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Write a research paper with AI agents

AI agents can speed up every stage of a paper, but they also invent references, inflate claims and produce recognizable “AI prose”. This workflow keeps you, the author, in control and uses skills to enforce the checks that stop those failures.

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The workflow

  1. Collect the evidence first. Put results tables, figures, analysis notebooks and your notes in one folder. Ask the agent to summarize what the data shows before any drafting (scientific-critical-thinking, statistical-analysis).
  2. Outline the argument. Ask for a one-sentence contribution, then a section outline in which every paragraph has one claim and its supporting figure or table (scientific-writing, or ml-paper-writing for ML venues).
  3. Draft section by section. Start with Methods and Results, then Discussion, then Introduction, and write the Abstract and Title last (abstract-and-title). Review each section before moving on.
  4. Cite from real records only. Find papers with literature-review / paper-lookup, or use firecrawl-research-index for hosted discovery and passage reads. Export BibTeX from the publisher or Crossref, and never let the agent write a reference from memory.
  5. Verify every citation. Run citation-verification on the .bib. Fix or remove anything flagged mismatch, doi-not-found or not-found. Then check that each cited paper supports its sentence.
  6. Clean the bibliography. bibtex-hygiene removes duplicates, fixes DOIs and protects acronym capitalization.
  7. Remove the slop. Run unslop-academic-writing: fix content (vague claims, missing numbers) before words. Aim for a slop index under 5 in the abstract and introduction.
  8. Format for the venue. Use the journal skill (nature-portfolio, science-aaas, cell-press, ieee-transactions, acm-sigconf, elsevier-cas, springer-lncs, plos, apa7) or venue-templates. The skill makes the agent read the current author guidelines.
  9. Prepare the statements. reproducibility-statement covers data and code availability, checklists, CRediT and AI-use disclosure.
  10. Submit. cover-letter-to-editor for the letter and reviewer suggestions, and arxiv-submission for the preprint.
  11. Revise. rebuttal-and-response-to-reviewers triages the reviews and drafts point-by-point responses.

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Rules that protect you

  • The author is responsible for every sentence. Read everything the agent writes.
  • Disclose AI assistance as your venue requires. Never list an AI as an author.
  • Never let an agent invent data, results, statistics or references.
  • Keep your analysis reproducible: the numbers in the text must come from code you can rerun.
Thesis and dissertation · No-slop academic writing · Systematic reviews