deep-research

Files (47)

• SKILL.md
• bibliography_agent.md · agents/
• devils_advocate_agent.md · agents/
• editor_in_chief_agent.md · agents/
• ethics_review_agent.md · agents/
• meta_analysis_agent.md · agents/
• monitoring_agent.md · agents/
• report_compiler_agent.md · agents/
• research_architect_agent.md · agents/
• research_question_agent.md · agents/
• risk_of_bias_agent.md · agents/
• socratic_mentor_agent.md · agents/
• source_verification_agent.md · agents/
• synthesis_agent.md · agents/
• exploratory_research.md · examples/
• fact_check_mode.md · examples/
• handoff_to_paper.md · examples/
• policy_analysis.md · examples/
• review_mode.md · examples/
• socratic_guided_research.md · examples/
• systematic_review.md · examples/
• apa7_style_guide.md · references/
• argumentation_reasoning_framework.md · references/
• changelog.md · references/
• cross_agent_quality_definitions.md · references/
• equator_reporting_guidelines.md · references/
• ethics_checklist.md · references/
• failure_paths.md · references/
• interdisciplinary_bridges.md · references/
• irb_decision_tree.md · references/
• literature_monitoring_strategies.md · references/
• logical_fallacies.md · references/
• methodology_patterns.md · references/
• mode_selection_guide.md · references/
• preregistration_guide.md · references/
• semantic_scholar_api_protocol.md · references/
• socratic_mode_protocol.md · references/
• socratic_questioning_framework.md · references/
• source_quality_hierarchy.md · references/
• systematic_review_protocol.md · references/
• systematic_review_toolkit.md · references/
• evidence_assessment_template.md · templates/
• literature_matrix_template.md · templates/
• preregistration_template.md · templates/
• prisma_protocol_template.md · templates/
• prisma_report_template.md · templates/
• research_brief_template.md · templates/

SKILL.md (first lines)

# 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?

From LUNARTECH-X/superpowers, MIT.

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