datasets
Training and evaluation data, with the modality, task and licence stated up front. Listed live from the Hugging Face Hub.
3D-ADAMRepository for the 3D-ADAM (3D Anomaly Detection in Additive Manufacturing) Dataset. This is the raw data for our complete dataset, separated by part-instance to allow users to utilise the dataset as desired.
We provide a single-camera (using the MechMind-Nano) subset prepared for unsupervised training at anomaly detection, localisation and segementation tasks through the anomalib library in a separate repository: here
Our ArXiv paper can also be found here: 3D-ADAM Dataset
This project has… See the full description on the dataset page: https://huggingface.co/datasets/pmchard/3D-ADAM.PMC
Data collected from PMC
Only CC-BY, CC-BY-SA licenses are included.
For all records, check the jsonl files in the data folder
PMC-VQA
PMC-VQA Dataset
PMC-VQA Dataset
Daraset Structure
Sample
Dataset Structure
PMC-VQA (version-1: 227k VQA pairs of 149k images).
train.csv: metafile of train set
test.csv: metafile of test set
test_clean.csv: metafile of test clean set
images.zip: images folder
(update version-2: noncompound images).
train2.csv: metafile of train set
test2.csv: metafile of test set
images2.zip: images folder
Sample
A row in train.csv is shown bellow… See the full description on the dataset page: https://huggingface.co/datasets/RadGenome/PMC-VQA.open-pmc-18m
OPEN-PMC
Arxiv: Arxiv
|
Code: Open-PMC Github
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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.… See the full description on the dataset page: https://huggingface.co/datasets/vector-institute/open-pmc-18m.pmc_oaFoundation models trained on large-scale dataset gain a recent surge in CV and NLP. In contrast, development in biomedical domain lags far behind due to data scarcity.
To address this issue, we build and release PMC-OA, a biomedical dataset with 1.6M image-caption pairs collected from PubMedCentral's OpenAccess subset, which is 8 times larger than before.
PMC-OA covers diverse modalities or diseases, with majority of the image-caption samples aligned at finer-grained level, i.e., subfigure and subcaption.
While pretraining a CLIP-style model on PMC-OA, our model named PMC-CLIP achieves state-of-the-art results on various downstream tasks,
including image-text retrieval on ROCO, MedMNIST image classification, Medical VQA, i.e. +8.1% R@10 on image-text retrieval, +3.9% accuracy on image classification.PMC-Treatment
🔭 Overview
R2MED: First Reasoning-Driven Medical Retrieval Benchmark
R2MED is a high-quality, high-resolution synthetic information retrieval (IR) dataset designed for medical scenarios. It contains 876 queries with three retrieval tasks, five medical scenarios, and twelve body systems.
Dataset
#Q
#D
Avg. Pos
Q-Len
D-Len
Biology
103
57359
3.6
115.2
83.6
Bioinformatics77
47473
2.9
273.8
150.5
Medical Sciences
88
34810
2.8
107.1
122.7
MedXpertQA-Exam
97… See the full description on the dataset page: https://huggingface.co/datasets/R2MED/PMC-Treatment.PMC-Clinical
🔭 Overview
R2MED: First Reasoning-Driven Medical Retrieval Benchmark
R2MED is a high-quality, high-resolution synthetic information retrieval (IR) dataset designed for medical scenarios. It contains 876 queries with three retrieval tasks, five medical scenarios, and twelve body systems.
Dataset
#Q
#D
Avg. Pos
Q-Len
D-Len
Biology
103
57359
3.6
115.2
83.6
Bioinformatics77
47473
2.9
273.8
150.5
Medical Sciences
88
34810
2.8
107.1
122.7
MedXpertQA-Exam
97… See the full description on the dataset page: https://huggingface.co/datasets/R2MED/PMC-Clinical.PMC-Clinical-VQA
PMC-VQA: A Large-Scale Visual Question Answering Dataset for Clinical Figures
This dataset contains over 1,700,000 Visual Question Answering (VQA) samples derived from figures and charts in biomedical articles from PubMed Central (PMC).
This is a preliminary release. A full dataset card and an accompanying research paper are currently in preparation.
Raw version of this dataset with licenses and metadata can be found on Hugging Face: DermaVLM/pmc_clinical_VQA_raw
Dataset… See the full description on the dataset page: https://huggingface.co/datasets/DermaVLM/PMC-Clinical-VQA.pmc_open_access_xml
Dataset Card for PMC Open Access XML
Dataset Summary
The XML Open Access includes more than 3.4 million journal articles and preprints that are made available under
license terms that allow reuse.
Not all articles in PMC are available for text mining and other reuse, many have copyright protection, however articles
in the PMC Open Access Subset are made available under Creative Commons or similar licenses that generally allow more
liberal redistribution and reuse than a… See the full description on the dataset page: https://huggingface.co/datasets/TomTBT/pmc_open_access_xml.pmc_open_access_sectionPMC-VQA-1
PMC-VQA-1
This dataset is a streaming-friendly version of the PMC-VQA dataset, specifically containing the "Compounded Images" version (version-1). It is designed to facilitate efficient training and evaluation of Visual Question Answering (VQA) models in the medical domain, straight from the repository
Dataset Description
The original PMC-VQA dataset, available at https://huggingface.co/datasets/xmcmic/PMC-VQA, comprises Visual Question Answering pairs derived from… See the full description on the dataset page: https://huggingface.co/datasets/hamzamooraj99/PMC-VQA-1.PMC-Patients
Dataset Card for PMC-Patients
News
We released PMC-Patients-V2 (in JSON format with the same keys), which is based on 2024 PMC baseline and contains 250,294 patients.
The data collection pipeline remains the same except for using more PMC articles.
Dataset Summary
PMC-Patients is a first-of-its-kind dataset consisting of 167k patient summaries extracted from case reports in PubMed Central (PMC), 3.1M patient-article relevance and 293k patient-patient similarity… See the full description on the dataset page: https://huggingface.co/datasets/zhengyun21/PMC-Patients.PMC-Patients-ReCDS
Dataset Card for PMC-Patients-ReCDS
Dataset Summary
PMC-Patients is a first-of-its-kind dataset consisting of 167k patient summaries extracted from case reports in PubMed Central (PMC), 3.1M patient-article relevance and 293k patient-patient similarity annotations defined by PubMed citation graph.
Supported Tasks and Leaderboards
Based on PMC-Patients, we define two tasks to benchmark Retrieval-based Clinical Decision Support (ReCDS) systems: Patient-to-Article… See the full description on the dataset page: https://huggingface.co/datasets/zhengyun21/PMC-Patients-ReCDS.PMC-VQA-refinedMedVLThinker-pmc_vqaCode: https://github.com/UCSC-VLAA/MedVLThinker
Project Page: https://ucsc-vlaa.github.io/MedVLThinker/
📊 Datasets
Available Datasets
Our project provides several curated datasets for medical vision-language understanding and training:
Dataset
Modality
Description
Download
MedVLThinker-m23k-tokenized
Text-only
Tokenized version of the m23k dataset
🤗 HF
MedVLThinker-pmc_vqa-gpt_4o_reasoning-tokenized
Image-Text
Tokenized PMC-VQA dataset with GPT-4o generated… See the full description on the dataset page: https://huggingface.co/datasets/UCSC-VLAA/MedVLThinker-pmc_vqa.open-pmc
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.… See the full description on the dataset page: https://huggingface.co/datasets/vector-institute/open-pmc.pmc_open_access_figure_comm3D-ADAM_anomalibRepository for the 3D-ADAM (3D Anomaly Detection in Additive Manufacturing) Dataset.
This is a single-camera (using the MechMind-Nano) subset prepared for unsupervised training at anomaly detection, localisation and segementation tasks through the anomalib library.
The full training, test and validation sets can be viewed and interacted with in this repository, and we also provide a zipped copy of the data which can be accessed automatically when using the dataset through the anomalib… See the full description on the dataset page: https://huggingface.co/datasets/pmchard/3D-ADAM_anomalib.pmc_llama_instructionsThis repo provides part of the dataset used for PMC-LLaMA-13B's instruction tuning.
Data
Size
Link
ChatDoctor
100K
https://www.yunxiangli.top/ChatDoctor/
MedQA
10.2K
https://huggingface.co/datasets/GBaker/MedQA-USMLE-4-options
MedMCQA
183K
https://huggingface.co/datasets/medmcqa
PubmedQA
211K
https://huggingface.co/datasets/pubmed_qa
LiveQA
635
https://huggingface.co/datasets/truehealth/liveqa
MedicationQA
690
https://huggingface.co/datasets/truehealth/medicationqa
UMLS… See the full description on the dataset page: https://huggingface.co/datasets/axiong/pmc_llama_instructions.soda-vec-data-full_pmc_title_abstract
SODA-VEC Clean Dataset
This is a cleaned and filtered version of the SODA-VEC dataset, containing high-quality biomedical title-abstract pairs from PubMed Central (PMC) articles.
Dataset Overview
Total examples: 26,573,900
Training set: 26,473,900 examples (99.6%)
Validation set: 50,000 examples (0.2%)
Test set: 50,000 examples (0.2%)
Quality Filtering Applied
This dataset has been processed with the following quality filters:
Abstract Length… See the full description on the dataset page: https://huggingface.co/datasets/EMBO/soda-vec-data-full_pmc_title_abstract.open_accessThe PMC Open Access Subset includes more than 3.4 million journal articles and preprints that are made available under
license terms that allow reuse.
Not all articles in PMC are available for text mining and other reuse, many have copyright protection, however articles
in the PMC Open Access Subset are made available under Creative Commons or similar licenses that generally allow more
liberal redistribution and reuse than a traditional copyrighted work.
The PMC Open Access Subset is one part of the PMC Article Datasetspmc_open_access_figure_noncommsoda-vec-data-full_pmc_title_abstract_paired
SODA-VEC Paired Dataset for Negative Sampling
This is a paired version of the SODA-VEC dataset, specifically formatted for negative sampling training with MultipleNegativesRankingLoss.
Dataset Overview
Total examples: 26,573,900
Format: Paired (anchor-positive) for contrastive learning
Source: EMBO/soda-vec-data-full_pmc_title_abstract
Purpose: Training sentence transformers with negative sampling
Data Format
Each example contains:
anchor (string): The title… See the full description on the dataset page: https://huggingface.co/datasets/EMBO/soda-vec-data-full_pmc_title_abstract_paired.PMC-Patients-MetaDataMeta data for PMC-Patients that might facilitate reproduction or usage of our dataset, consisting of the following files (most of which can be derived from our main files above).
PMIDs.json
PMIDs of articles from which PMC-Patients are extracted.
List of string, length 140,897.
train_PMIDs.json & dev_PMIDs.json & test_PMIDs.json
PMIDs of articles in training / dev / test split.
List of string.
train_patient_uids.json & dev_patient_uids.json &… See the full description on the dataset page: https://huggingface.co/datasets/zhengyun21/PMC-Patients-MetaData.pmc-articles-dataset-mentions-snippets
PMC Articles Dataset Mentions Snippets
Text snippets from PubMed Central articles paired with structured dataset citations. Designed for training models to extract dataset references from scientific literature.
Description
Task: Extract structured dataset info (identifier, repository, webpage) from article text
Source: PMC open-access articles
Format: Text snippet → JSON output
Examples: Positive (with datasets) and negative (no datasets)
Fields… See the full description on the dataset page: https://huggingface.co/datasets/vida-nyu/pmc-articles-dataset-mentions-snippets.euro_pmc_chemistry_paperspmc_vqa_basePMC-VQA
PMC-VQA - PubMed Central Visual Question Answering
Description
This dataset contains visual question answering data from PubMed Central medical literature. Questions are designed as multiple choice format requiring understanding of medical figures and images. 16 reasoning traces were collected for each example in this task by sampling with GPT-4o, available in the responses column. We greatly appreciate and build from the original data source available at… See the full description on the dataset page: https://huggingface.co/datasets/OctoMed/PMC-VQA.train_valid_split_pmc_neuroscience_2002-2022_filtered_subsetData from PubMed for abstracts and PubMed Central Open Access Subset (PMC OAS) for full-text articles using the Entrez Programming Utilities (E-utilities) API
and the pubget Python package, respectively. The data span publication dates from 2002 to 2022. For science general journals, a keyword filter of ``Neuroscience" was applied (all sourced journals are below).
Data extraction efforts yielded 332,807 abstracts and 123,085 full-text articles, totaling 1.3 billion tokens.
Figures and tables… See the full description on the dataset page: https://huggingface.co/datasets/BrainGPT/train_valid_split_pmc_neuroscience_2002-2022_filtered_subset.PMC-VQA_small