stopping-criteria

name	stopping-criteria
description	Decide when to stop investigating and prepare final report
category	workflow

Stopping Criteria

When to Use This Skill

• When approaching iteration limit
• When considering if investigation is "done"
• When deciding between continuing vs synthesizing

The Core Question

"Have we learned enough to answer the research question?"

Hard Stops (Must Stop)

These are non-negotiable stopping points:

1. Iteration Budget Exhausted

• You've reached max_iterations
• Action: Begin final synthesis immediately

2. Budget Exceeded

• Cost exceeds allowed threshold
• Action: Stop and synthesize with what you have

3. Catastrophic Failure

• Data is fundamentally flawed
• Analysis approach is wrong
• Action: Document the issue, stop investigation

Soft Stops (Consider Stopping)

These indicate you MIGHT be done:

1. Coherent Mechanistic Model

Criteria:

• You can explain the phenotype with a plausible mechanism
• Multiple findings support the same model
• No major contradictions remain

Example:

Research question: "Why is hypothermia neuroprotective?"

Model:
1. Hypothermia → metabolic shift to energy-efficient pathways
2. Nucleotide salvage increased (evidence: precursor depletion)
3. Membrane remodeling with PUFA enrichment (evidence: PC changes)
4. Enhanced antioxidant capacity (evidence: uronic acid pathway)

This is coherent ✓

Action: Consider stopping to synthesize

2. Diminishing Returns

Signs:

• Last 5 iterations produced no new insights
• All high-priority hypotheses tested
• Only low-impact questions remain
• Repeating similar analyses

Example:

Iteration 45: No new findings
Iteration 46: Tested marginal hypothesis (p=0.3)
Iteration 47: Re-analyzed previous finding
Iteration 48: Explored irrelevant variable
Iteration 49: ???

Action: Stop and synthesize rather than continue unproductively

3. Sufficient Coverage

Criteria:

• Tested all major pathway classes
• Addressed both positive and negative controls
• Examined key confounders (sex, age, etc.)
• Answered sub-questions of main research question

Check:

• Addressed the "why" not just the "what"
• Tested alternative explanations
• Identified mechanistic basis
• Connected findings into story

Action: If all checked, consider stopping

4. Satisfactory Answer Count

Guidelines by study complexity:

• Simple question: 2-3 major findings
• Moderate complexity: 3-5 major findings
• Complex multi-omics: 5-8 major findings

Quality > Quantity: Better to have 3 well-supported findings than 10 marginal ones

Should You Continue?

Continue if:

✅ High-priority hypotheses remain untested ✅ Recent findings opened promising new directions ✅ Current findings are contradictory (need resolution) ✅ Still < 70% of iteration budget used ✅ Each iteration is still productive

Stop if:

🛑 Reached iteration limit 🛑 Last 5+ iterations unproductive 🛑 All high-priority hypotheses tested 🛑 Coherent mechanistic model established 🛑 No promising leads remain

The Synthesis Test

Try this mental exercise:

"Can I explain the research question to a colleague right now with supporting evidence?"

If YES:

• You have the core answer
• Additional iterations = diminishing returns
• Consider stopping

If NO:

• Major gaps remain
• Continue investigating

Decision Framework

Are you at iteration limit?
│
YES → STOP (mandatory)
│
NO → Continue
    │
    Have you answered the research question with mechanistic model?
    │
    YES → STOP and synthesize
    │
    NO → Continue
        │
        Are last 5 iterations productive?
        │
        NO → STOP (diminishing returns)
        │
        YES → Continue
            │
            Do high-priority hypotheses remain?
            │
            YES → CONTINUE testing
            │
            NO → STOP and synthesize

Endgame Strategy (Last 20% of Iterations)

When you're in the final 20% of your iteration budget:

Shift Priorities

STOP doing:

• ❌ Broad exploration
• ❌ Low-priority hypotheses (score <30)
• ❌ Tangential questions
• ❌ Over-analyzing confirmed findings

START doing:

• ✅ Test remaining high-priority hypotheses only
• ✅ Record all unrecorded findings
• ✅ Resolve contradictions
• ✅ Connect findings into coherent story
• ✅ Identify knowledge gaps

Triage Ruthlessly

Example endgame (iterations 41-50):

Iteration 41: Test last high-priority hypothesis (H8)
Iteration 42: Record findings from H8
Iteration 43: Resolve contradiction between F3 and F5
Iteration 44: Search literature for knowledge gaps
Iteration 45: Test secondary hypothesis if time
Iteration 46-50: Reserve for synthesis and cleanup

Common Mistakes

❌ Stopping too early

• Only 1-2 findings
• Major alternative explanations untested
• Research question not actually answered

❌ Continuing too long

• Repeating similar analyses
• Testing trivial hypotheses
• Avoiding synthesis work

❌ Perfectionism

• Waiting for "complete" understanding
• Science is incremental - you won't solve everything

❌ Ignoring negative space

• What you DIDN'T find is also important
• Document what was ruled out

What "Done" Looks Like

A successful investigation concludes with:

✅ Clear answer to research question

• "Hypothermia is neuroprotective because..."
• Backed by statistical evidence

✅ Mechanistic model

• Not just correlations
• Plausible biological explanation

✅ Multiple supporting findings

• 3-5 major discoveries
• Mutually reinforcing evidence

✅ Acknowledged limitations

• What couldn't be tested
• What remains unknown

✅ Documented process

• Knowledge graph populated
• All findings recorded
• Analysis log complete

Final Checklist

Before stopping, verify:

• Research question is answered (or declared unanswerable)
• Major findings are recorded in knowledge graph
• Mechanistic model is articulated
• Alternative explanations were tested
• Knowledge gaps are identified
• Ready to synthesize final report

Example: Deciding to Stop

Situation: Iteration 42 of 50

Current state:

• 5 major findings recorded
• Coherent mechanistic model
• All high-priority hypotheses tested
• Last 3 iterations only found marginal results

Endgame options:

1. Continue testing low-priority hypotheses (8 iterations left)
2. Stop now and synthesize

Decision: STOP

Rationale:

• Research question is answered ✓
• Mechanistic model is coherent ✓
• High-priority work is done ✓
• Continuing = diminishing returns
• Better to synthesize well than chase marginal findings

Key Principle

Know when to stop digging and start synthesizing.

Perfect understanding is impossible. Good science is about answering the question with the evidence you can gather.

If you've:

1. Answered the research question
2. Built a mechanistic model
3. Tested major alternatives
4. Hit diminishing returns

STOP and write an excellent final report.

That's more valuable than 10 more iterations of marginal analyses.