Rethinking LLM Verification: Evidence Structure, Uncertainty, and Selective Refinement

Abstract

Large language models (LLMs) often rely on shortcuts rather than systematic reasoning, raising safety concerns in medical applications. Allowing models to abstain when uncertain improves reliability but introduces a coverage accuracy tradeoff. We propose a two-stage framework for medical hypothesis verification in multiple-choice settings that manages this tradeoff through targeted ontology grounding, applied only when the model abstains. We show that abstention is not random but reflects genuine uncertainty, with abstained predictions associated with lower confidence. Across two frontier models (GPT-5.5, accessed via the Azure OpenAI API, and DeepSeek-R1), the proposed framework improves question-level accuracy by 9.6 percentage points (82.9% to 92.5%) and hypothesis-level accuracy by 4.2 percentage points (92.0% to 96.2%). Our experiments conducted on MedReason and MedQA show that abstention can be repurposed as a control signal for selective reasoning refinement, achieving knowledge-graph-level performance without explicit knowledge graph construction.