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Skillsresearch-paper

research-paper

Writing & research

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Updated 10-16 06:24

About this skill

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:

  1. 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.
  2. 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 (can be declared in parallel with CLAIM)
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:

  1. Study type + target venue/journal — routes structure and checklist (above).
  2. 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).
  3. References pool — user's Zotero/bib, or run the lit-search skill for a defensible related-work corpus (its references.bib drops straight in).
  4. 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(column names follow the references/QUALITY_CHECKLIST.md schema header).

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: "you decide" → 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:

  1. Every citation in the section is from the verified pool (rules: references/CITATION_INTEGRITY.md).
  2. Every number in the section reconciles against results_ledger.csv.
  3. Self-check against the AI-tell list and style rules (references/WRITING_STYLE.md) — the Phase 5 grep gates make these checkable, not aspirational.
  4. 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):

# 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 — Chinese skeleton

learnings: review before rewriting

Before modifying references or scaffold, first scan learnings/; after rework or discovering a self-contradiction, append one entry, named by date (format see 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.