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How Ground Truth Shapes Retrieval Scores: Evidence-Aware Evaluation of a Retrieval-Augmented Generation System for Breast Lesions

Miguel Mochizuki Silva, Samuel Ismael, Mateus C. Dias, Thaís Gaudêncio, Yuri Malheiros, Barufaldi · 2026 · arXiv

DOI: 10.48550/arXiv.2610.31606 · open-access PDF

Abstract

Purpose: To describe an evidence-aware retrieval evaluation protocol for a clinical retrieval-augmented generation (RAG) system over breast lesion management literature, addressing the dependence of retrieval scores on annotation coverage. Methods: An 18-document corpus and an 18-query development benchmark, with one Yes/No or WH-question per document, were used. Retrieval combined dense embeddings, BM25, and cross-encoder reranking. Chunk sizes of 128 to 1024 tokens, overlaps of 0 to 20%, and four retriever configurations were evaluated. Relevance was defined by evidence spans mapped to all c

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