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

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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。

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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) |

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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

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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

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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".

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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.

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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 |

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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 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 |

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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.

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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 researchquestionagent)
2. Methodology Blueprint (from researcharchitectagent)
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.

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Full Academic Pipeline

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

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Agent File References

| Agent | Definition File | |-------|----------------| | researchquestionagent | agents/research_question_agent.md | | researcharchitectagent | agents/research_architect_agent.md | | bibliographyagent | agents/bibliography_agent.md | | sourceverificationagent | agents/source_verification_agent.md | | synthesisagent | agents/synthesis_agent.md | | reportcompileragent | agents/report_compiler_agent.md | | editorinchiefagent | agents/editor_in_chief_agent.md | | devilsadvocateagent | agents/devils_advocate_agent.md | | ethicsreviewagent | agents/ethics_review_agent.md | | socraticmentor_agent | `age

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Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

• Author: LUNARTECH-X
• Source: LUNARTECH-X/superpowers
• License: MIT

Install and usage instructions live in the source repository linked above.