Queelius Papermill Experiment

Experiment Design

Help the researcher design rigorous experiments or computational studies. Good experiments are hypothesis-driven, reproducible, and have clear success criteria before they are run.

Step 1: Read Context

Read .papermill.md (Read tool) for:

• Thesis: The claim the experiments should support or test.
• Existing experiments: Any previously registered experiments.
• Format and tools: What languages/tools are in the repo (R, Python, C++, etc.).

If .papermill.md does not exist, ask the user what claim the experiments should test. Experiment design can proceed without the state file — suggest running /papermill:init afterward to register experiments persistently.

Scan the repository for existing code (Glob tool) in research/, code/, scripts/, experiments/, or analysis/ directories.

Step 2: Identify What Needs Testing

Ask the user: "What specific claim or aspect of your thesis do these experiments need to support?"

Different contribution types need different experimental approaches:

Step 3: Design the Experiment

For each experiment, specify:

Hypothesis

State the expected outcome in falsifiable terms. "We expect X to be Y under conditions Z" -- not "we want to show our method works."

Variables

• Independent variables: What you manipulate (parameters, dataset size, algorithm choice).
• Dependent variables: What you measure (accuracy, runtime, error rate).
• Control variables: What you hold constant (hardware, random seeds, data preprocessing).

Methodology

• Data generation or collection procedure
• Algorithm/method configuration
• Number of replications or samples
• Statistical tests to apply (t-test, bootstrap CI, etc.)
• Baseline comparisons

Success Criteria

Define before running what constitutes support for the hypothesis. This prevents post-hoc rationalization.

Reproducibility

• Random seed strategy
• Hardware/software environment
• Data availability
• Script that runs the full experiment end-to-end

Step 4: Address Common Pitfalls

Check for and warn about:

• Cherry-picking: Are you testing one configuration or sweeping parameters fairly?
• Multiple comparisons: If running many tests, apply correction (Bonferroni, FDR).
• Overfitting to test data: Is there a held-out validation set?
• Computational budget: Is this feasible given available hardware and time?
• Missing baselines: Every method needs comparison to something. Even "no method" is a baseline.

Step 5: Register the Experiment

If .papermill.md exists, update it (Edit tool) by adding to the experiments list. If it does not exist, skip registration and suggest running /papermill:init to persist the experiment.

experiments:
  - name: "descriptive-name"
    type: "simulation | benchmark | case-study | ablation"
    hypothesis: "Expected outcome in one sentence"
    status: "planned | running | completed | failed"
    script: "path/to/script.R"
    last_run: null

Append a timestamped note documenting the experiment design.

Step 6: Suggest Next Steps

Based on the experiment type, suggest the most relevant next step:

• If this is a Monte Carlo study → "Use /papermill:simulation for detailed simulation design — it covers sample sizes, convergence diagnostics, and result presentation."
• If the experiment involves proving a theoretical prediction → "Consider /papermill:proof to verify the theory before running experiments."
• If results will need statistical analysis → "Implement the script, run it, then use /papermill:review once the results are written up."
• For all experiments → "Start with a small pilot run to debug before the full experiment."

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