{"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/joint-and-individual-analysis-of-breast","title":"Joint and individual analysis of breast cancer histologic images and genomic covariates","arxiv_id":"1912.00434","date":"2020-04-14","proceeding":null,"authors":[],"abstract":"A key challenge in modern data analysis is understanding connections between\ncomplex and differing modalities of data. For example, two of the main\napproaches to the study of breast cancer are histopathology (analyzing visual\ncharacteristics of tumors) and genetics. While histopathology is the gold\nstandard for diagnostics and there have been many recent breakthroughs in\ngenetics, there is little overlap between these two fields. We aim to bridge\nthis gap by developing methods based on Angle-based Joint and Individual\nVariation Explained (AJIVE) to directly explore similarities and differences\nbetween these two modalities. Our approach exploits Convolutional Neural\nNetworks (CNNs) as a powerful, automatic method for image feature extraction to\naddress some of the challenges presented by statistical analysis of\nhistopathology image data. CNNs raise issues of interpretability that we\naddress by developing novel methods to explore visual modes of variation\ncaptured by statistical algorithms (e.g. PCA or AJIVE) applied to CNN features.\nOur results provide many interpretable connections and contrasts between\nhistopathology and genetics.","url_abs":"http://arxiv.org/abs/1912.00434v3","url_pdf":"http://arxiv.org/pdf/1912.00434v3.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":"joint-and-individual-analysis-of-breast","repo_url":"https://github.com/idc9/breast_cancer_image_analysis","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":null},{"paper_slug":"joint-and-individual-analysis-of-breast","repo_url":"https://github.com/taebinkim7/med-ajive","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"pytorch","reach":null}],"tasks":[],"methods":[],"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}