{"id":1263,"date":"2018-06-08T15:10:01","date_gmt":"2018-06-08T19:10:01","guid":{"rendered":"http:\/\/mlmed.org\/w\/?p=1166"},"modified":"2019-06-19T01:17:38","modified_gmt":"2019-06-19T05:17:38","slug":"gene-graph-convolutions","status":"publish","type":"post","link":"https:\/\/josephpcohen.com\/w\/gene-graph-convolutions\/","title":{"rendered":"Gene Graph Convolutions"},"content":{"rendered":"<p><a href=\"http:\/\/josephpcohen.com\/w\/wp-content\/uploads\/gene-graph-convs.png\"><img decoding=\"async\" loading=\"lazy\" class=\"aligncenter wp-image-1295 size-large\" src=\"http:\/\/josephpcohen.com\/w\/wp-content\/uploads\/gene-graph-convs-1024x213.png\" alt=\"\" width=\"1024\" height=\"213\" srcset=\"https:\/\/josephpcohen.com\/w\/wp-content\/uploads\/gene-graph-convs-1024x213.png 1024w, https:\/\/josephpcohen.com\/w\/wp-content\/uploads\/gene-graph-convs-300x62.png 300w, https:\/\/josephpcohen.com\/w\/wp-content\/uploads\/gene-graph-convs-768x160.png 768w, https:\/\/josephpcohen.com\/w\/wp-content\/uploads\/gene-graph-convs.png 1600w\" sizes=\"(max-width: 1024px) 100vw, 1024px\" \/><\/a><\/p>\n<p>We discuss how gene-gene interaction graphs (same pathway, protein-protein, co-expression, or research paper text association) can be used to impose a bias on a deep neural network model similar to the spatial bias imposed by convolutions on an image. We find this approach provides an advantage for particular tasks in a low data regime but is very dependent on the quality of the graph used. More info: <a href=\"https:\/\/arxiv.org\/abs\/1806.06975\" target=\"_blank\" rel=\"noopener noreferrer\">Paper<\/a> <a href=\"https:\/\/docs.google.com\/presentation\/d\/1AtfDYbfJ1VN675uy84cQzugmza-t7QWUmUZJNA3w0Dk\/edit\" target=\"_blank\" rel=\"noopener noreferrer\">Slides<\/a> <a href=\"https:\/\/github.com\/mila-iqia\/gene-graph-conv\" target=\"_blank\" rel=\"noopener noreferrer\">Code<\/a><\/p>\n<p><strong>Citation<\/strong><\/p>\n<p>Francis Dutil, Joseph Paul Cohen, Martin Weiss, Georgy Derevyanko, Yoshua Bengio. &#8220;Towards Gene Expression Convolutions Using Gene Interaction Graphs.&#8221; International Conference on Machine Learning (ICML) Workshop on Computational Biology (WCB), 2018, http:\/\/arxiv.org\/abs\/1806.06975.<\/p>\n<p><strong>News<\/strong><\/p>\n<p>Oct, 24th 2018: Martin Weiss received the &#8220;Best Presentation Award&#8221; for presenting this project at the <a href=\"https:\/\/www.iric.ca\/symposium\/program\" target=\"_blank\" rel=\"noopener noreferrer\">2018 IRIC symposium<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<div class=\"mh-excerpt\"><p>We discuss how gene-gene interaction graphs (same pathway, protein-protein, co-expression, or research paper text association) can be used to impose a bias on a deep <a class=\"mh-excerpt-more\" href=\"https:\/\/josephpcohen.com\/w\/gene-graph-convolutions\/\" title=\"Gene Graph Convolutions\">[&#8230;]<\/a><\/p>\n<\/div>","protected":false},"author":1,"featured_media":1295,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":[],"categories":[17,23,18,22],"tags":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v21.1 - 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