submission-audit

Submission Audit

Overview

Use this skill for late-stage manuscript QA. It is narrower than manuscript-optimizer: do not use it to redesign a paper from scratch. Use it when the structure mostly exists and the main task is to catch the failures that survive normal revision cycles.

The core rule is simple: never treat a clean-looking manuscript as submission-ready until the front half, figures, legends, methods, supplement, and venue expectations have been checked against each other.

Use the helper script when you want a fast local pass over figure citations:

python ~/.agents/skills/submission-audit/scripts/check_figure_refs.py path/to/manuscript.md
# Claude Code (global install): replace ~/.agents/skills with ~/.claude/skills
# Claude Code (project-local install): replace ~/.agents/skills with .claude/skills

When To Use

Use this skill when:

The draft is near submission, resubmission, or internal circulation
Figures and legends are mostly finalized
The paper needs a last pass for overclaim, missing references, or cross-section drift
A revision round compressed the prose and may have dropped supporting detail
The supplement exists and may no longer match the main text

Do not use this skill for:

Early brainstorming
Initial section drafting
Citation discovery from scratch
Heavy structural rewrites that belong in manuscript-optimizer

Audit Order

Front-half alignment
- check title, abstract, introduction, and discussion against the actual Results
- flag any claim stronger than the downstream evidence
- check the broad positions against the Readers section of paper-workflow's references/section-contracts.md: a front matter written for specialists is a reader-friction finding, not a polish item
Figure and legend coverage
- verify that every main-figure panel and supplementary panel cited in the paper actually exists
- verify that panel letters, metrics, datasets, and numbers agree across figure, legend, and main text
Methods and supplement anchoring
- check that methods are cited where needed from Results
- check that supplementary figures, tables, and notes are referenced precisely enough to be usable
Terminology and metrics
- enforce one canonical name per concept
- check abbreviations, metric naming, domain-shift labels, cohort names, and model names
Risk pass
- overclaim
- evidence gaps
- unsupported mechanism language
- venue-specific style drift
- Statistical analysis declares only statistics the paper reports (see stats-reporting-audit)
- voice: audit, defensive or self-critical writing in the main text, SI, legends and data statements (run the anti-defensive-writing detection pass)
Venue preflight: what the target venue's editors and reviewers check
- Nature Portfolio:
  - reporting-summary readiness
  - data and code availability statements
  - accession IDs, repositories, and disclosure of sharing restrictions
  - image-integrity and raw-data readiness
  - end matter: competing interests, author contributions whose initials match the byline, a generative-AI statement in the Methods scoped to actual use with no AI-generated images, and code availability consistent with the released repository
  - preprint, related-manuscript, and conference-proceedings disclosure
- ML conference (conference-paper-writing, What Reviewers Check, in the optional set installed with --set all):
  - one statement that test data played no part in model or configuration selection
  - the number of runs behind each reported number, and their spread
  - no configuration chosen on evaluation data without the default configuration's result beside it
  - reproducibility and LLM-use statements as the current year's guide asks
Initials are checked against full names, not treated as unique identifiers. A missing or ambiguous contribution mapping is a finding for the authors. It is not authorization to remove a byline entry, change correspondence or assign a contribution role.
Source hygiene
- LaTeX comments become public when the source leaves the authors, on arXiv or as supplementary material
- strip internal paths and notes with arxiv_latex_cleaner or an equivalent step, and confirm the cleaned source compiles
Reviewer-side rejection pass
- contribution sufficiency
- writing clarity and reproducibility
- empirical strength
- evaluation completeness
- design or framework soundness
A finding from this pass is fixed with evidence, a precise definition or a narrower claim, never with an added caveat. Anything this audit adds to the manuscript is held to rule zero of anti-defensive-writing, because this audit runs after the posture pass.

Required Checks

Does every substantive abstract claim map to a figure, table, or supplement item?
Does every Results subsection cite the correct panel range?
Does every figure legend still reflect the current plot content?
Are Methods cross-references present where interpretation depends on setup or metric definition?
Is the supplement indexed precisely enough, including panel letters when needed?
Are strong causal or mechanism words used only where direct evidence exists?
Are title, abstract, and discussion consistent about the paper's actual contribution type?
Could a scientist outside the subfield say, from the title and abstract alone, what problem was addressed, what was found and why it matters?
If the target is Nature Portfolio, are the reporting-summary inputs, data/code statements, image-integrity materials, and disclosure items actually ready rather than merely planned?
If a submission form or portal draft already exists, do the title, abstract, keywords, availability statements, and related metadata still match the manuscript exactly?
Has the paper been pressure-tested against the main rejection dimensions: insufficient contribution, weak clarity, weak empirical effect, incomplete evaluation, and questionable design?

For a supplied LaTeX manuscript with typesetting in scope, use scientific-writing's references/latex-layout.md to check the numbered formulas, figure/caption placement, table parts and paragraph continuity in the rendered PDF. A navigation-only paragraph is assessed by function; a short scientific finding may be valid. Check the chosen numbering convention and existing labels, not a blanket requirement to number every display. Apply template, venue and project-specific placement rules to the relevant deliverable; separate figure legends or a genuinely long table can be intentional. If compilation or visual inspection is unavailable, identify it as unchecked.

Finding Format

Report findings in this order:

High: submission-blocking or claim-distorting issues
Medium: credibility or reader-friction issues
Low: consistency and polish issues

Each finding should include:

exact file reference
what is wrong
why it matters
the minimum safe fix

If no major problems exist, say that explicitly and then list only the residual risks or final checks still worth doing.

Common Failure Modes

Abstract promise stronger than Results support
Front matter whose first two sentences state no specific problem, or that reports findings only as metric gains over other methods
Figure panel mentioned in text but not actually indexed or explained
Legend still describing an old version of the plot
Supplementary figure cited at whole-figure level when the argument depends on one panel
Metric names drifting between sections
Discussion slipping into mechanism-level language not earned by the evidence
Nature Portfolio submission blocked late by missing accession IDs, undeclared sharing restrictions, undisclosed AI use, or missing raw image support
Submission-form title or abstract drifting away from the latest manuscript
The manuscript reading cleanly on the surface while still failing a reviewer-style contribution or evaluation check

Output Standard

End the audit with:

a one-sentence readiness assessment
the top remaining risk
the next highest-leverage fix before submission