Negation is Not Semantic: Diagnosing Dense Retrieval Failure Modes for Trade-offs in Contradiction-Aware Biomedical QA

Abstract: LLMs have demonstrated strong capabilities in biomedical question answering, yet their tendency to generate plausible but unverified claims poses serious risks in clinical settings. To mitigate these risks, the TREC 2025 BioGen track mandates grounded answers that explicitly surface contradictory evidence (Task A) and the generation of narrative driven, fully attributed responses (Task B). Addressing the absence of target ground truth, we present a proxy-based development framework using the SciFact dataset to systematically optimize retrieval architectures. Our iterative evaluation revealed a "Simplicity Paradox": complex adversarial dense retrieval strategies failed catastrophically at contradiction detection (MRR 0.023) due to Semantic Collapse, where negation signals become indistinguishable in vector space. We further identify a Retrieval Asymmetry: filtering dense embeddings improves contradiction detection but degrades support recall, compromising reliability. We resolve this via a Decoupled Lexical Architecture built on a unified BM25 backbone, balancing semantic support recall (0.810) with precise contradiction surfacing (0.750). This approach achieves the highest Weighted MRR (0.790) on the proxy benchmark while remaining the only viable strategy for scaling to the 30 million document PubMed corpus. For answer generation, we introduce Narrative Aware Reranking and One-Shot In-Context Learning, improving citation coverage from 50% (zero-shot) to 100%. Official TREC results confirm our findings: our system ranks 2nd on Task A contradiction F1 and 3rd out of 50 runs on Task B citation coverage (98.77%), achieving zero citation contradict rate. Our work transforms LLMs from stochastic generators into honest evidence synthesizers, showing that epistemic integrity in biomedical AI requires precision and architectural scalability isolated metric optimization.