README.md

metadata

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() to resolve full node/edge attributes beyond what's inlined in each item.

Source

Generated from data\processed\noncoding_qa_dataset.jsonl in 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.