| --- |
| pretty_name: GraphRareBench |
| license: mit |
| tags: |
| - rare-disease |
| - phenotype-driven-diagnosis |
| - benchmark |
| - knowledge-graph |
| - graph-evidence |
| - hpo |
| - mondo |
| --- |
| |
| # GraphRareBench Dataset |
|
|
| This release is the single frozen GraphRareBench benchmark described in the |
| AAAI 2027 submission. It contains 2,365 ontology-derived |
| rare-disease ranking cases and 18,093 labeled |
| target-confounder pairs. |
|
|
| ## Layout |
|
|
| ```text |
| dataset/ |
| cases/graphrarebench_cases.jsonl |
| sidecars/evidence_bundle.jsonl |
| sidecars/graph_path_alignment.jsonl |
| metadata/manifest.json |
| metadata/release_summary.json |
| metadata/checksums.sha256 |
| schema/case_public_schema.json |
| schema/evidence_bundle_public_schema.json |
| provenance/source_provenance.csv |
| ``` |
|
|
| ## Case File |
|
|
| `cases/graphrarebench_cases.jsonl` is the benchmark anchor. Each row contains: |
|
|
| - `case_id`, `split`, and `partition_strategy`; |
| - `query_phenotypes`: the coarsened HPO query visible to evaluated methods; |
| - `candidate_pools.full`: the closed full candidate set; |
| - `candidate_pools.hard`: the target plus graph-defined hard confounders; |
| - `target_disease` and `hard_confounders`: evaluator-only labels for scoring; |
| - `evidence_bundle_id` and `graph_path_alignment_refs` for source-linked audit. |
|
|
| The public split is gene-component-aware: 1,892 |
| train, 236 dev, and 237 |
| test cases. Test cases have a median of 69 |
| full-pool candidates and a median of 5 |
| hard confounders. |
|
|
| ## Evaluation |
|
|
| Full-pool ranking uses `candidate_pools.full`. The tool-mediated hard-pool |
| audit uses `candidate_pools.hard`. Evaluated systems should receive only the |
| query, candidate IDs/names, and permitted evidence interface; target labels, |
| hard-confounder labels, and mechanism annotations are evaluator-only. |
|
|
