DiscoUQ: Structured Disagreement Analysis for Uncertainty Quantification in LLM Agent Ensembles

Multi-agent LLM systems, where multiple prompted instances of a language model independently answer questions, are increasingly used for complex reasoning tasks. However, existing methods for quantifying the uncertainty of their collective outputs rely on shallow voting statistics that discard the rich semantic information in agents' reasoning. We introduce DiscoUQ, a framework that extracts and leverages the structure of inter-agent disagreement -- both linguistic properties (evidence overlap, argument strength, divergence depth) and embedding geometry (cluster distances, dispersion, cohesion) -- to produce well-calibrated confidence estimates. We propose three methods of increasing complexity: DiscoUQ-LLM (logistic regression on LLM-extracted structure features), DiscoUQ-Embed (logistic regression on embedding geometry), and DiscoUQ-Learn (a neural network combining all features). Evaluated on four diverse benchmarks (StrategyQA, MMLU, TruthfulQA, ARC-Challenge) with a 5-agent system using Qwen3.5-27B, DiscoUQ-LLM achieves an average AUROC of 0.802, outperforming the best baseline (LLM Aggregator, 0.791) while being substantially better calibrated (ECE 0.036 vs. 0.098). The learned features generalize across benchmarks with near-zero performance degradation and provide the largest improvements where they are most needed: in the ambiguous "weak disagreement" tier where simple vote counting fails.