Academic Paper — Academic Paper Writing Agent Team

A general-purpose academic paper writing tool — 12-agent pipeline covering all disciplines, with higher education domain as the default reference.

v2.5 adds two writing quality features:

• Style Calibration (intake Step 10, optional) — Provide 3+ past papers and the pipeline learns your writing voice (sentence rhythm, vocabulary preferences, citation integration style). Applied as a soft guide during drafting; discipline conventions always take priority. See shared/style_calibration_protocol.md.
• Writing Quality Check (references/writing_quality_check.md) — A writing quality checklist applied during the draft self-review step. Catches overused AI-typical terms, em dash overuse, throat-clearing openers, uniform paragraph lengths, and monotonous sentence rhythm. These are good writing rules, not detection evasion.

Quick Start

Minimal command:

Write a paper on the impact of AI on higher education quality assurance

Write a paper on the impact of declining birth rates on private university management strategies

Execution flow:

1. Configuration interview — paper type, discipline, citation format, output format
2. Literature search — systematic search strategy, source screening
3. Architecture design — paper structure, outline, word count allocation
4. Argumentation construction — claim-evidence chains, logical flow
5. Full-text drafting — section-by-section draft, register adjustment
6. Citation compliance + bilingual abstract (parallel)
7. Peer review — five-dimension scoring, revision suggestions
8. Output formatting — LaTeX/DOCX (via Pandoc)/PDF/Markdown

Trigger Conditions

Trigger Keywords

English: write paper, academic paper, paper outline, write abstract, revise paper, literature review paper, check citations, convert to LaTeX, convert format, format paper, conference paper, journal article, thesis chapter, research paper, guide my paper, help me plan my paper, step by step paper, draft manuscript, write methodology, write discussion, parse reviews, revision roadmap, help me with my revision, I got reviewer comments, convert citations

繁體中文: 寫論文, 學術論文, 論文大綱, 寫摘要, 修改論文, 文獻回顧論文, 檢查引用, 轉 LaTeX, 轉換格式, 研討會論文, 期刊文章, 學位論文, 研究論文, 引導我寫論文, 幫我規劃論文, 逐步寫論文, 寫方法論, 寫討論, 審查意見, 修訂路線圖, 幫我修改, 我收到審查意見, 轉換引用格式

Plan Mode Activation

Activate plan mode when the user wants guidance, step-by-step planning, or expresses uncertainty about paper structure. Default rule: when ambiguous between plan and full, prefer plan.

See references/plan_mode_protocol.md for full intent signals and activation rules.

Does NOT Trigger

Distinction from deep-research

Agent Team (12 Agents)

Output Formats

Text Formats

LaTeX (.tex + .bib), DOCX (via Pandoc), PDF (via LaTeX or Pandoc), Markdown.

Figures

When the paper contains quantitative results, the visualization_agent can generate publication-ready figures in Python (matplotlib/seaborn) or R (ggplot2) with APA 7.0 formatting and colorblind-safe palettes. Figures are delivered as runnable code + LaTeX \includegraphics integration code. See references/statistical_visualization_standards.md for chart type decision trees and code templates.

Citation Formats

APA 7.0 (default), Chicago (Author-Date or Notes-Bibliography), MLA 9, IEEE, Vancouver. The formatter_agent supports late-stage citation format conversion between any two supported formats via "Convert citations to [format]".

Orchestration Workflow (8 Phases)

Phase 0: CONFIG        -> [intake_agent]              -> Paper Configuration Record
Phase 1: RESEARCH      -> [literature_strategist]      -> Search Strategy + Source Corpus
Phase 2: ARCHITECTURE  -> [structure_architect]        -> Paper Outline + Evidence Map
Phase 3: ARGUMENTATION -> [argument_builder]           -> Argument Blueprint
Phase 4: DRAFTING      -> [draft_writer]               -> Complete Draft
Phase 5a: CITATIONS    -> [citation_compliance] ──┐    -> Citation Audit Report
Phase 5b: ABSTRACT     -> [abstract_bilingual]   ─┘    -> Bilingual Abstract + Keywords  (parallel)
Phase 6: PEER REVIEW   -> [peer_reviewer]              -> Review Report (max 2 revision loops)
Phase 7: FORMAT        -> [formatter]                  -> Final Output Package

See references/workflow_phase_details.md for detailed per-phase agent behavior and output descriptions.

Checkpoint Rules

1. ⚠️ IRON RULE: User must confirm Paper Configuration Record before proceeding to Phase 1
2. Phase 2 -> 3: User must approve outline (can request restructuring)
3. ⚠️ IRON RULE: Max 2 revision loops; unresolved items -> "Acknowledged Limitations"
4. Peer Review Critical-severity issues block progression to Phase 7
5. User can skip Phase 1 (literature) if providing own sources

v3.4.0 compliance (applies to full mode): Before finalization, compliance_agent runs RAISE principles-only check (warn-only; primary research is outside PRISMA-trAIce scope). Warnings are listed in the disclosure statement but never block the pipeline. See shared/raise_framework.md §Scope disclaimer.

Operational Modes (10 Modes)

See references/mode_selection_guide.md for details.

Quick Mode Selection Guide

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 plan — it will guide you step by step. disclosure is a finishing step — run it after the paper is drafted, targeting the venue you plan to submit to.

Mode Selection Logic

See references/mode_selection_guide.md for trigger-to-mode mappings and the full selection flowchart.

Plan Mode: Chapter-by-Chapter Guided Planning

Socratic mode that guides users through paper planning one chapter at a time. Builds a complete Paper Blueprint through structured dialogue.

See references/plan_mode_protocol.md for the full chapter-by-chapter dialogue flow and Paper Blueprint structure.

Handoff Protocol: deep-research -> academic-paper

intake_agent automatically detects deep-research materials (RQ Brief / Bibliography / Synthesis / INSIGHT Collection) and skips redundant steps. See deep-research/SKILL.md Handoff Protocol for the complete handoff material format.

Failure Paths

See references/failure_paths.md for details. Quick reference:

Full Academic Pipeline

See academic-pipeline/SKILL.md for the complete workflow.

Phase 0: Configuration Interview

See agents/intake_agent.md for the complete field definitions of the Phase 0 configuration interview. The interview covers 9 items: paper type, discipline, target journal, citation format, output format, language, abstract, word count, and existing materials. Outputs a Paper Configuration Record, awaiting user confirmation.

File Structure

Agent definitions: agents/{agent_name}.md — one file per agent (12 total, matching Agent Team table above).

References (19 files in references/):

• Citation: apa7_extended_guide, apa7_chinese_citation_guide, citation_format_switcher
• Writing: academic_writing_style, writing_quality_check, writing_judgment_framework
• Structure: paper_structure_patterns (6 types), abstract_writing_guide
• Domain: hei_domain_glossary (bilingual), journal_submission_guide, latex_template_reference
• Process: failure_paths (12 scenarios), mode_selection_guide (10 modes), plan_mode_protocol, workflow_phase_details
• Ethics: credit_authorship_guide (CRediT 14 roles), funding_statement_guide, statistical_visualization_standards
• Disclosure (v3.2): disclosure_mode_protocol (venue-specific AI-usage statement generation), venue_disclosure_policies (v1 database: ICLR, NeurIPS, Nature, Science, ACL, EMNLP)
• Also: deep-research/references/apa7_style_guide.md (base reference, extended here)

Templates (11 files in templates/): imrad, literature_review, case_study, theoretical_paper, policy_brief, conference_paper, latex_article_template.tex, bilingual_abstract, credit_statement, funding_statement, revision_tracking (4 status types).

Examples (5 files in examples/): imrad_hei_example, literature_review_example, plan_mode_guided_writing, chinese_paper_example, revision_mode_example.

Anti-Patterns

Explicit prohibitions to prevent common failure modes:

Quality Standards

Writing Quality

1. Every claim must have a citation or be supported by the paper's own data
2. Zero citation orphans — in-text citations <-> reference list must perfectly match
3. Consistent register — academic tone appropriate for the discipline
4. Logical flow — clear transitions between paragraphs and sections
5. Word count compliance — within +/-10% of target

Bilingual Abstract Quality

6. Independent writing — zh-TW and EN abstracts are independently composed, NOT mechanical translations
7. Structural alignment — both abstracts cover the same key points in the same order
8. Keywords — 5-7 per language, reflecting the paper's core concepts
9. Word count — EN: 150-300 words; zh-TW: 300-500 characters

Citation Quality

10. Format compliance — 100% adherence to selected citation style
11. ⚠️ IRON RULE: DOI inclusion — every source with a DOI must include it; every citation must be verified via DOI or WebSearch
12. Currency — flag sources older than 10 years (unless seminal works)
13. Self-citation ratio — flag if >15%

Peer Review

14. Five dimensions — Originality (20%), Methodological Rigor (25%), Evidence Sufficiency (25%), Argument Coherence (15%), Writing Quality (15%)
15. Actionable feedback — every criticism must include a specific suggestion
16. Max 2 revision rounds — unresolved items become Acknowledged Limitations

Mandatory Inclusions

⚠️ IRON RULE: Every paper MUST include: Data Availability Statement, Ethics Declaration, Author Contributions (CRediT), Conflict of Interest Statement, Funding Acknowledgment. 17. AI disclosure statement — every paper must include a statement on AI tool usage 18. Limitations section — explicitly discuss study limitations 19. Ethics statement — when applicable (human subjects, sensitive data)

Output Language

Follows the user's language. Academic terminology is kept in English. Bilingual abstracts are always provided regardless of the main text language.

Integration with Other Skills

academic-paper + tw-hei-intelligence  -> Evidence-based HEI paper with real MOE data
academic-paper + deep-research        -> Deep research phase -> paper writing phase (auto-handoff)
academic-paper + report-to-website    -> Interactive web version of the paper
academic-paper + notebooklm-slides-generator -> Presentation slides from paper
academic-paper + academic-paper-reviewer -> Peer review -> revision loop

Version Info

Version History

See references/changelog.md for full version history.