bibtools

bibtidy cross-checks BibTeX entries against Google Scholar, CrossRef, and conference/journal sites. It upgrades arXiv/bioRxiv preprints to published versions (even when the title changed upon publication), corrects metadata (authors, pages, venues), and flags duplicate entries.

Install

Claude Code

Add the marketplace source:

/plugin marketplace add mathpluscode/bibtools

Install the plugin:

/plugin install bibtools@mathpluscode-bibtools

Reload plugins:

/reload-plugins

Codex

Tell Codex to fetch and follow the install instructions:

Fetch and follow instructions from https://raw.githubusercontent.com/mathpluscode/bibtools/main/.codex/INSTALL.md

Examples

Hallucinated reference (https://openreview.net/forum?id=75SJoY9gTN) +1 -6 not found

+% bibtidy: NOT FOUND — no matching paper on CrossRef or web search; verify this reference exists
-@article{wang2021identity,
-  title={On the identity of the representation learned by pre-trained language models},
-  author={Wang, Zijie J and Choi, Yuhao and Wei, Dongyeop},
-  journal={arXiv preprint arXiv:2109.01819},
-  year={2021}
-}

Hallucinated metadata (real paper, wrong title and authors) +4 -2 fix

+% bibtidy: https://openreview.net/forum?id=HSi4VetQLj
+% bibtidy: corrected title and authors
 @inproceedings{aichberger2025semantically,
-  title={Semantically Diverse Language Generation},
-  author={Aichberger, Franz and Chen, Lily and Smith, John},
+  title={Improving Uncertainty Estimation through Semantically Diverse Language Generation},
+  author={Aichberger, Lukas and Schweighofer, Kajetan and Ielanskyi, Mykyta and Hochreiter, Sepp},
   booktitle={International Conference on Learning Representations},
   year={2025}
 }

Wrong co-author (editor listed as author) +5 -3 author fix

+% bibtidy: https://jmlr.org/papers/v6/hyvarinen05a.html
+% bibtidy: removed "Dayan, Peter" — journal editor, not co-author; number 4 → 24
 @article{hyvarinen2005estimation,
-  title={Estimation of non-normalized statistical models by score matching.},
-  author={Hyv{\"a}rinen, Aapo and Dayan, Peter},
+  title={Estimation of non-normalized statistical models by score matching},
+  author={Hyv{\"a}rinen, Aapo},
   journal={Journal of Machine Learning Research},
   volume={6},
-  number={4},
+  number={24},
   year={2005}
 }

arXiv preprint with published version available +5 -3 preprint → published

+% bibtidy: https://openreview.net/forum?id=PqvMRDCJT9t
+% bibtidy: published at ICLR 2023 (was arXiv preprint)
-@article{lipman2022flow,
+@inproceedings{lipman2022flow,
   title={Flow matching for generative modeling},
   author={Lipman, Yaron and Chen, Ricky TQ and Ben-Hamu, Heli and Nickel, Maximilian and Le, Matt},
-  journal={arXiv preprint arXiv:2210.02747},
-  year={2022}
+  booktitle={International Conference on Learning Representations},
+  year={2023}
 }

Formatting issues (DOI URL prefix, single-hyphen pages) +4 -2 formatting fix

+% bibtidy: https://doi.org/10.48550/arXiv.2006.11239
+% bibtidy: stripped DOI URL prefix, fixed page range hyphen
 @article{ho2020denoising,
   title={Denoising diffusion probabilistic models},
   author={Ho, Jonathan and Jain, Ajay and Abbeel, Pieter},
   journal={Advances in Neural Information Processing Systems},
   volume={33},
-  pages={6840-6851},
+  pages={6840--6851},
   year={2020},
-  doi={https://doi.org/10.48550/arXiv.2006.11239}
+  doi={10.48550/arXiv.2006.11239}
 }

Duplicate pair (bioRxiv preprint + published version) +1 duplicate detected

+% bibtidy: DUPLICATE of watson2023novo — consider removing
 @article{watson2022broadly,
   title={Broadly applicable and accurate protein design by integrating structure prediction networks and diffusion generative models},
   author={Watson, Joseph L and Juergens, David and Bennett, Nathaniel R and Trippe, Brian L and Yim, Jason and Eisenach, Helen E and Ahern, Woody and Borst, Andrew J and Ragotte, Robert J and Milles, Lukas F and others},
   journal={BioRxiv},
   pages={2022--12},
   year={2022},
   publisher={Cold Spring Harbor Laboratory}
 }
 
 @article{watson2023novo,
   title={De novo design of protein structure and function with RFdiffusion},
   author={Watson, Joseph L and Juergens, David and Bennett, Nathaniel R and Trippe, Brian L and Yim, Jason and Eisenach, Helen E and Ahern, Woody and Borst, Andrew J and Ragotte, Robert J and Milles, Lukas F and others},
   journal={Nature},
   volume={620},
   pages={1089--1100},
   year={2023},
   publisher={Nature Publishing Group UK London}
 }

Wrong page numbers (should be corrected via CrossRef) +3 -1 page fix

+% bibtidy: https://doi.org/10.1109/iccv48922.2021.00717
+% bibtidy: corrected page range 7262--7272 → 7242--7252
 @inproceedings{strudel2021segmenter,
   title={Segmenter: Transformer for semantic segmentation},
   author={Strudel, Robin and Garcia, Ricardo and Laptev, Ivan and Schmid, Cordelia},
   booktitle={Proceedings of the IEEE/CVF international conference on computer vision},
-  pages={7262--7272},
+  pages={7242--7252},
   year={2021}
 }

arXiv preprint where published title changed +6 -3 preprint → published

+% bibtidy: https://doi.org/10.1038/s41598-023-34341-2
+% bibtidy: updated from arXiv to published version (Scientific Reports 2023), title updated
 @article{khader2022medical,
-  title={Medical Diffusion--Denoising Diffusion Probabilistic Models for 3D Medical Image Generation},
+  title={Denoising Diffusion Probabilistic Models for 3D Medical Image Generation},
   author={Khader, Firas and Mueller-Franzes, Gustav and Arasteh, Soroosh Tayebi and Han, Tianyu and Haarburger, Christoph and Schulze-Hagen, Maximilian and Schad, Philipp and Engelhardt, Sandy and Baessler, Bettina and Foersch, Sebastian and others},
-  journal={arXiv preprint arXiv:2211.03364},
-  year={2022}
+  journal={Scientific Reports},
+  volume={13},
+  year={2023}
 }

Correct entry (should be left unchanged) unchanged

 @inproceedings{vaswani2017attention,
   title={Attention is All you Need},
   author={Vaswani, Ashish and Shazeer, Noam and Parmar, Niki and Uszkoreit, Jakob and Jones, Llion and Gomez, Aidan N and Kaiser, {\L}ukasz and Polosukhin, Illia},
   booktitle={Advances in Neural Information Processing Systems},
   volume={30},
   year={2017}
 }

Published article should not be downgraded to preprint unchanged

 @article{tzou2022coronavirus,
   title={Coronavirus Resistance Database (CoV-RDB): SARS-CoV-2 susceptibility to monoclonal antibodies, convalescent plasma, and plasma from vaccinated persons},
   author={Tzou, Philip L and Tao, Kaiming and Pond, Sergei L Kosakovsky and Shafer, Robert W},
   journal={Plos one},
   volume={17},
   number={3},
   pages={e0261045},
   year={2022},
   publisher={Public Library of Science San Francisco, CA USA}
 }