Priya Deshpande | Searcharxiv

arXiv2026

Model Retirement Creates Reproducibility Risk in Biomedical AI Publications

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.

cs.AI↗

arXiv2024

Autocompletion of Chief Complaints in the Electronic Health Records using Large Language Models

The Chief Complaint (CC) is a crucial component of a patient's medical record as it describes the main reason or concern for seeking medical care. It provides critical information for healthcare providers to make informed decisions about patient care. However, documenting CCs can be time-consuming for healthcare providers, especially in busy emergency departments. To address this issue, an autocompletion tool that suggests accurate and well-formatted phrases or sentences for clinical notes can be a valuable resource for triage nurses. In this study, we utilized text generation techniques to develop machine learning models using CC data. In our proposed work, we train a Long Short-Term Memory (LSTM) model and fine-tune three different variants of Biomedical Generative Pretrained Transformers (BioGPT), namely microsoft/biogpt, microsoft/BioGPT-Large, and microsoft/BioGPT-Large-PubMedQA. Additionally, we tune a prompt by incorporating exemplar CC sentences, utilizing the OpenAI API of GPT-4. We evaluate the models' performance based on the perplexity score, modified BERTScore, and cosine similarity score. The results show that BioGPT-Large exhibits superior performance compared to the other models. It consistently achieves a remarkably low perplexity score of 1.65 when generating CC, whereas the baseline LSTM model achieves the best perplexity score of 170. Further, we evaluate and assess the proposed models' performance and the outcome of GPT-4.0. Our study demonstrates that utilizing LLMs such as BioGPT, leads to the development of an effective autocompletion tool for generating CC documentation in healthcare settings.

cs.CL↗