Evidence map›Paper›PMID 39836495›Full record

ArticleJournal of the American Medical Informatics Association : JAMIA2025

Collaborative large language models for automated data extraction in living systematic reviews.

Muhammad Ali Khan, Umair Ayub, Syed Arsalan Ahmed Naqvi, Kaneez Zahra Rubab Khakwani, Zaryab Bin Riaz Sipra, Ammad Raina, Sihan Zhou, Huan He, Amir Saeidi, Bashar Hasan and 11 more

Abstract read
In one paragraph

Article in Journal of the American Medical Informatics Association : JAMIA, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.

0numbers the graph read from it
0cells of the map it votes in
15citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

15 citing papers in PubMed.

  1. Structured Schemas for Provenance-Rich, LLM-Assisted QSP Model Calibration.CPT: pharmacometrics & systems pharmacology · 2026
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  14. Harnessing the power of large language models for clinical tasks and synthesis of scientific literature.Journal of the American Medical Informatics Association : JAMIA · 2025
    Article
  15. Advancing the application and evaluation of large language models in health and biomedicine.Journal of the American Medical Informatics Association : JAMIA · 2025
    Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

21 authors.

Muhammad Ali KhanDepartment of Medicine, Mayo Clinic, Phoenix, AZ, 85054, United States.
Umair AyubDepartment of Medicine, Mayo Clinic, Phoenix, AZ, 85054, United States.
Syed Arsalan Ahmed NaqviDepartment of Medicine, Mayo Clinic, Phoenix, AZ, 85054, United States.
Kaneez Zahra Rubab KhakwaniDepartment of Medicine, University of Arizona, Tucson, AZ, 85721, United States.
Zaryab Bin Riaz SipraDepartment of Medicine and Surgery, Rashid Latif Medical College, Lahore, Punjab, 54000, Pakistan.
Ammad RainaDepartment of Medicine, Canyon Vista Hospital, Sierra Vista, AZ, 85635, United States.
Sihan ZhouDepartment of Medicine, Mayo Clinic, Phoenix, AZ, 85054, United States.
Huan HeDepartment of Biomedical Informatics and Data Science, Yale University, New Haven, CT, 06520, United States.ORCID 0000-0003-1312-4195
Amir SaeidiDepartment of Medicine, Mayo Clinic, Phoenix, AZ, 85054, United States.
Bashar HasanDepartment of Medicine, Mayo Clinic, Rochester, MN, 55905, United States.
Robert Bryan RumbleAmerican Society of Clinical Oncology, Alexandria, VA, 22314, United States.
Danielle S BittermanDepartment of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, United States.
Jeremy L WarnerDepartment of Medicine, Brown University, Providence, RI, 02912, United States.
Jia ZouDepartment of Computing and Augmented Intelligence, Arizona State University, Tempe, AZ, 85287, United States.
Amye J TevaarwerkDepartment of Oncology, Mayo Clinic, Rochester, MN, 55905, United States.
Konstantinos LeventakosDepartment of Medicine, Mayo Clinic, Rochester, MN, 55905, United States.
Kenneth L KehlDepartment of Medicine, Dana-Farber Cancer Institute, Boston, MA, 02215, United States.
Jeanne M PalmerDepartment of Medicine, Mayo Clinic, Phoenix, AZ, 85054, United States.
Mohammad Hassan MuradDepartment of Medicine, Mayo Clinic, Rochester, MN, 55905, United States.
Chitta BaralDepartment of Computing and Augmented Intelligence, Arizona State University, Tempe, AZ, 85287, United States.
Irbaz Bin RiazDepartment of Medicine, Mayo Clinic, Phoenix, AZ, 85054, United States.

Funding

Enhancing the HemOnc Knowledgebase of Chemotherapy Drugs and RegimensU24CA265879 · NCI · RHODE ISLAND HOSPITAL · PI Jeremy L Warner · 2022 to 2026
$3.4M
AstraZenecaNCI NIH HHS U24 CA265879NIH HHS U24 CA265879
6 · The paper itself

Abstract

objectiveData extraction from the published literature is the most laborious step in conducting living systematic reviews (LSRs). We aim to build a generalizable, automated data extraction workflow leveraging large language models (LLMs) that mimics the real-world 2-reviewer process. MATERIALS AND

methodsA dataset of 10 trials (22 publications) from a published LSR was used, focusing on 23 variables related to trial, population, and outcomes data. The dataset was split into prompt development (n = 5) and held-out test sets (n = 17). GPT-4-turbo and Claude-3-Opus were used for data extraction. Responses from the 2 LLMs were considered concordant if they were the same for a given variable. The discordant responses from each LLM were provided to the other LLM for cross-critique. Accuracy, ie, the total number of correct responses divided by the total number of responses, was computed to assess performance.

resultsIn the prompt development set, 110 (96%) responses were concordant, achieving an accuracy of 0.99 against the gold standard. In the test set, 342 (87%) responses were concordant. The accuracy of the concordant responses was 0.94. The accuracy of the discordant responses was 0.41 for GPT-4-turbo and 0.50 for Claude-3-Opus. Of the 49 discordant responses, 25 (51%) became concordant after cross-critique, increasing accuracy to 0.76. DISCUSSION: Concordant responses by the LLMs are likely to be accurate. In instances of discordant responses, cross-critique can further increase the accuracy.

conclusionLarge language models, when simulated in a collaborative, 2-reviewer workflow, can extract data with reasonable performance, enabling truly "living" systematic reviews.

Indexed as

Data MiningInformation Storage and RetrievalNatural Language ProcessingSystematic Reviews as TopicHumansLarge Language ModelsWorkflowdata extractionlarge language modelsmeta-analysisnatural language processingsystematic review

Identifiers

PMID39836495
PMCPMC12005628

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.