shaun-z/paper-write

Override for Codex users who want Gemini, not a second Codex agent, to act as the reviewer. Install this package after skills/skills-codex/*.

Paper Write: Section-by-Section LaTeX Generation

Draft a LaTeX paper based on: $ARGUMENTS

Constants

• REVIEWER_MODEL = gemini-review — Gemini reviewer invoked through the local gemini-review MCP bridge. Set GEMINI_REVIEW_MODEL if you need a specific Gemini model override.
• TARGET_VENUE = ICLR — Default venue. Supported: ICLR, NeurIPS, ICML. Determines style file and formatting.
• ANONYMOUS = true — If true, use anonymous author block. Set false for camera-ready.
• MAX_PAGES = 9 — Main body page limit. Counts from first page to end of Conclusion section. References and appendix are NOT counted.
• DBLP_BIBTEX = true — Fetch real BibTeX from DBLP/CrossRef instead of LLM-generated entries. Eliminates hallucinated citations. Zero install required. Set false to use legacy behavior (LLM search + [VERIFY] markers).

Inputs

1. PAPER_PLAN.md — outline with claims-evidence matrix, section plan, figure plan (from /paper-plan)
2. NARRATIVE_REPORT.md — the research narrative (primary source of content)
3. Generated figures — PDF/PNG files in figures/ (from /paper-figure)
4. LaTeX includes — figures/latex_includes.tex (from /paper-figure)
5. Bibliography — existing .bib file, or will create one

If no PAPER_PLAN.md exists, ask the user to run /paper-plan first or provide a brief outline.

Templates

Venue-Specific Setup

The skill includes conference templates in templates/. Select based on TARGET_VENUE:

ICLR:

\documentclass{article}
\usepackage{iclr2026_conference,times}
% \iclrfinalcopy  % Uncomment for camera-ready

NeurIPS:

\documentclass{article}
\usepackage[preprint]{neurips_2025}
% \usepackage[final]{neurips_2025}  % Camera-ready

ICML:

\documentclass[accepted]{icml2025}
% Use [accepted] for camera-ready

Project Structure

Generate this file structure:

paper/
├── main.tex                    # master file (includes sections)
├── iclr2026_conference.sty     # or neurips_2025.sty / icml2025.sty
├── math_commands.tex           # shared math macros
├── references.bib              # bibliography (filtered — only cited entries)
├── sections/
│   ├── 0_abstract.tex
│   ├── 1_introduction.tex
│   ├── 2_related_work.tex
│   ├── 3_method.tex            # or preliminaries, setup, etc.
│   ├── 4_experiments.tex
│   ├── 5_conclusion.tex
│   └── A_appendix.tex          # proof details, extra experiments
└── figures/                    # symlink or copy from project figures/

Section files are FLEXIBLE: If the paper plan has 6-8 sections, create corresponding files (e.g., 4_theory.tex, 5_experiments.tex, 6_analysis.tex, 7_conclusion.tex).

Workflow

Step 0: Backup and Clean

If paper/ already exists, back up to paper-backup-{timestamp}/ before overwriting. Never silently destroy existing work.

CRITICAL: Clean stale files. When changing section structure (e.g., 5 sections → 7 sections), delete section files that are no longer referenced by main.tex. Stale files (e.g., old 5_conclusion.tex left behind when conclusion moved to 7_conclusion.tex) cause confusion and waste space.

Step 1: Initialize Project

1. Create paper/ directory
2. Copy venue template from templates/ — the template already includes:
   • All standard packages (amsmath, hyperref, cleveref, booktabs, etc.)
   • Theorem environments with \crefname{assumption} fix
   • Anonymous author block
3. Generate math_commands.tex with paper-specific notation
4. Create section files matching PAPER_PLAN structure

Author block (anonymous mode):

\author{Anonymous Authors}

Step 2: Generate math_commands.tex

Create shared math macros based on the paper's notation:

% math_commands.tex — shared notation
\newcommand{\R}{\mathbb{R}}
\newcommand{\E}{\mathbb{E}}
\DeclareMathOperator*{\argmin}{arg\,min}
\DeclareMathOperator*{\argmax}{arg\,max}
% Add paper-specific notation here

Step 3: Write Each Section

Process sections in order. For each section:

1. Read the plan — what claims, evidence, citations belong here
2. Read NARRATIVE_REPORT.md — extract relevant content, findings, and quantitative results
3. Draft content — write complete LaTeX (not placeholders)
4. Insert figures/tables — use snippets from figures/latex_includes.tex
5. Add citations — use \citep{} / \citet{} (all three venues use natbib)

Section-Specific Guidelines

§0 Abstract:

• Must be self-contained (understandable without reading the paper)
• Structure: problem → approach → key result → implication
• Include one concrete quantitative result
• 150-250 words (check venue limit)
• No citations, no undefined acronyms
• No \begin{abstract} — that's in main.tex

§1 Introduction:

• Open with a compelling hook (1-2 sentences, problem motivation)
• State the gap clearly ("However, ...")
• List contributions as a numbered or bulleted list
• End with a brief roadmap ("The rest of this paper is organized as...")
• Include the main result figure if space allows
• Target: 1.5 pages

§2 Related Work:

• MINIMUM 1 full page (3-4 substantive paragraphs). Short related work sections are a common reviewer complaint.
• Organize by category using \paragraph{Category Name.}
• Each category: 1 paragraph summarizing the line of work + 1-2 sentences positioning this paper
• Do NOT just list papers — synthesize and compare
• End each paragraph with how this paper relates/differs

§3 Method / Preliminaries / Setup:

• Define notation early (reference math_commands.tex)
• Use \begin{definition}, \begin{theorem} environments for formal statements
• For theory papers: include proof sketches of key results in main body, full proofs in appendix
• For theory papers: include a comparison table of prior bounds vs. this paper
• Include algorithm pseudocode if applicable (algorithm2e or algorithmic)
• Target: 1.5-2 pages

§4 Experiments:

• Start with experimental setup (datasets, baselines, metrics, implementation details)
• Main results table/figure first
• Then ablations and analysis
• Every claim from the introduction must have supporting evidence here
• Target: 2.5-3 pages

§5 Conclusion:

• Summarize contributions (NOT copy-paste from intro — rephrase)
• Limitations (be honest — reviewers appreciate this)
• Future work (1-2 concrete directions)
• Ethics statement and reproducibility statement (if venue requires)
• Target: 0.5 pages

Appendix:

• Proof details (full proofs of main-body theorems)
• Additional experiments, ablations
• Implementation details, hyperparameter tables
• Additional visualizations

Step 4: Build Bibliography

CRITICAL: Only include entries that are actually cited in the paper.

1. Scan all \citep{} and \citet{} references in the drafted sections
2. Build a citation key list
3. For each citation key:
   • Check existing .bib files in the project/narrative docs
   • If not found and DBLP_BIBTEX = true, use the verified fetch chain below
   • If not found and DBLP_BIBTEX = false, search arXiv/Scholar for correct BibTeX
   • NEVER fabricate BibTeX entries — mark unknown ones with [VERIFY] comment
4. Write references.bib containing ONLY cited entries (no bloat)

Verified BibTeX Fetch (when DBLP_BIBTEX = true)

Three-step fallback chain — zero install, zero auth, all real BibTeX:

Step A: DBLP (best quality — full venue, pages, editors)

# 1. Search by title + first author
curl -s "https://dblp.org/search/publ/api?q=TITLE+AUTHOR&format=json&h=3"
# 2. Extract DBLP key from result (e.g., conf/nips/VaswaniSPUJGKP17)
# 3. Fetch real BibTeX
curl -s "https://dblp.org/rec/{key}.bib"

Step B: CrossRef DOI (fallback — works for arXiv preprints)

# If paper has a DOI or arXiv ID (arXiv DOI = 10.48550/arXiv.{id})
curl -sLH "Accept: application/x-bibtex" "https://doi.org/{doi}"

Step C: Mark [VERIFY] (last resort) If both DBLP and CrossRef return nothing, mark the entry with % [VERIFY] comment. Do NOT fabricate.

Why this matters: LLM-generated BibTeX frequently hallucinates venue names, page numbers, or even co-authors. DBLP and CrossRef return publisher-verified metadata. Upstream skills (/research-lit, /novelty-check) may mention papers from LLM memory — this fetch chain is the gate that prevents hallucinated citations from entering the final .bib.

Automated bib cleaning — use this Python pattern to extract only cited entries:

import re
# 1. Grep all \citep{...} and \citet{...} from all .tex files
# 2. Extract unique keys (handle multi-cite like \citep{a,b,c})
# 3. Parse the full .bib file, keep only entries whose key is in the cited set
# 4. Write the filtered bib

This prevents bib bloat (e.g., 948 lines → 215 lines in testing).

Citation verification rules (from claude-scholar + Imbad0202):

1. Every BibTeX entry must have: author, title, year, venue/journal
2. Prefer published venue versions over arXiv preprints (if published)
3. Use consistent key format: {firstauthor}{year}{keyword} (e.g., ho2020denoising)
4. Double-check year and venue for every entry
5. Remove duplicate entries (same paper with different keys)

Step 5: De-AI Polish (from kgraph57/paper-writer-skill)

After drafting all sections, scan for common AI writing patterns and fix them:

Content patterns to fix:

• Significance inflation ("groundbreaking", "revolutionary" → use measured language)
• Formulaic transitions ("In this section, we..." → remove or vary)
• Generic conclusions ("This work opens exciting new avenues" → be specific)

Language patterns to fix (watch words):

• Replace: delve, pivotal, landscape, tapestry, underscore, noteworthy, intriguingly
• Remove filler: "It is worth noting that", "Importantly,", "Notably,"
• Avoid rule-of-three lists ("X, Y, and Z" appearing repeatedly)
• Don't start consecutive sentences with "This" or "We"

Step 6: Cross-Review with REVIEWER_MODEL

Send the complete draft to Gemini review:

mcp__gemini-review__review_start:
  prompt: |
    Review this [VENUE] paper draft (main body, excluding appendix).

    Focus on:
    1. Does each claim from the intro have supporting evidence?
    2. Is the writing clear, concise, and free of AI-isms?
    3. Any logical gaps or unclear explanations?
    4. Does it fit within [MAX_PAGES] pages (to end of Conclusion)?
    5. Is related work sufficiently comprehensive (≥1 page)?
    6. For theory papers: are proof sketches adequate?
    7. Are figures/tables clearly described and properly referenced?

    For each issue, specify: severity (CRITICAL/MAJOR/MINOR), location, and fix.

    [paste full draft text]

After this start call, immediately save the returned jobId and poll mcp__gemini-review__review_status with a bounded waitSeconds until done=true. Treat the completed status payload's response as the reviewer output, and save the completed threadId for any follow-up round.

Apply CRITICAL and MAJOR fixes. Document MINOR issues for the user.

Step 7: Reverse Outline Test (from Research-Paper-Writing-Skills)

After drafting all sections:

1. Extract topic sentences — pull the first sentence of every paragraph
2. Read them in sequence — they should form a coherent narrative on their own
3. Check claim coverage — every claim from the Claims-Evidence Matrix must appear
4. Check evidence mapping — every experiment/figure must support a stated claim
5. Fix gaps — if a topic sentence doesn't advance the story, rewrite the paragraph

Step 8: Final Checks

Before declaring done:

• [ ] All \ref{} and \label{} match (no undefined references)
• [ ] All \citep{} / \citet{} have corresponding BibTeX entries
• [ ] No author information in anonymous mode
• [ ] Figure/table numbering is correct
• [ ] Page count within MAX_PAGES (main body to Conclusion end)
• [ ] No TODO/FIXME/XXX markers left in the text
• [ ] No [VERIFY] markers left unchecked
• [ ] Abstract is self-contained (understandable without reading the paper)
• [ ] Title is specific and informative (not generic)
• [ ] Related work is ≥1 full page
• [ ] references.bib contains ONLY cited entries (no bloat)
• [ ] No stale section files — every .tex in sections/ is \inputed by main.tex
• [ ] Section files match main.tex — file numbering and \input paths are consistent

Output Protocols

Follow these shared protocols for all output files:

• Output Versioning Protocol — write timestamped file first, then copy to fixed name
• Output Manifest Protocol — log every output to MANIFEST.md
• Output Language Protocol — respect the project's language setting

Key Rules

• Large file handling: If the Write tool fails due to file size, immediately retry using Bash (cat << 'EOF' > file) to write in chunks. Do NOT ask the user for permission — just do it silently.

• Do NOT generate author names, emails, or affiliations — use anonymous block or placeholder

• Write complete sections, not outlines — the output should be compilable LaTeX

• One file per section — modular structure for easy editing

• Every claim must cite evidence — cross-reference the Claims-Evidence Matrix

• Compile-ready — the output should compile with latexmk without errors (modulo missing figures)

• No over-claiming — use hedging language ("suggests", "indicates") for weak evidence

• Venue style matters — all three venues (ICLR/NeurIPS/ICML) use natbib (\citep/\citet)

• Page limit = main body to Conclusion — references and appendix do NOT count

• Clean bib — references.bib must only contain entries that are actually \cited

• Section count is flexible — match PAPER_PLAN structure, don't force into 5 sections

• Backup before overwrite — never destroy existing paper/ directory without backing up

Writing Quality Reference

Principles from Research-Paper-Writing-Skills:

1. One message per paragraph — each paragraph makes exactly one point
2. Topic sentence first — the first sentence states the paragraph's message
3. Explicit transitions — connect paragraphs with logical connectors
4. Reverse outline test — extract topic sentences; they should form a coherent narrative

De-AI patterns from kgraph57/paper-writer-skill:

5. No AI watch words — delve, pivotal, landscape, tapestry, underscore
6. No significance inflation — groundbreaking, revolutionary, paradigm shift
7. No formulaic structures — vary sentence openings and transitions

Acknowledgements

Writing methodology adapted from Research-Paper-Writing-Skills (CCF award-winning methodology). Citation verification from claude-scholar and Imbad0202/academic-research-skills. De-AI polish from kgraph57/paper-writer-skill. Backup mechanism from baoyu-skills.