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# OpenPMC-VL

Please replace all dataset names everywhere with OpenPMC

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OpenPMC-VL

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[![license](https://img.shields.io/github/license/VectorInstitute/aieng-template.svg)](https://github.com/VectorInstitute/pmc-data-extraction/blob/main/LICENSE.md)

A toolkit to download, augment, and benchmark OpenPMC-VL; a large dataset of image-text pairs extracted from open-access scientific articles on PubMedCentral.

OpenPMC

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OpenPMC-VL

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## Download and parse image-caption pairs from Pubmed Articles
The codebase used to download Pubmed articles and parse image-text pairs from them is stored in `openpmcvl/foundation`.

openpmc

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For more details, see the following resources:
- **arXiv Paper:** [PMC-CLIP: Contrastive Language-Image Pre-training using Biomedical Documents](http://arxiv.org/abs/2503.14377)

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[arXiv Paper:] (http://arxiv.org/abs/2503.14377)

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arXiv Paper

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For more details, see the following resources:
- **arXiv Paper:** [PMC-CLIP: Contrastive Language-Image Pre-training using Biomedical Documents](http://arxiv.org/abs/2503.14377)

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PMC-CLIP: Contrastive Language-Image Pre-training using Biomedical Documents

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README.md line 13 at r2 (raw file):

For more details, see the following resources:
- **arXiv Paper:** [PMC-CLIP: Contrastive Language-Image Pre-training using Biomedical Documents](http://arxiv.org/abs/2503.14377)
- **Dataset on Hugging Face:** [Open_PMC Dataset on Hugging Face](https://huggingface.co/datasets/vector-institute/open-pmc)

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Dataset on Hugging Face

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- **arXiv Paper:** [PMC-CLIP: Contrastive Language-Image Pre-training using Biomedical Documents](http://arxiv.org/abs/2503.14377)
- **Dataset on Hugging Face:** [Open_PMC Dataset on Hugging Face](https://huggingface.co/datasets/vector-institute/open-pmc)
- **Model Checkpoint on Hugging Face:** [Open_PMC_CLIP Model Checkpoint on Hugging Face](https://huggingface.co/vector-institute/open-pmc-clip)

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Model Checkpoint

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- **Dataset:** [Open_PMC Dataset on Hugging Face](https://huggingface.co/datasets/vector-institute/open_pmc)
- **Checkpoint:** [Open_PMC_CLIP Model Checkpoint on Hugging Face](https://huggingface.co/vector-institute/open_pmc_clip)

This section is already above, right?

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## Hugging Face Dataset and Checkpoint

- **Dataset:** [Open_PMC Dataset on Hugging Face](https://huggingface.co/datasets/vector-institute/open_pmc)
- **Checkpoint:** [Open_PMC_CLIP Model Checkpoint on Hugging Face](https://huggingface.co/vector-institute/open_pmc_clip)

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@article{baghbanzadeh2025advancing,
  title={Advancing Medical Representation Learning Through High-Quality Data},
  author={Baghbanzadeh, Negin and Fallahpour, Adibvafa and Parhizkar, Yasaman and Ogidi, Franklin and Roy, Shuvendu and Ashkezari, Sajad and Khazaie, Vahid Reza and Colacci, Michael and Etemad, Ali and Afkanpour, Arash and others},

Only Elham's name is missing here. Replace others with her name if possible.

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others

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  journal={arXiv preprint arXiv:2303.07240},
  year={2023}
}

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## References
<a id="1">[1]</a> PMC-OA paper:
latex
@article{lin2023pmc,
  title={PMC-CLIP: Contrastive Language-Image Pre-training using Biomedical Documents},
  author={Lin, Weixiong and Zhao, Ziheng and Zhang, Xiaoman and Wu, Chaoyi and Zhang, Ya and Wang, Yanfeng and Xie, Weidi},
  journal={arXiv preprint arXiv:2303.07240},
  year={2023}
}

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README.md line 18 at r5 (raw file):

For more details, see the following resources:
- **[arXiv Paper]:** [http://arxiv.org/abs/2503.14377](http://arxiv.org/abs/2503.14377)

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arXiv Preprint:

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For more details, see the following resources:
- **[arXiv Paper]:** [http://arxiv.org/abs/2503.14377](http://arxiv.org/abs/2503.14377)
- **[Dataset]:** [Hugging Face](https://huggingface.co/datasets/vector-institute/open-pmc)

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README.md line 19 at r5 (raw file):

For more details, see the following resources:
- **[arXiv Paper]:** [http://arxiv.org/abs/2503.14377](http://arxiv.org/abs/2503.14377)
- **[Dataset]:** [Hugging Face](https://huggingface.co/datasets/vector-institute/open-pmc)

delete [Hugging Face] and just use the link.

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[Hugging Face]

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- **[arXiv Paper]:** [http://arxiv.org/abs/2503.14377](http://arxiv.org/abs/2503.14377)
- **[Dataset]:** [Hugging Face](https://huggingface.co/datasets/vector-institute/open-pmc)
- **[Model Checkpoint]:** [Hugging Face](https://huggingface.co/vector-institute/open-pmc-clip)

ditto.

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[Model Checkpoint]:** [Hugging Face]

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