Conducting Deep Research

This skill uses an iterative methodology treating research as a diffusion process: start with noise (rough draft), apply guidance (research brief), denoise through cycles of critique → research → refine until quality converges.

Use TodoWrite to track these mandatory steps:

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1. Clarify scope (if ambiguous)
2. Write research brief (guidance signal)
3. Generate initial draft from knowledge (noisy starting point)
4. Red team critique (identify noise)
5. Targeted web_search with reflection
6. Score sources and track contradictions
7. Refine draft (denoise)
8. Evaluate quality (score < 7? repeat 4-7, max 3 cycles)
9. Finalize

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Step 1: Clarify Scope

Ask me clarifying questions only if:

• Topic has multiple interpretations
• Key constraints missing (timeframe, geography, industry)
• Success criteria unclear

Skip for well-defined requests.

Step 2: Research Brief (Guidance Signal)

RESEARCH BRIEF
Topic: [Specific question]
Scope: [Included/excluded]
Key Questions:
1. [Primary]
2. [Secondary]
3. [Tertiary]
Constraints: [Limits]
Language: [Match user's language]

Step 3: Initial Draft (Noisy Starting Point)

Write from existing knowledge only, marking gaps:

• [NEEDS VERIFICATION] - uncertain claims
• [RESEARCH NEEDED] - missing information
• [CONFIDENCE: LOW/MED/HIGH] - flag uncertainty levels

This draft intentionally contains "noise" - the refinement loop will denoise it.

Step 4: Red Team Critique

Attack the draft for:

• Logic: Circular reasoning, false dichotomies, unsupported claims
• Gaps: Missing perspectives, incomplete coverage
• Sources: Unsourced claims, single-source reliance

Rate each issue 1-10 severity. See references/critique-framework.md.

Step 5: Targeted Research with Reflection

Search budget by complexity:

• Simple verification: 1-2 searches
• Moderate topics: 3-5 searches
• Complex research: 5-10 searches

CRITICAL: Think after EVERY search. After each web_search, pause and reflect:

REFLECTION:
- What key facts did I find?
- What gaps remain?
- Do sources agree or conflict?
- Is another search needed, or do I have enough?

Parallel research triggers - pursue multiple threads when:

• Comparing alternatives (search each separately)
• Multiple independent sub-questions exist
• Different source types needed (academic vs news vs official)

See references/search-patterns.md for query techniques.

Step 6: Source Scoring and Contradiction Handling

Score each source (1-100 confidence):

Adjust based on: recency, author credentials, citation quality.

Track facts with attribution:

FACT: [Statement]
SOURCE: [URL]
CONFIDENCE: [1-100]
DISPUTED: [Yes/No - conflicts with other sources?]

When sources contradict:

1. Note the contradiction explicitly
2. Check publication dates (prefer recent)
3. Evaluate source authority
4. Search for additional sources to break tie
5. If unresolved, present both views with confidence levels

See references/source-evaluation.md for detailed guidance.

Step 7: Refine Draft (Denoise)

Refine by:

1. Replacing [NEEDS VERIFICATION] with sourced facts
2. Adding inline citations with confidence: "According to [Source] (high confidence), ..."
3. Qualifying or removing unsupported claims
4. Addressing contradictions explicitly
5. Adding counterarguments

Context management: If accumulating too much research, compress raw notes into key findings before continuing. Discard redundant/low-value information.

Step 8: Evaluate Quality

Score 1-10 on:

• Comprehensiveness: All key questions addressed?
• Accuracy: Claims well-sourced with appropriate confidence?

Track across iterations:

QUALITY LOG:
Iteration 1: Comprehensiveness 5, Accuracy 4, Avg 4.5
Iteration 2: Comprehensiveness 7, Accuracy 6, Avg 6.5
Iteration 3: Comprehensiveness 8, Accuracy 8, Avg 8.0 ✓

If average < 7: Return to Step 4 (max 3 cycles). If score drops between iterations: Focus critique on what regressed.

Step 9: Finalize

# [Title]

## Executive Summary
[Key findings in 2-3 paragraphs]

## Findings
[Organized by research questions, with inline citations]

## Methodology
[Brief: sources consulted, confidence levels, any unresolved contradictions]

## Limitations
[Gaps, uncertainties, disputed claims]

## Sources
[Numbered list with confidence indicators]

See references/report-templates.md for format variants.

Example

Input: "Research the current state of nuclear fusion energy"

Research Brief:

Topic: Current state of nuclear fusion energy
Key Questions:
1. What are the leading approaches and projects?
2. What milestones have been achieved recently?
3. What are realistic timelines for commercial fusion?
Constraints: Focus on scientific/engineering progress, not policy

Draft Excerpt (before research):

Nuclear fusion has made significant progress [CONFIDENCE: LOW]. 
The National Ignition Facility achieved ignition [NEEDS VERIFICATION].
Private companies like [RESEARCH NEEDED] are also pursuing fusion.

Post-search reflection:

REFLECTION after search 1 (NIF ignition):
- Found: NIF achieved ignition Dec 2022, 3.15 MJ from 2.05 MJ input
- Source: Lawrence Livermore (official) - Confidence 95
- Gap: Private sector landscape still unknown
- Next: Search for private fusion companies

Source tracking:

FACT: NIF achieved fusion ignition December 2022
SOURCE: llnl.gov/news/...
CONFIDENCE: 95
DISPUTED: No

Quality log:

Iteration 1: Comp 5, Acc 4 → Need private sector + timelines
Iteration 2: Comp 8, Acc 7 → Good coverage, strengthen citations
Iteration 3: Comp 9, Acc 8 → Done ✓

When to Use

Use: Complex questions, comparisons, due diligence, state-of-art surveys Don't use: Simple lookups (use web_search directly), opinions, creative writing

References

• references/search-patterns.md - Query techniques, parallel research
• references/critique-framework.md - Red team methodology
• references/source-evaluation.md - Confidence scoring, contradictions
• references/report-templates.md - Output formats

User Interaction

Use the AskUserQuestion tool at key decision points throughout the deep research workflow:

When to Use

• Scope clarification (Step 1): Topic has multiple interpretations or unclear constraints
• Research direction (Step 3-4): Multiple valid approaches, prioritization needed
• Quality iteration (Step 8): Decide whether to continue refining or finalize
• Contradiction resolution (Step 6): Sources disagree and user judgment would help

Example Invocations

Scope clarification (Step 1):

Topic: "Research renewable energy"
→ Use AskUserQuestion tool:
  Question: "Renewable energy is broad. What aspect should I focus on?"
  Options:
  - "Current technology comparison (solar, wind, etc.)"
  - "Economic viability and cost trends"
  - "Policy and regulatory landscape"
  - "Specific geography or market"

Research brief validation (Step 2):

After drafting research brief
→ Use AskUserQuestion tool:
  Question: "Does this research brief capture your needs?"
  Options:
  - "Yes, proceed with research"
  - "Adjust scope (I'll specify)"
  - "Add specific questions to address"
  - "Change constraints or focus"

Quality iteration decision (Step 8):

Iteration 2: Comprehensiveness 6, Accuracy 7, Avg 6.5
→ Use AskUserQuestion tool:
  Question: "Quality at 6.5/10 after 2 iterations. Continue or finalize?"
  Options:
  - "Continue to iteration 3 (target 7+)" (Recommended)
  - "Good enough, finalize now"
  - "Focus on specific gaps: [describe]"

Source contradiction (Step 6):

Major sources disagree: Source A (confidence 85) says X, Source B (confidence 80) says Y
→ Use AskUserQuestion tool:
  Question: "Authoritative sources conflict. How to resolve?"
  Options:
  - "Present both views with confidence levels"
  - "Search for additional tiebreaker sources"
  - "Favor more recent source"
  - "Flag as unresolved, note in limitations"

Report depth selection (Step 9):

Research complete, ready for final report
→ Use AskUserQuestion tool:
  Question: "What level of detail in the final report?"
  Options:
  - "Full report with all methodology details"
  - "Executive summary with key findings"
  - "Detailed findings, minimal methodology"
  - "Just the sources with confidence ratings"

Benefits of Interactive Research

• Aligned scope: Research matches user's actual needs
• Informed trade-offs: User decides depth vs breadth
• Quality control: User approves iteration decisions
• Transparent methodology: User understands how conclusions reached