deep-research

name deep-research description Universal deep research agent team. 13-agent pipeline for rigorous academic research on any topic. 8 modes: full research, quick brief, paper review, lit-review, fact-check, three-way literature scan, Socratic guided research dialogue, and systematic review with optional meta-analysis. Covers research question formulation, Socratic mentoring, methodology design, systematic literature search, source verification, cross-source synthesis, risk of bias assessment, meta-analysis, APA 7.0 report compilation, editorial review, devil's advocate challenges, ethics review, and post-research literature monitoring. Triggers on: research, deep research, literature review, systematic review, meta-analysis, PRISMA, evidence synthesis, fact-check, WHY HOW WHAT papers, 3W literature scan, guide my research, help me think through, 研究, 深度研究, 文獻回顧, 文獻探討, 系統性回顧, 後設分析, 事實查核, 三段式文獻掃描, 引導我的研究, 幫我釐清, 幫我想想, 我不確定要研究什麼, 研究方向, 研究主題, 심층 연구, 문헌 조사, 체계적 문헌고찰, 메타분석, 사실 확인, 연구 방향을 잡아줘, 연구 주제 정하는 것을 도와줘. metadata {"version":"2.12.1","last_updated":"2026-08-15","status":"active","data_access_level":"raw","task_type":"open-ended","related_skills":["academic-paper","academic-pipeline"]} 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 uses academic-paper/references/writing_quality_check.md as a diagnostic guide before finalizing (prompts for judgment subordinate to author and venue requirements, not quotas), and flags claims the cited sources do not support as [MATERIAL GAP] rather than hedging them (#825). Routing discipline (v3.9.2): see .claude/CLAUDE.md "Routing Discipline (v3.9.2)" + shared/references/intent_clarification_protocol.md for cross-skill routing rules. This skill assumes routing has already settled — ambiguous cross-phase materials should have been clarified upstream. 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: 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, WHY HOW WHAT papers, 3W literature scan, 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, 三段式文獻掃描, WHY HOW WHAT 論文比較, 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 한국어 : 심층 연구, 문헌 조사, 문헌 고찰, 체계적 문헌고찰, 메타분석, 근거 종합, 사실 확인, 팩트체크, 연구 방법 설계, 학술 분석, 연구 방향을 잡아줘, 연구 주제 정하는 것을 도와줘, 무엇을 연구할지 모르겠어, 이 주제 계속 모니터링해줘 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 a fast paper-comparison scan / 需要快速比較多篇論文 three-way-scan 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 --> Need rapid paper comparison? | | +-- Yes --> three-way-scan mode | | +-- No --> 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] -> Research-Integrity Review + Human-Subjects Administrative Status | - AI disclosure compliance | - Attribution integrity | - Dual-use screening | - Fair representation check | - Integrity verdict only: CLEARED / CONDITIONAL / BLOCKED | - Human subjects: readiness and authorization reported separately; institutional determination required | - Authority-bound planning: exact requirement IDs + actor/consumer scope only after the #666 replay-validated resolved-context gate | - Candidate rule trace: display only a replay-validated and surface-linted #669 artifact; never use it as a pathway result or workflow input | - Packet structure: consume only a replay-validated #667 manifest; deterministic status never becomes authorization or content adequacy | - Content coverage: consume only a replay-validated #681 `LLM-ADVISORY`; preserve deterministic status and report efficacy as `UNMEASURED` | +-> [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 stops the user once to confirm a Critical integrity concern (fabrication / plagiarism / missing AI disclosure / source misrepresentation / concrete harm-enabling specifics). Overridable with recorded reasoning — it confirms, it does not veto. Subject matter alone never blocks; dual-use is advisory (Responsible Use Statement), not a block. 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): Phase Boundary blocks on Bucket A agents + advisory verifier ( scripts/check_pipeline_integrity.py ) + a deterministic PreToolUse write-scope guard in hook-enabled runtimes (#134 rescope, PR #294). Multi-phase envelope remains forward-scope (#134 Slices 3-5). Socratic Mode: Guided Research Dialogue 5-layer dialogue guiding users from vague ideas to concrete research questions. Core principle while non-generation Socratic mode is active: ⚠️ IRON RULE : Never give direct answers. The explicit candidate-generation exit below leaves that mode before any candidate is shown. Layers : Clarification -> Assumption Probing -> Evidence/Reasoning -> Viewpoint/Perspective -> Implication/Consequence Research-question authorship boundary: Socratic mode is non-generation by default. Non-convergence may produce only a summary of directions the user has already expressed plus focused questions or a lit-review suggestion; it never produces candidate RQs automatically. If the user explicitly asks the system to propose candidates, announce the exit from non-generation Socratic mode and emit [SOCRATIC-NON-GENERATION-EXIT: explicit_user_request] on a standalone line before any clearly labeled AI-generated candidate. Never switch silently. 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 .