bibtex-updater 1.3.0

Replace preprint BibTeX entries with published versions and validate bibliography references

BibTeX Updater

Tools for managing BibTeX bibliographies: automatically update preprints to published versions, validate references against external databases, and filter to only cited references.

Installation

From PyPI (Recommended)

pip install bibtex-updater

# With Google Scholar support
pip install bibtex-updater[scholarly]

# With Zotero support
pip install bibtex-updater[zotero]

# All optional dependencies
pip install bibtex-updater[all]

From Source (Recommended)

git clone https://github.com/rpatrik96/bibtexupdater.git
cd bibtexupdater
uv sync --extra dev --extra all

Using uv (No Installation)

Run directly without cloning using uv:

# Run any command directly
uv run --with "bibtex-updater[all]" bibtex-update references.bib -o updated.bib

# Or use the provided wrapper script
./scripts/bibtex-x update references.bib -o updated.bib
./scripts/bibtex-x check references.bib
./scripts/bibtex-x filter paper.tex -b references.bib -o filtered.bib

CLI Commands

Command	Description
bibtex-update	Replace preprints with published versions
bibtex-check	Validate references exist with correct metadata
bibtex-filter	Filter to only cited entries
bibtex-zotero	Update preprints in Zotero library
bibtex-zotero-organize	Organize Zotero items into collections by research taxonomy
bibtex-obsidian-keywords	AI-powered keyword generation for Obsidian paper notes

Quick Start

Update Preprints

# Update preprints to published versions
bibtex-update references.bib -o updated.bib

# Preview changes (dry run)
bibtex-update references.bib --dry-run --verbose

Validate References (Fact-Check)

# Check if references exist and have correct metadata
bibtex-check references.bib --report report.json

# Strict mode: exit with error if hallucinated/not-found entries
bibtex-check references.bib --strict

Filter Bibliography

# Filter to only cited entries
bibtex-filter paper.tex -b references.bib -o filtered.bib

# Multiple tex files
bibtex-filter *.tex -b references.bib -o filtered.bib

Update Zotero Library

# Set credentials (get from zotero.org/settings/keys)
export ZOTERO_LIBRARY_ID="your_user_id"
export ZOTERO_API_KEY="your_api_key"

# Preview changes
bibtex-zotero --dry-run

# Apply updates
bibtex-zotero

Sync BibTeX Updates to Zotero

When updating a .bib file, you can simultaneously update matching entries in your Zotero library:

# Set Zotero credentials
export ZOTERO_LIBRARY_ID="your_user_id"
export ZOTERO_API_KEY="your_api_key"

# Update bib file AND sync to Zotero
bibtex-update references.bib -o updated.bib --zotero

# Preview Zotero changes only (bib changes still apply)
bibtex-update references.bib -o updated.bib --zotero --zotero-dry-run

# Limit to a specific Zotero collection
bibtex-update references.bib -o updated.bib --zotero --zotero-collection ABCD1234

The sync matches bib entries to Zotero items by:

1. arXiv ID - Most reliable for preprints
2. DOI - For preprints with DOIs (e.g., bioRxiv)
3. Title + Author - Fuzzy matching as fallback

Standalone Scripts

For environments without pip (e.g., Overleaf), filter_bibliography.py can be used directly as it has no dependencies:

# Copy the script and run directly
python filter_bibliography.py paper.tex -b references.bib -o filtered.bib

Documentation

Document	Description
docs/BIBTEX_UPDATER.md	Full BibTeX updater documentation
docs/REFERENCE_FACT_CHECKER.md	Full reference fact-checker documentation
docs/ZOTERO_UPDATER.md	Full Zotero updater documentation
docs/FILTER_BIBLIOGRAPHY.md	Full filter documentation
docs/LANDSCAPE.md	Databases, competing tools, and ecosystem landscape
benchmarks/HALLMARK.md	bibtex-check v1.2.0 detection metrics on HALLMARK v1.1.1 (all splits) + reproduction
examples/	Example workflows and configuration files

Overleaf Integration

Both tools integrate with Overleaf via GitHub Actions or latexmkrc.

GitHub Actions (Recommended)

1. Enable GitHub sync in Overleaf (Menu -> Sync -> GitHub)
2. Copy a workflow from examples/workflows/ to .github/workflows/
3. Changes synced from Overleaf automatically trigger updates

latexmkrc (Direct Overleaf)

For filter_bibliography.py only (no dependencies required):

1. Upload filter_bibliography.py to your Overleaf project
2. Create .latexmkrc based on examples/latexmkrc
3. Recompile - filtered bibliography appears in your file list

Features

BibTeX Updater (bibtex-update)

• Multi-source resolution: arXiv, OpenAlex, Europe PMC, Crossref, DBLP, ACL Anthology, OpenReview, Semantic Scholar, Google Scholar
• High accuracy: Title and author fuzzy matching with confidence thresholds
• ACL Anthology support: Zero-overhead resolution for NLP papers (ACL, EMNLP, NAACL, etc.)
• Batch processing: Multiple files with concurrent workers (default: 8)
• Deduplication: Merge duplicates by DOI or normalized title+authors
• Smart caching: On-disk cache + semantic resolution cache with TTL
• Per-service rate limiting: Optimized rate limits per API (Crossref, S2, DBLP, ACL Anthology, arXiv, OpenAlex, Europe PMC, OpenReview)
• Batch API support: Faster bulk lookups via arXiv/S2/Crossref batch endpoints
• Resolution tracking: --mark-resolved tags updated entries to skip on re-runs

Zotero Updater (bibtex-zotero)

• Direct Zotero integration: Fetches and updates items via Zotero API
• Same resolution pipeline: Uses the same multi-source resolution
• Preserves metadata: Keeps notes, tags, and attachments intact
• Idempotent: Already-published papers are automatically skipped
• Dry-run mode: Preview changes before applying
• Tag-based chunking: Track processing state with preprint-upgraded/preprint-checked/preprint-error tags

Zotero Organizer (bibtex-zotero-organize)

• AI-powered taxonomy: Organize items into hierarchical collections automatically
• Multiple backends: Claude, OpenAI, or local embeddings for classification
• Caching: Classification results cached to reduce API calls
• Batch processing: Configurable limits and dry-run mode

Obsidian Keywords (bibtex-obsidian-keywords)

• AI-powered keywords: Generate [[wikilinks]] for Obsidian paper notes
• Multiple backends: Claude, OpenAI, or local embeddings
• Smart skipping: --min-keywords to skip notes that already have enough keywords
• Topics file: Provide existing topics for consistent tagging across notes
• Dry-run mode: Preview changes before modifying files

Reference Fact-Checker (bibtex-check)

v1.2.0 carries v1.1.0's held-out FPR work into the catch-rate dimension: ~110 previously-abstained hallucinations are now flagged as problematic, the SCoRe wrong-venue leak class is caught, and a --strict evaluation mode tuned for arXiv's 2026 hallucinated-reference policy (1-year ban followed by peer-review-first requirement) is available for high-stakes audits. Against the corrected HALLMARK v1.0 gold:

• Held-out test FPR steady at 2.32% (8.94% in v1.0.0 → 2.32% in v1.1.0+v1.2.0; −74% vs v1.0.0). Dev FPR 1.59% → 1.99% (+0.4pp; 3 small documented regression FPs)
• Caught-on-hallucinated: dev 60% → 75%, test 58% → 74% (+15pp on both splits) — driven by the new cross-source venue verification (catches SCoRe-shape leaks), the ID-anchored venue/year mismatch helper, and the relaxed-author retrieval fallback
• Leak rate: 0.65% dev (4 entries), 0.57% test (3 entries; SCoRe caught — was 4 in v1.1.0); policy-adjusted 0.32% / 0.38% — remaining "leaks" are mostly 1-character title perturbations; hyphen-only differences are explicitly not counted as leaks in default mode (hyphenation is bibliographic noise that varies across DBLP/Crossref/publisher records — flagging it would generate false positives on most legit refs). --strict catches every 1-char title diff (Levenshtein-1, hyphen included) for arXiv-style high-stakes audits, plus tolerance-0 year, single-source author-fab detection, and truncated-author flagging. See docs/KNOWN_LEAKS.md for the per-leak enumeration and policy
• Could-not-verify on real refs dropped ~70% via venue + retrieval refinements (OpenReview/PMLR track-suffix normalization, TMLR/JMLR ISO-4 alias expansion, diacritic-preserving paperhash)

The "leak" headline is mostly benchmark noise: HALLMARK PR #9 corrects 30 entries — including FlashAttention, DDPM, Imagen, SimCLR, Performers, ViT-vs-CNN, Chain-of-Thought (Wei), Zero-Shot Reasoner (Kojima), MERLOT — that the v1.0 auto-labeller flagged as fabricated but are in fact real, correctly-cited papers (arXiv DOIs register with DataCite, not CrossRef, so the auto-labeller's "no resolve" check returned false). The corrected leak rate isolates genuine catch opportunities.

The full per-split detection grid (DR / FPR / Precision / F1 / MCC / Coverage on dev_public, test_public, stress_test, test_crossdomain) against the corrected HALLMARK v1.1.1 gold lives in benchmarks/HALLMARK.md, with a reproducible eval script (scripts/eval_hallmark.py):

# Score bibtex-check on a HALLMARK split and emit detection metrics
export S2_API_KEY=...   # optional: lifts Semantic Scholar rate limits
python scripts/eval_hallmark.py --split /path/to/hallmark/data/v1.0/test_public.jsonl --out test_public.json

• Multi-source validation: Crossref, OpenAlex, DBLP, OpenReview, Semantic Scholar
• Detailed mismatch detection: Title, author, year, venue comparisons
• Integrity checks: DOI- and arXiv-ID-target consistency, ID-anchored author fabrication, chimeric-title detection
• Hallucination detection: Reserves hallucinated for positive evidence (fabricated DOI, future/invalid year, ID misattribution); abstains (not_found) on weak matches
• Structured reports: JSON and JSONL output formats
• CI/CD integration: Strict mode with exit codes for automation

Cascading verification

Inspired by Abbonato 2026 (CheckIfExist), verification runs a single cascade — CrossRef → OpenAlex → DBLP → OpenReview → Semantic Scholar — that short-circuits as soon as one source produces a high-confidence match (≥0.95). Each step retrieves top-K candidates and re-ranks them by title similarity; combined with cross-source author intersection, this catches swapped-author / chimeric citations that single-source verification misses.

The order is throughput-aware: CrossRef and OpenAlex (polite pool, ~100 req/min) come first, then DBLP and OpenReview (~30 req/min) as the CS-conference and ICLR/NeurIPS/TMLR authorities, so the slow keyless Semantic Scholar fallback (~10 req/min) is only reached on hard entries. Set a Semantic Scholar API key (--s2-api-key or S2_API_KEY) to lift S2 from ~10 to ~60 req/min.

OpenReview owns the submission record for most ML conferences, so it positively confirms ICLR/NeurIPS/TMLR papers that the DOI- and CS-index sources above can only leave in the "could-not-verify" bucket. Retrieval uses fielded title search (CrossRef query.title, OpenAlex title.search) rather than a free-text title+author blob, which keeps DOI-less ML-conference titles ranked correctly.

# Verification with top-3 candidates per source
bibtex-check references.bib --top-k 3 --jsonl out.jsonl

# Polite OpenAlex pool (recommended)
bibtex-check references.bib --openalex-mailto [e-mail]

A 0–100 numeric confidence_score (additive in the JSONL output) summarizes per-field similarity with explicit penalty/bonus contributions:

• Multi-source bonus: +10 when ≥2 sources confirm the same authors
• Penalties: title-mismatch -20, author-mismatch -20, journal-mismatch -15, fabricated-author -10 each (capped at -20)
• Asymmetric formula for the high-title-low-author chimeric case: confidence = S_title − 0.5 × (100 − S_author)

Verdicts: verified vs. could-not-verify vs. problematic

VERIFIED requires every claimed field to be positively confirmed against the matched record — not merely "not contradicted". When a record is found but a claimed field can't be confirmed (e.g. a published venue backed only by a preprint, or an incomplete author list), the entry is reported as could-not-verify (UNCONFIRMED/NOT_FOUND), distinct from a problematic flag (*_mismatch, doi_mismatch, chimeric, …) which is positive evidence of a defect. A "could-not-verify" is not a clean pass: it means the tool couldn't decide, and such entries warrant review.

For full transparency, every residual VERIFIED-on-a-real-leak case against the corrected HALLMARK v1.0 gold is enumerated in docs/KNOWN_LEAKS.md, with the perturbation, the default verdict, and the --strict rule that catches it.

Author handling

All sources return authors in as-published order, so a multiset-equal reordering is treated as a real swapped-authors defect — except when the API record is alphabetized (Crossref NeurIPS/ICML proceedings deposits, prefix 10.52202, sort contributors A–Z; that's a record-sort artifact, not a swap). Surname comparison uses each source's structured family field where available (Crossref, OpenAlex, OpenReview ~Given_Family handles), so family-first/CJK names like "Chen Xing" ↔ "Xing Chen" match cleanly; when the matched source lacks structured names, a Crossref structured-name lookup vets a potential author mismatch before reporting it.

The lead author's given name is graded via classify_given_pair: diacritic / initial / abbreviation / nickname / transliteration variants pass; a true substitution (e.g. "Shunyu Zhou" vs canonical "Denny Zhou") flags as GIVEN_NAME_SUBSTITUTION. The cross-source author-fabrication check downgrades the author outcome to AUTHOR_MISMATCH when the entry contributes ≥2 surnames absent from every order-reliable candidate's full author set (no and others sentinel, ≥2 sources contributing), catching fabricated trailing authors that slip past the prefix-N slice. DBLP-scraped XML entities (', &) are decoded before any matching, so d'Amore, D'Hondt, Ch'ng no longer trigger spurious mismatches.

Strict mode (--strict)

For high-stakes submissions where the asymmetric cost is leak ≫ FP — arXiv as of May 2026 imposes a 1-year ban for incontrovertible hallucinated references, thereafter requiring submissions to be accepted by a reputable peer-reviewed venue first — --strict (or BIBTEX_CHECK_STRICT=1) tightens the verdict gate:

• Title: Levenshtein-1 catches 1-character typos and added/removed hyphens ("Privacy"/"Privacys", "Schema Variable"/"Schema-Variable").
• Year: tolerance 0; a preprint-twin record returns STRICT_WARN_PREPRINT_YEAR instead of silently confirming.
• Author-set: even a single entry-side surname absent from a single complete canonical record flags AUTHOR_MISMATCH (the default requires ≥2 absent across ≥2 sources, to avoid false positives on stub records).
• Author order: the alphabetized-record escape is disabled — every same-multiset reordering on an order-reliable source flags.
• Truncated author list without an and others/et al sentinel flags AUTHOR_TRUNCATED (silent truncation is a misrepresentation; an explicit sentinel discloses it).

The companion --strict-warn-cnv subflag (requires --strict) promotes unconfirmed/not_found to a fourth visible category STRICT_WARN_CNV, so CI integrations can fail on entries the tool couldn't anchor. Default mode keeps the principled three-way verdict unchanged.

# Strict pass for an arXiv submission
bibtex-check references.bib --strict --strict-warn-cnv --jsonl strict.jsonl

Non-generative-AI mode (--non-generative)

For venue-policy compliance (ACL ARR, ICML 2026) the --non-generative flag (or BIBTEX_CHECK_NON_GENERATIVE=1 env var) refuses to load any LLM backend at runtime. Today the package has no LLM backends, so this is a forward-compat guard plus a startup banner:

bibtex-check references.bib --non-generative --strict
# bibtex-check running in non-generative mode (no LLM calls).
# Compliant with ICML 2026 / ACL ARR LLM-in-review policies.

Filter Bibliography (bibtex-filter)

• Zero dependencies: Uses only Python standard library
• Works on Overleaf: No pip install needed
• Multiple bib files: Merge and filter from multiple sources
• Citation detection: Supports natbib, biblatex, and standard LaTeX citations

Python API

from bibtex_updater import Detector, Resolver, Updater, HttpClient, RateLimiter, DiskCache

# Create HTTP client with rate limiting and caching
rate_limiter = RateLimiter(req_per_min=30)
cache = DiskCache(".cache.json")
http_client = HttpClient(
    timeout=30.0,
    user_agent="bibtex-updater/0.5.0",
    rate_limiter=rate_limiter,
    cache=cache
)

# Detect preprints
detector = Detector()
detection = detector.detect(entry)

if detection.is_preprint:
    # Resolve to published version
    resolver = Resolver(http_client)
    candidate = resolver.resolve(detection)

    if candidate and candidate.confidence >= 0.9:
        # Update the entry
        updater = Updater()
        updated_entry = updater.update_entry(entry, candidate.record, detection)

Development

# Clone and install in development mode
git clone https://github.com/rpatrik96/bibtexupdater.git
cd bibtexupdater
uv sync --extra dev --extra all

# Run tests
uv run pytest tests/ -v

# Run tests with coverage
uv run pytest tests/ -v --cov=bibtex_updater --cov-report=term-missing

# Code quality
pre-commit run --all-files

# Build package
uv build

# Check package
uv run twine check dist/*

License

MIT License - see LICENSE for details.