Paper Writing

Override inline: /paper-writing "NARRATIVE_REPORT.md" — venue: NeurIPS, illustration: gemini, human checkpoint: true IEEE example: /paper-writing "NARRATIVE_REPORT.md" — venue: IEEE_JOURNAL

Inputs

This pipeline accepts one of:

1. NARRATIVE_REPORT.md (best) — structured research narrative with claims, experiments, results, figures
2. Research direction + experiment results — the skill will help draft the narrative first
3. Existing PAPER_PLAN.md — skip Phase 1, start from Phase 2

The more detailed the input (especially figure descriptions and quantitative results), the better the output.

Pipeline

Phase 1: Paper Plan

Invoke /paper-plan to create the structural outline:

/paper-plan "$ARGUMENTS"

What this does:

• Parse NARRATIVE_REPORT.md for claims, evidence, and figure descriptions
• Build a Claims-Evidence Matrix — every claim maps to evidence, every experiment supports a claim
• Design section structure (5-8 sections depending on paper type)
• Plan figure/table placement with data sources
• Scaffold citation structure
• GPT-5.4 reviews the plan for completeness

Output: PAPER_PLAN.md with section plan, figure plan, citation scaffolding.

Checkpoint: Present the plan summary to the user.

📐 Paper plan complete:
- Title: [proposed title]
- Sections: [N] ([list])
- Figures: [N] auto-generated + [M] manual
- Target: [VENUE], [PAGE_LIMIT] pages

Shall I proceed with figure generation?

• User approves (or AUTO_PROCEED=true) → proceed to Phase 2.
• User requests changes → adjust plan and re-present.

Phase 2: Figure Generation

Invoke /paper-figure to generate data-driven plots and tables:

/paper-figure "PAPER_PLAN.md"

What this does:

• Read figure plan from PAPER_PLAN.md
• Generate matplotlib/seaborn plots from JSON/CSV data
• Generate LaTeX comparison tables
• Create figures/latex_includes.tex for easy insertion
• GPT-5.4 reviews figure quality and captions

Output: figures/ directory with PDFs, generation scripts, and LaTeX snippets.

Scope: paper-figure covers data plots and comparison tables. Architecture diagrams, pipeline figures, and method illustrations are handled in Phase 2b below.

Phase 2b: Architecture & Illustration Generation

Skip this step entirely if illustration: false.

If the paper plan includes architecture diagrams, pipeline figures, audit cascades, or method illustrations, invoke the appropriate generator based on the illustration parameter:

When illustration: figurespec (default) — invoke /figure-spec:

/figure-spec "[architecture/workflow description from PAPER_PLAN.md]"

• Deterministic JSON → SVG vector rendering (editable, reproducible)
• Best for: system architecture, workflow pipelines, audit cascades, layered topology
• Output: figures/*.svg + figures/*.pdf (via rsvg-convert) + figures/specs/*.json
• No external API, runs fully local

When illustration: gemini — invoke /paper-illustration:

/paper-illustration "[method description from PAPER_PLAN.md or NARRATIVE_REPORT.md]"

• Claude plans → Gemini optimizes → Nano Banana Pro renders → Claude reviews (score ≥ 9)
• Best for: qualitative method illustrations, natural-style diagrams, result grids
• Output: figures/ai_generated/*.png
• Requires GEMINI_API_KEY environment variable

When illustration: mermaid — invoke /mermaid-diagram:

/mermaid-diagram "[method description from PAPER_PLAN.md]"

• Generates Mermaid syntax diagrams (flowchart, sequence, class, state, etc.)
• Best for: lightweight flowcharts, state machines, simple sequence diagrams
• Output: figures/*.mmd + figures/*.png
• Free, no API key needed

When illustration: false — skip entirely. All non-data figures must be created manually (draw.io, Figma, TikZ) and placed in figures/ before Phase 3.

Choosing the right mode:

• Formal architecture / workflow / topology figures → figurespec (default)
• Method concept illustrations with natural style → gemini
• Quick flowchart / state machine → mermaid
• Full manual control → false

These are complementary, not mutually exclusive: you can run multiple generators for different figures in the same paper by re-invoking with different illustration overrides.

Checkpoint: List generated vs manual figures.

📊 Figures complete:
- Data plots (auto, Phase 2): [list]
- Architecture/illustrations (auto, Phase 2b, mode=<illustration>): [list]
- Manual (need your input): [list]
- LaTeX snippets: figures/latex_includes.tex

[If manual figures needed]: Please add them to figures/ before I proceed.
[If all auto]: Shall I proceed with LaTeX writing?

Phase 3: LaTeX Writing

Invoke /paper-write to generate section-by-section LaTeX:

/paper-write "PAPER_PLAN.md"

What this does:

• Write each section following the plan, with proper LaTeX formatting
• Insert figure/table references from figures/latex_includes.tex
• Build references.bib from citation scaffolding
• Clean stale files from previous section structures
• Automated bib cleaning (remove uncited entries)
• De-AI polish (remove "delve", "pivotal", "landscape"...)
• GPT-5.4 reviews each section for quality

Output: paper/ directory with main.tex, sections/*.tex, references.bib, math_commands.tex.

Checkpoint: Report section completion.

✍️ LaTeX writing complete:
- Sections: [N] written ([list])
- Citations: [N] unique keys in references.bib
- Stale files cleaned: [list, if any]

Shall I proceed with compilation?

Phase 4: Compilation

Invoke /paper-compile to build the PDF:

/paper-compile "paper/"

What this does:

• latexmk -pdf with automatic multi-pass compilation
• Auto-fix common errors (missing packages, undefined refs, BibTeX syntax)
• Up to 3 compilation attempts
• Post-compilation checks: undefined refs, page count, font embedding
• Precise page verification via pdftotext
• Stale file detection

Output: paper/main.pdf

Checkpoint: Report compilation results.

🔨 Compilation complete:
- Status: SUCCESS
- Pages: [X] (main body) + [Y] (references) + [Z] (appendix)
- Within page limit: YES/NO
- Undefined references: 0
- Undefined citations: 0

Shall I proceed with the improvement loop?

Phase 4.5: Proof Verification (theory papers only)

Skip this phase if the paper contains no theorems, lemmas, or proofs.

if paper contains \begin{theorem} or \begin{lemma} or \begin{proof}:
    Run /proof-checker "paper/"
    This invokes GPT-5.4 xhigh to:
    - Verify all proof steps (hypothesis discharge, interchange justification, etc.)
    - Check for logic gaps, quantifier errors, missing domination conditions
    - Attempt counterexamples on key lemmas
    - Generate PROOF_AUDIT.md with issue list + severity

    If FATAL or CRITICAL issues found:
        Fix before proceeding to improvement loop
    If only MAJOR/MINOR:
        Proceed, improvement loop may address remaining issues