vector-institute/open-pmc-clip
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] | train-0000-000000 | hf://datasets/vector-institute/open-pmc@a7add5e1b0d8659281931898b1377d27c0d1a2dd/train-0000.tar |
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] | train-0000-000001 | hf://datasets/vector-institute/open-pmc@a7add5e1b0d8659281931898b1377d27c0d1a2dd/train-0000.tar |
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] | train-0000-000002 | hf://datasets/vector-institute/open-pmc@a7add5e1b0d8659281931898b1377d27c0d1a2dd/train-0000.tar |
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] | train-0000-000003 | hf://datasets/vector-institute/open-pmc@a7add5e1b0d8659281931898b1377d27c0d1a2dd/train-0000.tar |
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] | train-0000-000004 | hf://datasets/vector-institute/open-pmc@a7add5e1b0d8659281931898b1377d27c0d1a2dd/train-0000.tar |
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] | train-0000-000005 | hf://datasets/vector-institute/open-pmc@a7add5e1b0d8659281931898b1377d27c0d1a2dd/train-0000.tar |
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] | train-0000-000006 | hf://datasets/vector-institute/open-pmc@a7add5e1b0d8659281931898b1377d27c0d1a2dd/train-0000.tar |
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] | train-0000-000007 | hf://datasets/vector-institute/open-pmc@a7add5e1b0d8659281931898b1377d27c0d1a2dd/train-0000.tar |
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] | train-0000-000008 | hf://datasets/vector-institute/open-pmc@a7add5e1b0d8659281931898b1377d27c0d1a2dd/train-0000.tar |
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] | train-0000-000009 | hf://datasets/vector-institute/open-pmc@a7add5e1b0d8659281931898b1377d27c0d1a2dd/train-0000.tar |
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] | train-0000-000010 | hf://datasets/vector-institute/open-pmc@a7add5e1b0d8659281931898b1377d27c0d1a2dd/train-0000.tar |
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] | train-0000-000011 | hf://datasets/vector-institute/open-pmc@a7add5e1b0d8659281931898b1377d27c0d1a2dd/train-0000.tar |
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] | train-0000-000012 | hf://datasets/vector-institute/open-pmc@a7add5e1b0d8659281931898b1377d27c0d1a2dd/train-0000.tar |
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] | train-0000-000013 | hf://datasets/vector-institute/open-pmc@a7add5e1b0d8659281931898b1377d27c0d1a2dd/train-0000.tar |
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] | train-0000-000016 | hf://datasets/vector-institute/open-pmc@a7add5e1b0d8659281931898b1377d27c0d1a2dd/train-0000.tar |
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] | train-0000-000017 | hf://datasets/vector-institute/open-pmc@a7add5e1b0d8659281931898b1377d27c0d1a2dd/train-0000.tar |
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] | train-0000-000018 | hf://datasets/vector-institute/open-pmc@a7add5e1b0d8659281931898b1377d27c0d1a2dd/train-0000.tar |
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] | train-0000-000019 | hf://datasets/vector-institute/open-pmc@a7add5e1b0d8659281931898b1377d27c0d1a2dd/train-0000.tar |
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] | train-0000-000020 | hf://datasets/vector-institute/open-pmc@a7add5e1b0d8659281931898b1377d27c0d1a2dd/train-0000.tar |
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] | train-0000-000021 | hf://datasets/vector-institute/open-pmc@a7add5e1b0d8659281931898b1377d27c0d1a2dd/train-0000.tar |
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] | train-0000-000022 | hf://datasets/vector-institute/open-pmc@a7add5e1b0d8659281931898b1377d27c0d1a2dd/train-0000.tar |
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] | train-0000-000023 | hf://datasets/vector-institute/open-pmc@a7add5e1b0d8659281931898b1377d27c0d1a2dd/train-0000.tar |
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] | train-0000-000024 | hf://datasets/vector-institute/open-pmc@a7add5e1b0d8659281931898b1377d27c0d1a2dd/train-0000.tar |
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] | train-0000-000025 | hf://datasets/vector-institute/open-pmc@a7add5e1b0d8659281931898b1377d27c0d1a2dd/train-0000.tar |
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] | train-0000-000026 | hf://datasets/vector-institute/open-pmc@a7add5e1b0d8659281931898b1377d27c0d1a2dd/train-0000.tar |
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] | train-0000-000027 | hf://datasets/vector-institute/open-pmc@a7add5e1b0d8659281931898b1377d27c0d1a2dd/train-0000.tar |
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] | train-0000-000028 | hf://datasets/vector-institute/open-pmc@a7add5e1b0d8659281931898b1377d27c0d1a2dd/train-0000.tar |
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] | train-0000-000029 | hf://datasets/vector-institute/open-pmc@a7add5e1b0d8659281931898b1377d27c0d1a2dd/train-0000.tar |
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] | train-0000-000030 | hf://datasets/vector-institute/open-pmc@a7add5e1b0d8659281931898b1377d27c0d1a2dd/train-0000.tar |
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in Data Studio
OPEN-PMC
Arxiv: Arxiv | Code: Open-PMC Github | Model Checkpoint: Hugging Face
Dataset Summary
This dataset consists of image-text pairs extracted from medical papers available on PubMed Central. It has been curated to support research in medical image understanding, particularly in natural language processing (NLP) and computer vision tasks related to medical imagery. The dataset includes:
- Extracted images from research articles.
- Associated captions and sub-captions with each image.
- All pairs are filtered medical image-text pairs.
- All images are decomposed compound figures with their respective sub-captions.
- Summarized in-text references to corresponding images for better model training.
Supported Tasks and Benchmarks
This dataset is designed for research in:
- Medical Image Captioning: Training and evaluating models that generate descriptions for medical images.
- Multimodal Learning: Studying the relationship between medical images and their textual descriptions.
- Image-Text Retrieval: Enabling models to retrieve relevant images based on textual queries and vice versa.
- Medical Language Understanding: Assisting in understanding complex medical terminology in images.
Languages
The dataset primarily contains text in English.
Dataset Structure
Data Fields
Each record in the dataset contains:
- PMC_ID: Unique identifier from PubMed Central.
- Image: Filename of the extracted image.
- Sub-caption: Caption corresponding to a sub-part of a compound figure (if applicable).
- Full caption: Original figure caption from the research paper.
- In-text references summary: Summarized reference to the image from the body text of the paper.
- In-text references: The full in-text reference associated with the image.
- Modality: Image modality classification.
Data Splits
The dataset does not contain predefined splits. Users can split the data as needed for training, validation, and testing.
Dataset Creation
Source Data
Initial Data Collection and Processing
- Data Collection: We gathered medical papers from PubMed Central, extracting image-text pairs from these research articles.
- Filtering: Non-medical image-text pairs were removed to ensure a focused dataset.
- Compound Figure Decomposition: Multi-panel figures were split into individual sub-figures, and associated sub-captions were assigned.
- In-text Reference Extraction: In-text references to images were extracted from the articles.
- Summarization: For cases where in-text references existed, a summarization process was applied to generate concise descriptions useful for training models.
Annotations
The dataset does not contain additional manual annotations.
Uses
This dataset is designed for research purposes only and should not be used for:
- Clinical diagnosis.
- Medical decision-making.
- Any real-world patient care applications.
Ethical Considerations
- This dataset is derived from open-access publications available on PubMed Central.
- Researchers should comply with ethical guidelines and ensure that their work does not imply clinical utility.
- The dataset is intended strictly for academic and research purposes.
Citation
If you find the code useful for your research, please consider citing
@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},
journal={arXiv preprint arXiv:2503.14377},
year={2025}
}
License
This dataset is licensed under CC-BY-4.0, meaning it can be used for research purposes with appropriate attribution.
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Size of the auto-converted Parquet files (First 5GB per split):
10.8 GB
Number of rows (First 5GB per split):
696,579
Estimated number of rows:
1,981,451
Models trained or fine-tuned on vector-institute/open-pmc