deep-research

$2b

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:

• Scoping — Research question + methodology blueprint

• Investigation — Systematic literature search + source verification

• Analysis — Cross-source synthesis + bias check

• Composition — Full APA 7.0 report

• Review — Editorial + ethics + vulnerability scan

• 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):

• User has no clear research question and wants guided thinking

• User asks to be "led", "guided", or "mentored" through research

• User expresses uncertainty about what to research or where to start

• User wants to brainstorm, explore, or clarify a research direction

• 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

• ⚠️ IRON RULE: Devil's Advocate has 3 mandatory checkpoints; Critical-severity issues block progression

• Revision loops capped at 2 iterations; remaining issues become "acknowledged limitations"

• ⚠️ IRON RULE: Ethics Review can halt delivery for Critical ethics concerns

• User confirmation required after Phase 1 before proceeding

Phase-by-phase Invocation Contract (v3.9.2)

ARS pipeline runs in 6 phases. Two invocation modes:

Mode A — orchestrator-driven (default): pipeline_orchestrator_agent (in academic-pipeline skill) runs all phases end-to-end with state tracking via Material Passport.

Mode B — phase-by-phase (cross-session resume): User invokes one agent per phase across sessions for long-running projects. Common pattern via ARS_PASSPORT_RESET=1 + resume_from_passport=<hash> (see academic-pipeline/references/passport_as_reset_boundary.md).

In Mode B, **single-phase agents (Bucket A per docs/design/2026-05-18-ars-v3.9.2-agent-phase-classification.md) stay strictly within their assigned phase for writes**. Reads from upstream phases are allowed. Multi-phase agents (Bucket B: devils_advocate_agent, report_compiler_agent) do exactly the work specified by the caller's invocation for that phase — no extension to other phases in the same call.

Routing into Mode B requires explicit user signal — /ars-<mode> slash command or [direct-mode] prefix. Ambiguous cross-phase input defaults to clarification per .claude/CLAUDE.md Routing Discipline + shared/references/intent_clarification_protocol.md.

Enforcement (v3.9.2): prompt-level via Phase Boundary blocks on Bucket A agents + advisory verifier (scripts/check_pipeline_integrity.py). Deterministic PreToolUse hook + multi-phase envelope deferred to v3.10 active conductor (#134).

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:

• Research Question Brief (from research_question_agent)

• Methodology Blueprint (from research_architect_agent)

• Annotated Bibliography (from bibliography_agent)

• Synthesis Report (from synthesis_agent)

• [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

• ⚠️ IRON RULE: Every claim must have a citation — no unsupported assertions

• Evidence hierarchy — meta-analyses > RCTs > cohort studies > case reports > expert opinion

• Contradiction disclosure — if sources disagree, report both sides with evidence quality comparison

• Limitation transparency — every report must have an explicit limitations section

• AI disclosure — all reports include a statement that AI-assisted research tools were used

• Reproducibility — search strategies, inclusion criteria, and analytical methods must be documented for replication

• 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.