AI-assisted scoping review of code sharing in clinical prediction model research

Abstract Clinical prediction models are increasingly deployed to support diagnostic and prognostic decisions, making reproducibility essential for assessing their reliability and generalizability. Analytical code supports independent assessment of these processes, yet its availability in the literature remains limited. This scoping review quantifies current practices in sharing analytical code to inform the development of TRIPOD-Code, a reporting guideline for code availability and reproducibility. Here a large-language-model-assisted pipeline was developed to screen articles citing TRIPOD or TRIPOD+AI, extract repository links and assess retrieved repositories against 14 predefined reproducibility-related features. Among 3,967 articles, 482 (12.2%) included code-sharing statements. Sharing prevalence varied widely by journal and country. Repository assessment showed substantial heterogeneity in reproducibility features. These findings underscore the need for clearer expectations beyond code availability, including documentation, dependency specification and executable structure. Strengthening these practices may improve the usability of clinical prediction model studies and support their deployment in real-world clinical settings.

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Publication Details

Journal
Nature Medicine
Published
2026-10-09
DOI
https://doi.org/10.1038/s41591-026-04691-1
Primary Topic
Meta-analysis and systematic reviews
Type
article
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article

AI-assisted scoping review of code sharing in clinical prediction model research

Raffaele Giancotti, Hyung‐Chul Lee, Hyeonhoon Lee, Lasai Barreñada et al.
Nature Medicine
Meta-analysis and systematic reviews
article

AI-assisted scoping review of code sharing in clinical prediction model research

Raffaele Giancotti, Hyung‐Chul Lee, Hyeonhoon Lee, Lasai Barreñada, Leo Anthony Celi, Catherine A. Gao, Professor Gary S. Collins, Karel G.M. Moons, Tom Pollard, Charlotta Lindvall, Thomas Sounack
article en

Abstract

Abstract Clinical prediction models are increasingly deployed to support diagnostic and prognostic decisions, making reproducibility essential for assessing their reliability and generalizability. Analytical code supports independent assessment of these processes, yet its availability in the literature remains limited. This scoping review quantifies current practices in sharing analytical code to inform the development of TRIPOD-Code, a reporting guideline for code availability and reproducibility. Here a large-language-model-assisted pipeline was developed to screen articles citing TRIPOD or TRIPOD+AI, extract repository links and assess retrieved repositories against 14 predefined reproducibility-related features. Among 3,967 articles, 482 (12.2%) included code-sharing statements. Sharing prevalence varied widely by journal and country. Repository assessment showed substantial heterogeneity in reproducibility features. These findings underscore the need for clearer expectations beyond code availability, including documentation, dependency specification and executable structure. Strengthening these practices may improve the usability of clinical prediction model studies and support their deployment in real-world clinical settings.

Nature Medicine
Northwestern University (US), University Hospitals Birmingham NHS Foundation Trust (GB), Harvard University (US), Seoul National University (KR), Seoul National University Hospital (KR), University Medical Center Utrecht (NL), Dana-Farber Cancer Institute (US), University of Calabria (IT), Massachusetts Institute of Technology (US), University of Birmingham (GB), KU Leuven (BE)
Openalex Percentile: Top 10%
Meta-analysis and systematic reviews
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