Agent-Skills.md

Agent Skills: Paper Audit Skill v5.1

Deep-review-first audit for Chinese and English academic papers across LaTeX, Typst, and PDF formats. Use whenever the user wants reviewer-style paper critique, pre-submission readiness checks, pass/fail gate decisions, structured revision roadmaps, journal-style peer review reports, or re-audits of revised manuscripts. Trigger even if the user only says "review my paper", "check if this is ready to submit", "audit this PDF", "simulate peer review", "write a SCI review report", "give me Summary / Major Issues / Minor Issues / Recommendation", "find the biggest problems in this manuscript", or "re-check whether I fixed the review issues". Do not use for direct source editing or compilation-heavy repair; route those to the format-specific writing skills instead.

[auditdeep-reviewpaperpdflatextypstchineseenglishreviewergatere-audit]
academic-writingID: bahayonghang/academic-writing-skills/paper-audit
11014

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pnpm dlx add-skill https://github.com/bahayonghang/academic-writing-skills/tree/HEAD/academic-writing-skills/paper-audit

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academic-writing-skills/paper-audit/SKILL.md

Skill Metadata

Name
paper-audit
Description
Reviewer-style audit and submission gate for Chinese and English academic papers in LaTeX, Typst, or PDF format. Use for peer-review critique, pre-submission readiness checks, pass/fail gate decisions, blocker triage, structured revision roadmaps, journal-style review reports, or re-audits of revised manuscripts. Trigger for prompts like "review my paper", "act as a reviewer", "audit this PDF", "is this ready to submit", "gate-check before submission", "write an SCI review report with Summary/Major/Minor/Recommendation", "re-check whether I fixed the review issues", "审稿", "帮我审稿", "投稿门控", "投稿前体检", "重新审一遍", "看看能不能投", or "重大/次要问题清单". Do not use for source editing, sentence polishing, or compilation repair; route those to latex-paper-en, latex-thesis-zh, or typst-paper instead.

Paper Audit Skill v5.1

paper-audit is deep-review-first. Its core job is to behave like a serious reviewer: find technical, methodological, claim-level, and cross-section issues; keep script-backed findings separate from reviewer judgment; and return a structured issue bundle plus a revision roadmap.

This version ships a script-backed PRESUBMISSION layer for final-week mechanical checks (em dashes, AI-tone term frequency, abstract completeness, LaTeX citation/label/equation hygiene, paragraph-shape weak signals, concrete captions). It plugs into existing modes; it is not a separate public mode. See references/PRESUBMISSION_GUIDE.md for mode integration.

Use it for audit and review. Do not use it as the first tool for source editing, sentence rewriting, or build fixing.

What This Skill Produces

  • quick-audit: fast submission-readiness screen with script-backed findings, including PRESUBMISSION
  • deep-review: reviewer-style structured issue bundle with major/moderate/ minor findings
  • gate: PASS/FAIL decision calibrated for submission blockers; PRESUBMISSION Major/Minor findings remain advisory
  • re-audit: compare current issue bundle against a previous audit, including mechanical regression findings
  • polish: precheck-only handoff into a polishing workflow

The primary product is no longer just a score. For deep-review, the main outputs are:

  • final_issues.json
  • overall_assessment.txt
  • review_report.md
  • peer_review_report.md
  • revision_roadmap.md

Do Not Use

  • direct source surgery on .tex / .typ
  • compilation debugging as the main task
  • free-form literature survey writing
  • paragraph-level related-work rewriting
  • cosmetic grammar cleanup without an audit goal

Critical Rules

  • Don't rewrite the paper source — paper-audit is a reviewer, not an editor; switch skills explicitly if the user wants prose changes, so review evidence stays separable from edits.
  • Don't fabricate references, baselines, or reviewer evidence — invented citations and made-up reviewer voices undermine every other finding in the bundle.
  • Distinguish [Script] from [LLM] findings — script-backed items have a deterministic anchor the user can rerun, while LLM findings need a quote or section to be falsifiable.
  • Anchor every reviewer finding to a quote, section, or exact textual location — unanchored complaints become impossible to audit on a re-pass.
  • Be conservative with OCR noise, formatting quirks, and copy-editing trivia — flagging cosmetic noise inflates the report and buries the real issues.
  • Read like a careful reader before flagging — understand the author's intended meaning first so the issue captures a real misread, not a strawman.
  • For literature findings, judge whether the gap is evidence-backed and fairly positioned, and don't rewrite the prose inside paper-audit — keep prose rewrites in the format-specific writing skills where they can be reviewed in isolation.
  • For PRESUBMISSION, map CRITICAL / MAJOR / MINOR to Critical / Major / Minor script severities; only Critical or failed checklist items can fail gate — otherwise mechanical findings drown out the substantive ones. Full mode-integration matrix lives in references/PRESUBMISSION_GUIDE.md.
  • In PDF mode, do not guess source-only hygiene. Report text-proven items and note that LaTeX/Typst source checks were skipped.

Mode Selection

| Requested intent | Mode | |---|---| | "check my paper", "quick audit", "submission readiness", "pre-submission review", "投稿前检查" | quick-audit | | "review my paper", "simulate peer review", "harsh review", "deep review" | deep-review | | "is this ready to submit", "gate this submission", "blockers only" | gate | | "did I fix these issues", "re-audit", "compare against old review" | re-audit | | "polish the writing, but only if safe" | polish |

Legacy aliases still work for one compatibility cycle:

  • self-check -> quick-audit
  • review -> deep-review

For per-mode workflow steps, input resolution rules, presentation surface rules, and committee focus routing, see references/MODE_GUIDE.md.

Review Standard

Read these references before running reviewer-style work:

  1. references/REVIEW_CRITERIA.md
  2. references/DEEP_REVIEW_CRITERIA.md
  3. references/CHECKLIST.md
  4. references/CONSOLIDATION_RULES.md
  5. references/ISSUE_SCHEMA.md
  6. references/PRE_SUBMISSION_RULES.md
  7. references/PRESUBMISSION_GUIDE.md
  8. references/CLAIM_EVIDENCE_CONTRACT.md
  9. references/DATA_AVAILABILITY_ADVISORY.md
  10. references/MODE_GUIDE.md
  11. references/editorial_decision_standards.md
  12. references/quality_rubrics.md

The deep-review workflow uses a 16-part issue taxonomy:

  1. formula / derivation errors
  2. notation inconsistency
  3. prose vs formal object mismatch
  4. numerical inconsistency
  5. missing justification
  6. overclaim or claim inaccuracy
  7. ambiguity that can mislead a careful reader
  8. underspecified methods / missing information
  9. internal contradiction
  10. self-consistency of standards
  11. table structure violations
  12. abstract structural incompleteness
  13. theory contribution deficiency
  14. qualitative methodology opacity
  15. pseudo-innovation / straw man
  16. paragraph-level argument incoherence

Workflow

Each mode has the same shape: parse $ARGUMENTS, lock the paper path, infer mode/report-style/focus/language if not provided, then run the canonical command. Detailed phase steps are in references/MODE_GUIDE.md.

quick-audit

uv run python -B "$SKILL_DIR/scripts/audit.py" <paper> --mode quick-audit ...

Present Submission Blockers -> Quality Improvements -> checklist; call out PRESUBMISSION mechanical findings with [Script] provenance. Escalate to deep-review when the user wants reviewer-depth critique.

deep-review

Five phases (see references/MODE_GUIDE.md for full detail):

  1. Workspace prep: 
    uv run python -B "$SKILL_DIR/scripts/prepare_review_workspace.py" <paper> --output-dir ./review_results
  2. Phase 0 automated audit: 
    uv run python -B "$SKILL_DIR/scripts/audit.py" <paper> --mode deep-review ...
  3. Phase 3A committee — dispatch 5 committee agents (editor, theory, literature, methodology, logic) and write committee/consensus.md.
  4. Phase 3B section + cross-cutting lanes — section, claims-vs-evidence, notation, evaluation fairness, self-consistency, prior-art, and pre-submission readiness (full/editor focus only).
  5. Consolidation: 
    uv run python -B "$SKILL_DIR/scripts/consolidate_review_findings.py" <review_dir>
uv run python -B "$SKILL_DIR/scripts/verify_quotes.py" <review_dir> --write-back
uv run python -B "$SKILL_DIR/scripts/render_deep_review_report.py" <review_dir>

When the user explicitly asks for journal-review prose, set --report-style peer-review so peer_review_report.md becomes the Primary View while review_report.md stays as the richer evidence bundle.

gate

uv run python -B "$SKILL_DIR/scripts/audit.py" <paper> --mode gate ...

Run EIC Screening (Phase 0.5) using agents/editor_in_chief_agent.md first; report PASS/FAIL; verdict -> EIC -> blockers -> advisory. A desk-reject verdict is a gate blocker. Critical PRESUBMISSION only blocks the gate.

re-audit

Requires --previous-report PATH.

uv run python -B "$SKILL_DIR/scripts/audit.py" <paper> --mode re-audit --previous-report <path> ...
uv run python -B "$SKILL_DIR/scripts/diff_review_issues.py" <old_final_issues.json> <new_final_issues.json>

Present root-cause-aware status labels: FULLY_ADDRESSED, PARTIALLY_ADDRESSED, NOT_ADDRESSED, NEW.

polish

uv run python -B "$SKILL_DIR/scripts/audit.py" <paper> --mode polish ...

If blockers exist, stop and report them. Only proceed into polishing if the precheck is safe.

Output Contract

For deep-review, the final issue schema is:

{
  "title": "short issue title",
  "quote": "exact quote from paper",
  "explanation": "why this matters and what remains problematic",
  "comment_type": "methodology|claim_accuracy|presentation|missing_information",
  "severity": "major|moderate|minor",
  "confidence": "high|medium|low|unverified",
  "source_kind": "script|llm",
  "source_section": "methods",
  "related_sections": ["results", "appendix"],
  "root_cause_key": "shared-normalized-key",
  "review_lane": "claims_vs_evidence",
  "evidence_anchor": [
    {"type": "citation|figure_or_table|metric|section|analysis_artifact", "text": "visible anchor"}
  ],
  "claim_strength": "unsupported|observed|supported|strong",
  "missing_evidence": ["specific support that is absent or unverified"],
  "allowed_wording": "bounded wording that stays within the evidence",
  "forbidden_wording": ["unbounded wording that would require stronger evidence"],
  "gate_blocker": false,
  "quote_verified": true
}

Always prefer:

  • exact quotes over vague paraphrase
  • evidence-backed findings over style commentary
  • issue bundle + roadmap over raw script dumps

References

| File | Purpose | |---|---| | references/MODE_GUIDE.md | per-mode workflow detail, phase steps, committee focus routing | | references/PRESUBMISSION_GUIDE.md | PRESUBMISSION mode-integration behavior matrix | | references/REVIEW_CRITERIA.md | top-level audit scoring and mapping | | references/DEEP_REVIEW_CRITERIA.md | deep-review-specific issue taxonomy and leniency rules | | references/CONSOLIDATION_RULES.md | deduplication and root-cause merge policy | | references/ISSUE_SCHEMA.md | canonical JSON schema | | references/CLAIM_EVIDENCE_CONTRACT.md | optional claim candidate / evidence anchor contract | | references/DATA_AVAILABILITY_ADVISORY.md | source-data and FAIR metadata advisory boundary | | references/REVIEW_LANE_GUIDE.md | section lanes and cross-cutting lanes | | references/PRE_SUBMISSION_RULES.md | final-week mechanical audit rules and term list | | references/SUBAGENT_TEMPLATES.md | reviewer task templates | | references/QUICK_REFERENCE.md | CLI and mode cheat sheet | | references/editorial_decision_standards.md | cross-reviewer arbitration rules and decision matrix | | references/quality_rubrics.md | five-dimension scoring rubric with calibrated tiers | | references/TROUBLESHOOTING.md | operational errors plus review-quality failure paths (F1-F8) |

Scripts

| Script | Purpose | |---|---| | scripts/audit.py | Phase 0 audit and mode entrypoint | | scripts/pre_submission_check.py | deterministic PRESUBMISSION mechanical audit layer | | scripts/prepare_review_workspace.py | create deep-review workspace | | scripts/build_claim_map.py | extract headline claims, closure targets, and additive claim_candidates | | scripts/consolidate_review_findings.py | deduplicate comment JSONs | | scripts/verify_quotes.py | verify exact quote presence | | scripts/render_deep_review_report.py | render final Markdown report | | scripts/diff_review_issues.py | compare old vs new issue bundles |

Reviewer Lanes

Committee agents (deep-review default):

  • committee_editor_agent.md
  • committee_theory_agent.md
  • committee_literature_agent.md
  • committee_methodology_agent.md
  • committee_logic_agent.md

Default deep-review lanes live in agents/:

  • section_reviewer_agent.md
  • claims_evidence_reviewer_agent.md
  • notation_consistency_reviewer_agent.md
  • evaluation_fairness_reviewer_agent.md
  • self_consistency_reviewer_agent.md
  • prior_art_reviewer_agent.md
  • synthesis_agent.md
  • editor_in_chief_agent.md — EIC desk-reject screener (used in gate mode)
  • revision_coach_agent.md — parse free-form reviewer letters into a structured roadmap (used in re-audit mode)

Specialized deep-review agents (read their files for activation criteria):

  • critical_reviewer_agent.md — devil's advocate with C3-C5 checks
  • domain_reviewer_agent.md — domain expertise with A1-A7 assessments
  • methodology_reviewer_agent.md — methodology rigor with B3-B10 checks
  • literature_reviewer_agent.md — evidence-based literature verification (optional, --literature-search)

Examples

  • "Review this manuscript like a serious conference reviewer and tell me the biggest validity risks."
  • "Run a quick audit on paper.tex and tell me what blocks submission."
  • "Gate this IEEE submission and separate blockers from recommendations."
  • "Re-audit this revision against my previous report."
  • "Audit only the literature positioning and tell me whether the claimed gap is real or fabricated by selective citation."