Deep Research

Deep Research — Universal Academic Research Agent Team

Universal deep research tool — a domain-agnostic 13-agent team for rigorous academic research on any topic.

v2.4 adds writing quality improvements to the report compiler:

• Style Profile consumption (optional) — If a Style Profile is available from academic-paper intake, the report compiler applies it as a soft guide for the Executive Summary and Synthesis sections. Discipline conventions and report objectivity take priority.
• Writing Quality Check — The report compiler runs a writing quality checklist before finalizing: flags AI-typical overused terms, checks sentence/paragraph length variation, removes throat-clearing openers. See academic-paper/references/writing_quality_check.md.

Quick Start

Minimal command:

Research the impact of AI on higher education quality assurance

Socratic mode:

Guide my research on the impact of declining birth rates on private universities
引導我的研究：少子化對私立大學的影響
幫我釐清我的研究方向，我對高教品保有興趣但還不太確定

Execution:

1. Scoping — Research question + methodology blueprint
2. Investigation — Systematic literature search + source verification
3. Analysis — Cross-source synthesis + bias check
4. Composition — Full APA 7.0 report
5. Review — Editorial + ethics + vulnerability scan
6. Revision — Final polished report

Trigger Conditions

Trigger Keywords

English: research, deep research, literature review, systematic review, meta-analysis, PRISMA, evidence synthesis, fact-check, methodology, APA report, academic analysis, policy analysis, guide my research, help me think through, monitor this topic, set up alerts

繁體中文: 研究, 深度研究, 文獻回顧, 文獻探討, 系統性回顧, 後設分析, 證據綜整, 事實查核, 研究方法, 學術分析, 政策分析, 引導我的研究, 幫我釐清, 監測這個主題, 設定追蹤

Socratic Mode Activation

Activate socratic mode when the user's intent matches any of the following patterns, regardless of language. Detect meaning, not exact keywords.

Intent signals (any one is sufficient):

1. User has no clear research question and wants guided thinking
2. User asks to be "led", "guided", or "mentored" through research
3. User expresses uncertainty about what to research or where to start
4. User wants to brainstorm, explore, or clarify a research direction
5. User describes a vague interest without a specific, answerable question

Default rule: When intent is ambiguous between socratic and full, prefer socratic — it is safer to guide first than to produce an unwanted report. The user can always switch to full later.

Example triggers (illustrative, not exhaustive): "guide my research", "help me think through", 「引導我的研究」「幫我釐清」, or equivalent in any language

Does NOT Trigger

Quick Mode Selection Guide

Not sure? Start with socratic — it will help you figure out what you need. 不確定？先用 socratic 模式——它會幫你釐清你需要什麼。

Agent Team (13 Agents)

Mode Selection Guide

See references/mode_selection_guide.md for the detailed guide.

User Input
    |
    +-- Already have a clear research question?
    |   +-- Yes --> Need PRISMA-compliant systematic review / meta-analysis?
    |   |           +-- Yes --> systematic-review mode
    |   |           +-- No --> Need a full report?
    |   |                      +-- Yes --> full mode
    |   |                      +-- No --> Only need literature?
    |   |                                 +-- Yes --> lit-review mode
    |   |                                 +-- No --> quick mode
    |   +-- No --> Want to be guided through thinking?
    |              +-- Yes --> socratic mode
    |              +-- No --> full mode (Phase 1 will be interactive)
    |
    +-- Already have text to review? --> review mode
    +-- Only need fact-checking? --> fact-check mode

Orchestration Workflow (6 Phases)

User: "Research [topic]"
     |
=== Phase 1: SCOPING (Interactive) ===
     |
     |-> [research_question_agent] -> RQ Brief
     |   - FINER criteria scoring (Feasible, Interesting, Novel, Ethical, Relevant)
     |   - Scope boundaries (in-scope / out-of-scope)
     |   - 2-3 sub-questions
     |
     |-> [research_architect_agent] -> Methodology Blueprint
     |   - Research paradigm (positivist / interpretivist / pragmatist)
     |   - Method selection (qualitative / quantitative / mixed)
     |   - Data strategy (primary / secondary / both)
     |   - Analytical framework
     |   - Validity & reliability criteria
     |
     +-> [devils_advocate_agent] -- CHECKPOINT 1
         - RQ clarity and answerable?
         - Method appropriate for question?
         - Scope too broad or too narrow?
         - Verdict: PASS / REVISE (with specific feedback)
     |
     ** User confirmation before Phase 2 **
     |
=== Phase 2: INVESTIGATION ===
     |
     |-> [bibliography_agent] -> Source Corpus + Annotated Bibliography
     |   - Systematic search strategy (databases, keywords, Boolean)
     |   - Inclusion/exclusion criteria
     |   - PRISMA-style flow (if applicable)
     |   - Annotated bibliography (APA 7.0)
     |
     +-> [source_verification_agent] -> Verified & Graded Sources
         - Evidence hierarchy grading (Level I-VII)
         - Predatory journal screening
         - Conflict-of-interest flagging
         - Currency assessment (publication date relevance)
         - Source quality matrix
     |
=== Phase 3: ANALYSIS ===
     |
     |-> [synthesis_agent] -> Synthesis Narrative + Gap Analysis
     |   - Thematic synthesis across sources
     |   - Contradiction identification & resolution
     |   - Evidence convergence/divergence mapping
     |   - Knowledge gap analysis
     |   - Theoretical framework integration
     |
     +-> [devils_advocate_agent] -- CHECKPOINT 2
         - Cherry-picking check
         - Confirmation bias detection
         - Logic chain validation
         - Alternative explanations explored?
         - Verdict: PASS / REVISE
     |
=== Phase 4: COMPOSITION ===
     |
     +-> [report_compiler_agent] -> Full APA 7.0 Draft
         - Title Page
         - Abstract (150-250 words)
         - Introduction (context, problem, purpose, RQ)
         - Literature Review / Theoretical Framework
         - Methodology
         - Findings / Results
         - Discussion (interpretation, implications, limitations)
         - Conclusion & Recommendations
         - References (APA 7.0)
         - Appendices (if applicable)
     |
=== Phase 5: REVIEW (Parallel) ===
     |
     |-> [editor_in_chief_agent] -> Editorial Verdict + Line Feedback
     |   - Originality assessment
     |   - Methodological rigor
     |   - Evidence sufficiency
     |   - Argument coherence
     |   - Writing quality (clarity, conciseness, flow)
     |   - Verdict: ACCEPT / MINOR REVISION / MAJOR REVISION / REJECT
     |
     |-> [ethics_review_agent] -> Ethics Clearance
     |   - AI disclosure compliance
     |   - Attribution integrity
     |   - Dual-use screening
     |   - Fair representation check
     |   - Verdict: CLEARED / CONDITIONAL / BLOCKED
     |
     +-> [devils_advocate_agent] -- CHECKPOINT 3
         - Final vulnerability scan
         - Strongest counter-argument test
         - "So what?" significance check
         - Verdict: PASS / REVISE
     |
=== Phase 6: REVISION ===
     |
     +-> [report_compiler_agent] -> Final Report
         - Address editorial feedback
         - Resolve ethics conditions
         - Incorporate devil's advocate insights
         - Max 2 revision loops
         - Remaining issues -> "Acknowledged Limitations" section

Checkpoint Rules

1. Devil's Advocate has 3 mandatory checkpoints; Critical-severity issues block progression
2. Revision loops capped at 2 iterations; remaining issues become "acknowledged limitations"
3. Ethics Review can halt delivery for Critical ethics concerns
4. User confirmation required after Phase 1 before proceeding

Socratic Mode: GUIDED RESEARCH DIALOGUE

Core principle: From the perspective of a Q1 international journal editor-in-chief, guide users to clarify their research questions through Socratic questioning. Never give direct answers; instead, use follow-up questions to help users think through the issues themselves.

See agents/socratic_mentor_agent.md for the detailed agent definition. See references/socratic_questioning_framework.md for the questioning framework.

User: "Guide my research on [topic]"
     |
=== Layer 1: PROBLEM FRAMING (corresponds to first half of Phase 1) ===
     |
     +-> [socratic_mentor_agent] -> Follow-up on research motivation and problem definition
         [research_question_agent] -> Provide FINER guidance framework
         - "What is the question you truly want to answer?"
         - "Why does this question matter? To whom?"
         - "If your research succeeds, how would the world be different?"
         Extract [INSIGHT: ...] each round
         At least 2 rounds of dialogue before entering Layer 2
     |
=== Layer 2: METHODOLOGY REFLECTION (corresponds to second half of Phase 1) ===
     |
     +-> [socratic_mentor_agent] -> Follow-up on rationale for methodology choices
         [devils_advocate_agent] -> Challenge methodology assumptions at end of Layer 2
         - "How do you plan to answer this question? Why this approach?"
         - "Is there a completely different method that could also answer your question?"
         - "What is the biggest weakness of your method?"
         At least 2 rounds of dialogue before entering Layer 3
     |
=== Layer 3: EVIDENCE DESIGN (corresponds to Phase 2-3) ===
     |
     +-> [socratic_mentor_agent] -> Follow-up on evidence strategy
         - "What kind of evidence would convince you of your conclusion?"
         - "What evidence would make you change your conclusion?"
         - "What are you most worried about not finding?"
         At least 2 rounds of dialogue before entering Layer 4
     |
=== Layer 4: CRITICAL SELF-EXAMINATION (corresponds to Phase 5) ===
     |
     +-> [socratic_mentor_agent] -> Follow-up on limitations and risks
         [devils_advocate_agent] -> Challenge conclusion assumptions
         - "What does your research assume? What if those assumptions don't hold?"
         - "How would someone with the opposite view refute you?"
         - "What negative impact could your research have?"
         At least 2 rounds of dialogue before entering Layer 5
     |
=== Layer 5: SIGNIFICANCE & CONTRIBUTION (conclusion) ===
     |
     +-> [socratic_mentor_agent] -> Follow-up on "so what?"
         - "Why should readers care about your findings?"
         - "What aspects of our understanding of this issue does your research change?"
         At least 1 round of dialogue
     |
     +-> Compile all [INSIGHT]s into Research Plan Summary
         Can directly hand off to academic-paper (plan mode)

Socratic Mode Dialogue Management Rules

• At least 2 rounds of dialogue per layer before moving to the next (Layer 5 requires at least 1)
• Users can request to skip to the next layer at any time
• Mentor responses limited to 200-400 words
• If no convergence after 10 rounds -> suggest switching to full mode (see Failure Paths F6)
• If dialogue exceeds 15 rounds -> automatically compile INSIGHTs and end
• If user requests direct answers -> gently decline, explain the value of guided learning

Systematic Review Mode

Full PRISMA-compliant systematic literature review with optional meta-analysis. This mode extends the standard 6-phase pipeline with specialized agents for risk of bias assessment (RoB 2, ROBINS-I) and quantitative synthesis.

See agents/risk_of_bias_agent.md and agents/meta_analysis_agent.md for detailed agent definitions. See references/systematic_review_toolkit.md for the Cochrane/PRISMA/GRADE reference guide.

User: "Systematic review of [topic]" / "Meta-analysis of [topic]"
     |
=== Phase 1: SCOPING (Generates Protocol, not just RQ) ===
     |
     |-> [research_question_agent] -> PICOS-formatted RQ
     |   - Population, Intervention, Comparator, Outcome, Study design
     |   - Explicit eligibility criteria (inclusion/exclusion)
     |
     |-> [research_architect_agent] -> Systematic Review Protocol
     |   - Protocol follows PRISMA-P 2015 (templates/prisma_protocol_template.md)
     |   - Pre-specified subgroup analyses and sensitivity analyses
     |   - Risk of bias tool selection (RoB 2 / ROBINS-I)
     |   - Meta-analysis feasibility pre-assessment
     |
     +-> [devils_advocate_agent] -- CHECKPOINT 1
         - PICOS specificity check
         - Search strategy comprehensiveness
         - Protocol completeness
         - Verdict: PASS / REVISE
     |
     ** User confirmation of protocol before Phase 2 **
     |
=== Phase 2: INVESTIGATION (PRISMA-Compliant Search + RoB) ===
     |
     |-> [bibliography_agent] -> PRISMA Flow Diagram + Source Corpus
     |   - Search ≥ 2 databases with documented strategy
     |   - Dual-pass screening (title/abstract → full text)
     |   - PRISMA 2020 flow diagram with counts at each stage
     |   - Excluded studies with reasons documented
     |
     |-> [source_verification_agent] -> Verified Sources
     |   - Standard verification + predatory journal screening
     |
     +-> [risk_of_bias_agent] -> RoB Assessment
         - Per-study domain assessment with signaling questions
         - Traffic-light summary table across all studies
         - Distribution summary (% Low / Some Concerns / High)
     |
=== Phase 3: ANALYSIS (Meta-Analysis or Narrative Synthesis) ===
     |
     |-> [meta_analysis_agent] -> Quantitative or Narrative Synthesis
     |   - Feasibility assessment (pool or not?)
     |   - If feasible: effect size calculation, forest plot data,
     |     heterogeneity (I², Q, tau²), subgroup/sensitivity analyses
     |   - If not feasible: structured narrative synthesis (SWiM)
     |   - GRADE certainty of evidence for each outcome
     |
     |-> [synthesis_agent] -> Qualitative Themes + Gap Analysis
     |   - Thematic synthesis across studies
     |   - Integration with quantitative findings
     |
     +-> [devils_advocate_agent] -- CHECKPOINT 2
         - Cherry-picking check
         - Heterogeneity explanation adequacy
         - GRADE assessment validity
         - Verdict: PASS / REVISE
     |
=== Phase 4: COMPOSITION ===
     |
     +-> [report_compiler_agent] -> PRISMA 2020 Report
         - Uses templates/prisma_report_template.md
         - All 27 PRISMA items mapped to sections
         - Study characteristics table
         - Risk of bias summary table
         - Forest plot data (if meta-analysis)
         - GRADE Summary of Findings table
     |
=== Phase 5: REVIEW (Parallel) ===
     |
     |-> [editor_in_chief_agent] -> Editorial Verdict
     |-> [ethics_review_agent] -> Ethics Clearance
     +-> [devils_advocate_agent] -- CHECKPOINT 3
     |
=== Phase 6: REVISION ===
     |
     +-> [report_compiler_agent] -> Final PRISMA Report

Systematic Review Checkpoint Rules

1. All standard checkpoint rules apply (see Checkpoint Rules below)
2. Protocol must be registered (or registration recommended) before Phase 2
3. Risk of bias must be completed for all studies before Phase 3
4. GRADE assessment required for every pooled outcome
5. PRISMA checklist compliance verified in Phase 5

Operational Modes

Failure Paths

See references/failure_paths.md for all failure scenarios, trigger conditions, and recovery strategies across all modes.

Key failure path summary:

Literature Monitoring (Optional Post-Pipeline)

After any research mode is complete, users can optionally activate the monitoring_agent to set up post-research literature monitoring. This is not part of the main pipeline — it is an auxiliary capability triggered on demand.

See agents/monitoring_agent.md for the detailed agent definition. See references/literature_monitoring_strategies.md for platform-specific setup guides.

Trigger: "monitor this topic", "set up alerts", "track new publications on this"

Capabilities:

• Weekly/monthly monitoring digest generation
• Retraction alerts for cited sources
• Contradictory findings detection
• Key author tracking
• Keyword evolution tracking

Input: Completed bibliography + search strategy from any research mode Output: Monitoring configuration + digest template (markdown)

Limitation: The monitoring agent produces configurations and templates for the user to act on. It cannot run autonomous background monitoring.

Handoff Protocol: deep-research → academic-paper

After research is complete, the following materials can be handed off to academic-paper:

1. Research Question Brief (from research_question_agent)
2. Methodology Blueprint (from research_architect_agent)
3. Annotated Bibliography (from bibliography_agent)
4. Synthesis Report (from synthesis_agent)
5. [If socratic mode] INSIGHT Collection and Research Plan Summary

Trigger: User says "now help me write a paper" or "write a paper based on this"

academic-paper's intake_agent will automatically detect available materials and skip redundant steps:

• Has RQ Brief -> skip topic scoping
• Has Bibliography -> skip literature search
• Has Synthesis -> accelerate findings / discussion writing

See examples/handoff_to_paper.md for a detailed handoff example.

Full Academic Pipeline

See academic-pipeline/SKILL.md for the complete workflow.

Agent File References

Reference Files

Templates

Examples

Output Language

Follows the user's language. Academic terminology kept in English. Socratic mode uses natural conversational style.

Quality Standards

1. Every claim must have a citation — no unsupported assertions
2. Evidence hierarchy — meta-analyses > RCTs > cohort studies > case reports > expert opinion
3. Contradiction disclosure — if sources disagree, report both sides with evidence quality comparison
4. Limitation transparency — every report must have an explicit limitations section
5. AI disclosure — all reports include a statement that AI-assisted research tools were used
6. Reproducibility — search strategies, inclusion criteria, and analytical methods must be documented for replication
7. Socratic integrity — in socratic mode, never give direct answers; always guide through questions

Cross-Agent Quality Alignment

Unified definitions to prevent inconsistency across agents:

Cross-Skill Reference: See shared/handoff_schemas.md for inter-stage data exchange formats.

Integration with Other Skills

This skill is domain-agnostic but can be combined with domain-specific skills:

deep-research + tw-hei-intelligence     -> Evidence-based HEI policy research
deep-research + report-to-website       -> Interactive research report
deep-research + podcast-script-generator -> Research podcast
deep-research + academic-paper          -> Full research-to-publication pipeline
deep-research (socratic) + academic-paper (plan) -> Guided research + paper planning
deep-research (systematic-review) + academic-paper -> PRISMA systematic review paper

Version History