MRAgent: an LLM-based automated agent for causal knowledge discovery in disease via Mendelian randomization

Understanding causality in medical research is essential for developing effective interventions and diagnostic tools. Mendelian Randomization (MR) is a pivotal method for inferring causality through genetic data. However, MR analysis often requires pre-identification of exposure-outcome pairs from clinical experience or literature, which can be challenging to obtain. This poses difficulties for clinicians investigating causal factors of specific diseases. To address this, we introduce MRAgent, an innovative automated agent leveraging Large Language Models (LLMs) to enhance causal knowledge discovery in disease research. MRAgent autonomously scans scientific literature, discovers potential exposure-outcome pairs, and performs MR causal inference using extensive Genome-Wide Association Study data. We conducted both automated and human evaluations to compare different LLMs in operating MRAgent and provided a proof-of-concept case to demonstrate the complete workflow. MRAgent's capability to conduct large-scale causal analyses represents a significant advancement, equipping researchers and clinicians with a robust tool for exploring and validating causal relationships in complex diseases. Our code is public at https://github.com/xuwei1997/MRAgent.