# Where Does Retrieval-Based Open-Ended Evaluation Fail? Automatic Taxonomy Induction from Long-Form Medical Answer Factuality Verification

arXiv: https://arxiv.org/abs/2609.30467 · HTML: https://mlsanity.com/paper/2609.30467/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 14 of its 23 references that are in the map.
- First posted on arXiv 24 Sep 2026.

## Builds on (most cited first, 14 of 14)

- [Efficient Memory Management for Large Language Model Serving with PagedAttention](https://mlsanity.com/paper/2309.06180/) (2023)
- [FEVER: a large-scale dataset for Fact Extraction and VERification](https://mlsanity.com/paper/1803.05355/) (2018)
- [FActScore: Fine-grained Atomic Evaluation of Factual Precision in Long Form Text Generation](https://mlsanity.com/paper/2305.14251/) (2023)
- [Qwen3 Embedding: Advancing Text Embedding and Reranking Through Foundation Models](https://mlsanity.com/paper/2506.05176/) (2025)
- [Unsupervised Dense Information Retrieval with Contrastive Learning](https://mlsanity.com/paper/2112.09118/) (2021)
- [Fact or Fiction: Verifying Scientific Claims](https://mlsanity.com/paper/2004.14974/) (2020)
- [SPECTER: Document-level Representation Learning using Citation-informed Transformers](https://mlsanity.com/paper/2004.07180/) (2020)
- [Benchmarking Retrieval-Augmented Generation for Medicine](https://mlsanity.com/paper/2402.13178/) (2024)
- [MedCPT: Contrastive Pre-trained Transformers with Large-scale PubMed Search Logs for Zero-shot Biomedical Information Retrieval](https://mlsanity.com/paper/2307.00589/) (2023)
- [COVID-Fact: Fact Extraction and Verification of Real-World Claims on COVID-19 Pandemic](https://mlsanity.com/paper/2106.03794/) (2021)
- [SciFact-Open: Towards open-domain scientific claim verification](https://mlsanity.com/paper/2210.13777/) (2022)
- [Explainable Automated Fact-Checking: A Survey](https://mlsanity.com/paper/2011.03870/) (2020)
- [Classifying and Addressing the Diversity of Errors in Retrieval-Augmented Generation Systems](https://mlsanity.com/paper/2510.13975/) (2025)
- [MedScore: Generalizable Factuality Evaluation of Free-Form Medical Answers by Domain-adapted Claim Decomposition and Verification](https://mlsanity.com/paper/2505.18452/) (2025)

## Abstract (arXiv)

Retrieval-based factuality evaluation, where LLM-generated claims are verified against evidence from authoritative medical corpora, has become the dominant paradigm for scalable hallucination detection in high-stakes clinical settings. Despite the urgency of reliable and transparent medical fact verification, most systems measure performance with aggregate metrics like F1, which obscure where and why failures occur. Existing RAG diagnostics require gold answers or annotated gold evidence, neither of which exists in this regime. We introduce two comprehensive taxonomies, grounded in a case study on the open-ended MedExpert dataset and 3 closed-ended datasets, decomposing failures into retrieval-stage errors along five quality dimensions, and verifier-reasoning errors into six consecutive steps. We adapt an automatic pattern induction pipeline using LLM-as-Judge to label evidence quality and classify verifier reasoning errors at scale, and then stress-test our findings across 4 retrieval methods and 6 frontier verifier models. Our analysis reveals that scaling model size, adding reasoning effort, expanding to authoritative web sources, and applying medical fine-tuning do not resolve these failure modes, demonstrating that they represent fundamental limitations of the retrieve-then-verify paradigm in open-ended medical settings rather than artifacts of outdated systems. We release our code and data at https://anonymous.4open.science/r/Medical_RAG_eval-4AB5 for the full reproducibility of our results.