Evaluating Generative AI’s Ability to Identify Cancer Subtypes in Publicly Available Structured Genetic Datasets

Background: Genetic data play a crucial role in diagnosing and treating various diseases, reflecting a growing imperative to integrate these data into clinical care. However, significant barriers such as the structure of electronic health records (EHRs), insurance costs for genetic testing, and the interpretability of genetic results impede this integration. Methods: This paper explores solutions to these challenges by combining recent technological advances with informatics and data science, focusing on the diagnostic potential of artificial intelligence (AI) in cancer research. AI has historically been applied in medical research with limited success, but recent developments have led to the emergence of large language models (LLMs). These transformer-based generative AI models, trained on vast datasets, offer significant potential for genetic and genomic analyses. However, their effectiveness is constrained by their training on predominantly human-written text rather than comprehensive, structured genetic datasets. Results: This study reevaluates the capabilities of LLMs, specifically GPT models, in performing supervised prediction tasks using structured gene expression data. By comparing GPT models with traditional machine learning approaches, we assess their effectiveness in predicting cancer subtypes, demonstrating the potential of AI models to analyze real-world genetic data for generating real-world evidence.