How Effectively Can Large Language Models Connect SNP Variants and ECG Phenotypes for Cardiovascular Risk Prediction?
Menon, Niranjana Arun Farooq, Iqra Li, Yulong Ahmed, Sara Xie, Yutong Cvssp, Muhammad Awais Razzak, Imran
Menon, Niranjana Arun
Farooq, Iqra
Li, Yulong
Ahmed, Sara
Xie, Yutong
Cvssp, Muhammad Awais
Razzak, Imran
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Computational Biology
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Abstract
Cardiovascular disease (CVD) prediction remains a tremendous challenge due to its multifactorial etiology and global burden of morbidity and mortality. Despite the growing availability of genomic and electrophysiological data, extracting biologically meaningful insights from such high-dimensional, noisy, and sparsely annotated datasets remains a non-trivial task. Recently, LLMs has been applied effectively to predict structural variations in biological sequences. In this work, we explore the potential of fine-tuned LLMs to predict cardiac diseases and SNPs potentially leading to CVD risk using genetic markers derived from high-throughput genomic profiling. We investigate the effect of genetic patterns associated with cardiac conditions and evaluate how LLMs can learn latent biological relationships from structured and semi-structured genomic data obtained by mapping genetic aspects that are inherited from the family tree. By framing the problem as a Chain of Thought (CoT) reasoning task, the models are prompted to generate disease labels and articulate informed clinical deductions across diverse patient profiles and phenotypes. The findings highlight the promise of LLMs in contributing to early detection, risk assessment, and ultimately, the advancement of personalized medicine in cardiac care.
Citation
N.A. Menon, I. Farooq, Y. Li, S. Ahmed, Y. Xie, M.A. Cvssp, I. Razzak, "How Effectively Can Large Language Models Connect SNP Variants and ECG Phenotypes for Cardiovascular Risk Prediction?," 2026, pp. 7625-7632.
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2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
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31 Biological Sciences, 3105 Genetics, 3 Good Health and Well Being
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2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
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IEEE