Experiment Design Checklist

Prevent the "I ran experiments for 3 months and they're meaningless" disaster through rigorous upfront design.

The Core Principle

Before running ANY experiment, you should be able to answer:

1. What specific claim will this experiment support or refute?
2. What would convince a skeptical reviewer?
3. What could go wrong that would invalidate the results?

Process

Step 1: State the Hypothesis Precisely

Convert your research question into falsifiable predictions:

Template:

If [intervention/method], then [measurable outcome], because [mechanism].

Examples:

• "If we add auxiliary contrastive loss, then downstream task accuracy increases by >2%, because representations become more separable."
• "If we use learned positional encodings, then performance on sequences >4096 tokens improves, because the model can extrapolate beyond training length."

Null hypothesis: What does "no effect" look like? This is what you're trying to reject.

Step 2: Identify Variables

Independent Variables (what you manipulate):

Variable	Levels	Rationale
[Var 1]	[Level A, B, C]	[Why these levels]

Dependent Variables (what you measure):

Metric	How Measured	Why This Metric
[Metric 1]	[Procedure]	[Justification]

Control Variables (what you hold constant):

Variable	Fixed Value	Why Fixed
[Var 1]	[Value]	[Prevents confound X]

Step 3: Choose Baselines

Every experiment needs comparisons. No result is meaningful in isolation.

Baseline Hierarchy:

1. Random/Trivial Baseline

   • What does random chance achieve?
   • Sanity check that the task isn't trivial

2. Simple Baseline

   • Simplest reasonable approach
   • Often embarrassingly effective

3. Standard Baseline

   • Well-known method from literature
   • Apples-to-apples comparison

4. State-of-the-Art Baseline

   • Current best published result
   • Only if you're claiming SOTA

5. Ablated Self

   • Your method minus key components
   • Shows each component contributes

For each baseline, document:

• Source (paper, implementation)
• Hyperparameters used
• Whether you re-ran or used reported numbers
• Any modifications made

Step 4: Design Ablations

Ablations answer: "Is each component necessary?"

Ablation Template:

Variant	What's Removed/Changed	Expected Effect	If No Effect...
Full Model	Nothing	Best performance	-
w/o Component A	Remove A	Performance drops X%	A isn't helping
w/o Component B	Remove B	Performance drops Y%	B isn't helping
Component A only	Only A, no B	Shows A's isolated contribution	-

Good ablations are:

• Surgical (one change at a time)
• Interpretable (clear what was changed)
• Informative (result tells you something)

Step 5: Address Confounds

Things that could explain your results OTHER than your hypothesis:

Common Confounds:

Confound	How to Check	How to Control
Hyperparameter tuning advantage	Same tuning budget for all	Report tuning procedure
Compute advantage	Matched FLOPs/params	Report compute used
Data leakage	Check train/test overlap	Strict separation
Random seed luck	Multiple seeds	Report variance
Implementation bugs (baseline)	Verify baseline numbers	Use official implementations
Cherry-picked examples	Random or systematic selection	Pre-register selection criteria

Step 6: Statistical Rigor

Sample Size:

• How many random seeds? (Minimum: 3, better: 5+)
• How many data splits? (If applicable)
• Power analysis: Can you detect expected effect size?

What to Report:

• Mean ± standard deviation (or standard error)
• Confidence intervals where appropriate
• Statistical significance tests if claiming "better"

Appropriate Tests:

Comparison	Test	Assumptions
Two methods, normal data	t-test	Normality, equal variance
Two methods, unknown dist	Mann-Whitney U	Ordinal data
Multiple methods	ANOVA + post-hoc	Normality
Multiple methods, unknown	Kruskal-Wallis	Ordinal data
Paired comparisons	Wilcoxon signed-rank	Same test instances

Avoid:

• p-hacking (running until significant)
• Multiple comparison problems (Bonferroni correct)
• Reporting only favorable metrics

Step 7: Compute Budget

Before running, estimate:

Component	Estimate	Notes
Single training run	X GPU-hours	[Details]
Hyperparameter search	Y runs × X hours	[Search strategy]
Baselines	Z runs × W hours	[Which baselines]
Ablations	N variants × X hours	[Which ablations]
Seeds	M seeds × above	[How many seeds]
Total	T GPU-hours	Buffer: 1.5-2x

Go/No-Go Decision: Is this feasible with available resources?

Step 8: Pre-Registration (Optional but Recommended)

Write down BEFORE running:

• Exact hypotheses
• Primary metrics (not chosen post-hoc)
• Analysis plan
• What would constitute "success"

This prevents unconscious goal-post moving.

Output: Experiment Design Document

# Experiment Design: [Title]

## Hypothesis
[Precise statement]

## Variables
### Independent
[Table]

### Dependent
[Table]

### Controls
[Table]

## Baselines
1. [Baseline 1]: [Source, details]
2. [Baseline 2]: [Source, details]

## Ablations
[Table]

## Confound Mitigation
[Table]

## Statistical Plan
- Seeds: [N]
- Tests: [Which tests for which comparisons]
- Significance threshold: [α level]

## Compute Budget
[Table with total estimate]

## Success Criteria
- Primary: [What must be true]
- Secondary: [Nice to have]

## Timeline
- Phase 1: [What, when]
- Phase 2: [What, when]

## Known Risks
1. [Risk 1]: [Mitigation]
2. [Risk 2]: [Mitigation]

Red Flags in Experiment Design

🚩 "We'll figure out the metrics later" 🚩 "One run should be enough" 🚩 "We don't need baselines, it's obviously better" 🚩 "Let's just see what happens" 🚩 "We can always run more if it's not significant" 🚩 No compute estimate before starting 🚩 Vague success criteria