Accelerating Causal Network Discovery of Alzheimer Disease Biomarkers via Scientific Literature-based Retrieval Augmented Generation

The causal relationships between biomarkers are essential for disease diagnosis and medical treatment planning. One notable application is Alzheimer's disease (AD) diagnosis, where certain biomarkers may influence the presence of others, enabling early detection, precise disease staging, targeted treatments, and improved monitoring of disease progression. However, understanding these causal relationships is complex and requires extensive research. Constructing a comprehensive causal network of biomarkers demands significant effort from human experts, who must analyze a vast number of research papers, and have bias in understanding diseases' biomarkers and their relation. This raises an important question: Can advanced large language models (LLMs), such as those utilizing retrieval-augmented generation (RAG), assist in building causal networks of biomarkers for further medical analysis? To explore this, we collected 200 AD-related research papers published over the past 25 years and then integrated scientific literature with RAG to extract AD biomarkers and generate causal relations among them. Given the high-risk nature of the medical diagnosis, we applied uncertainty estimation to assess the reliability of the generated causal edges and examined the faithfulness and scientificness of LLM reasoning using both automatic and human evaluation. We find that RAG enhances the ability of LLMs to generate more accurate causal networks from scientific papers. However, the overall performance of LLMs in identifying causal relations of AD biomarkers is still limited. We hope this study will inspire further foundational research on AI-driven analysis of AD biomarkers causal network discovery.

@article{zhou2025_2504.08768,
  title={ Accelerating Causal Network Discovery of Alzheimer Disease Biomarkers via Scientific Literature-based Retrieval Augmented Generation },
  author={ Xiaofan Zhou and Liangjie Huang and Pinyang Cheng and Wenpen Yin and Rui Zhang and Wenrui Hao and Lu Cheng },
  journal={arXiv preprint arXiv:2504.08768},
  year={ 2025 }
}