{"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/self-supervised-visualisation-of-medical","title":"Self-supervised Visualisation of Medical Image Datasets","arxiv_id":"2402.14566","date":"2024-02-22","proceeding":null,"authors":["Ifeoma Veronica Nwabufo","Jan Niklas Böhm","Philipp Berens","Dmitry Kobak"],"abstract":"Self-supervised learning methods based on data augmentations, such as SimCLR, BYOL, or DINO, allow obtaining semantically meaningful representations of image datasets and are widely used prior to supervised fine-tuning. A recent self-supervised learning method, $t$-SimCNE, uses contrastive learning to directly train a 2D representation suitable for visualisation. When applied to natural image datasets, $t$-SimCNE yields 2D visualisations with semantically meaningful clusters. In this work, we used $t$-SimCNE to visualise medical image datasets, including examples from dermatology, histology, and blood microscopy. We found that increasing the set of data augmentations to include arbitrary rotations improved the results in terms of class separability, compared to data augmentations used for natural images. Our 2D representations show medically relevant structures and can be used to aid data exploration and annotation, improving on common approaches for data visualisation.","url_abs":"https://arxiv.org/abs/2402.14566v2","url_pdf":"https://arxiv.org/pdf/2402.14566v2.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":"self-supervised-visualisation-of-medical","repo_url":"https://github.com/berenslab/medical-t-simcne","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":null}],"tasks":[{"task_slug":"contrastive-learning","task_name":"Contrastive Learning"},{"task_slug":"self-supervised-learning","task_name":"Self-Supervised Learning"}],"methods":[{"method_slug":"attention","method_name":"Attention"},{"method_slug":"average-pooling","method_name":"Average Pooling"},{"method_slug":"byol","method_name":"BYOL"},{"method_slug":"colorjitter","method_name":"ColorJitter"},{"method_slug":"contrastive-learning","method_name":"Contrastive Learning"},{"method_slug":"convolution","method_name":"Convolution"},{"method_slug":"dino","method_name":"DINO"},{"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":"layer-normalization","method_name":"Layer Normalization"},{"method_slug":"linear-layer","method_name":"Linear Layer"},{"method_slug":"max-pooling","method_name":"Max Pooling"},{"method_slug":"multi-head-attention","method_name":"Multi-Head Attention"},{"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-connection","method_name":"Residual Connection"},{"method_slug":"set","method_name":"SET"},{"method_slug":"simclr","method_name":"SimCLR"},{"method_slug":"softmax","method_name":"Softmax"},{"method_slug":"vision-transformer","method_name":"Vision Transformer"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}