Alterlab 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. v2.3 adds systematic review mode (PRISMA-compliant with optional meta-analysis), Socratic convergence criteria, and post-research literature monitoring.

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)	alterlab-paper-writer
Reviewing a paper (structured review)	alterlab-paper-reviewer
Full research-to-paper pipeline	alterlab-research-pipeline

Quick Mode Selection Guide

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

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)

The standard pipeline runs six phases: 1. Scoping (RQ Brief + Methodology Blueprint, Checkpoint 1) → 2. Investigation (Source Corpus + verified/graded sources) → 3. Analysis (Synthesis + gap analysis, Checkpoint 2) → 4. Composition (full APA 7.0 draft) → 5. Review (editorial + ethics + Checkpoint 3, parallel) → 6. Revision (final report, max 2 loops).

Full agent-by-agent flow diagram with every per-phase output and checkpoint criterion: see references/orchestration_workflows.md (Standard Orchestration Workflow 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

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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.

Socratic mode advances through five layers: 1. Problem Framing → 2. Methodology Reflection → 3. Evidence Design → 4. Critical Self-Examination → 5. Significance & Contribution. Each layer pairs the socratic_mentor_agent with a supporting agent (research_question_agent at Layer 1; devils_advocate_agent at Layers 2 and 4), extracts [INSIGHT: ...] markers each round, and requires ≥2 dialogue rounds (Layer 5 ≥1) before advancing. Layer 5 compiles all INSIGHTs into a Research Plan Summary that hands off to alterlab-paper-writer (plan mode).

Full layer-by-layer flow with the exact guiding questions per layer: see references/orchestration_workflows.md (Socratic Mode Layer Flow section).

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

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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.

This mode reuses the six phases but with PRISMA-specific outputs: 1. Scoping produces a PICOS RQ and a full PRISMA-P protocol (not just an RQ); 2. Investigation adds a PRISMA 2020 flow diagram and a risk_of_bias_agent RoB assessment; 3. Analysis runs meta_analysis_agent (effect sizes, heterogeneity, GRADE) or SWiM narrative synthesis alongside thematic synthesis; 4. Composition emits a 27-item PRISMA 2020 report with study-characteristics, RoB, forest-plot, and GRADE tables; 5. Review and 6. Revision mirror the standard pipeline.

Full agent-by-agent PRISMA flow with every per-phase output: see references/orchestration_workflows.md (Systematic Review Mode Pipeline section).

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

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Operational Modes

Mode	Agents Active	Output	Word Count
full (default)	All 9 core (excluding socratic_mentor, risk_of_bias, meta_analysis, monitoring)	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 < 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

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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.

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Handoff Protocol: alterlab-deep-research → alterlab-paper-writer

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

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"

alterlab-paper-writer'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 alterlab-research-pipeline/SKILL.md for the complete workflow.

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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

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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/orchestration_workflows.md	Detailed 6-phase, Socratic 5-layer, and systematic-review flow diagrams	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

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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)

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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	alterlab-deep-research full mode handoff to alterlab-paper-writer
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

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Output Language

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

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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:

Concept	Definition	Applies To
Peer-reviewed	Published in a journal with formal peer review process (editorial review alone does not qualify). Conference proceedings count only if explicitly peer-reviewed	bibliography_agent, source_verification_agent
Currency Rule	Default: published within 5 years. Override by domain: CS/AI = 3 years, History/Philosophy = 20 years, Law = depends on jurisdiction changes. Seminal works exempt regardless of age	bibliography_agent, ethics_review_agent
CRITICAL severity	Issue that, if unresolved, would invalidate a core conclusion or constitute academic misconduct. Requires immediate resolution before pipeline can proceed	All agents
Source Tier	tier_1 = top-quartile peer-reviewed journal; tier_2 = other peer-reviewed; tier_3 = academic but not peer-reviewed; tier_4 = grey literature	bibliography_agent, source_verification_agent
Minimum Source Count	full = 15+, quick = 5-8, lit-review = 25+, systematic-review = all eligible (no limit), fact-check = 3+ per claim	bibliography_agent
Verification Threshold	100% DOI check + 50% WebSearch spot-check	source_verification_agent, ethics_review_agent

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

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Integration with Other Skills

This skill is domain-agnostic but composes with other AlterLab skills:

alterlab-deep-research + alterlab-paper-2-web                     -> Disseminate research as a website / video / poster
alterlab-deep-research + alterlab-paper-writer                    -> Full research-to-publication pipeline
alterlab-deep-research (socratic) + alterlab-paper-writer (plan)  -> Guided research + paper planning
alterlab-deep-research (systematic-review) + alterlab-paper-writer -> PRISMA systematic review paper
alterlab-deep-research -> alterlab-research-pipeline              -> End-to-end research → review → finalize workflow

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Version History

Current: v2.3 (see frontmatter metadata.version). Latest change: added the systematic-review mode (PRISMA 2020 pipeline with risk_of_bias_agent and meta_analysis_agent, PRISMA protocol/report templates, systematic_review_toolkit reference) and the optional post-pipeline monitoring_agent, bringing the team to 13 agents and 7 modes.