Skills
skills/imbad0202/academic-research-skills/deep-research

deep-research

Installation
SKILL.md

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

Scenario Use Instead
Writing a paper (not researching) academic-paper
Reviewing a paper (structured review) academic-paper-reviewer
Full research-to-paper pipeline academic-pipeline

Quick Mode Selection Guide

Your Situation 你的狀況 Recommended Mode Spectrum
Vague idea, need guidance / 有模糊想法，需要引導 socratic originality
Clear RQ, need comprehensive research / 有明確 RQ，需要完整研究 full balanced
Need a quick brief (30 min) / 需要快速摘要 quick fidelity
Have a paper to evaluate before citing / 有論文需要評估 review balanced
Need literature review for a topic / 需要文獻回顧 lit-review fidelity
Need to verify specific claims / 需要查核特定事實 fact-check fidelity
Need systematic review / meta-analysis / 系統性回顧或後設分析 systematic-review fidelity

Spectrum (v3.2): fidelity = template-heavy, predictable output; balanced = default; originality = exploratory, template-light. See shared/mode_spectrum.md for the full cross-skill spectrum table.

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)

# Agent Role Phase
1 research_question_agent Transforms vague topics into precise, FINER-scored research questions with scope boundaries Phase 1, Socratic Layer 1
2 research_architect_agent Designs methodology blueprint: paradigm, method, data strategy, analytical framework, validity criteria Phase 1
3 bibliography_agent Systematic literature search, source screening, annotated bibliography in APA 7.0 Phase 2
4 source_verification_agent Fact-checking, source grading (evidence hierarchy), predatory journal detection, conflict-of-interest flagging Phase 2
5 synthesis_agent Cross-source integration, contradiction resolution, thematic synthesis, gap analysis Phase 3
6 report_compiler_agent Drafts complete APA 7.0 report (Title -> Abstract -> Intro -> Method -> Findings -> Discussion -> References) Phase 4, 6
7 editor_in_chief_agent Q1 journal editorial review: originality, rigor, evidence sufficiency, verdict (Accept/Revise/Reject) Phase 5
8 devils_advocate_agent Challenges assumptions, tests for logical fallacies, finds alternative explanations, confirmation bias checks Phase 1, 3, 5, Socratic Layer 2, 4
9 ethics_review_agent AI-assisted research ethics, attribution integrity, dual-use screening, fair representation Phase 5
10 socratic_mentor_agent Q1 journal editor persona; guides research thinking through Socratic questioning across 5 layers Socratic Mode (Layer 1-5)
11 risk_of_bias_agent Assesses risk of bias using RoB 2 (RCTs) and ROBINS-I (non-randomized); traffic-light visualization Systematic Review (Phase 2)
12 meta_analysis_agent Designs and executes meta-analysis or narrative synthesis; effect sizes, heterogeneity, GRADE Systematic Review (Phase 3)
13 monitoring_agent Post-research literature monitoring: digests, retraction alerts, contradictory findings detection Optional (post-pipeline)

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. ⚠️ IRON RULE: 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. ⚠️ IRON RULE: Ethics Review can halt delivery for Critical ethics concerns
  4. User confirmation required after Phase 1 before proceeding

Socratic Mode: Guided Research Dialogue

5-layer dialogue guiding users from vague ideas to concrete research questions. Core principle: ⚠️ IRON RULE: Never give direct answers.

Layers: Clarification -> Assumption Probing -> Evidence/Reasoning -> Viewpoint/Perspective -> Implication/Consequence

See references/socratic_mode_protocol.md for the full 5-layer dialogue flow, management rules, and auto-end conditions.

Opt-in Reading Probe (v3.5.1)

Setting ARS_SOCRATIC_READING_PROBE=1 enables a one-time honesty probe during goal-oriented Socratic sessions. When the user cites a specific paper, the Mentor asks them to paraphrase one passage. Decline is logged without penalty. Default OFF. See agents/socratic_mentor_agent.md §"Optional Reading Probe Layer".

Systematic Review Mode

PRISMA 2020-compliant systematic review with optional meta-analysis. Follows 5-phase protocol: Protocol Registration -> Systematic Search -> Screening & Selection -> Data Extraction & RoB -> Synthesis & Reporting.

v3.4.0 compliance: systematic-review mode triggers compliance_agent at Stage 2.5 (Methods items) and Stage 4.5 (remaining items + RAISE 8-role matrix). PRISMA-trAIce Mandatory failures block the pipeline. See shared/compliance_checkpoint_protocol.md.

See references/systematic_review_protocol.md for full PRISMA pipeline, checkpoint rules, and meta-analysis procedures.

Operational Modes

Mode Agents Active Output Word Count
full (default) All 9 core (excluding socratic_mentor, RoB, meta-analysis) Full APA 7.0 report 3,000-8,000
quick RQ + Biblio + Verification + Report Research brief 500-1,500
review Editor + Devil's Advocate + Ethics Reviewer report on provided text N/A
lit-review Biblio + Verification + Synthesis Annotated bibliography + synthesis 1,500-4,000
fact-check Source Verification only Verification report 300-800
socratic Socratic Mentor + RQ + Devil's Advocate Research Plan Summary (INSIGHT collection) N/A (iterative)
systematic-review RQ + Architect + Biblio + Verification + RoB + Meta-Analysis + Synthesis + Report + Editor + Ethics + DA Full PRISMA 2020 report + forest plot data + GRADE table 5,000-15,000

Failure Paths

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

Key failure path summary:

Failure Scenario Trigger Condition Recovery Strategy
RQ cannot converge Phase 1 / Layer 1 exceeds multiple rounds while still vague Provide 3 candidate RQs or suggest lit-review
Insufficient literature bibliography_agent finds < 5 sources Expand search strategy, alternative keywords
Methodology mismatch RQ type misaligned with method capability Return to Phase 1, suggest 3 alternative methods
Devil's Advocate CRITICAL Fatal logical flaw discovered STOP, explain the issue, require correction
Ethics BLOCKED Serious ethical issue STOP, list issues and remediation path
Socratic non-convergence > 10 rounds without convergence Suggest switching to full mode
User abandons mid-process Explicitly states they don't want to continue Save progress, provide re-entry path
Only Chinese-language literature English search returns empty Switch to Chinese academic databases

Literature Monitoring (Optional Post-Pipeline)

Optional post-research monitoring for new publications in the research area.

See references/literature_monitoring_strategies.md for setup instructions across academic databases.

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

Agent Definition File
research_question_agent agents/research_question_agent.md
research_architect_agent agents/research_architect_agent.md
bibliography_agent agents/bibliography_agent.md
source_verification_agent agents/source_verification_agent.md
synthesis_agent agents/synthesis_agent.md
report_compiler_agent agents/report_compiler_agent.md
editor_in_chief_agent agents/editor_in_chief_agent.md
devils_advocate_agent agents/devils_advocate_agent.md
ethics_review_agent agents/ethics_review_agent.md
socratic_mentor_agent agents/socratic_mentor_agent.md
risk_of_bias_agent agents/risk_of_bias_agent.md
meta_analysis_agent agents/meta_analysis_agent.md
monitoring_agent agents/monitoring_agent.md

Reference Files

Reference Purpose Used By
references/apa7_style_guide.md APA 7th edition quick reference report_compiler, editor_in_chief
references/source_quality_hierarchy.md Evidence pyramid + grading rubric source_verification, bibliography
references/methodology_patterns.md Research design templates research_architect
references/logical_fallacies.md 30+ fallacies catalog devils_advocate
references/ethics_checklist.md AI disclosure, attribution, dual-use ethics_review
references/interdisciplinary_bridges.md Cross-discipline connection patterns synthesis, research_architect
references/socratic_questioning_framework.md 6 types of Socratic questions + 30+ prompt patterns socratic_mentor
references/failure_paths.md 12 failure scenarios with triggers and recovery paths all agents
references/mode_selection_guide.md Mode selection flowchart and comparison table orchestrator
references/irb_decision_tree.md IRB decision tree + Taiwan process + HE quick reference ethics_review, research_architect
references/equator_reporting_guidelines.md EQUATOR reporting guideline mapping research_architect, report_compiler
references/preregistration_guide.md Preregistration decision tree + platforms + checklist research_architect
references/systematic_review_toolkit.md Cochrane v6.4, PRISMA 2020, RoB 2, ROBINS-I, I² guide, GRADE, protocol registration risk_of_bias, meta_analysis, bibliography, report_compiler
references/literature_monitoring_strategies.md Google Scholar alerts, PubMed alerts, RSS feeds, Retraction Watch, citation tracking, monitoring cadence monitoring_agent
references/argumentation_reasoning_framework.md Cognitive framework for evaluating argument strength: Toulmin model, causal reasoning (Bradford Hill), inference to best explanation, epistemic status classification synthesis, devils_advocate, source_verification, socratic_mentor, research_architect
references/socratic_mode_protocol.md Full 5-layer Socratic dialogue flow, management rules, auto-end conditions socratic_mentor, research_question
references/systematic_review_protocol.md Full PRISMA pipeline, checkpoint rules, meta-analysis procedures risk_of_bias, meta_analysis, bibliography, report_compiler
references/cross_agent_quality_definitions.md Peer-reviewed source tiers, currency standards, severity definitions all agents
references/changelog.md Full version history —

Templates

Template Purpose
templates/research_brief_template.md Quick mode output format
templates/literature_matrix_template.md Source x Theme analysis matrix
templates/evidence_assessment_template.md Per-source quality assessment card
templates/preregistration_template.md OSF standard 21-item preregistration template
templates/prisma_protocol_template.md PRISMA-P 2015 systematic review protocol template
templates/prisma_report_template.md PRISMA 2020 systematic review report template (27 items)

Examples

Example Demonstrates
examples/exploratory_research.md Full 6-phase pipeline walkthrough
examples/systematic_review.md PRISMA-style literature review
examples/policy_analysis.md Applied comparative policy research
examples/socratic_guided_research.md Complete Socratic mode multi-turn dialogue (12 rounds)
examples/handoff_to_paper.md deep-research full mode handoff to academic-paper
examples/review_mode.md Review mode: 3-agent review pipeline for policy recommendation text
examples/fact_check_mode.md Fact-check mode: source verification of HEI claims with per-claim verdicts

Output Language

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

Anti-Patterns

Explicit prohibitions to prevent common failure modes:

# Anti-Pattern Why It Fails Correct Behavior
1 Confirmation bias in source selection Only finding sources that support the hypothesis Devil's Advocate checkpoint must include counter-evidence search
2 Cherry-picking evidence Citing one supportive study while ignoring three contradicting ones Report the full evidence landscape including conflicting findings
3 Vibe citing Mixing elements from 2-3 real papers into a fabricated reference Every reference must be verified independently; mashup fabrication is the hardest to detect
4 ⚠️ IRON RULE: Treating "difficult to verify" as acceptable Marking a reference as "uncertain" instead of FAIL Gray zone = FAIL. If you cannot confirm it exists, it does not go in the report
5 Skipping phases Jumping to synthesis before completing source verification Complete each phase fully; Phase N output is Phase N+1 input
6 Shallow Socratic mode Giving answers disguised as questions ("Wouldn't you say X is true?") Ask genuine questions that expose assumptions; never lead to predetermined conclusions
7 Source tier inflation Treating a blog post as equivalent to a peer-reviewed journal Apply evidence hierarchy strictly: Tier 1 (peer-reviewed) > Tier 2 (preprint) > Tier 3 (gray lit)

Quality Standards

  1. ⚠️ IRON RULE: 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 across all agents. ⚠️ IRON RULE: CRITICAL severity = issue that would invalidate a core conclusion or constitute academic misconduct. Requires immediate resolution.

See references/cross_agent_quality_definitions.md for full peer-reviewed source tiers, currency standards, and severity definitions.

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 Info

Item Content
Skill Version 2.9.3
Last Updated 2026-04-30
Maintainer Cheng-I Wu
Dependent Skills academic-paper v1.0+ (downstream)

Version History

See references/changelog.md for full version history.

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