{"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-learning-of-phenotypic","title":"Self-Supervised Learning of Phenotypic Representations from Cell Images with Weak Labels","arxiv_id":"2209.07819","date":"2022-09-16","proceeding":null,"authors":["Jan Oscar Cross-Zamirski","Guy Williams","Elizabeth Mouchet","Carola-Bibiane Schönlieb","Riku Turkki","Yinhai Wang"],"abstract":"We propose WS-DINO as a novel framework to use weak label information in learning phenotypic representations from high-content fluorescent images of cells. Our model is based on a knowledge distillation approach with a vision transformer backbone (DINO), and we use this as a benchmark model for our study. Using WS-DINO, we fine-tuned with weak label information available in high-content microscopy screens (treatment and compound) and achieve state-of-the-art performance in not-same-compound mechanism of action prediction on the BBBC021 dataset (98%), and not-same-compound-and-batch performance (96%) using the compound as the weak label. Our method bypasses single cell cropping as a pre-processing step, and using self-attention maps we show that the model learns structurally meaningful phenotypic profiles.","url_abs":"https://arxiv.org/abs/2209.07819v2","url_pdf":"https://arxiv.org/pdf/2209.07819v2.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-learning-of-phenotypic","repo_url":"https://github.com/crosszamirski/ws-dino","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":null}],"tasks":[{"task_slug":"knowledge-distillation","task_name":"Knowledge Distillation"},{"task_slug":"self-supervised-learning","task_name":"Self-Supervised Learning"}],"methods":[{"method_slug":"attention","method_name":"Attention"},{"method_slug":"dense-connections","method_name":"Dense Connections"},{"method_slug":"knowledge-distillation","method_name":"Knowledge Distillation"},{"method_slug":"layer-normalization","method_name":"Layer Normalization"},{"method_slug":"linear-layer","method_name":"Linear Layer"},{"method_slug":"multi-head-attention","method_name":"Multi-Head Attention"},{"method_slug":"residual-connection","method_name":"Residual Connection"},{"method_slug":"softmax","method_name":"Softmax"},{"method_slug":"vision-transformer","method_name":"Vision Transformer"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":"https://syntology.ai/paper/2209.07819","atlas_url":"https://app.syntology.ai/?focus=2209.07819","mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}