/academic-paper

Mode Selection Guide

This guide helps users and the intake_agent select the most appropriate operational mode.

Mode Selection Flowchart

User Input →
│
├── Already have complete research?
│   ├── Yes → Want a full paper?
│   │   ├── Yes ─────────────────────────→ full mode
│   │   └── No → Just need an outline?
│   │       ├── Yes ─────────────────────→ outline-only mode
│   │       └── No → Just need an abstract?
│   │           ├── Yes ──────────────────→ abstract-only mode
│   │           └── No → Just need a literature review?
│   │               ├── Yes ─────────────→ lit-review mode
│   │               └── No ──────────────→ full mode
│   │
│   └── No → Want guided thinking?
│       ├── Yes ─────────────────────────→ plan mode ★ NEW
│       └── No ──────────────────────────→ full mode (Phase 0 will conduct an interview)
│
├── Have an existing paper to revise? ──────────────────────→ revision mode
├── Have comments explicitly identified as coming from a real committee or institutional review office?
│   └── Need tracking / response preparation ───────────────→ revision-coach committee-correspondence variant
├── Have reviewer comments to handle?
│   ├── Comments only, no response written yet ──────────→ revision-coach mode
│   └── Comments + an existing rebuttal/response draft ──→ rebuttal-audit mode
├── Need an AI-usage disclosure statement? ─────────────────→ disclosure mode
├── Just need format conversion? ────────────────────────→ format-convert mode
└── Just need a citation check? ────────────────────────→ citation-check mode

Detailed Description of Each Mode

full mode — Complete Paper Writing

Applicable Scenarios:

• User has a clear research question and (partial) materials
• Needs to produce a complete paper from start to finish
• Includes all phases: Interview → Literature → Structure → Argumentation → Writing → Citation → Review → Formatting

Not Applicable When:

• User has no idea about research direction (→ use deep-research first)
• Only need a specific section (→ use another specialized mode)

Expected Output: Complete paper draft + references + bilingual abstract + review report Expected Duration: Long (all 8 Phases fully executed) Agents Used: All 9 + socratic_mentor (if needed)

outline-only mode — Outline Generation

Applicable Scenarios:

• Only need the paper structure and outline
• A proposal to submit to an advisor for review
• Need to quickly plan the paper structure

Not Applicable When:

• Need complete paper content (→ full mode)
• Need guided thinking (→ plan mode)

Expected Output: Detailed outline + evidence allocation + word count distribution Expected Duration: Short (Phase 0-2) Agents Used: intake → literature_strategist → structure_architect

plan mode — Chapter-by-Chapter Guided Planning ★ NEW

Applicable Scenarios:

• User has ideas but they are not yet clear enough
• Wants guided thinking for each chapter's content
• First-time academic paper writer
• Wants to think through every section before writing
• Just received materials from deep-research and needs to transform them into a paper plan

Not Applicable When:

• Already knows exactly what to write (→ full mode is faster)
• Only needs an outline without deep thinking (→ outline-only mode)
• Time-pressured and needs rapid output (→ full mode)

Expected Output: Chapter Plan + INSIGHT Collection Expected Duration: Medium (Step 0-3, approximately 20-30 rounds of conversation) Agents Used: intake → socratic_mentor → structure_architect → argument_builder

Subsequent Connections:

• Chapter Plan → full mode (produce complete paper)
• Chapter Plan → academic-paper-reviewer (review the plan)

revision mode — Paper Revision

Applicable Scenarios:

• Already have a completed paper draft
• Received reviewer comments requiring revision
• Feel certain sections need improvement

Not Applicable When:

• No existing paper draft (→ full mode)
• Only need to check citation format (→ citation-check mode)

Expected Output: Revised paper + revision notes (tracked changes) Expected Duration: Medium Agents Used: peer_reviewer → draft_writer → citation_compliance

Prerequisite: User must provide existing paper content

abstract-only mode — Abstract Writing

Applicable Scenarios:

• Paper is already complete, only need an abstract
• Need to submit a conference abstract
• Need a bilingual abstract

Not Applicable When:

• No paper content to summarize (→ full mode or plan mode)

Expected Output: Bilingual abstract in the run's declared output language pair (output_language_pair; default zh-TW + EN) + keywords Expected Duration: Short Agents Used: intake → abstract_bilingual

lit-review mode — Literature Review

Applicable Scenarios:

• Need a literature review on a specific topic
• Preparing the Literature Review chapter of a paper
• Need a systematic search strategy and literature matrix

Not Applicable When:

• Need a complete paper (→ full mode)
• Need an in-depth research investigation (→ deep-research)

Expected Output: Annotated bibliography + literature matrix + synthesis analysis Expected Duration: Medium Agents Used: intake → literature_strategist

format-convert mode — Format Conversion

Applicable Scenarios:

• Already have paper content, need format conversion
• Markdown → LaTeX / DOCX / PDF
• Need to comply with a specific journal's formatting requirements

Not Applicable When:

• No existing content (→ full mode)
• Need content modifications (→ revision mode)

Expected Output: Document in target format Expected Duration: Short Agents Used: formatter used standalone

citation-check mode — Citation Check

Applicable Scenarios:

• Already have a paper, only need to check citation format
• Final check before submission
• Switching citation format (e.g., APA → IEEE)

Not Applicable When:

• No existing citation list (→ full mode)
• Need to modify paper content (→ revision mode)

Expected Output: Citation error report + automatic correction suggestions Expected Duration: Short Agents Used: citation_compliance used standalone

revision-coach mode — Reviewer-Comment Triage

Applicable Scenarios:

• Received reviewer comments / a decision letter and need them parsed into a structured plan
• Want a Revision Roadmap that classifies, maps, and prioritizes each comment
• Need a Response Letter Skeleton to start drafting replies
• Deciding whether to address or push back on a comment (disagreement posture)
• Non-journal scopes: conference rebuttal, grant-panel response, transfer-after-review

Not Applicable When:

• Already have a written rebuttal/response draft you want QA'd (→ rebuttal-audit mode)
• The paper itself needs rewriting based on the comments (→ revision mode)

Expected Output: Revision Roadmap + optional Tracking Template + Response Letter Skeleton Expected Duration: Short-Medium Agents Used: revision_coach_agent used standalone (no prior pipeline execution required)

Committee-correspondence variant: when the user explicitly identifies comments from a real committee or institutional review office, this same entrypoint loads committee_correspondence_protocol.md and emits the separate #668 byte-accounted concern tracker plus placeholder response skeleton. It does not emit the reviewer Roadmap, Schema 11, priority/severity, a determination, or a resolution claim. Formal tone alone never activates the variant.

disclosure mode — AI-Usage Disclosure Outcome

Applicable Scenarios:

• Paper is drafted and you need venue-specific disclosure text or a policy action checklist
• Submitting under a covered policy target (ICLR, NeurIPS, Nature, Science, ACL, EMNLP, or a covered medical-publishing target: ICMJE, NEJM, The Lancet, JAMA, BMJ, PLOS, Frontiers, publisher-wide 中华护理杂志社, journal-level 国际眼科杂志)
• Need placement/action guidance for every required manuscript or submission channel

Not Applicable When:

• No paper drafted yet — disclosure is a finishing step (→ full mode first)
• The venue is not in the policy database (confirm the venue's current policy manually)

Expected Output: Default venue path — REQUIRED / ACTION_ONLY / NOT_REQUIRED / UNKNOWN applicability plus typed halt status; policy-anchor path — anchor-specific render Expected Duration: Short Agents Used: formatter agent's standalone disclosure branch, which loads the disclosure protocol before the venue policy database or policy-anchor lookup; it does not run normal Phase 7 formatting

rebuttal-audit mode — Rebuttal-Draft QA

Applicable Scenarios:

• You already wrote a rebuttal/response-to-reviewers draft and want it checked before sending
• Need a per-comment coverage table (which reviewer concerns the draft addresses, partially addresses, or misses)
• Want risk flags for tone (too combative), unsupported claims, or a response that misreads the reviewer's point

Not Applicable When:

• You have reviewer comments but have not written a response yet (→ revision-coach mode, which generates a skeleton)
• The manuscript itself needs revising (→ revision mode)

Input gate: requires BOTH (a) the reviewer comments / decision letter AND (b) an existing rebuttal draft. Comments only → route to revision-coach. If intent is ambiguous, clarify rather than guess.

Expected Output: Advisory QA report — per-comment coverage + gap list + risk flags. Generates no new response. Expected Duration: Short Agents Used: revision_coach_agent's comment-parsing capability, run standalone (advisory)

Integrity boundary: a standalone invocation runs outside the pipeline, so rebuttal-audit does not emit a Schema 11 ledger, does not write the Material Passport, and does not mark anything ready_to_submit or verified. The output is advisory QA only.

Paths from deep-research

deep-research completed
  │
  ├── deep-research (full mode) outputs:
  │   RQ Brief + Methodology Blueprint + Annotated Bibliography + Synthesis Report
  │   │
  │   ├── Want to write the paper directly ──→ academic-paper (full mode)
  │   │   intake_agent auto-detects materials, skips redundant questions
  │   │
  │   └── Want to plan before writing ──→ academic-paper (plan mode)
  │       socratic_mentor leverages existing materials to accelerate guidance
  │
  └── deep-research (socratic mode) outputs:
      INSIGHT Collection + Synthesis Report
      │
      ├── INSIGHTs are sufficiently clear ──→ academic-paper (full mode)
      │
      └── Need more guidance ──→ academic-paper (plan mode)
          socratic_mentor continues deepening from INSIGHTs

Connecting to academic-paper-reviewer

academic-paper completed
  │
  ├── full mode produces complete paper ──→ academic-paper-reviewer (full / guided)
  │   Complete peer review + revision suggestions
  │
  ├── plan mode produces Chapter Plan ──→ academic-paper-reviewer (guided)
  │   Review the plan's feasibility and completeness
  │
  └── reviewer feedback ──→ academic-paper (revision mode)
      Revise paper based on review comments

Common Misselection Scenarios

Quick Decision Table

Plan to Full Mode Conversion Protocol

When a user completes plan mode and wants to proceed to full mode for actual paper writing:

Conversion Checklist

Quality Gate

Before conversion, ALL of the following must be true:

• Every chapter in the Chapter Plan has at least 1 argument sketch rated adequate or above
• The overall paper structure maps to a recognized pattern in paper_structure_patterns.md
• At least 5 potential references have been identified (seeds for literature_strategist)
• The research question is finalized (not still evolving from Socratic dialogue)

What Gets Discarded

• Conversational filler from Socratic dialogue (greetings, confirmations, repetitions)
• Tentative ideas explicitly marked as "maybe" or "not sure" by the user
• Plan mode's iterative drafts (only the final version of each chapter plan carries over)

Trigger-to-Mode Mapping Examples

"Write a paper on SDGs in HEI"           -> full
"Give me a paper outline for..."         -> outline-only
"Revise this paper based on feedback"    -> revision
"Write an abstract for this paper"       -> abstract-only
"Do a literature review on..."           -> lit-review
"Convert this paper to LaTeX"            -> format-convert
"Convert citations to IEEE"              -> format-convert
"Check the citations in this paper"      -> citation-check
"guide my paper"                         -> plan
"help me plan my paper"                  -> plan
"I got reviewer comments"               -> revision-coach
"parse these reviews"                    -> revision-coach
"help me with my revision"              -> revision-coach
"should we push back on reviewer 2"     -> revision-coach
"conference rebuttal" / "grant response" -> revision-coach
"track these committee comments"          -> revision-coach committee-correspondence variant (only with explicit real-source identity)
"audit my rebuttal draft"               -> rebuttal-audit (needs comments + an existing draft)
"did I miss any reviewer comment"       -> rebuttal-audit
"AI disclosure for Nature"              -> disclosure
"generate an AI usage statement"        -> disclosure