MedMNIST Classification Decathlon: A Lightweight AutoML Benchmark for Medical Image Analysis

This data repository for MedMNIST v1 is out of date! Please check the latest version of MedMNIST v2. <strong>Abstract</strong> We present MedMNIST, a collection of 10 pre-processed medical open datasets. MedMNIST is standardized to perform classification tasks on lightweight 28x28 images, which requires no background knowledge. Covering the primary data modalities in medical image analysis, it is diverse on data scale (from 100 to 100,000) and tasks (binary/multi-class, ordinal regression and multi-label). MedMNIST could be used for educational purpose, rapid prototyping, multi-modal machine learning or AutoML in medical image analysis. Moreover, MedMNIST Classification Decathlon is designed to benchmark AutoML algorithms on all 10 datasets; We have compared several baseline methods, including open-source or commercial AutoML tools. The datasets, evaluation code and baseline methods for MedMNIST are publicly available at https://medmnist.github.io/. Please note that this dataset is <strong>NOT</strong> intended for clinical use. We recommend our official code to download, parse and use the MedMNIST dataset: <pre>pip install medmnist</pre> <strong>Citation and Licenses</strong> If you find this project useful, please cite our ISBI'21 paper as:<br> <em> Jiancheng Yang, Rui Shi, Bingbing Ni. "MedMNIST Classification Decathlon: A Lightweight AutoML Benchmark for Medical Image Analysis," arXiv preprint arXiv:2010.14925, 2020.</em><br> <br> or using bibtex:<br> <em> @article{medmnist,<br> title={MedMNIST Classification Decathlon: A Lightweight AutoML Benchmark for Medical Image Analysis},<br> author={Yang, Jiancheng and Shi, Rui and Ni, Bingbing},<br> journal={arXiv preprint arXiv:2010.14925},<br> year={2020}<br> }</em> Besides, please cite the corresponding paper if you use any subset of MedMNIST. Each subset uses the <strong>same license</strong> as that of the source dataset. <strong>PathMNIST</strong> Jakob Nikolas Kather, Johannes Krisam, et al., "Predicting survival from colorectal cancer histology slides using deep learning: A retrospective multicenter study," PLOS Medicine, vol. 16, no. 1, pp. 1–22, 01 2019. <em><strong>License</strong>: CC BY 4.0</em> <strong>ChestMNIST</strong> Xiaosong Wang, Yifan Peng, et al., "Chestx-ray8: Hospital-scale chest x-ray database and benchmarks on weakly-supervised classification and localization of common thorax diseases," in CVPR, 2017, pp. 3462–3471. <em><strong>License</strong>: CC0 1.0</em> <strong>DermaMNIST</strong> Philipp Tschandl, Cliff Rosendahl, and Harald Kittler, "The ham10000 dataset, a large collection of multisource dermatoscopic images of common pigmented skin lesions," Scientific data, vol. 5, pp. 180161, 2018. Noel Codella, Veronica Rotemberg, Philipp Tschandl, M. Emre Celebi, Stephen Dusza, David Gutman, Brian Helba, Aadi Kalloo, Konstantinos Liopyris, Michael Marchetti, Harald Kittler, and Allan Halpern: “Skin Lesion Analysis Toward Melanoma Detection 2018: A Challenge Hosted by the International Skin Imaging Collaboration (ISIC)”, 2018; arXiv:1902.03368. <em><strong>License</strong>: CC BY-NC 4.0</em> <strong>OCTMNIST/PneumoniaMNIST</strong> Daniel S. Kermany, Michael Goldbaum, et al., "Identifying medical diagnoses and treatable diseases by image-based deep learning," Cell, vol. 172, no. 5, pp. 1122 – 1131.e9, 2018. <em><strong>License</strong>: CC BY 4.0</em> <strong>RetinaMNIST</strong> DeepDR Diabetic Retinopathy Image Dataset (DeepDRiD), "The 2nd diabetic retinopathy – grading and image quality estimation challenge," https://isbi.deepdr.org/data.html, 2020. <em><strong>License</strong>: CC BY 4.0</em> <strong>BreastMNIST</strong> Walid Al-Dhabyani, Mohammed Gomaa, Hussien Khaled, and Aly Fahmy, "Dataset of breast ultrasound images," Data in Brief, vol. 28, pp. 104863, 2020. <em><strong>License</strong>: CC BY 4.0</em> <strong>OrganMNIST_{Axial,Coronal,Sagittal}</strong> Patrick Bilic, Patrick Ferdinand Christ, et al., "The liver tumor segmentation benchmark (lits)," arXiv preprint arXiv:1901.04056, 2019. Xuanang Xu, Fugen Zhou, et al., "Efficient multiple organ localization in ct image using 3d region proposal network," IEEE Transactions on Medical Imaging, vol. 38, no. 8, pp. 1885–1898, 2019. <em><strong>License</strong>: CC BY 4.0</em>