o4-mini-high and Claude-Sonnet-4 achieved perfect duration agreement (r = 1.000, n = 19) while Llama-4-Maverick diverged substantially (r < 0.12). Validation against an expert gold standard (100% inter-annotator agreement on a 20-trial overlap) confirmed high extraction accuracy across all features (mean 93.7-98.9%). Crucially, the low agreement on anatomical targets proved to be an artifact of exact-string scoring: under the same semantic matching used to measure accuracy, inter-model agreement rose to 97.0%, coinciding with the 95.5% expert accuracy. Inter-model agreement therefore tracks accuracy once both are measured on a common basis. (4) Conclusions: Exact-string inter-model agreement decreases with task complexity, but this decline largely reflects interchangeable free-text wording rather than reduced accuracy. Evaluated semantically, agreement and expert accuracy are both high and closely aligned. A residual risk is not low accuracy but the rare error shared across all models, which agreement cannot detect, and which overall accuracy can itself mask when one class dominates. These findings inform hybrid human-AI systematic review pipelines in which targeted expert oversight focuses on shared-error and minority-class detection.
    Keywords:  API integration; Parkinson’s disease; clinical trial data extraction; evidence synthesis; large language models; neuromodulation; research automation; systematic review methodology; transcranial direct current stimulation
    DOI:  https://doi.org/10.3390/bioengineering13070773
  6. JMIR AI. 2026 Jul 29. 5 e95565
       Background: Large language models (LLMs) can accurately classify biomedical documents, but strong benchmark performance does not establish that predictions are grounded in the supplied text. In biomedical literature tasks, titles, abstracts, digital object identifiers (DOIs), journal metadata, and trial identifiers may have been seen during pretraining and can trigger parametric knowledge or learned associations.
    Objective: This study aimed to test whether oncology randomized trial success classification is driven by abstract evidence or by identifier-conditioned prior knowledge, and assess whether models follow counterfactual outcome evidence when it conflicts with original trial identifiers.
    Methods: We evaluated 250 two-arm oncology randomized controlled trials from 7 major journals published between 2005 and 2023, each with a single primary endpoint and previously adjudicated positive or negative ground-truth label. The corpus included 58.4% (146/250) positive and 41.6% (104/250) negative trials. GPT-5.2, Gemini 3 Flash, and Claude Opus 4.5 were queried via vendor APIs under default settings using a single-token output instruction. For each trial, we created 5 deterministic input conditions: title+abstract, title only, DOI only, counterfactual title+abstract in which the primary endpoint outcome statement was minimally flipped, and the same counterfactual input paired with the original DOI to create an identifier-text conflict. Performance was assessed using valid format rate, accuracy, sensitivity, specificity, and F1-score.
    Results: The models showed high format adherence, with valid prediction rates of 97.2% to 100%. In the title+abstract condition, all models achieved high and balanced performance (accuracy and F1-score=0.96-0.97; sensitivity=0.96-0.97; specificity=0.96-0.98). Removing evidence reduced performance stepwise: title-only accuracy and F1-score fell to 0.79 to 0.88, and DOI-only performance fell to 0.63-0.67, exceeding the 58.4% majority class baseline but indicating limited identifier-driven signal. Counterfactual edits were concentrated in outcome-bearing text, with the Results and Conclusions sections modified for all trials, whereas the titles and Methods sections required edits in only 5.2% (13/250) and 1.6% (4/250) of trials. Against inverted labels, models followed counterfactual evidence with near-ceiling performance (accuracy and F1-score=0.96-0.99). Reintroducing the original DOI caused little change for GPT-5.2 (accuracy and F1-score=0.99) but modestly reduced F1-scores for Gemini (0.97) and Claude (0.95), mainly through lower sensitivity.
    Conclusions: The evaluated LLMs robustly followed explicit end point statements in abstracts, including when those statements contradicted original trial outcomes. However, above-chance title-only and DOI-only performance, together with small decrements under counterfactual DOI conflicts, showed that identifiers can carry predictive signal and occasionally compete with textual evidence. Progressive content removal combined with counterfactual identifier-text conflicts offers a practical, reproducible audit for grounding in biomedical LLM evaluations.
    Keywords:  context grounding; large language models; memory; natural language processing; parametric knowledge; reasoning models
    DOI:  https://doi.org/10.2196/95565
  7. Cureus. 2026 Jun;18(6): e111768
       BACKGROUND: Appropriate statistical test selection is essential for producing valid and reproducible findings in healthcare research. However, many investigators encounter difficulties when determining the most suitable statistical methods for their study design and dataset. Recently, artificial intelligence-based large language models (LLMs) have emerged as potential tools capable of assisting researchers with methodological decisions, including statistical analysis.
    OBJECTIVE: The objective of this study was to evaluate whether artificial intelligence-based LLMs can accurately and reliably recommend appropriate statistical tests for healthcare research studies.
    METHODS: Four LLM platforms (ChatGPT (OpenAI, San Francisco, California, USA), Google Gemini (Google LLC, Mountain View, California, USA), Microsoft Copilot (Microsoft Corporation, Redmond, Washington, USA), and Grok (xAI, Palo Alto, California, USA)) and two traditional search engines (Google (Google LLC, Mountain View, California, USA) and Bing (Microsoft Corporation, Redmond, Washington, USA)) were evaluated. Forty published research articles were selected across four common study designs: systematic reviews, randomized controlled trials, cohort studies, and case-control studies (10 articles per category). Each article's primary objective and statistical analysis were used to generate a standardized prompt describing the study scenario. These prompts were submitted to each LLM and search engine. Model responses were recorded and compared with the statistical tests used in the original studies. Accuracy was defined as agreement between the model's recommendation and the statistical test used in the published article.
    RESULTS: LLMs demonstrated moderate-to-high accuracy in recommending appropriate statistical tests. Grok and Microsoft Copilot achieved the highest accuracy (34/40 correct recommendations), followed by Google Gemini (32/40) and ChatGPT (30/40). In contrast, traditional search engines (Google and Bing) did not provide statistical recommendations that matched the statistical tests used in the selected studies.
    CONCLUSION: LLMs demonstrated promising capability in identifying appropriate statistical tests for healthcare research scenarios and outperformed traditional search engines in this task. While these findings suggest that LLMs may serve as useful decision-support tools for researchers, their recommendations should be interpreted cautiously and verified by individuals with statistical expertise. Continued evaluation of AI-based tools will be necessary to ensure their responsible integration into scientific research workflows.
    Keywords:  artificial intelligence; healthcare research; large language models; statistical analysis; statistical test
    DOI:  https://doi.org/10.7759/cureus.111768
  8. Heart Lung Circ. 2026 Jul 27. pii: S1443-9506(26)00479-8. [Epub ahead of print]
       BACKGROUND & AIM: Accurate extraction of clinical and methodological features from published literature is essential for supporting evidence-based cardiovascular rehabilitation. With the rapid expansion of research outputs, manual data extraction is time-consuming and prone to errors. Large language models (LLMs) may help automate evidence synthesis tasks, but their performance in document extraction for cardiovascular rehabilitation nursing research remains unclear. We aimed to evaluate the ability of LLMs to extract key literature features in the field of cardiovascular exercise rehabilitation nursing.
    METHOD: A diagnostic accuracy study was conducted using a reference standard established by two independent experts in cardiovascular rehabilitation. A structured extraction framework covering study characteristics, participant profiles, intervention components, and outcome domains was applied. LLM outputs were compared with the reference standard, and sensitivity, specificity, and area under the curve (AUC) were calculated.
    RESULTS: LLMs demonstrated high sensitivity (0.96-0.98) in identifying essential study features, indicating a low risk of missed information. Specificity ranged from moderate to high (0.70-0.77) and improved notably after incorporating nursing-specific chain-of-thought prompting. Overall diagnostic performance was excellent, with a post-hoc analysis AUC reaching 0.98. Error patterns were primarily related to ambiguous intervention descriptions and multi-component rehabilitation programs.
    CONCLUSIONS: LLMs show strong potential as an efficient and accurate tools for automating literature feature extraction in cardiovascular exercise-based rehabilitation nursing. Their use may enhance the speed and reliability of evidence synthesis, and support clinical decision-making. Further optimisation of prompting strategies and domain-specific tuning is warranted before widespread clinical adoption.
    Keywords:  Cardiovascular rehabilitation; Evidence synthesis; Feature extraction; Large language model; Nursing
    DOI:  https://doi.org/10.1016/j.hlc.2026.05.032
  9. JMIR AI. 2026 Jul 30. 5 e87034
       BACKGROUND: Large language models (LLMs) have the potential to provide individualized preventive care guidance at scale. Research, however, has found mixed performance among a small set of LLMs queried about select preventive care activities. These findings call for testing a larger set of LLMs on a wider range of preventive care topics.
    OBJECTIVE: This study aims to assess whether various popular LLMs generate outputs about preventive care consistent with a comprehensive set of recommendations from the US Preventive Services Task Force (USPSTF).
    METHODS: We investigated whether 35 popular LLMs produced outputs consistent with all publicly available USPSTF recommendations (n=142) published as of May 2025. The study occurred in 2 waves (wave 1, 2025: 28 LLMs; wave 2, 2026: 10 LLMs; 3 LLMs overlapping across waves). LLMs received queries from simulated users who, in baseline prompts, sought nonbinding, hypothetical advice about whether to participate in particular preventive care activities given their inclusion in a relevant population. LLM raters assessed LLM-USPSTF concordance (interrater reliability, wave 1: κ=0.8893; wave 2: κ=0.9366). Wave 2 tested chain-of-thought, few-shot, and role-based prompts (3 variants each for 426 tests per prompting approach per model). Wave 2 also tested an iterative prompt that sought clarification about previous LLM responses and a prompt that eliminated the user's reference to nonbinding, hypothetical advice. Automated methods classified responses to detect sources of LLM-USPSTF discrepancy. Further tests prompted LLMs to rate preventive care activities for relevant populations using the USPSTF grading scale.
    RESULTS: Focusing on cases where LLM raters agreed, the study found in its baseline prompts that the LLM with the highest concordance rate generated responses consistent with USPSTF recommendations in 66.92% (89/133) of tests in wave 1 and 87.77% (122/139) of tests in wave 2; the LLM with the lowest rate accorded with USPSTF recommendations in 45.19% (61/135) of tests in wave 1 and in 50.36% (69/137) of tests in wave 2. Eliminating reference to nonbinding, hypothetical advice did not alter the highest-performing model's rate of concordance (122/139, 87.77%). The highest concordance rate increased with chain-of-thought (404/421, 95.96%), role-based (371/416, 89%), and iterative prompting (127/140, 90.71%); however, it moderately decreased with few-shot prompting (361/419, 86.15%). Automated content analysis found high rates of LLMs avoiding definitive recommendations. When prompted to grade preventive care activities, the highest-performing LLM matched USPSTF grades in 85.92% (122/142) of tests in wave 1 and in 94.37% (134/142) of tests in wave 2.
    CONCLUSIONS: LLMs' consistency with USPSTF recommendations varies. Deviations result mainly from LLMs' avoidance of definitive statements. LLM-USPSTF concordance has improved markedly in newer models, and this concordance increases with particular prompting approaches.
    Keywords:  LLM; generative artificial intelligence; health promotion; large language model; preventive health services; preventive medicine; primary prevention; public health
    DOI:  https://doi.org/10.2196/87034
  10. Cureus. 2026 Jun;18(6): e111207
      Background Artificial intelligence (AI), particularly large language models (LLMs) such as ChatGPT, is increasingly being used for statistical interpretation and research support. While traditional statistical software such as IBM SPSS remains the gold standard for transparent and reproducible analyses, concerns persist regarding the accuracy, consistency, and reproducibility of LLM-generated statistical outputs. Given the continuous evolution of LLMs, replication studies are needed to evaluate whether newer models demonstrate improved statistical reliability and alignment with established analytic standards. Methodology In total, 14 statistical procedures were applied to real datasets that previously generated peer‑reviewed, published scientific articles. The analyses encompassed descriptive statistics, Pearson product-moment correlation coefficient (Pearson r), multiple correlation using Pearson r, Spearman's rho, simple linear regression, one-sample and paired t‑tests, two independent‑sample t‑tests, multiple linear regression, one-way analysis of variance (ANOVA), repeated‑measures ANOVA, two‑way (factorial) ANOVA, and multivariate analysis of variance (MANOVA). Datasets were collected within a systematically defined timeframe (2012-2023), ensuring temporal consistency and representativeness. All analyses were executed by copying and pasting prompts into GPT-5.5, accompanied by the corresponding SPSS 31.0 variable names copied and pasted directly from the original SPSS datasets. Results Results demonstrated concordance between SPSS 31.0 and GPT-5.5 across most descriptive and inferential statistical procedures, although notable discrepancies did occur. Identical or near-identical findings were observed for descriptive statistics, Pearson correlations, one-sample t-tests, paired t-tests, two independent-sample t-tests, simple and multiple linear regression, and one-way ANOVA. Correlation coefficients, effect sizes, confidence intervals, and significance values were mostly consistent across platforms. Discrepancies emerged in selected nonparametric analyses, factorial ANOVA, MANOVA, and repeated-measures ANOVA procedures. Despite these computational differences, the overall substantive interpretations and statistical conclusions remained largely consistent between SPSS 31.0 and GPT-5.5, but not perfectly. These findings suggest GPT-5.5 demonstrates some statistical consistency with traditional statistical software for many common analytic procedures, while more advanced multivariate analyses may still require independent verification using established statistical platforms. Conclusions GPT-5.5 demonstrated considerable agreement with SPSS 31.0 across many commonly used statistical procedures, including descriptive statistics, correlations, regression analyses, t-tests, and one-way ANOVA. However, more notable discrepancies emerged in several analyses, particularly more complex procedures such as factorial ANOVA, MANOVA, and repeated-measures ANOVA. These findings suggest that GPT-5.5 may serve as a useful adjunct for statistical interpretation and exploratory research, but AI-generated statistical outputs should be interpreted with caution. Validated statistical software and appropriate methodological oversight remain essential for confirmatory analyses and research involving clinical decision-making.
    Keywords:  ai-assisted statistics; alignment; chatgpt; ibm spss; large language models
    DOI:  https://doi.org/10.7759/cureus.111207
  11. Clin Pharmacol Ther. 2026 Jul 29.
      Pharmacovigilance is the science involving the detection, assessment, understanding, and prevention of adverse events associated with drugs, biologics, or medical devices. In pharmacovigilance, information that suggests a new potential causal relationship between an intervention and an adverse event is called a safety signal. Following their detection, safety signals are assessed via a comprehensive, structured analysis to more fully elucidate whether a correlation exists. This key process often requires the manual assessment of many individual case safety report (ICSR) narratives to extract meaningful information in a labor-intensive, time-consuming, and variability-prone manner. In this retrospective feasibility study, we describe the potential utility of an intelligent automation system leveraging the GPT-4o large language model to automate the extraction of case elements of interest from a series of ICSR narratives while maintaining human expert oversight. Our proprietary platform allowed users to extract the presence or absence of risk factors and responses to dechallenge and rechallenge via instructional prompts built on a common template structure. Case elements for five historical signal assessments were selected based on need for and feasibility of artificial intelligence extraction. Performance ranged from F1 = 0.444 to 1.000 for risk factors and from F1 = 0.429 to 0.909 for responses to dechallenge and rechallenge. Even when considering the need to verify GPT-4o outputs for accuracy, potential time savings were identified. To the best of our knowledge, our results are the first to demonstrate an intelligent automation platform that may streamline signal management workflows using a machine-first, human-verified operational workflow while maintaining regulatory compliance.
    DOI:  https://doi.org/10.1002/cpt.70409