Research Paper Writer
Draft an original research article from the user's actual completed work: their experiments, data, figures, and references. Two disciplines govern everything:
- Results-first. Methods and Results are written from materials the user
supplied (result tables, metrics dumps, figures, code notebooks). Anything
not supplied is flagged
[PENDING: …]— never filled with a plausible number. A fabricated result is worse than a fabricated citation: it is data fraud, not a style slip. - Citation integrity (this repository's shared five-rule core, instantiated
for author-year/numeric journal styles — see
references/CITATION_INTEGRITY.md):
every reference verified to exist before it enters the bibliography;
[UNVERIFIED]flags for the rest; no invented DOIs, authors, or numbers.
Scenario routing
| Study type | Structure | Binding checklist (Phase 1) |
|---|---|---|
| Imaging-AI method / model paper | IMRaD, methods-forward | CLAIM 2024 |
| Prediction / risk model | IMRaD + model development emphasis | TRIPOD+AI |
| Diagnostic accuracy study | IMRaD, test-vs-reference emphasis | STARD 2015 (可与 CLAIM 并行声明) |
| Observational / cohort study | IMRaD, methods after hypotheses | STROBE |
| (Rare here) trial, systematic review | Out of scope — say so and stop | CONSORT / PRISMA via the right skill |
| CS/eng venue paper (CVPR/NeurIPS style) | Abstract → Intro → Related Work → Method → Experiments → Discussion → Conclusion | venue's own checklist/reproducibility statement |
Read references/STRUCTURE_GUIDE.md for section-by-section construction and references/REPORTING_CHECKLISTS.md for what the binding checklist actually requires.
Phase 1: Intake (record, don't improvise)
Use AskUserQuestion to collect:
- Study type + target venue/journal — routes structure and checklist (above).
- Materials in hand — result tables/CSVs, metric numbers, figures, prior drafts/notes, code notebook. If the user has no results yet, stop: this skill writes papers about completed work, not imagined work (that is research-proposal territory).
- References pool — user's Zotero/bib, or run the lit-search skill for
a defensible related-work corpus (its
references.bibdrops straight in). - Language and length — en/zh; word limit from the venue's guide.
Record the intake as a short paper_plan.md (study type, venue, checklist,
materials list, citation style). Headless runs: record inline and continue.
Phase 2: Materials audit (before any prose)
Inventory every number that will appear in Results:
- Each metric → its source artifact (file, table, cell). Untraceable numbers
are
[PENDING], and the user is told before drafting starts. - Each figure → real file or a
[PENDING: figure]placeholder with a content description. Redrawing/schematics follow the same honesty rules as scholar-slides (label what is not data). - This inventory becomes
results_ledger.csv(see references/QUALITY_CHECKLIST.md) — the paper-side sibling of the review skill's claim ledger: one row per load-bearing number,claim_id → section → claim_text → value（列名以 references/QUALITY_CHECKLIST.md 的 schema 表头为准）.
Phase 3: Outline + approval (red line)
Section skeleton per references/STRUCTURE_GUIDE.md, with per-section bullet content mapped to Phase 2 materials. Present the outline and wait for explicit approval (same rules as research-proposal: "你看着办" → state assumptions, re-present, proceed).
Phase 4: Write-with-verify (per section)
Draft section by section into a single working file paper_draft.md (the
Phase 5 gates grep exactly that filename — a renamed draft makes them scan an
empty file and report a false zero-hit); after each section, before starting the next:
- Every citation in the section is from the verified pool (rules: references/CITATION_INTEGRITY.md).
- Every number in the section reconciles against
results_ledger.csv. - Self-check against the AI-tell list and style rules (references/WRITING_STYLE.md) — the Phase 5 grep gates make these checkable, not aspirational.
- Tense/register per section (Methods: past, what was done; Results: past, what was found — no interpretation; Discussion: present, what it means).
Phase 5: Gates + reporting checklist + submission pack
Mechanical gates (paste command output as evidence):
bash# 1) Placeholder gate — zero hits (or disclosed [UNVERIFIED]/[PENDING]) grep -nE "xxx|XXXX|\[TBD\]|\[PENDING|\[UNVERIFIED[^]]*\]|10\.xxxx|doi:10\.[a-z]+/x" paper_draft.md # 2) AI-tell gate — zero hits grep -nEi "over the past ((few|several|two|three) )?(decades?|years)|in recent years,|it is worth noting|plays a (crucial|pivotal) role|has garnered significant attention|delves into|a testament to|众所周知|近年来，?随着|日益受到(广泛)?关注" paper_draft.md
Then: work through the binding reporting checklist item by item (references/REPORTING_CHECKLISTS.md); assemble the submission pack — title page, abstract in the venue's format, keywords, cover letter, author contributions (CRediT) / conflicts (references/SUBMISSION_PACK.md).
Reference Files
Read only the file for the phase you are in.
| File | Read when |
|---|---|
| references/STRUCTURE_GUIDE.md | Phase 3 — IMRaD construction per study type |
| references/CITATION_INTEGRITY.md | Phase 2/4/5 — the five rules + Phase 5 reconciliation gate |
| references/REPORTING_CHECKLISTS.md | Phase 1/5 — checklist selection + item-by-item pass |
| references/WRITING_STYLE.md | Phase 4 — register, tense, cohesion, AI-tells |
| references/SUBMISSION_PACK.md | Phase 5 — abstract/cover letter/reproducibility statement |
| references/QUALITY_CHECKLIST.md | Phase 2/5 — Phase 2 reads the ledger schema; Phase 5 runs the gates |
| assets/paper_scaffold_en.md | Phase 4 — English skeleton |
| assets/paper_scaffold_zh.md | Phase 4 — 中文骨架 |
learnings：复盘先于重写
修改 references 或 scaffold 之前先扫 learnings/；返工或发现
自相矛盾后追加一篇，日期命名（格式见 lit-search/learnings/）。
Error handling
- No results materials — stop and say so; suggest research-proposal if the work is still planned.
- A claimed number can't be traced —
[PENDING]+ explicit disclosure, never a placeholder that looks real. - Reference can't be verified —
[UNVERIFIED]+ disclosure (never dropped silently, never fabricated). - Venue requires a checklist this skill doesn't carry — say so, point to the
official source, and record it as a manual gate in
paper_plan.md.
