paper-preflight

<!-- mcp-name: io.github.amos689/paper-preflight --> <div align="center">  **Check every reference of a LaTeX paper against real scholarly records before you submit.<br> No LLM guessing, no false accusations.** [](https://github.com/amos689/paper-preflight/actions/workflows/ci.yml) [](https://pypi.org/project/paper-preflight/) [](LICENSE) [](https://glama.ai/mcp/servers/amos689/paper-preflight) [](pyproject.toml) [](#quick-start) [](#how-it-works) [](#design-principles) [](docs/mcp.md) [](https://github.com/amos689/paper-preflight/actions/workflows/ci.yml) [](README.zh-CN.md) **English** · [简体中文](README.zh-CN.md) · [Quick start](#quick-start) · [Releases](https://github.com/amos689/paper-preflight/releases) · [Feedback](https://github.com/amos689/paper-preflight/issues/new/choose) </div>  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) 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 - Has it been retracted?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: v0.4, an early release.** False positives are the bugs we most want to hear > about: please [open an issue](https://github.com/amos689/paper-preflight/issues). The repository's [demo paper](examples/demo-paper) cites eleven works, several of them wrong on purpose. A real run, against the live sources: ```text $ paper-preflight check examples/demo-paper paper-preflight 0.4.0 · 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 error REF004 refs.bib:73 'wakefield1998ileal' has been retracted (reported by Crossref, OpenAlex).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:127 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:111 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:86 'goodfellow2016deep' could not be verified: grey literature without an identifier (book, report, software, web page). info REF090 refs.bib:94 '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:115 Entry 'lecun1998gradient' is never cited. References: 6 verified · 1 metadata mismatch · 1 identifier conflict · 1 not found · 2 cannot determine 5 error(s) · 4 warning(s) · 4 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, and the two books without identifiers are 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`) | | CIT001–CIT008 | Undefined, duplicate, unused or near-duplicate citation keys; broken `.bib` syntax | | REF090 | Cannot determine, always with the reason (source unavailable, grey literature, …) | `paper-preflight explain REF003` describes any rule. ## 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 | **135 (89%)** | 16 | **0** | - **None of them is verified.** The 16 left undecided are web pages and blog posts, titles too short to search with confidence, real titles given with invented authors where several works share the title, and two references the plain-text reader could not take apart. Each is listed with its reason in [`evals/results/gptzero.md`](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 The bibliographies of 20 arXiv papers first submitted in mid-August 2026 (cs, stat, q-bio, quant-ph and astro-ph), chosen mechanically and collected only after every fix in this release, with every warning and error reviewed by hand: | References | Flags | Real problems | False positives | Unclear | False positives per 100 references | |---|---|---|---|---|---| | 753 | 86 | 77 | 9 | 0 | 1.2 | - **One false alarm every two papers** (38 references on average), against 77 real problems: 36 errors in the entries (invented authors and titles, wrong given names, years and titles, identifiers written so that links break) and 41 cited preprints that have since been published. - **The false alarms are mostly registry records with errors of their own** (two misspelt titles, an affiliation mark inside a name, a workshop filed under a joint volume) **and real works no source describes as cited** (a Substack post, a technical report, a database cited by its access year, an article's early-access year). - **Six 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). Details in [`evals/README.md`](evals/README.md#real-papers). ### Next to other tools [Badalova & Mayr (2026)](https://doi.org/10.5281/zenodo.21457492) 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`](evals/results/badalova-mayr.md). ### On a benchmark: HALLMARK [HALLMARK](https://github.com/rpatrik96/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 | 98.1% | 88.9% | 2.2% | 97.0% | | | Fabrication | 99.0% | 49.0% | 0.6% | 97.0% | | `dev_public`: 1,119 entries, used during development | Any issue | 97.6% | 90.7% | 2.1% | 98.4% | | | Fabrication | 98.1% | 52.7% | 1.0% | 98.4% | HALLMARK v1.2.3, every entry of both public splits, run on 2026-10-04. *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:** the same precision and two points less recall on entries no rule was ever tuned on. - **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`](evals/hallmark_disputed.toml). - **What is still missed:** invented venues on papers known only as preprints (an arXiv record cannot contradict a venue) and author lists that merely leave people out. See [`evals/results/`](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/`](evals/README.md). ## Quick start With [uv](https://docs.astral.sh/uv/) nothing needs installing (or `pip install paper-preflight`): ```bash 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). No LaTeX at all? A reference list as plain text works too, in the common styles (APA, IEEE, ACM, Nature, Vancouver, Springer, Elsevier, Chicago, MLA), one reference per line, per paragraph or numbered: ```bash 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. ```bash uvx paper-preflight check arxiv:2607.06922 ``` Only the PDF? Its reference list is read too, with the `pdf` extra: ```bash 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) | | `--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 | ## 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: ```bash paper-preflight bib fetch 1810.04805 ``` ```bibtex % 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`: ```bash paper-preflight bib fix path/to/paper --level unsafe ``` ```diff --- 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, and removes identifiers that point to another work. 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: ```bibtex % 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. ## 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. ```bash pip install "paper-preflight[support]" ``` ```bash 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`](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 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. ```bash claude plugin marketplace add amos689/paper-preflight ``` ```bash 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: ```bash 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](docs/mcp.md). **pre-commit** — check citation keys and cached verdicts on every commit in seconds; see [docs/pre-commit.md](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](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 | `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) - Next: catch more of what is still missed (real titles with invented authors, references without titles, invented venues), each round measured on a new week of real papers - Later: Chinese-language references Progress is tracked in [docs/PROGRESS.md](docs/PROGRESS.md) (in Chinese) and the [changelog](CHANGELOG.md). ## Contributing Bug reports with a reproducible `.bib` entry are the most valuable contribution, especially false positives. See [CONTRIBUTING.md](CONTRIBUTING.md). ## License [MIT](LICENSE). See [THIRD_PARTY_NOTICES.md](THIRD_PARTY_NOTICES.md) for adapted code.