Research SOP

Use this skill as the main router for empirical research. Custom researcher, engineer, verifier, reviewer, and budgeter agents are optional helpers; when they are unavailable, execute the same role boundaries inline.

Inputs and promised output

Before doing expensive work, establish:

• the research question and decision the result should support;
• the active workspace and relevant files or datasets;
• whether the work is exploratory or confirmatory;
• cost, time, reserved-data, and external-service constraints;
• whether the user asked only for diagnosis or also authorized implementation.

Finish with a research handoff containing the question, literature basis, hypothesis node ids, comparison evidence, experiment manifest, verification status, unresolved risks, and the next justified action. Do not call a result publication-ready merely because code ran or unit tests passed.

1. Orient and resume

1. If Cockpit is useful, tell the user how to start it from the same workspace:

claudescientist cockpit --workspace <path> --lang zh.

1. Inspect the active frontier and ancestors. Reuse an existing question or

hypothesis when it already represents the task; otherwise create the question and candidate hypothesis nodes.

1. Call mcp__memory__match_signatures with the task and likely failure modes.

Read matching failures before choosing a method.

1. Query existing literature and contradictions. Record a snapshot before a

risky pruning decision or when resuming an interrupted investigation.

Expected state: a question node or explicit task statement, known prior failures, and a short list of missing evidence.

2. Establish the evidence base

1. Call mcp__memory__query_literature, find_baselines_for, and

find_contradictions as relevant.

1. Use arXiv or OpenAlex only when those optional MCPs are available. If they

are absent, continue with repository sources and say what literature search remains incomplete; do not invent citations.

1. Ingest structured paper summaries that materially affect the decision.
2. Separate established facts, reported claims, assumptions, and open gaps.

Pause for user direction when the research question can be interpreted in materially different ways or when the required data/source is unavailable.

Expected state: a concise evidence table and a defensible gap statement.

3. Generate comparable hypotheses

Create 3-5 falsifiable candidates when the question genuinely has competing explanations. Each candidate needs:

• a mem_nodes hypothesis id and one-sentence statement;
• mechanism or rationale;
• expected observation and a result that would refute it;
• feasible experiment and cost estimate;
• known supporting and contradicting evidence.

Do not pad the list with paraphrases. With only one credible candidate, state that limitation and skip the tournament.

4. Select without overstating uncertainty

When at least three candidates compete, run $bt-tournament. The current leaderboard is a joint batch MAP Bradley-Terry fit. Its lcb and ucb fields are retained for compatibility but represent an uncalibrated approximate posterior interval, not a guaranteed 95% confidence interval. Always surface the returned interval_calibrated=False flag in a handoff. The underlying loop is mcp__memory__judge_hypotheses followed by mcp__memory__record_judgement, then mcp__memory__get_bt_leaderboard; keep those calls auditable even when the Skill performs the routing.

Use comparisons to organize judgment, not manufacture certainty. Stop when every serious candidate has enough direct evidence for a decision, the ranking is stable to reasonable judging criteria, the budget is exhausted, or the user chooses. Record the chosen path and why the alternatives were deferred. A pause suggestion is advisory unless explicit auto-prune is enabled.

Expected state: selected hypothesis ids, comparison counts, approximate intervals with the calibration caveat, and a recorded selection rationale.

5. Choose exploratory or confirmatory mode

Exploratory mode may prototype, inspect outcomes, and pin results, but every claim stays labelled exploratory.

Confirmatory mode must lock the target before observing the confirmatory run:

1. Invoke $preregister.
2. Define family_id and fixed family_size for related tests before the

first family member is resolved.

1. Lock metric, direction, threshold, alpha, seed count, and optional reserved

dataset.

1. Pass every prereg_id into later experiment and verification records.

Never retroactively call an observed exploratory result confirmatory.

6. Plan and implement the experiment

1. Check configured budgets before expensive, remote, reserved-data, or long

proof work. Missing budget configuration is advisory for low-cost work and a reason to ask before material cost.

1. Run leakage_check before training or evaluation code touches data splits.
2. Specify baselines, metrics, seeds, config files, input files, and the exact

command before execution.

1. Implement only within the user's authorization. Preserve diagnosis-only

boundaries when the user did not request a fix.

1. Record failures through record_failure; do not silently switch methods

after a failed run.

1. Record and pin central metrics. v5.1 automatically attaches a run manifest

containing experiment code, inputs, configs, lockfiles, Git state, command, seeds, runtime, and safe environment fields. Still pass input_files and config_files explicitly so domain data is complete.

Expected state: reproducible command, code/config/data fingerprints, results, budget use, and failure records.

7. Verify independently

Treat verification as a separate role even when performed by the same host:

1. Check provenance and call refresh_claim; stale central evidence blocks

promotion.

1. Re-run or inspect leakage checks.
2. Use seed_perturb for central experimental metrics and link the run to the

metric pin. An unstable result must be narrowed or remain exploratory.

1. Run baseline_fairness for method-versus-baseline claims.
2. Access sequestered data only through query_heldout; budget is reserved

before execution.

1. Resolve confirmatory preregistrations. A missed or open target cannot be

rewritten as met.

Expected state: pin ids, fresh run manifests, seed verdict, fairness verdict, reserved-data audit, and preregistration status.

8. Review and hand off to writing

Invoke $writeup-sop only after the claim inventory is ready. Publication- critical claims require reviewer JSON with verdict="accept"; a non-empty blocker list means revise or reject. Theorem-shaped claims also invoke $prove-sop and its diagnostic/formalization checks.

Failure and recovery paths

• Literature insufficient: report searched sources and missing access; keep

hypotheses provisional.

• No reproducible baseline: stop comparative claims and record the blocker.
• Experiment fails: use $debug-sop, record the failure, then resume here from

the last valid checkpoint.

• Budget exhausted: preserve state and offer a lower-cost next experiment.
• Verification fails or evidence is stale: do not write the central claim;

rerun, narrow, downgrade to exploratory, or remove it.

• Interrupted work: inspect the graph, latest snapshot, preregistrations,

pins, and manifests; do not restart from memory alone.

Completion criteria

The research loop is complete only when the chosen hypothesis and alternatives are traceable, experiment inputs and environment are fingerprinted, central metrics have fresh provenance, required seed/fairness/preregistration checks have explicit verdicts, failures and caveats are recorded, and the final claim language matches the strength of that evidence.