| --- |
| license: unknown |
| task_categories: |
| - question-answering |
| tags: |
| - genomics |
| - knowledge-graph |
| - multi-hop-reasoning |
| - biology |
| pretty_name: GenBench CoCG QA Dataset |
| --- |
| |
| # GenBench CoCG QA Dataset |
|
|
| Multi-hop genetic reasoning QA items generated from GenBench's knowledge |
| graph (Ensembl, ClinVar, VEP, BioGRID, STRING, Reactome, UniProt, GO, |
| SIGNOR, OmniPath, KEGG, DisGeNET, OpenTargets, PubTator3, GTEx, and more), |
| built for CoCG (Co-Evolving Confidence Graph) agent training. |
|
|
| **8159 items across 11 task types.** |
|
|
| ## Task types |
|
|
| | task_type | count | |
| |---|---| |
| | `coding_variant` | 159 | |
| | `conservation_reasoning` | 800 | |
| | `counterfactual` | 800 | |
| | `disease_reasoning` | 800 | |
| | `evidence_attribution` | 800 | |
| | `hallucination_detection` | 800 | |
| | `interaction_propagation` | 800 | |
| | `mechanistic_explanation` | 800 | |
| | `path_traversal` | 800 | |
| | `structural_effect` | 800 | |
| | `tissue_specific` | 800 | |
|
|
| ## Schema |
|
|
| Each item has: |
| - `id`, `task_type`, `pipeline` (`coding_variant`/`noncoding_regulatory`), `difficulty` |
| - `question`, `answer`, `choices` (MCQ options, when applicable) |
| - `context` -- either a templated chain narration, or (if `llm_rewrite` was |
| applied) an LLM-rewritten fluent Step/Evidence/Interpretation/Conclusion |
| narrative |
| - `reasoning_chain` -- the grounded, machine-checkable multi-hop path |
| (`steps`: each with `source_node_id`/`target_node_id`/`edge_relation`/ |
| `edge_confidence`/`edge_source_db`), never touched by any LLM step |
| - `modality_data` -- raw modality payloads (sequence, structural, |
| transcriptomic, post_translational, signaling_role, etc.) attached to the |
| chain's anchor nodes |
| - `evidence` -- supporting evidence entries with source database/PMID |
| - `path_confidence_score` -- continuous, confidence-derived difficulty score |
|
|
| ## Companion graph |
|
|
| `graph.json` (if included in this repo) is the exact knowledge graph these |
| items' `reasoning_chain` node IDs refer to -- load it with |
| [GenBench's `GraphBuilder.load()`](https://github.com/murk07/GenBench) to |
| resolve full node/edge attributes beyond what's inlined in each item. |
|
|
| ## Source |
|
|
| Generated from `data\curated\qa_dataset.jsonl` in [GenBench](https://github.com/murk07/GenBench), |
| the substrate for CoCG (Co-Evolving Confidence Graph) agent training -- |
| per-edge, per-modality KG confidence that co-adapts with an RL policy |
| during training rather than treating the KG as a frozen oracle. |
|
|
