{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/large-scale-pretraining-on-pathological","title":"Large-scale pretraining on pathological images for fine-tuning of small pathological benchmarks","arxiv_id":"2303.15693","date":"2023-03-28","proceeding":null,"authors":["Masataka Kawai","Noriaki Ota","Shinsuke Yamaoka"],"abstract":"Pretraining a deep learning model on large image datasets is a standard step before fine-tuning the model on small targeted datasets. The large dataset is usually general images (e.g. imagenet2012) while the small dataset can be specialized datasets that have different distributions from the large dataset. However, this 'large-to-small' strategy is not well-validated when the large dataset is specialized and has a similar distribution to small datasets. We newly compiled three hematoxylin and eosin-stained image datasets, one large (PTCGA200) and two magnification-adjusted small datasets (PCam200 and segPANDA200). Major deep learning models were trained with supervised and self-supervised learning methods and fine-tuned on the small datasets for tumor classification and tissue segmentation benchmarks. ResNet50 pretrained with MoCov2, SimCLR, and BYOL on PTCGA200 was better than imagenet2012 pretraining when fine-tuned on PTCGA200 (accuracy of 83.94%, 86.41%, 84.91%, and 82.72%, respectively). ResNet50 pre-trained on PTCGA200 with MoCov2 exceeded the COCOtrain2017-pretrained baseline and was the best in ResNet50 for the tissue segmentation benchmark (mIoU of 63.53% and 63.22%). We found re-training imagenet-pretrained models (ResNet50, BiT-M-R50x1, and ViT-S/16) on PTCGA200 improved downstream benchmarks.","url_abs":"https://arxiv.org/abs/2303.15693v2","url_pdf":"https://arxiv.org/pdf/2303.15693v2.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"large-scale-pretraining-on-pathological","repo_url":"https://github.com/enigmanx20/patchtcga","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":{"status":"ok"}}],"tasks":[{"task_slug":"self-supervised-learning","task_name":"Self-Supervised Learning"}],"methods":[{"method_slug":"1x1-convolution","method_name":"1x1 Convolution"},{"method_slug":"average-pooling","method_name":"Average Pooling"},{"method_slug":"byol","method_name":"BYOL"},{"method_slug":"batch-normalization","method_name":"Batch Normalization"},{"method_slug":"bottleneck-residual-block","method_name":"Bottleneck Residual Block"},{"method_slug":"colorjitter","method_name":"ColorJitter"},{"method_slug":"convolution","method_name":"Convolution"},{"method_slug":"dense-connections","method_name":"Dense Connections"},{"method_slug":"feedforward-network","method_name":"Feedforward Network"},{"method_slug":"global-average-pooling","method_name":"Global Average Pooling"},{"method_slug":"kaiming-initialization","method_name":"Kaiming Initialization"},{"method_slug":"max-pooling","method_name":"Max Pooling"},{"method_slug":"nt-xent","method_name":"NT-Xent"},{"method_slug":"random-gaussian-blur","method_name":"Random Gaussian Blur"},{"method_slug":"random-resized-crop","method_name":"Random Resized Crop"},{"method_slug":"relu","method_name":"ReLU"},{"method_slug":"residual-block","method_name":"Residual Block"},{"method_slug":"residual-connection","method_name":"Residual Connection"},{"method_slug":"simclr","method_name":"SimCLR"}],"datasets_introduced":[{"slug":"pcam200","name":"PCam200","full_name":"Patch Camelyon in 200 microns by 512 px"},{"slug":"ptcga200","name":"PTCGA200","full_name":"Patch TCGA in 200 microns by 512 px"},{"slug":"segpanda200","name":"SegPANDA200","full_name":"Segmentation task on PANDA challenge in 200 microns by 512px"}],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=2303.15693","mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}