Evidence map›Paper›PMID 39399004›Full record

ArticlemedRxiv : the preprint server for health sciences2024

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 Zou, Huan He, Seyyed Amir Hossein, Bashar Hasan and 11 more

Abstract readPreprint
In one paragraph

Article in medRxiv : the preprint server for health sciences, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing 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

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

21 authors.

Muhammad Ali KhanDepartment of Medicine, Mayo Clinic, Phoenix, United States of America.
Umair AyubDepartment of Medicine, Mayo Clinic, Phoenix, United States of America.
Syed Arsalan Ahmed NaqviDepartment of Medicine, Mayo Clinic, Phoenix, United States of America.
Kaneez Zahra Rubab KhakwaniDepartment of Medicine, University of Arizona, Tucson, United States of America.
Zaryab Bin Riaz SipraDepartment of Medicine and Surgery, Rashid Latif Medical College, Lahore, Pakistan.
Ammad RainaDepartment of Medicine, Canyon Vista Hospital, Sierra Vista, United States of America.
Sihan ZouDepartment of Medicine, Mayo Clinic, Phoenix, United States of America.
Huan HeDepartment of Biomedical Informatics and Data Science, Yale University, New Haven, United States of America.
Seyyed Amir HosseinDepartment of Medicine, Mayo Clinic, Phoenix, United States of America.
Bashar HasanDepartment of Medicine, Mayo Clinic, Rochester, United States of America.
R Bryan RumbleAmerican Society of Clinical Oncology, Alexandria, United States of America.
Danielle S BittermanDepartment of Radiation Oncology, Dana-Farber Cancer Institute, Boston, United States of America.
Jeremy L WarnerDepartments of Medicine and Biostatistics, Brown University, Providence, United States of America.
Jia ZouDepartment of Computing and Augmented Intelligence, Arizona State University, Tempe, United States of America.
Amye J TevaarwerkDepartment of Oncology, Mayo Clinic, Rochester, United States of America.
Konstantinos LeventakosDepartment of Medicine, Mayo Clinic, Rochester, United States of America.
Kenneth L KehlDepartment of Medicine, Dana-Farber Cancer Institute, Boston, United States of America.
Jeanne M PalmerDepartment of Medicine, Mayo Clinic, Phoenix, United States of America.
M Hassan MuradDepartment of Medicine, Mayo Clinic, Rochester, United States of America.
Chitta BaralDepartment of Computing and Augmented Intelligence, Arizona State University, Tempe, United States of America.
Irbaz Bin RiazDepartment of Medicine, Mayo Clinic, Phoenix, United States of America.

Funding

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

Abstract

Objective: Data 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 two-reviewer process. Materials and Methods: A dataset of 10 clinical 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 two LLMs were compared for concordance. In instances with discordance, original responses from each LLM were provided to the other LLM for cross-critique. Evaluation metrics, including accuracy, were used to assess performance against the manually curated gold standard. Results: In 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, with an increase in 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. Conclusion: Large language models, when simulated in a collaborative, two-reviewer workflow, can extract data with reasonable performance, enabling truly 'living' systematic reviews.

Indexed as

Data ExtractionLarge Language ModelsMeta-AnalysisNatural Language ProcessingSystematic Review

Identifiers

PMID39399004
PMCPMC11469465

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

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.