paper-preflight

Check every reference of a LaTeX paper against real scholarly records before you submit.
No LLM guessing, no false accusations.

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Language models invent references, and copy-pasted BibTeX carries wrong years, wrong authors and dead DOIs. paper-preflight reads your .tex and .bib files and asks Crossref, dblp, arXiv, DataCite, PubMed and OpenAlex (and Semantic Scholar, if you have a key; Open Library for books without a DOI; GitHub, PyPI, CRAN, Hugging Face and OpenML for software, models and datasets) about every cited work:

• Does it exist?
• Does it match what you wrote?
• Has it been retracted?
• Has the preprint you cite been published since?

When it cannot tell, it says so instead of guessing.

Status: 0.x releases, on the way to a stable 1.0. False positives are the bugs we most want to hear about: please open an issue.

The repository's demo paper cites eleven works, several of them wrong on purpose. A real run, against the live sources:

$ paper-preflight check examples/demo-paper
paper-preflight 0.8.0 · main.tex · 12 entries, 12 cited keys

error   CIT001 main.tex:31
    Citation key 'nonexistent2023' is not defined in any bibliography file (1 use(s)).
error   REF001 refs.bib:43
    The doi of 'devlin2019bert' (10.1109/cvpr.2016.90) resolves to a different work in Crossref: "Deep Residual Learning for Image Recognition" (He et al., 2016).
error   REF003 refs.bib:66
    'lindqvist2024quantum' was not found in Crossref, dblp and Semantic Scholar, and every source responded. Check that the work exists and that its title is correct.
error   REF004 refs.bib:73
    'wakefield1998ileal' has been retracted (reported by Crossref, OpenAlex). Cite it only if the text discusses the retraction.
error   CIT002 refs.bib:128
    Entry key 'kingma2015adam' is already defined at line 47; BibTeX ignores this one.
warning REF015 refs.bib:31
    'he2015residual' cites a preprint that has been published in CVPR (2016), DOI 10.1109/cvpr.2016.90. Cite the published version and keep the eprint field.
warning CIT004 refs.bib:37
    Entries 'devlin2019bert' and 'he2016deep' look like the same work (same DOI).
warning REF013 refs.bib:51
    'kingma2015adam' gives the year 2016, but dblp records 2014, 2015.
warning REF017 refs.bib:112
    The doi of 'tacl2019example' contains LaTeX escapes: '10.1162/tacl\_a\_00276'. Write it as: 10.1162/tacl_a_00276
info    REF005 refs.bib:73
    'wakefield1998ileal' has a published correction (reported by Crossref).
info    REF090 refs.bib:95
    'zhou2016ml' could not be verified: non-Latin titles are not supported yet; grey literature without an identifier (book, report, software, web page).
info    CIT003 refs.bib:116
    Entry 'lecun1998gradient' is never cited.

References: 7 verified · 1 metadata mismatch · 1 identifier conflict · 1 not found · 1 cannot determine
5 error(s) · 4 warning(s) · 3 info

Each finding is backed by a record (or by every source answering "no"). The correct NeurIPS paper is verified through dblp even though Crossref only holds fake copies of it, the book without an identifier is confirmed by Open Library, and the Chinese one, whose script is not supported yet, is reported as "cannot determine" instead of "not found".

What it catches

Rule	Finding
REF001	The DOI or arXiv ID points to a different paper
REF002	The DOI or arXiv ID does not exist
REF003	The work was not found in any source, and every source answered
REF004 · REF005	The work was retracted, or has an expression of concern or a correction
REF010–REF014	Authors, title, year or venue differ from the real record
REF015	A cited preprint has been formally published
REF016	The registry has a DOI the entry lacks (offered as a safe fix)
REF017	An identifier is written so that links break (10.1162/tacl\_a\_00276, …v1)
REF018	A cited arXiv preprint was withdrawn by its authors
REF019 · REF021	A linked repository, package or dataset does not exist; a linked web page is gone, with no archived copy
REF020	A preprint is cited with a venue no catalogue of journals and conferences has
CIT001–CIT008	Undefined, duplicate, unused or near-duplicate citation keys; broken .bib syntax
REF090	Cannot determine, always with the reason (source unavailable, grey literature, …)

Every rule has a page: what it checks, when it can be wrong, and what to do. paper-preflight explain REF003 prints it in the terminal.

How accurate is it?

Four measurements, all against the live sources: hallucinations found in published papers, the bibliographies of real papers, a head-to-head with published tools, and a public benchmark.

On hallucinations that got past peer review

GPTZero published 151 hallucinated references it found in NeurIPS 2025 papers and ICLR 2026 submissions, each confirmed by its staff. Pasted as plain text, as the papers printed them:

References	Flagged	Cannot determine	Verified
151	142 (94%)	9	0

• None of them is verified. The 9 left undecided are web pages and blog posts, a workshop no source indexes, real titles given with invented authors where several works share the title, and two references too garbled to search. Each is listed with its reason in evals/results/gptzero.md.
• GPTZero's own tool found these, so they are the hallucinations a search can find; recall on every kind of hallucination is lower (see HALLMARK below).

On real papers

Weeks of arXiv papers (20 each, cs, stat, q-bio, quant-ph and astro-ph), chosen mechanically, each list fixed before the changes it measures, run once, with every warning and error reviewed by hand:

Papers first submitted	Version	References	Flags	Real problems	False positives	Unclear	False positives per 100 references
2026-08-19..25	0.5.0	962	53	41	10	2	1.0
2026-08-26..09-01	0.5.1	780	101	81	19	1	2.4
2026-09-02..08	0.5.2	975	48	31	13	4	1.3
2026-09-09..15	0.5.3	1,067	98	83	14	1	1.3
2026-09-16..22	0.6.0 candidate	868	89	76	13	0	1.5
2026-09-23..29	0.6.0	786	48	42	6	0	0.8
2026-09-30..10-06	0.7.0	1,014	89	79	7	3	0.7
2026-06-24..30, an earlier week	0.8.0	1,127	143	132	10	1	0.9

• 0.8.0: one false alarm every two papers (56 references on average), against 132 real problems: 93 cited preprints since published, 17 identifiers written as links, wrong authors or given names in 10 entries (in four, most given names are invented), 6 wrong years, 2 misquoted titles, a wrong venue, a DOI that does not exist and an arXiv ID of another paper. Six false alarms are registries' own writing ('Ueber' for 'Über', a title that lost its '3/4'), three are author fields written by hand ('and 324 others'), one an ITU-R report no source indexes. This week was sampled from before the first one, never used until then, so that 0.8.0 need not wait for next week's papers; checked months after it was written, it may read a little better than a fresh week, which follows as a control.
• 0.7.0: about one false alarm every three papers, against 79 real problems. The false alarms are three articles a registry dates only by their online appearance, a book against its online edition, two symbols a registry writes its own way, and a paper's code offered as its published version; all are fixed in 0.8.0.
• The two weeks before (0.6.0): 1.5, then 0.8. 8 of the first week's 13 false alarms were registries' own errors (a short author list, misspelt names, an HTML entity, a typo, a wrong year); 5 are fixed in 0.6.0.
• One week was over our target of 1.5 (2.4); 11 of its 19 false alarms are fixed in 0.5.2.
• In the first week, one false alarm every two papers (48 references on average), against 41 real problems: 16 errors in the entries (wrong years, given names and titles, a missing first author, one paper's title with another's authors, identifiers written so that links break) and 25 cited preprints that have since been published.
• The false alarms are mostly registry records with errors of their own (author lists that stop short, a garbled symbol, an English given name) and collaboration names in author lists ("MAGPI Team"); two come from a title cited without its last words.
• Seven earlier batches of 20 papers were used to find false positives, each first measured as it came out (0.1.0: 4.5 per 100 references; 0.1.1: 2.3; 0.1.2 before its last fixes: 3.0; 0.1.2: 1.7; 0.2.1: 1.9; 0.3.0: 1.9; 0.4.0: 1.2). Details in evals/README.md.

Next to other tools

Badalova & Mayr (2026) checked 104 references by hand and published what five tools flagged. On the same references, with their labels:

Tool	Precision [95% CI]	Recall	False flags per 100 correct references
CheckIfExist	47.7% [36.0%, 59.6%]	93.9%	47.9
HalluCiteChecker	47.4% [32.5%, 62.7%]	54.5%	28.2
Hallucinator	50.9% [38.3%, 63.4%]	87.9%	39.4
HalRef	31.2% [21.9%, 42.2%]	72.7%	74.6
RefChecker	47.1% [35.7%, 58.8%]	97.0%	50.7
paper-preflight	72.5% [57.2%, 83.9%]	87.9%	15.5

The sample is small, so the intervals are wide. Some flags count as false here because the study labels a reference correct when the work exists: five of paper-preflight's flags on such references point at real errors (a wrong author, a broken DOI). Two causes of false flags found in this data were fixed, and four names the study's CSV garbled were restored, before the run above; the first run measured 62.8%. See evals/results/badalova-mayr.md.

On a benchmark: HALLMARK

HALLMARK is a public benchmark of real and hallucinated BibTeX entries.

Split	Mode	Precision	Recall	False-positive rate	Coverage
test_public: 831 entries, never used during development	Any issue	98.5%	93.5%	1.9%	97.7%
	Fabrication	99.0%	50.2%	0.6%	97.7%
dev_public: 1,119 entries, used during development	Any issue	97.7%	94.3%	2.1%	98.9%
	Fabrication	98.2%	53.7%	1.0%	98.9%

HALLMARK v1.2.3, every entry of both public splits, run with 0.8.0 on 2026-10-09. Fabrication counts a wrong identifier, a work not found and no author in common; any issue also counts wrong authors, title, year or venue.

• The held-out split confirms the development numbers: a little higher precision and less than a point less recall on entries no rule was ever tuned on. 0.8.0 catches 97% of invented venues (78% in 0.7.0) and 85% of near-miss titles (70%).
• Every flag on a dev_public entry labelled VALID was checked by hand. The 11 that remain are not correct citations: DOIs that belong to other papers, author lists naming people who did not write the paper, a shifted year and a truncated title.
• Without them, both modes reach 100% precision and 0% false positives. The list, each item with a reason one lookup confirms, is in evals/hallmark_disputed.toml.
• What is still missed: author lists that merely leave people out (named in an info until held-out weeks show the check never fires on a correct list) and invented entries that borrow a title several real works share. See evals/results/ for every hallucination type.

Precision comes first: a reference is called fabricated only on positive evidence, and an unanswered or ambiguous lookup is reported as "cannot determine", never as "not found". The evaluation harness and every run's summary are in evals/.

Quick start

With uv nothing needs installing (or pip install paper-preflight):

uvx paper-preflight check path/to/paper

path/to/paper is the project directory, its main .tex file, or a single .bib file. A project that ships no .bib, as many arXiv sources do, is read from its compiled .bbl (checked, but never edited).

Writing in Word, Markdown or Typst? The manuscript is checked the same way:

uvx paper-preflight check paper.docx     # Word: Zotero, Mendeley or EndNote citations, or the typed list
uvx paper-preflight check paper.qmd      # Markdown, Quarto, R Markdown: [@key] against its bibliography
uvx paper-preflight check paper.typ      # Typst: @key against #bibliography(...), .bib or Hayagriva .yml

In a Word manuscript, citations inserted by Zotero, Mendeley or EndNote carry the reference manager's own record of each work (field codes), which is read first; Word's source manager next; else the reference list as typed, after its "References" heading. A bibliography may also be checked on its own as CSL-JSON (.json), RIS (.ris) or YAML (.yml, Hayagriva or CSL).

No manuscript at all? A reference list as plain text works too, in the common styles (APA, IEEE, ACM, Nature, Vancouver, Springer, Elsevier, MDPI, GOST, Chicago, MLA), one reference per line, per paragraph or numbered:

uvx paper-preflight check references.txt
pbpaste | uvx paper-preflight check -      # or from stdin

Any arXiv paper, by its ID: the source is downloaded to a temporary folder, checked, and deleted.

uvx paper-preflight check arxiv:2607.06922

Only the PDF? Its reference list is read too, with the pdf extra:

uvx --from 'paper-preflight[pdf]' paper-preflight check paper.pdf

Option	Effect
--format json / --format sarif	Machine-readable output (SARIF works with GitHub code scanning)
--offline	Never touch the network; use only answers already in the local cache
--refresh	Ask every source again instead of using cached answers (after a correction, say)
--recheck	Search again now for references found too new to be indexed on earlier runs (otherwise once a day)
--fail-on warning	Make warnings fail the run too (the default is errors)
--details	List every finding; by default a suggestion that applies to many entries (published preprints, available DOIs) is one line
--lang zh	Chinese messages (also chosen automatically from your locale)

Exit codes:

Code	Meaning
0	Nothing at or above --fail-on was found
1	Blocking findings
2	No blocking findings, but a source was unavailable and nothing could answer in its place, so the paper cannot be called clean yet
3	Usage error
4	Internal error (please report it)

The JSON report follows a published JSON Schema (schema_version 0.1): fields may be added, but none is removed or changes meaning without a new schema_version. The tests check every report against it.

Fetch verified BibTeX

Instead of writing an entry from memory, ask for it by DOI, arXiv ID or title. Every field comes from the registry record, which a comment above the entry names:

paper-preflight bib fetch 1810.04805

% Verified with paper-preflight against dblp (conf/naacl/DevlinCLT19), 2026-10-03
@inproceedings{devlin2019bert,
  title         = {{BERT:} Pre-training of Deep Bidirectional Transformers for Language Understanding},
  author        = {Devlin, Jacob and Chang, Ming-Wei and Lee, Kenton and Toutanova, Kristina},
  booktitle     = {NAACL-HLT (1)},
  year          = {2019},
  doi           = {10.18653/v1/n19-1423},
  eprint        = {1810.04805},
  archivePrefix = {arXiv},
}

• Preprints: an arXiv preprint that has been published comes back as the published version, with its eprint kept (--prefer preprint for the preprint itself).
• Titles: --title (with --author/--year if needed) lists the candidates instead of choosing when several works match.
• Retractions: a retracted work comes with a warning.
• Agents: --format json is for scripts and agents.

Fix the bibliography

bib fix turns findings into edits of your .bib files, taken from the verified records. It prints a diff and changes nothing until you add --apply:

paper-preflight bib fix path/to/paper --level unsafe

--- a/refs.bib
+++ b/refs.bib
@@ -48,7 +47,7 @@
   title     = {Adam: A Method for Stochastic Optimization},
   author    = {Kingma, Diederik P. and Ba, Jimmy},
   booktitle = {International Conference on Learning Representations (ICLR)},
-  year      = {2016},
+  year      = {2015},
 }

• --level safe (the default) only fixes what cannot change which work is cited: identifiers written so that links break, and DOIs the registry has but the entry lacks.
• --level unsafe also rewrites authors, title, year and venue from the record, removes identifiers that point to another work, and cites a preprint as its published version (the entry type, venue, year, volume, pages and DOI; the eprint is kept). Review the diff first.
• Only the affected fields change; comments, formatting, line endings and encoding are kept. A reference nobody could find is never "fixed": only you can say what was meant.

Silence a finding you have checked

A comment directly above an entry silences rules for that entry, with an optional reason:

% preflight: ignore[REF003] reason="internal technical report, not indexed anywhere"
@techreport{lab2024internal,
  ...
}

The verdict stays in the JSON report; only the finding is dropped. A suppression that silenced nothing is reported as CFG001 (info), so stale comments do not pile up. Reference rules are only judged after a complete online run, since offline answers and outages may leave them unrun.

A finding you believe is wrong: where false alarms come from, and what to do.

Project settings

For a whole project, put the settings in paper-preflight.toml next to the paper (or in a folder above it, up to the repository's root), or in [tool.paper-preflight] of pyproject.toml:

ignore-rules = ["REF016"]                  # never report these rules
ignore-keys = ["internal2024*"]            # nor anything about these entries
severity = { REF015 = "info" }             # report published preprints as infos
disable-sources = ["s2"]                   # optional sources only
fail-on = "warning"                        # as --fail-on; the command line wins

check --config <path> names the file instead. The optional sources are s2, openlibrary, github, pypi, cran, huggingface, openml, web (links to web pages) and wayback; the registries that judge a reference cannot be turned off, and a mistake in the file (an unknown rule or setting) is an error, never silently ignored. The JSON report names the file in run.notes; the MCP server reads it too.

Experimental: find the passage behind each citation

support looks in each cited work for a passage that says what the citing sentence claims. It reads the work's text: the arXiv source, an open-access full text or PDF, or else the abstract. A small local model (HHEM-2.1-open, 0.4 GB) then scores the passages ranked best for the claim.

pip install "paper-preflight[support]"

paper-preflight support path/to/paper --download-model --all

--download-model fetches the model's weights once. --all also lists the confirmed citations with their quotes, and arxiv:<id> works as a target, as it does for check.

• What it says: "confirmed", with the passage quoted word for word, or "could not confirm". A citation it could not confirm comes with the reason: no text, only the abstract, or no passage close enough. A citation that only names what it cites ("Adam \cite{...}") is confirmed when the cited work's title carries the name.
• It never calls a citation wrong. On a gold set of 298 citations, 93% of its confirmations were right [95% CI 82%, 98%]. But it confirms only about one real citation in six, and a low score pointed at a mis-citation less than half the time. The gold set's labels were made by AI models, not experts; see evals/results/support.md.
• Or let your agent judge. The MCP tool preflight_cited_passages returns each claim with the cited work's best passages, for Claude, Codex or another agent to judge by the same rules. It needs no model and no support extra. On 100 gold-set citations, a Claude agent judging from it confirmed 39% of the real ones, against HHEM's 9%, and every confirmation was at least partially supported (the labels come from the same model family).
• What leaves your machine: the claims are scored locally. Only the cited works' identifiers go out, to fetch their text, which is then kept in the local cache.

Use it from Python

import paper_preflight

report = paper_preflight.check_paper("paper/")
for ref in report.references:
    print(ref.key, ref.verdict, [f.rule for f in ref.findings])

The results are plain, frozen dataclasses; see docs/python-api.md.

Use it from your coding agent

Claude Code — install the plugin. It bundles an MCP server and a skill that makes Claude check the references before calling a paper finished, fix only what is proven wrong, and never invent a reference.

claude plugin marketplace add amos689/paper-preflight

claude plugin install paper-preflight@paper-preflight

Codex, Gemini CLI, Copilot, Cursor and other agents — install the same skill. It runs the CLI when no MCP server is configured:

npx skills add amos689/paper-preflight

gh skill install amos689/paper-preflight paper-preflight installs it too.

MCP clients (Codex, Cursor, VS Code, …) — run paper-preflight mcp. The tools are read-only and confined to your workspace; see docs/mcp.md.

pre-commit — check citation keys and cached verdicts on every commit in seconds; see docs/pre-commit.md.

GitHub Actions — uses: amos689/paper-preflight@main checks the paper on every push, with the report in the job summary and optional code-scanning alerts; see docs/github-action.md.

Better results with free credentials

paper-preflight works without any account. These optional environment variables make it faster and more complete; their values are never printed or logged.

Variable	Effect
PAPER_PREFLIGHT_EMAIL	Crossref's polite pool: faster, more reliable lookups
OPENALEX_API_KEY	A larger OpenAlex budget for retraction checks
S2_API_KEY	Semantic Scholar as a rescue source for references nobody else found
GITHUB_TOKEN	GitHub's larger budget (5,000 requests an hour, not 60) for references to repositories
NCBI_API_KEY	PubMed's larger budget (10 requests a second, not 3) for PMIDs and PMCIDs

paper-preflight doctor shows which are set and whether each source answers right now.

How it works

1. Source-first. It reads the LaTeX project as LaTeX sees it: comments, \iffalse blocks and \includeonly are respected, .aux files are used when they are fresh, and the first definition of a duplicated key wins, as in BibTeX.
2. Identifier-first routing. DOIs go to their registration agency (doi.org tells which: Crossref, DataCite, …). arXiv IDs go to arXiv, with DataCite as a fallback, and PMIDs and PMCIDs to PubMed (which also marks retracted articles). Entries without identifiers are searched by title in dblp and Crossref. dblp is read through its SPARQL endpoint, which still answers scripts now that dblp's search API is behind a bot challenge.
3. Field-by-field matching with guards. It compares titles (including earlier arXiv version titles), authors (tolerating transcriptions such as Reiß/Reis), year and venue. A search result is used only when enough of these agree and no other work fits as well; known fake DOI copies are skipped.
4. One verdict per reference: verified, metadata mismatch, identifier conflict, not found, or cannot determine with a reason. "Not found" needs every required source to answer "no".
5. No LLM anywhere in the verdict. Answers are cached locally (SQLite), so re-runs are fast and --offline works.

Design principles

• Positive confirmation or abstain. Rate limits, outages and unindexed works lead to "cannot determine", never to "not found".
• Neutral wording. Findings state observations ("not found in Crossref, dblp and Semantic Scholar, and every source responded"), never accusations.
• Local-first, no telemetry. Only the metadata of the cited works (DOIs, titles, authors) is sent to the public scholarly APIs above. Your manuscript never leaves your machine.

What it will never do

Help evade plagiarism or AI-text detection, scrape paywalled or bot-protected sites, recommend or "complete" references from memory, or name and shame authors.

Roadmap

• Done: releases on PyPI (v0.1); references from a .bbl, plain text, a PDF or an arXiv ID (v0.2); an experimental evidence finder for citations, support (v0.3); installs into more agents, an agent-judged support, and recall measured on hallucinations found in published papers (v0.4); references without titles found by journal, volume and page, short titles and real titles with invented authors judged where the sources allow it (v0.5); Chinese-language works cited in English no longer called "not found" (v0.5.2); fewer false alarms on double surnames, subtitles, workshop papers and books (v0.5.3); twice as fast, and references written whole in a note read as plain text (v0.6); Word, Markdown, Quarto, R Markdown and Typst manuscripts, and CSL-JSON, RIS and YAML bibliographies (v0.7); books, software, models, datasets, RFCs and web links checked against their own registries, invented venues and near-miss titles caught, project settings, a Python API and a page for every rule (v0.8)
• Next: a stable 1.0, once three held-out weeks average at most one false alarm per 100 references
• After 1.0: references in Chinese script, measured before anything ships

Progress is tracked in docs/PROGRESS.md (in Chinese) and the changelog.

Contributing

Bug reports with a reproducible .bib entry are the most valuable contribution, especially false positives. See CONTRIBUTING.md.

License

MIT. See THIRD_PARTY_NOTICES.md for adapted code.