--- name: Deep Research slug: deep-research-4 category: AI Engineering description: Deep Research is a 13-agent pipeline for rigorous academic research on any topic, from research question formulation and systematic literature search to source verification, synthesis, meta-analysis, and APA 7.0 report compilation. github: "https://github.com/Imbad0202/academic-research-skills/tree/main/deep-research" language: Python stars: 42257 forks: 3369 install: "npx degit https://github.com/Imbad0202/academic-research-skills/tree/main/deep-research ~/.claude/skills/deep-research" installs_to: ~/.claude/skills/deep-research source_path: deep-research/SKILL.md collection_size: 4 category_size: 2451 collection_url: "https://dirskills.com/collections/Imbad0202/academic-research-skills" added: 2026-08-13T07:36:59.085Z last_synced: 2026-08-13T07:36:59.085Z canonical_url: "https://dirskills.com/skills/deep-research-4" --- # Deep Research Deep Research is a 13-agent pipeline for rigorous academic research on any topic, from research question formulation and systematic literature search to source verification, synthesis, meta-analysis, and APA 7.0 report compilation. **Install:** ```bash npx degit https://github.com/Imbad0202/academic-research-skills/tree/main/deep-research ~/.claude/skills/deep-research ``` ## README # 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`. > **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:** 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, 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): 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 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 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** 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. 4. 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=` (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-` 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: ⚠️ **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 | | `three-way-scan` | Biblio + Verification (retrieval + WHY/HOW/WHAT extract) | Paper shortlist compared by WHY/HOW/WHAT + cross-paper synthesis | 800-2,000 | | `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 | --- ## Three-Way Scan Mode (WHY / HOW / WHAT) Use `three-way-scan` when the user needs a disciplined shortlist of papers compared in a stable frame, but does **not** yet need a full literature review report. - **WHY**: what problem or bottleneck the paper addresses and why it matters - **HOW**: what strategy, method, or technical route the paper uses - **WHAT**: what the paper found, built, or still leaves unresolved This mode is intentionally lighter than `lit-review`. It prioritizes: 1. candidate retrieval 2. deduplication 3. compact per-paper extraction 4. cross-paper synthesis of shared WHY, divergent HOW, and remaining gaps Recommended per-paper output: ```markdown ## Source: | Year: | Link: - WHY: ... - HOW: ... - WHAT: ... ``` Then add: - common `WHY` - divergent `HOW` - strongest `WHAT` - unresolved global gap If the user later wants a broader evidence matrix, thematic synthesis, or PRISMA-like coverage, escalate from `three-way-scan` to `lit-review` or `systematic-review`. --- ## 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 | Critical integrity issue (not subject matter) | Stop the user once to confirm; list issues + remediation path; overridable with recorded reasoning | | 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`: 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** 6. **Preregistration handoff** — exactly one builder-produced `preregistration-artifact/1.0` sidecar (including an unavailable recei