| # GraphRareBench Dataset Card |
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| ## Summary |
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| GraphRareBench is a provenance-preserving benchmark for phenotype-driven |
| rare-disease ranking. The frozen release contains 2,365 |
| ontology-derived cases, 18,093 |
| target-confounder pairs, coarsened HPO queries, fixed candidate pools, |
| graph-defined hard confounders, and source-linked evidence records. |
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| ## Intended Use |
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| Use the release to evaluate closed candidate-set rare-disease ranking methods, |
| target-over-confounder discrimination, mechanism-specific failures, and |
| tool-mediated evidence-access behavior. |
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| ## Splits |
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| - Train: 1,892 cases |
| - Dev: 236 cases |
| - Test: 237 cases |
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| Diseases connected through the same causal-gene component are assigned to the |
| same partition when gene annotations are available. |
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| ## Metrics |
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| The accompanying code computes MRR, Hit@1/5/10, ToC_case, ToC_pair, |
| AnyConfAbove, mechanism-sliced ToC_pair, case-level bootstrap confidence |
| intervals, paired bootstrap contrasts, and deterministic tool-trace audit |
| metrics. |
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