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CLIMB Dataset Information

This document provides detailed information about each dataset included in the Clinical Large-scale Integrative Multi-modal Benchmark (CLIMB). The datasets are organized by modality.

ECG (Electrocardiogram)

PTB-XL

  • Description: 12-lead ECGs from 18,869 patients (10 seconds each)
  • Classes: 7 (Normal, CD, HYP, MI, STTC, A. Fib/Aflutter, Other)
  • Size: 21,837 records (17,476 train, 4,361 test)
  • Source: PhysioNet
  • License: Creative Commons Attribution 4.0 International
  • Access: https://physionet.org/files/ptb-xl/1.0.3/

Chapman-Shaoxing

  • Description: 12-lead ECGs from 10,646 patients
  • Classes: 7 (Same as PTB-XL)
  • Size: 40,258 records (38,207 train, 2,051 test)
  • License: Creative Commons Attribution 4.0 International
  • Access: Available on Kaggle

Georgia

  • Description: 12-lead ECGs from 15,742 patients (10 seconds, 500 Hz)
  • Classes: 7 (Same as PTB-XL)
  • Size: 20,689 records (18,622 train, 2,067 test)
  • License: Creative Commons Public Domain
  • Access: Available on Kaggle

CPSC

  • Description: 12-lead Holter and 3-lead wearable ECG recordings
  • Classes: 7 (Same as PTB-XL)
  • Size: 6,192 records (4,815 train, 1,377 test)
  • License: Creative Commons Attribution 4.0 International
  • Access: Available on PhysioNet

EEG (Electroencephalogram)

IIIC

  • Description: EEG samples from 2,711 patients, annotated by 124 raters
  • Classes: 6 (SZ, LPD, GPD, LRDA, GRDA, Other)
  • Size: 134,450 segments
  • License: BDSP Restricted Health Data License 1.0.0
  • Access: Available through BDSP
  • Split: 60% train, 20% validation, 20% test (by patient groups)

TUAB

  • Description: 276 EEG recording sessions from 253 subjects
  • Classes: 2 (Normal, Abnormal)
  • Size: 409,500 total records
  • License: Custom (requires application)
  • Access: Available through Temple University

TUEV

  • Description: 518 EEG recording sessions from 368 subjects
  • Classes: 6 (SPSW, GPED, PLED, EYEM, ARTF, BCKG)
  • Size: 111,900 total records
  • License: Custom (requires application)
  • Access: Available through Temple University

Chest X-ray

MIMIC-CXR

  • Description: Large-scale chest X-ray dataset
  • Classes: 14 (Atelectasis, Cardiomegaly, Consolidation, Edema, Enlarged Cardiomediastinum, Fracture, Lung Lesion, Lung Opacity, Pleural Effusion, Pneumonia, Pneumothorax, Pleural Other, Support Devices, No Finding)
  • Size: 356,225 records (348,516 train, 7,709 test)
  • License: PhysioNet Credentialed Health Data License 1.5.0
  • Access: Requires credentialed account and CITI training

CheXpert

  • Description: Chest radiographs from Stanford Hospital
  • Classes: 14 (Same as MIMIC-CXR)
  • Size: 212,498 records (212,243 train, 225 test)
  • License: Stanford University Dataset Research Use Agreement
  • Access: Requires registration

VinDr-CXR

  • Description: Adult chest X-rays from Vietnamese hospitals
  • Classes: 6 (Lung tumor, Pneumonia, Tuberculosis, COPD, Other diseases, No finding)
  • Size: 18,000 records (15,000 train, 3,000 test)
  • License: PhysioNet Credentialed Health Data License 1.5.0
  • Access: Requires credentialed account

COVID-19

  • Description: Chest X-ray dataset for COVID-19 related diseases
  • Classes: 4 (Normal, Bacterial Pneumonia, COVID-19, Viral Pneumonia)
  • Size: 2,990 records (2,002 train, 988 test)
  • License: Creative Commons Attribution 4.0 International
  • Access: Available on Kaggle

CoronaHack

  • Description: Chest X-ray dataset from University of Montreal
  • Classes: 3 (Normal, Bacterial Pneumonia, Viral Pneumonia)
  • Size: 5,908 records (5,284 train, 624 test)
  • License: Creative Commons Attribution 4.0 International
  • Access: Available on Kaggle

Mammography

VinDr-Mammo

  • Description: Mammography from Vietnamese hospitals
  • Classes: 5 (BI-RAD 1-5)
  • Size: 20,000 records (16,000 train, 4,000 test)
  • License: PhysioNet Restricted Health Data License 1.5.0
  • Access: Requires data use agreement

CBIS-DDSM

  • Description: Curated subset of Digital Database for Screening Mammography
  • Classes: 6 (BI-RAD 0-5)
  • Size: 2,825 records (2,230 train, 595 test)
  • License: Creative Commons Attribution 3.0 Unported
  • Access: Available through Cancer Imaging Archive

CMMD

  • Description: Breast mammography dataset from China
  • Classes: 2 (Benign, Malignant)
  • Size: 1,872 records (1,404 train, 468 test)
  • License: Creative Commons Attribution 4.0 International
  • Access: Available through Cancer Imaging Archive
  • Note: Currently pending expert verification

Dermoscopy

ISIC-2020

  • Description: Dermoscopy of skin lesions from over 2000 patients
  • Classes: 2 (Malignant, Benign)
  • Size: 33,126 records (26,501 train, 6,625 test)
  • License: Creative Commons Attribution-Noncommercial 4.0 International
  • Access: Available through ISIC Archive

HAM10000

  • Description: Dermoscopy images from ISIC 2018 classification challenge
  • Classes: 5 (MEL, NV, BCC, AKIEC, OTHER)
  • Size: 10,015 records (8,012 train, 2,003 test)
  • License: Creative Commons Attribution-Noncommercial-Sharealike 4.0 International
  • Access: Available on Kaggle

PAD-UFES-20

  • Description: Dermoscopy images of 1641 skin lesions
  • Classes: 5 (Same as HAM10000)
  • Size: 2,298 records (1,839 train, 459 test)
  • License: Creative Commons Attribution 4.0 International
  • Access: Available on Kaggle

Fundus

Messidor-2

  • Description: Diabetic Retinopathy examinations
  • Classes: 5 (None, Mild DR, Moderate DR, Severe DR, PDR)
  • Size: 1,744 records (1,394 train, 350 test)
  • License: Creative Commons Public Domain
  • Access: Available on Kaggle

APTOS 2019

  • Description: Fundus images from rural India
  • Classes: 5 (No DR, Mild, Moderate, Severe, Proliferative DR)
  • Size: 3,662 records (2,929 train, 733 test)
  • License: Kaggle Competition Rules
  • Access: Available on Kaggle

Jichi

  • Description: Posterior pole fundus photography dataset from Japan
  • Classes: 3 (SDR, PPDR, PDR)
  • Size: 9,939 records (7,950 train, 1,989 test)
  • License: Creative Commons Attribution 4.0 International
  • Access: Available through PMC

CT (Computed Tomography)

LNDb

  • Description: Lung cancer CT scan dataset from Portugal
  • Classes: 3 (nodule ≥3mm, nodule <3mm, non-nodule)
  • Size: 5,561 records (4,130 train, 1,431 test)
  • License: Creative Commons Attribution 4.0 International
  • Access: Available through Zenodo

INSPECT

  • Description: Multi-modal dataset with CT images and reports
  • Classes: 5 (No PE, Acute Subsegmental-only PE, Acute PE, Subsegmental-only PE, Chronic PE)
  • Size: 23,240 records (17,434 train, 5,806 test)
  • License: Stanford University Dataset Research Use Agreement
  • Access: Requires registration

KiTS23

  • Description: Kidney Tumor Segmentation Challenge dataset
  • Classes: 2 (Benign, Malignant)
  • Size: 478 records (361 train, 117 test)
  • License: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International
  • Access: Available on GitHub

Hemorrhage

  • Description: Intracranial hemorrhage CT images
  • Classes: 2 (No Hemorrhage, Has Hemorrhage)
  • Size: 2,501 records (1,986 train, 515 test)
  • License: Creative Commons Attribution 4.0 International
  • Access: Available on Kaggle

RSPECT

  • Description: CT scans for Pulmonary Embolism
  • Classes: 3 (No PE, Chronic PE, Acute PE)
  • Size: 1,790,594 records (1,342,945 train, 447,649 test)
  • License: Kaggle competition rules
  • Access: Available on Kaggle

Ultrasound

EchoNet-Dynamic

  • Description: Echocardiography videos from Stanford
  • Task: Segmentation (not classification)
  • Size: 10,247 records (8,196 train, 2,051 test)
  • License: Stanford University Dataset Research Use Agreement
  • Access: Requires registration

BUSI

  • Description: Breast cancer ultrasound images
  • Classes: 3 (Normal, Malignant, Benign)
  • Size: 780 records (583 train, 197 test)
  • License: Creative Commons Public Domain
  • Access: Available on Kaggle

COVID-BLUES

  • Description: Lung ultrasound videos for COVID-19
  • Classes: 2 (Has COVID, No COVID)
  • Size: 362 records (266 train, 96 test)
  • License: Creative Commons Attribution-Noncommercial-NoDerivatives 4.0 International
  • Access: Available on GitHub

COVID-US

  • Description: COVID-related lung ultrasound videos
  • Classes: 3 (Covid, Pneumonia, Normal)
  • Size: 99 records (74 train, 25 test)
  • License: GNU Affero General Public License 3.0
  • Access: Available on GitHub

MRI (Magnetic Resonance Imaging)

Brain Tumor

  • Description: Brain MRI images for tumor classification
  • Classes: 4 (No Tumor, Pituitary Tumor, Glioma Tumor, Meningioma Tumor)
  • Size: 3,264 records (2,870 train, 394 test)
  • License: MIT License
  • Access: Available on Kaggle

Brain MRI

  • Description: Brain MRI dataset for tumor detection
  • Classes: 2 (Yes, No - presence of tumors)
  • Size: 253 records (202 train, 51 test)
  • License: No specific license
  • Access: Available on Kaggle

BrainNet

ABCD

  • Description: Adolescent brain cognitive development study
  • Classes: 2 (Normal, Abnormal)
  • Size: 9,563 records (7,650 train, 1,613 test)
  • License: Custom NIH license
  • Access: Available through NDA

ABIDE

  • Description: Autism brain MRI diagnosis dataset
  • Classes: 2 (ASD, Typical controls)
  • Size: 1,009 records (807 train, 202 test)
  • License: Creative Commons Attribution-NonCommercial-Share Alike
  • Access: Requires account registration

PPMI

  • Description: Parkinson's disease progression study
  • Classes: 2 (Control, PD patients)
  • Size: 718 records (572 train, 143 test)
  • License: Custom license
  • Access: Available through PPMI

Molecule

PROTEINS

  • Description: Protein structure graphs
  • Classes: 2 (Enzyme, Not enzyme)
  • Size: 1,113 records (890 train, 223 test)
  • License: No specific license
  • Access: Available through Papers with Code

PPI

  • Description: Protein-protein interaction dataset
  • Task: Protein interaction prediction
  • Size: 56,944 records (45,555 train, 11,389 test)
  • License: MIT License
  • Access: Available through Stanford SNAP

Tissues

LC25000

  • Description: Lung and colon histopathological images
  • Classes: 5 (Colon adenocarcinomas, Benign colon, Lung adenocarcinomas, Lung squamous cell carcinomas, Benign lung)
  • Size: 18,750 records (15,000 train, 3,750 test)
  • License: No specific license
  • Access: Available on GitHub

BCSS

  • Description: Breast cancer slides
  • Classes: 4 (Tumor, Stroma, Lymphocytic infiltrate, Necrosis/debris)
  • Size: 5,264 records (4,211 train, 1,053 test)
  • License: CC0 1.0 Universal
  • Access: Available on GitHub

Video

Cholec80

  • Description: Cholecystectomy surgery videos
  • Task: Surgery phase annotations and tool labels
  • Size: 7,200 records (5,760 train, 1,440 test)
  • License: Creative Commons Attribution-Noncommercial-Sharealike 4.0 International
  • Access: Requires request form

IMU (Inertial Measurement Unit)

HuGaDB

  • Description: Human gait analysis data
  • Classes: 4 (Sitting, Standing, Sitting down, Standing up)
  • Size: 364 records (291 train, 73 test)
  • License: No specific license
  • Access: Available on GitHub

Gene Expression

Expression Atlas

  • Description: RNA gene expression data across species and biological conditions
  • Task: Expression analysis and classification
  • Size: 4,506 records (3,605 train, 901 test)
  • License: Creative Commons Attribution-Noncommercial-NoDerivatives 4.0 International
  • Access: Available through EBI

Geo

  • Description: Functional genomics dataset supporting MIAME-compliant data submissions
  • Task: Expression analysis and classification
  • Size: 126,452 records (101,162 train, 25,290 test)
  • License: Custom NCBI license
  • Access: Available through NCBI

Multimodal

Vital

  • Description: Medical image-language dataset based on PMC-15, with GPT-4 generated instructions
  • Task: Multimodal understanding and instruction following
  • Size: 210,000 records (42,000 train, 168,000 test)
  • License: Apache License 2.0
  • Access: Available through Hugging Face

MIMIC-IV

  • Description: Multimodal medical dataset from Beth Israel Deaconess Medical Center
  • Modalities: EHR, vital signs, chest X-rays
  • Classes: 2 (48 Hour In-Hospital-Mortality: Yes/No)
  • Size:
    • Full dataset: 800,000 records (640,000 train, 160,000 test)
    • Multimodal subset: 207,769 records (166,215 train, 41,554 test)
  • License: PhysioNet Credentialed Health Data License 1.5.0
  • Access: Requires credentialed account and CITI training

Usage Guidelines

  1. Respect all data usage agreements and licenses
  2. Follow proper citation practices when using these datasets
  3. Maintain data privacy and security standards
  4. Check for updated versions of datasets
  5. Review specific ethical guidelines for each dataset

Citation

Please cite individual datasets as well as the CLIMB benchmark when using this data. Specific citation information is provided in the original paper.