Hypothesis generate literature

hypothesis-generate-literature

Goal:

• Generate exactly one literature-grounded hypothesis candidate for the active round.

Inputs:

• research_plan/RESEARCH_PLAN.json
• state/STRATEGY_PLAN.json
• literature/queries/<query_id>/EVIDENCE_BUNDLE.json produced by tools.search_literature(...)
• optional parent hypothesis and review artifacts when the round is part of an evolution continuation

Outputs:

• hypotheses/<id>/HYPOTHESIS.json
• hypotheses/<id>/HYPOTHESIS.md
• hypotheses/<id>/ORIGIN.json
• literature/queries/<query_id>/* search bridge artifacts for the evidence query used by this generation

Context Loading:

• Open skills/shared-references/schema-index.md.
• Open skills/shared-references/literature-search-contract.md.
• Read packages/agent_contracts/literature.py before building or consuming any search bridge request or evidence bundle.
• Read research_plan/RESEARCH_PLAN.json.
• Treat research_goal as the task anchor.
• Treat preferences as the quality axes that the hypothesis should optimize for.
• Treat constraints as hard boundaries that the hypothesis and experiment design must satisfy.
• Read state/STRATEGY_PLAN.json and confirm that the current round allows literature_exploration_generation.
• If the round is parented, read the selected parent hypothesis and its latest review summary before generating a child. Improve the known weaknesses instead of paraphrasing the parent.

Execution Prompt Contract:

• System Intent:
  • You are generating one scientifically grounded candidate hypothesis from literature exploration.
• Required Reasoning Focus:
  • Before generating the candidate, call tools.search_literature(run_dir, request) with consumer="hypothesis-generate-literature" and use the returned EvidenceBundleContract as the formal external evidence input.
  • Use relevant prior work, gaps, contradictions, or unexplored connections from the evidence bundle to motivate the candidate.
  • Produce a specific falsifiable claim with a mechanism and a concrete experiment path.
  • Make the mechanism explicit enough that another reviewer can critique it step by step.
  • When novelty depends on a conjectural link, keep that link explicit rather than hiding it in vague wording.
• Do Not Do:
  • Do not merely restate established literature.
  • Do not emit multiple final candidates in one round.
  • Do not ignore explicit constraints from the research plan.
  • Do not write an informal summary in place of the canonical hypothesis artifact.
  • Do not invent papers, DOIs, arXiv IDs, venues, citation counts, abstracts, or literature claims not present in the evidence bundle.
  • Do not treat model memory as a substitute for tools.search_literature(...).
• Output Shape:
  • Wrap the final result into the canonical shared HypothesisContract.
  • origin.content.statement: 2-3 sentences maximum.
  • origin.content.mechanism: 2-3 sentences maximum.
  • origin.content.experimental_design: one concise multiline string with 3-6 numbered steps.
  • origin.content.experimental_design must remain one string field containing embedded line breaks; do not emit it as a list, array, or nested object.
  • origin.content.summary: one concise sentence.
  • origin.content.category: 1-5 words.

Execution Steps:

1. Open skills/shared-references/schema-index.md, skills/shared-references/literature-search-contract.md, then read packages/agent_contracts/hypothesis.py and packages/agent_contracts/literature.py before writing hypotheses/<id>/HYPOTHESIS.json or consuming search bridge artifacts.
2. Read the required artifacts.
3. Confirm that this round is allowed to use literature exploration.
4. Build a focused SearchRequestContract for the active research goal and call tools.search_literature(run_dir, request).
5. Read the returned EvidenceBundleContract. If retrieval_metadata.status is blocked, stop or return a degraded state; do not write a literature-grounded hypothesis.
6. Identify one literature-grounded gap or underexplored mechanism from the evidence bundle that can answer the active research goal.
7. Generate exactly one candidate hypothesis for this round.
8. Wrap the result into the canonical HypothesisContract. Any origin.retrieval_results entries must be derived from the evidence bundle rather than invented in prompt text.
9. Write hypotheses/<id>/HYPOTHESIS.json, hypotheses/<id>/HYPOTHESIS.md, and hypotheses/<id>/ORIGIN.json.
10. Validate the emitted artifacts before declaring success.

Artifact Rules:

• hypotheses/<id>/HYPOTHESIS.json is the authoritative artifact and must serialize the canonical shared contract.
• ORIGIN.json may mirror the generation payload and grounding notes, but it does not replace the canonical hypothesis artifact.
• Formal external evidence must be traceable to literature/queries/<query_id>/EVIDENCE_BUNDLE.json.
• Because origin.strategy is literature_exploration_generation, the canonical hypothesis origin must include non-empty retrieval_results, evidence_bundle_ids, and literature_query_ids derived from the returned evidence bundle; validation fails if these bridge linkages are omitted or point to unknown artifacts.
• Any literature search or evidence-gathering notes that are not in the canonical evidence bundle should live in the trace, not be mixed into the contract fields.

Completion Rule:

• This skill is complete only when exactly one new canonical hypothesis artifact has been written from a non-blocked evidence bundle and the emitted files validate for downstream review.