@bohuyeshan/openagent-labforge-core 3.11.1 → 3.11.3

package/generated/skills-bundles/full/skills/research/document-authoring/auto-claude__paper-write/SKILL.md

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+---
+name: "auto-claude/paper-write"
+description: "Draft LaTeX paper section by section from an outline. Use when user says \"写论文\", \"write paper\", \"draft LaTeX\", \"开始写\", or wants to generate LaTeX content from a paper plan."
+argument-hint: ["venue-or-section"]
+allowed-tools: "Bash(*), Read, Write, Edit, Grep, Glob, Agent, WebSearch, WebFetch, mcp__codex__codex, mcp__codex__codex-reply"
+metadata:
+  category: "research/document-authoring"
+---
+# Paper Write: Section-by-Section LaTeX Generation
+
+Draft a LaTeX paper based on: **$ARGUMENTS**
+
+## Constants
+
+- **REVIEWER_MODEL = `gpt-5.4`** — Model used via Codex MCP for section review. Must be an OpenAI model.
+- **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.
+
+## 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:**
+```latex
+\documentclass{article}
+\usepackage{iclr2026_conference,times}
+% \iclrfinalcopy  % Uncomment for camera-ready
+```
+
+**NeurIPS:**
+```latex
+\documentclass{article}
+\usepackage[preprint]{neurips_2025}
+% \usepackage[final]{neurips_2025}  % Camera-ready
+```
+
+**ICML:**
+```latex
+\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):**
+```latex
+\author{Anonymous Authors}
+```
+
+### Step 2: Generate math_commands.tex
+
+Create shared math macros based on the paper's notation:
+
+```latex
+% 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, 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)
+
+**Automated bib cleaning** — use this Python pattern to extract only cited entries:
+
+```python
+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 GPT-5.4 xhigh:
+
+```
+mcp__codex__codex:
+  model: gpt-5.4
+  config: {"model_reasoning_effort": "xhigh"}
+  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]
+```
+
+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 `\input`ed by `main.tex`
+- [ ] **Section files match main.tex** — file numbering and `\input` paths are consistent
+
+## Key Rules
+
+- **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 `\cite`d
+- **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](https://github.com/Master-cai/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](https://github.com/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](https://github.com/Master-cai/Research-Paper-Writing-Skills) (CCF award-winning methodology). Citation verification from [claude-scholar](https://github.com/Galaxy-Dawn/claude-scholar) and [Imbad0202/academic-research-skills](https://github.com/Imbad0202/academic-research-skills). De-AI polish from [kgraph57/paper-writer-skill](https://github.com/kgraph57/paper-writer-skill). Backup mechanism from [baoyu-skills](https://github.com/jimliu/baoyu-skills).

package/generated/skills-bundles/full/skills/research/document-authoring/auto-claude__paper-write/templates/iclr2026.tex

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+% ICLR 2026 Paper Template
+% Generated by ARIS paper-write skill
+% Style file: download from https://iclr.cc/Conferences/2026/CallForPapers
+
+\documentclass{article}
+\usepackage{iclr2026_conference,times}
+
+% Math
+\usepackage{amsmath,amssymb,amsfonts,amsthm,mathtools}
+
+% Typography
+\usepackage[utf8]{inputenc}
+\usepackage[T1]{fontenc}
+\usepackage{hyperref}
+\usepackage{url}
+\usepackage{booktabs}
+\usepackage{nicefrac}
+\usepackage{microtype}
+\usepackage{xcolor}
+\usepackage{graphicx}
+\usepackage{subcaption}
+\usepackage{multirow}
+\usepackage{algorithm}
+\usepackage{algorithmic}
+
+% cleveref must be loaded AFTER hyperref
+\usepackage[capitalize,noabbrev]{cleveref}
+
+% Theorems
+\theoremstyle{plain}
+\newtheorem{theorem}{Theorem}[section]
+\newtheorem{proposition}[theorem]{Proposition}
+\newtheorem{lemma}[theorem]{Lemma}
+\newtheorem{corollary}[theorem]{Corollary}
+\theoremstyle{definition}
+\newtheorem{definition}[theorem]{Definition}
+\newtheorem{assumption}[theorem]{Assumption}
+\theoremstyle{remark}
+\newtheorem{remark}[theorem]{Remark}
+
+% cleveref names for custom theorem types
+\crefname{assumption}{Assumption}{Assumptions}
+\Crefname{assumption}{Assumption}{Assumptions}
+
+% Shared math commands
+\input{math_commands}
+
+% === ANONYMOUS SUBMISSION ===
+% Comment out \iclrfinalcopy for anonymous submission
+% Uncomment for camera-ready version
+% \iclrfinalcopy
+
+\title{Paper Title Here}
+
+% Authors — leave anonymous for submission
+% Uncomment and fill for camera-ready
+% \author{
+%   Author Name \\
+%   Affiliation \\
+%   \texttt{email@example.com}
+% }
+
+\begin{document}
+
+\maketitle
+
+\begin{abstract}
+\input{sections/0_abstract}
+\end{abstract}
+
+\input{sections/1_introduction}
+\input{sections/2_related_work}
+\input{sections/3_method}
+\input{sections/4_experiments}
+\input{sections/5_conclusion}
+
+\bibliography{references}
+\bibliographystyle{iclr2026_conference}
+
+\newpage
+\appendix
+\input{sections/A_appendix}
+
+\end{document}

package/generated/skills-bundles/full/skills/research/document-authoring/auto-claude__paper-write/templates/icml2025.tex

@@ -0,0 +1,87 @@
+% ICML 2025 Paper Template
+% Generated by ARIS paper-write skill
+% Style file: download from https://icml.cc/Conferences/2025/CallForPapers
+
+\documentclass[accepted]{icml2025}
+% For submission: remove [accepted]
+
+% Math
+\usepackage{amsmath,amssymb,amsfonts,amsthm,mathtools}
+
+% Typography
+\usepackage[utf8]{inputenc}
+\usepackage[T1]{fontenc}
+\usepackage{hyperref}
+\usepackage{url}
+\usepackage{booktabs}
+\usepackage{nicefrac}
+\usepackage{microtype}
+\usepackage{xcolor}
+\usepackage{graphicx}
+\usepackage{subcaption}
+\usepackage{multirow}
+\usepackage{algorithm}
+\usepackage{algorithmic}
+
+% cleveref must be loaded AFTER hyperref
+\usepackage[capitalize,noabbrev]{cleveref}
+
+% Theorems
+\theoremstyle{plain}
+\newtheorem{theorem}{Theorem}[section]
+\newtheorem{proposition}[theorem]{Proposition}
+\newtheorem{lemma}[theorem]{Lemma}
+\newtheorem{corollary}[theorem]{Corollary}
+\theoremstyle{definition}
+\newtheorem{definition}[theorem]{Definition}
+\newtheorem{assumption}[theorem]{Assumption}
+\theoremstyle{remark}
+\newtheorem{remark}[theorem]{Remark}
+
+% cleveref names for custom theorem types
+\crefname{assumption}{Assumption}{Assumptions}
+\Crefname{assumption}{Assumption}{Assumptions}
+
+% Shared math commands
+\input{math_commands}
+
+\icmltitlerunning{Paper Title Here}
+
+\begin{document}
+
+\twocolumn[
+\icmltitle{Paper Title Here}
+
+% Authors — leave anonymous for submission
+% Uncomment and fill for camera-ready
+% \icmlsetsymbol{equal}{*}
+% \begin{icmlauthorlist}
+% \icmlauthor{Author Name}{inst1}
+% \end{icmlauthorlist}
+% \icmlaffiliation{inst1}{Affiliation}
+% \icmlcorrespondingauthor{Author Name}{email@example.com}
+
+\vskip 0.3in
+]
+
+\printAffiliationsAndNotice{}
+
+\begin{abstract}
+\input{sections/0_abstract}
+\end{abstract}
+
+\input{sections/1_introduction}
+\input{sections/2_related_work}
+\input{sections/3_method}
+\input{sections/4_experiments}
+\input{sections/5_conclusion}
+
+\bibliography{references}
+\bibliographystyle{icml2025}
+
+\newpage
+\appendix
+\onecolumn
+\input{sections/A_appendix}
+
+\end{document}

package/generated/skills-bundles/full/skills/research/document-authoring/auto-claude__paper-write/templates/math_commands.tex

@@ -0,0 +1,48 @@
+% math_commands.tex — Shared notation for ML papers
+% Generated by ARIS paper-write skill
+% Add paper-specific notation below the common commands
+
+% === Common Math Shortcuts ===
+\newcommand{\R}{\mathbb{R}}
+\newcommand{\Z}{\mathbb{Z}}
+\newcommand{\N}{\mathbb{N}}
+\newcommand{\E}{\mathbb{E}}
+\newcommand{\Var}{\mathrm{Var}}
+\newcommand{\Cov}{\mathrm{Cov}}
+
+% Probability
+\newcommand{\Prob}{\mathbb{P}}
+\newcommand{\KL}{\mathrm{KL}}
+
+% Operators
+\DeclareMathOperator*{\argmin}{arg\,min}
+\DeclareMathOperator*{\argmax}{arg\,max}
+\DeclareMathOperator{\tr}{tr}
+\DeclareMathOperator{\diag}{diag}
+\DeclareMathOperator{\softmax}{softmax}
+
+% Vectors and matrices (bold)
+\newcommand{\vx}{\mathbf{x}}
+\newcommand{\vy}{\mathbf{y}}
+\newcommand{\vz}{\mathbf{z}}
+\newcommand{\vw}{\mathbf{w}}
+\newcommand{\vtheta}{\boldsymbol{\theta}}
+\newcommand{\mA}{\mathbf{A}}
+\newcommand{\mI}{\mathbf{I}}
+
+% Norms
+\newcommand{\norm}[1]{\left\|#1\right\|}
+\newcommand{\abs}[1]{\left|#1\right|}
+\newcommand{\inner}[2]{\langle #1, #2 \rangle}
+
+% Distributions
+\newcommand{\Normal}{\mathcal{N}}
+
+% Sets
+\newcommand{\cX}{\mathcal{X}}
+\newcommand{\cY}{\mathcal{Y}}
+\newcommand{\cD}{\mathcal{D}}
+\newcommand{\cL}{\mathcal{L}}
+
+% === Paper-Specific Notation ===
+% Add your paper's custom notation below this line

package/generated/skills-bundles/full/skills/research/document-authoring/auto-claude__paper-write/templates/neurips2025.tex

@@ -0,0 +1,80 @@
+% NeurIPS 2025 Paper Template
+% Generated by ARIS paper-write skill
+% Style file: download from https://neurips.cc/Conferences/2025/CallForPapers
+
+\documentclass{article}
+\usepackage[preprint]{neurips_2025}
+% For camera-ready: \usepackage[final]{neurips_2025}
+
+% Math
+\usepackage{amsmath,amssymb,amsfonts,amsthm,mathtools}
+
+% Typography
+\usepackage[utf8]{inputenc}
+\usepackage[T1]{fontenc}
+\usepackage{hyperref}
+\usepackage{url}
+\usepackage{booktabs}
+\usepackage{nicefrac}
+\usepackage{microtype}
+\usepackage{xcolor}
+\usepackage{graphicx}
+\usepackage{subcaption}
+\usepackage{multirow}
+\usepackage{algorithm}
+\usepackage{algorithmic}
+
+% cleveref must be loaded AFTER hyperref
+\usepackage[capitalize,noabbrev]{cleveref}
+
+% Theorems
+\theoremstyle{plain}
+\newtheorem{theorem}{Theorem}[section]
+\newtheorem{proposition}[theorem]{Proposition}
+\newtheorem{lemma}[theorem]{Lemma}
+\newtheorem{corollary}[theorem]{Corollary}
+\theoremstyle{definition}
+\newtheorem{definition}[theorem]{Definition}
+\newtheorem{assumption}[theorem]{Assumption}
+\theoremstyle{remark}
+\newtheorem{remark}[theorem]{Remark}
+
+% cleveref names for custom theorem types
+\crefname{assumption}{Assumption}{Assumptions}
+\Crefname{assumption}{Assumption}{Assumptions}
+
+% Shared math commands
+\input{math_commands}
+
+\title{Paper Title Here}
+
+% Authors — leave anonymous for submission
+% Uncomment and fill for camera-ready
+% \author{
+%   Author Name \\
+%   Affiliation \\
+%   \texttt{email@example.com}
+% }
+
+\begin{document}
+
+\maketitle
+
+\begin{abstract}
+\input{sections/0_abstract}
+\end{abstract}
+
+\input{sections/1_introduction}
+\input{sections/2_related_work}
+\input{sections/3_method}
+\input{sections/4_experiments}
+\input{sections/5_conclusion}
+
+\bibliography{references}
+\bibliographystyle{plainnat}
+
+\newpage
+\appendix
+\input{sections/A_appendix}
+
+\end{document}