| --- |
| license: unknown |
| task_categories: |
| - question-answering |
| tags: |
| - genomics |
| - knowledge-graph |
| - multi-hop-reasoning |
| - biology |
| pretty_name: GenBench CoCG QA Dataset |
| dataset_info: |
| features: |
| - name: id |
| dtype: string |
| - name: task_type |
| dtype: string |
| - name: pipeline |
| dtype: string |
| - name: difficulty |
| dtype: string |
| - name: num_hops |
| dtype: int64 |
| - name: question |
| dtype: string |
| - name: context |
| dtype: string |
| - name: reasoning_chain |
| struct: |
| - name: steps |
| list: |
| - name: hop |
| dtype: int64 |
| - name: source_node_id |
| dtype: string |
| - name: source_node_type |
| dtype: string |
| - name: source_node_label |
| dtype: string |
| - name: edge_relation |
| dtype: string |
| - name: edge_evidence_type |
| dtype: string |
| - name: edge_confidence |
| dtype: float64 |
| - name: edge_source_db |
| dtype: string |
| - name: target_node_id |
| dtype: string |
| - name: target_node_type |
| dtype: string |
| - name: target_node_label |
| dtype: string |
| - name: human_readable |
| dtype: string |
| - name: total_hops |
| dtype: int64 |
| - name: start_node_id |
| dtype: string |
| - name: end_node_id |
| dtype: string |
| - name: answer |
| dtype: string |
| - name: modalities |
| list: string |
| - name: modality_data |
| list: |
| - name: family |
| dtype: string |
| - name: tag |
| dtype: string |
| - name: anchor_node_id |
| dtype: string |
| - name: source_db |
| dtype: string |
| - name: payload |
| struct: |
| - name: gene |
| dtype: string |
| - name: tissues |
| list: string |
| - name: tpm_median |
| list: float64 |
| - name: n_tissues |
| dtype: int64 |
| - name: top_tissue |
| dtype: string |
| - name: chrom |
| dtype: string |
| - name: center |
| dtype: int64 |
| - name: start |
| dtype: int64 |
| - name: end |
| dtype: int64 |
| - name: width |
| dtype: int64 |
| - name: sequence |
| dtype: string |
| - name: biosample |
| dtype: string |
| - name: marks |
| struct: |
| - name: H3K4me1 |
| dtype: float64 |
| - name: H3K4me3 |
| dtype: float64 |
| - name: H3K27ac |
| dtype: float64 |
| - name: state |
| dtype: string |
| - name: hops |
| list: int64 |
| - name: evidence |
| list: |
| - name: source_db |
| dtype: string |
| - name: source_id |
| dtype: string |
| - name: text |
| dtype: string |
| - name: confidence |
| dtype: float64 |
| - name: metadata |
| struct: |
| - name: gene_a |
| dtype: string |
| - name: gene_b |
| dtype: string |
| - name: path_length |
| dtype: int64 |
| - name: gene |
| dtype: string |
| - name: tissue |
| dtype: string |
| - name: element_type |
| dtype: string |
| - name: variant |
| dtype: string |
| - name: pathway |
| dtype: string |
| - name: mode |
| dtype: string |
| - name: fabricated |
| dtype: string |
| - name: real_options |
| list: string |
| - name: protein |
| dtype: string |
| - name: threshold |
| dtype: int64 |
| - name: partner_count |
| dtype: int64 |
| - name: disease |
| dtype: string |
| - name: pathogenic_variants |
| list: string |
| - name: top_tissue |
| dtype: string |
| - name: top_tpm |
| dtype: float64 |
| - name: path_confidence_score |
| dtype: float64 |
| splits: |
| - name: train |
| num_bytes: 19898486 |
| num_examples: 4900 |
| download_size: 17322981 |
| dataset_size: 19898486 |
| configs: |
| - config_name: default |
| data_files: |
| - split: train |
| path: data/train-* |
| --- |
| |
| # 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. |
|
|
| **1464 items across 6 task types.** |
|
|
| ## Task types |
|
|
| | task_type | count | |
| |---|---| |
| | `disease_reasoning` | 244 | |
| | `hallucination_detection` | 244 | |
| | `interaction_propagation` | 244 | |
| | `mechanistic_explanation` | 244 | |
| | `path_traversal` | 244 | |
| | `regulatory_reasoning` | 244 | |
|
|
| ## 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\processed\noncoding_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. |
|
|
