@research-copilot/plugin 1.1.17 → 1.1.19

package/dist/skills/paper-write/SKILL.md

@@ -0,0 +1,411 @@
+---
+name: "paper-write"
+description: "Draft LaTeX paper section by section from an outline. Use when user says \\\"\u5199\u8bba\u6587\\\", \\\"write paper\\\", \\\"draft LaTeX\\\", \\\"\u5f00\u59cb\u5199\\\", or wants to generate LaTeX content from a paper plan."
+---
+
+# Paper Write: Section-by-Section LaTeX Generation
+
+Draft a LaTeX paper based on: **$ARGUMENTS**
+
+## Constants
+
+- **REVIEWER_MODEL = `gpt-5.5`** — Model used via a secondary Codex agent for section review. Must be an OpenAI model.
+- **TARGET_VENUE = `ICLR`** — Default venue. Supported: `ICLR`, `NeurIPS`, `ICML`, `CVPR` (also ICCV/ECCV), `ACL` (also EMNLP/NAACL), `AAAI`, `ACM` (ACM MM, SIGIR, KDD, CHI, etc.), `IEEE_JOURNAL` (IEEE Transactions / Letters, e.g., T-PAMI, JSAC, TWC, TCOM, TSP, TIP), `IEEE_CONF` (IEEE conferences, e.g., ICC, GLOBECOM, INFOCOM, ICASSP). Determines style file and formatting.
+- **ANONYMOUS = true** — If true, use anonymous author block. Set `false` for camera-ready. Note: most IEEE venues do NOT use anonymous submission — set `false` for IEEE.
+- **MAX_PAGES = 9** — Main body page limit. For ML conferences: counts from first page to end of Conclusion section, references and appendix NOT counted. **For IEEE venues: references ARE counted toward the page limit.** Typical limits: IEEE journal = no strict limit (but 12-14 pages typical for Transactions, 4-5 for Letters), IEEE conference = 5-8 pages including references.
+- **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.
+
+## Orchestra-Guided Writing Overlay
+
+Keep the existing workflow, file layout, and defaults. Use the shared references below only when they improve writing quality:
+
+- Read `../shared-references/writing-principles.md` before drafting the Abstract, Introduction, Related Work, or when prose feels generic
+- Read `../shared-references/venue-checklists.md` during the final write-up and submission-readiness pass
+- Read `../shared-references/citation-discipline.md` only when the built-in DBLP/CrossRef workflow is insufficient
+
+These references are support material, not extra workflow phases.
+
+## 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
+```
+
+**IEEE Journal** (Transactions, Letters):
+```latex
+\documentclass[journal]{IEEEtran}
+\usepackage{cite}  % IEEE uses \cite{}, NOT natbib
+% Author block uses \author{Name~\IEEEmembership{Member,~IEEE}}
+```
+
+**IEEE Conference** (ICC, GLOBECOM, INFOCOM, ICASSP, etc.):
+```latex
+\documentclass[conference]{IEEEtran}
+\usepackage{cite}  % IEEE uses \cite{}, NOT natbib
+% Author block uses \IEEEauthorblockN / \IEEEauthorblockA
+```
+
+### Project Structure
+
+Generate this file structure:
+
+```
+paper/
+├── main.tex                    # master file (includes sections)
+├── iclr2026_conference.sty     # or neurips_2025.sty / icml2025.sty / IEEEtran.cls + IEEEtran.bst
+├── 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** — for ML conferences (ICLR/NeurIPS/ICML/CVPR/ACL/AAAI): use `\citep{}` / `\citet{}` (natbib). **For IEEE venues**: use `\cite{}` (numeric style via `cite` package). Never mix natbib and cite commands.
+
+Before drafting the front matter, re-read the one-sentence contribution from `PAPER_PLAN.md`. The Abstract and Introduction should make that takeaway obvious before the reader reaches the full method.
+
+#### Section-Specific Guidelines
+
+**§0 Abstract:**
+- Use the 5-part flow from `../shared-references/writing-principles.md`: what, why hard, how, evidence, strongest result
+- 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 3.5: Theory Paper Consistency Pass (theory papers only)
+
+Run this pass after drafting all sections and before building the bibliography.
+
+Trigger it when `PAPER_PLAN.md` labels the paper as theory/analysis, or when the drafted sections contain five or more formal result environments (`theorem`, `lemma`, `proposition`, or `corollary`).
+
+**Proof source search:** search the workspace for standalone full-proof sources whose names or contents indicate a canonical proof version (`proof`, `appendix`, `full`, `complete`, `supplement`, `supplementary`). If one exists, ask:
+
+`Inline full proofs from {file}? [Y/n]`
+
+Default to `Y`. If accepted:
+
+- import the full theorem/lemma statement plus proof block into the appendix source;
+- use the main-body theorem statement as the canonical public statement;
+- do not leave placeholders such as "see supplementary proof document" or "proof omitted for brevity";
+- preserve theorem labels, equation labels, and proof structure exactly;
+- keep main-body proof sketches short, but never let the appendix be sketch-only when a full proof source exists.
+
+**Restatement audit:** compare every theorem/lemma/proposition statement restated in the appendix against the main-body version. Audit statements, hypotheses, case splits, quantifiers, domains, notation, variable names, and terminology for defined objects. Resolve all mismatches before Step 4.
+
+### 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)**
+```bash
+# 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)**
+```bash
+# 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`.
+
+If the DBLP/CrossRef flow is not enough, load `../shared-references/citation-discipline.md` for stricter fallback rules before adding placeholders.
+
+**Automated bib cleaning** — use this Python pattern to extract only cited entries:
+
+```python
+import re
+# 1. Grep all \citep{...}, \citet{...}, and \cite{...} from all .tex files
+# 2. Extract unique keys (handle multi-cite like \citep{a,b,c} or \cite{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: Scientific Writing Quality Pass (5 audit passes)
+
+After drafting all sections, run five sequential audit passes. De-AI polish is included as one part of this quality pass, not a replacement for it.
+
+**Pass 1: Clutter Extraction** — strip sentences to their cleanest components, remove filler, and remove AI-isms.
+
+**Pass 2: Active Voice and Verb Vitality** — identify who did what, convert unnecessary passive voice, and resurrect smothered verbs.
+
+**Pass 3: Sentence Architecture** — flag sentences over 40 words, keep subject and verb close, put familiar context first and new information later, and ensure each paragraph does one job.
+
+**Pass 4: Keyword Consistency** — apply the Banana Rule: do not rename defined technical terms just to avoid repetition. If Methods defines a group, variable, or technique name, Results, Discussion, tables, and captions must use the same term.
+
+**Pass 5: Numerical and Citation Integrity** — check sample sizes, percentages, significant figures, figure/table values, and whether citations support the claims they are attached to.
+
+After drafting all sections, scan for common AI writing patterns and fix them:
+
+First apply the sentence-level clarity rules from `../shared-references/writing-principles.md`:
+
+- keep subject and verb close together
+- put familiar context first and new information later
+- place the most important information near the end of the sentence
+- let each paragraph do one job
+- use verbs for actions instead of nominalized nouns
+
+**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-5.5 xhigh:
+
+```
+spawn_agent:
+  model: gpt-5.5
+  reasoning_effort: xhigh
+  message: |
+    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 citation commands (`\citep{}`/`\citet{}` for ML conferences, `\cite{}` for IEEE) 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
+- [ ] Venue-specific required sections/checklists satisfied (read `../shared-references/venue-checklists.md` if needed)
+- [ ] A skim reader can recover the main claim from the title, abstract, introduction, and Figure 1/captions
+
+## 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** — ML conferences (ICLR/NeurIPS/ICML) use `natbib` (`\citep`/`\citet`); **IEEE venues use `cite` package (`\cite{}`, numeric)**. Never mix.
+- **Page limit rules differ by venue** — ML conferences: main body to Conclusion, references/appendix NOT counted. **IEEE: references ARE counted toward the page limit.**
+- **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
+- **Front-load the contribution** — do not hide the payoff until the experiments or appendix
+
+## Writing Quality Reference
+
+- `../shared-references/writing-principles.md` — story framing, abstract/introduction patterns, sentence-level clarity, reviewer reading order
+- `../shared-references/venue-checklists.md` — ICLR/NeurIPS/ICML/IEEE submission requirements to check before declaring done
+- `../shared-references/citation-discipline.md` — stricter fallback for ambiguous citations
+
+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).