ClinicalBench: Stress-Testing Assertion-Aware Retrieval for Cross-Admission Clinical QA on MIMIC-IV
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| Format: | Preprint |
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2026
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| _version_ | 1866917481953624064 |
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| author | Stinard, Alex |
| author_facet | Stinard, Alex |
| contents | Reasoning benchmarks measure clinical performance on clean inputs. We evaluate the step before reasoning: retrieval over real EHR notes, where negation, temporality, and family-versus-patient attribution can flip a correct answer to a wrong one. EpiKG carries an assertion label and a temporality tag with every fact in a patient knowledge graph, then routes retrieval by question intent. ClinicalBench is a 400-question test over 43 MIMIC-IV patients across 9 assertion-sensitive categories. A 7-condition ablation tests each piece of EpiKG across six LLMs (Claude Opus 4.6, GPT-OSS 20B, MedGemma 27B, Gemma 4 31B, MedGemma 1.5 4B, Qwen 3.5 35B). Three physicians blindly adjudicated 100 paired items. The author-blind primary endpoint, leave-author-out paired exact McNemar on 50 unanimous-strict items rated by two external physicians, yields +22.0 percentage points (95 percent Newcombe CI [+5.1, +31.5], p=0.0192). The architectural novelty, intent-aware KG-RAG over a Contriever dense-RAG baseline (C2b to C4g_kw on the change-excluded n=362 endpoint), is +8.84 percentage points (paired McNemar p=1.79e-3); +12.43 percentage points under oracle intent. Sensitivities agree directionally: three-rater physician majority +24.0 percentage points (subject to single-author circularity); deterministic keyword reproducibility proxy +39.5 percentage points. Across the six models, the gain shrinks as the LLM-alone baseline rises (beta=-1.123, r=-0.921, p=0.009). With n=6 this looks more like regression to the mean than encoding substituting for model size. Physician adjudication identified 56 percent of auto-generated reference answers as defective, a methodological finding indicating that NLP-pipeline clinical-QA benchmarks require physician adjudication to be usable. ClinicalBench, the frozen evaluator, three-rater adjudication data, and the EpiKG output stack are publicly released. |
| format | Preprint |
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arxiv_https___arxiv_org_abs_2605_11143 |
| institution | arXiv |
| publishDate | 2026 |
| record_format | arxiv |
| spellingShingle | ClinicalBench: Stress-Testing Assertion-Aware Retrieval for Cross-Admission Clinical QA on MIMIC-IV Stinard, Alex Computation and Language Artificial Intelligence Information Retrieval Reasoning benchmarks measure clinical performance on clean inputs. We evaluate the step before reasoning: retrieval over real EHR notes, where negation, temporality, and family-versus-patient attribution can flip a correct answer to a wrong one. EpiKG carries an assertion label and a temporality tag with every fact in a patient knowledge graph, then routes retrieval by question intent. ClinicalBench is a 400-question test over 43 MIMIC-IV patients across 9 assertion-sensitive categories. A 7-condition ablation tests each piece of EpiKG across six LLMs (Claude Opus 4.6, GPT-OSS 20B, MedGemma 27B, Gemma 4 31B, MedGemma 1.5 4B, Qwen 3.5 35B). Three physicians blindly adjudicated 100 paired items. The author-blind primary endpoint, leave-author-out paired exact McNemar on 50 unanimous-strict items rated by two external physicians, yields +22.0 percentage points (95 percent Newcombe CI [+5.1, +31.5], p=0.0192). The architectural novelty, intent-aware KG-RAG over a Contriever dense-RAG baseline (C2b to C4g_kw on the change-excluded n=362 endpoint), is +8.84 percentage points (paired McNemar p=1.79e-3); +12.43 percentage points under oracle intent. Sensitivities agree directionally: three-rater physician majority +24.0 percentage points (subject to single-author circularity); deterministic keyword reproducibility proxy +39.5 percentage points. Across the six models, the gain shrinks as the LLM-alone baseline rises (beta=-1.123, r=-0.921, p=0.009). With n=6 this looks more like regression to the mean than encoding substituting for model size. Physician adjudication identified 56 percent of auto-generated reference answers as defective, a methodological finding indicating that NLP-pipeline clinical-QA benchmarks require physician adjudication to be usable. ClinicalBench, the frozen evaluator, three-rater adjudication data, and the EpiKG output stack are publicly released. |
| title | ClinicalBench: Stress-Testing Assertion-Aware Retrieval for Cross-Admission Clinical QA on MIMIC-IV |
| topic | Computation and Language Artificial Intelligence Information Retrieval |
| url | https://arxiv.org/abs/2605.11143 |