Model Retirement Creates Reproducibility Risk in Biomedical AI Publications

Nathan Wolfrath; Meghan Conroy; Thomas Kosten; Dave Bell; Bhabishya Neupane; Jonah Kindel; Anjishnu Banerjee; Priya Deshpande; Bradley Taylor; Anai N. Kothari

arXiv · 2609.04699

Model Retirement Creates Reproducibility Risk in Biomedical AI Publications

Nathan Wolfrath·Meghan Conroy·Thomas Kosten·Dave Bell·Bhabishya Neupane·Jonah Kindel·Anjishnu Banerjee·Priya Deshpande·Bradley Taylor·Anai N. Kothari

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Abstract

Background. Large language models (LLMs) are being adopted in biomedical research at a rapid and accelerating pace, yet commercial services that host many widely used models operate under deprecation schedules that can complicate scientific reproducibility. Methods. We searched PubMed for original research articles from 2022 through March 2026 that applied a specific LLM to a biomedical task. An extraction agent identified model names from 61,077 article abstracts with human reviewers validating a subset for extraction accuracy. Extracted model names were normalized to canonical model identifiers. Lifecycle data (release date, retirement date, status) were compiled for the 50 most frequently used models. Results. We identified 8,931 paper-model mentions spanning 5,242 unique publications after restricting the analysis to the 50 most frequently used models. Among these mentions, 77.7% cited a commercial closed-weight model. Overall, 42% involved a model that was already retired by the time of official publication or is scheduled to retire within two years of publication. The median interval from publication to model retirement was 538 days. Conclusion. Many biomedical publications using LLMs are on a trajectory toward computational non-reproducibility after publication. Model deprecation should be treated as a core reporting and preservation issue for biomedical research.

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Nathan Wolfrath, Meghan Conroy, Thomas Kosten, Dave Bell, Bhabishya Neupane, Jonah Kindel, Anjishnu Banerjee, Priya Deshpande, Bradley Taylor, Anai N. Kothari. 2026-09-04. Model Retirement Creates Reproducibility Risk in Biomedical AI Publications. https://arxiv.org/abs/2609.04699

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