{"id":4140,"date":"2024-07-19T09:16:04","date_gmt":"2024-07-19T01:16:04","guid":{"rendered":"https:\/\/nullthought.net\/?p=4140"},"modified":"2024-08-19T16:11:22","modified_gmt":"2024-08-19T08:11:22","slug":"%e4%b8%80%e4%b8%aa%e5%85%b8%e5%9e%8b%e7%9a%84%e6%97%a0%e7%9b%91%e7%9d%a3%e6%b7%b1%e5%ba%a6%e5%ad%a6%e4%b9%a0%e6%88%90%e5%8a%9f%e7%a0%94%e7%a9%b6%e6%a1%88%e4%be%8b%ef%bc%9aunsupervised-representation-l","status":"publish","type":"post","link":"https:\/\/nullthought.net\/?p=4140","title":{"rendered":"\u4e00\u4e2a\u5178\u578b\u7684\u65e0\u76d1\u7763\u6df1\u5ea6\u5b66\u4e60\u6210\u529f\u7814\u7a76\u6848\u4f8b\uff1aUnsupervised representation learning on high-dimensional clinical data improves genomic discovery and prediction"},"content":{"rendered":"\n<p>\u9ad8\u7ef4\u4e34\u5e8a\u6570\u636e\uff08HDCD\uff09\u5728\u751f\u7269\u94f6\u884c\uff08Biobank\uff09\u7ea7\u522b\u7684\u6570\u636e\u96c6\u4e2d\u8d8a\u6765\u8d8a\u591a\uff0c\u4f46\u5728\u9057\u4f20\u5b66\u7814\u7a76\u4e2d\u7684\u5e94\u7528\u4ecd\u5177\u6709\u6311\u6218\u6027\u3002\u8bba\u6587<strong><em><a href=\"https:\/\/www.nature.com\/articles\/s41588-024-01831-6\" target=\"_blank\" rel=\"noreferrer noopener\">Unsupervised representation learning on high-dimensional clinical data improves genomic discovery and prediction<\/a><\/em><\/strong>\u63d0\u51fa\u4e86\u4e00\u79cd\u65e0\u76d1\u7763\u6df1\u5ea6\u5b66\u4e60\u6a21\u578b\uff0c\u79f0\u4e3a\u4f4e\u7ef4\u5d4c\u5165\u7684\u9057\u4f20\u53d1\u73b0\u8868\u793a\u5b66\u4e60\uff08REGLE\uff09\uff0c\u7528\u4e8e\u53d1\u73b0\u9057\u4f20\u53d8\u5f02\u4e0eHDCD\u4e4b\u95f4\u7684\u5173\u8054\u3002REGLE\u5229\u7528\u53d8\u5206\u81ea\u7f16\u7801\u5668\uff08VAE\uff09\u8ba1\u7b97HDCD\u7684\u975e\u7ebf\u6027\u89e3\u7f20\u5d4c\u5165\uff0c\u8fd9\u4e9b\u5d4c\u5165\u6210\u4e3a\u5168\u57fa\u56e0\u7ec4\u5173\u8054\u7814\u7a76\uff08GWAS\uff09\u7684\u8f93\u5165\u3002<\/p>\n\n\n\n<p>\u6211\u7684\u521d\u6d45\u7406\u89e3\uff1a<strong>\u901a\u8fc7VAE\u628a\u9ad8\u7ef4\u4e34\u5e8a\u6570\u636e(HDCD)\u538b\u7f29\u5230\u8f83\u4f4e\u7ef4\u5ea6\u6f5c\u5728\u7a7a\u95f4\uff0c\u7136\u540e\u57fa\u4e8e\u57fa\u56e0\u5173\u8054\u548c\u4e13\u5bb6\u5b9a\u4e49\u7279\u5f81\uff08Expert-defined Features, EDFs\uff09\uff0c\u518d\u5bf9\u6f5c\u5728\u7a7a\u95f4\u7684\u6570\u636e\u8fdb\u884c\u5e72\u6d89\u548c\u8c03\u6574<\/strong>\u3002\ud83e\udd14<br>My basic understanding is: High-dimensional clinical data (HDCD) is compressed into a lower-dimensional latent space using a Variational Autoencoder (VAE). Then, based on gene associations and expert-defined features (EDFs), the data in the latent space is further manipulated and adjusted. <\/p>\n\n\n\n<figure class=\"wp-block-image aligncenter size-full\"><img loading=\"lazy\" decoding=\"async\" width=\"800\" height=\"599\" src=\"https:\/\/nullthought.net\/wp-content\/uploads\/2024\/07\/REGLE.png\" alt=\"\" class=\"wp-image-4141\" srcset=\"https:\/\/nullthought.net\/wp-content\/uploads\/2024\/07\/REGLE.png 800w, https:\/\/nullthought.net\/wp-content\/uploads\/2024\/07\/REGLE-300x225.png 300w, https:\/\/nullthought.net\/wp-content\/uploads\/2024\/07\/REGLE-768x575.png 768w\" sizes=\"auto, (max-width: 800px) 100vw, 800px\" \/><figcaption class=\"wp-element-caption\"><strong><em><a href=\"https:\/\/www.nature.com\/articles\/s41588-024-01831-6\" target=\"_blank\" rel=\"noreferrer noopener\">Unsupervised representation learning on high-dimensional clinical data improves genomic discovery and prediction<\/a><\/em><\/strong><\/figcaption><\/figure>\n\n\n\n<p>\u8be5\u7814\u7a76\u7531\u5982\u4e0b\u4eba\u5458\u5408\u4f5c\u5b8c\u6210\uff1a<em>Justin Cosentino, Babak Behsaz, Yuchen Zhou, Zachary R. McCaw, Howard Yang, Andrew Carroll, Cory Y. McLean (Google), Davin Hill (Northeastern University), Tae-Hwi Schwantes-An, Dongbing Lai (Indiana University), John Bates (Verily), Brian D. Hobbs, Michael H. Cho (Brigham and Women\u2019s Hospital &amp; Harvard Medical School), Robert Luben, Anthony P. Khawaja (Moorfields Eye Hospital &amp; University College London).&nbsp;<\/em><\/p>\n\n\n\n<p>\u4ee5\u4e0b\u4e3a\u8bba\u6587\u5185\u5bb9\u6982\u8981\uff08ChatGPT 4o\u751f\u6210\uff09\uff1a<\/p>\n\n\n\n<h4 class=\"wp-block-heading\">\u4e00\u3001\u65b9\u6cd5<\/h4>\n\n\n\n<ol class=\"wp-block-list\">\n<li><strong>\u6a21\u578b\u67b6\u6784\uff1a<\/strong>\n<ul class=\"wp-block-list\">\n<li><strong>VAE\u8bad\u7ec3\uff1a<\/strong> \u4f7f\u7528\u53d8\u5206\u81ea\u7f16\u7801\u5668\uff08VAE\uff09\u5bf9HDCD\u8fdb\u884c\u538b\u7f29\u548c\u91cd\u6784\uff0c\u751f\u6210\u4f4e\u7ef4\u7684\u975e\u7ebf\u6027\u5d4c\u5165\u3002<\/li>\n\n\n\n<li><strong>GWAS\uff1a<\/strong> \u5728\u6bcf\u4e2a\u5d4c\u5165\u5750\u6807\u4e0a\u72ec\u7acb\u8fdb\u884cGWAS\u3002<\/li>\n\n\n\n<li><strong>PRS\u6784\u5efa\uff1a<\/strong> \u4f7f\u7528\u5d4c\u5165\u5750\u6807\u7684\u591a\u57fa\u56e0\u98ce\u9669\u8bc4\u5206\uff08PRS\uff09\u4f5c\u4e3a\u4e00\u822c\u751f\u7269\u529f\u80fd\u7684\u9057\u4f20\u8bc4\u5206\uff0c\u7ed3\u5408\u5b83\u4eec\u4ee5\u521b\u5efa\u7279\u5b9a\u75be\u75c5\u6216\u7279\u5f81\u7684PRS\u3002<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li><strong>\u6570\u636e\u96c6\uff1a<\/strong>\n<ul class=\"wp-block-list\">\n<li>\u4f7f\u7528UK Biobank\u4e2d\u7684\u547c\u5438\u548c\u5faa\u73afHDCD\u6570\u636e\uff0c\u5206\u522b\u4e3a\u80ba\u529f\u80fd\u6d4b\u91cf\u7684\u547c\u5438\u56fe\u548c\u8840\u6db2\u4f53\u79ef\u53d8\u5316\u7684\u5149\u7535\u5bb9\u79ef\u56fe\uff08PPG\uff09\u3002<\/li>\n<\/ul>\n<\/li>\n<\/ol>\n\n\n\n<h4 class=\"wp-block-heading\">\u4e8c\u3001\u7ed3\u679c<\/h4>\n\n\n\n<ol class=\"wp-block-list\">\n<li><strong>\u5d4c\u5165\u751f\u6210\u4e0e\u89e3\u91ca\uff1a<\/strong>\n<ul class=\"wp-block-list\">\n<li><strong>\u547c\u5438\u56fe\uff08SPINCs\uff09\u548c\u6b8b\u5dee\u547c\u5438\u56fe\uff08RSPINCs\uff09\uff1a<\/strong> \u8bad\u7ec3\u5377\u79efVAE\u751f\u6210\u547c\u5438\u56fe\u5d4c\u5165\u3002\u901a\u8fc7\u6ce8\u5165\u4e94\u4e2a<strong>\u4e13\u5bb6\u5b9a\u4e49\u7279\u5f81EDFs<\/strong>\uff08FEV1\u3001FVC\u3001FEV1\/FVC\u3001PEF\u548cFEF25-75%\uff09\u4f5c\u4e3a\u89e3\u7801\u5668\u7684\u8f93\u5165\u6765\u751f\u6210RSPINCs\u3002<\/li>\n\n\n\n<li><strong>PPG\u5d4c\u5165\uff08PLENCs\uff09\u548c\u6b8b\u5deePPG\u5d4c\u5165\uff08RPLENCs\uff09\uff1a<\/strong> \u8bad\u7ec3\u5377\u79efVAE\u751f\u6210PPG\u5d4c\u5165\uff0c\u901a\u8fc7\u6ce8\u5165\u4e94\u4e2aPPG EDFs\u751f\u6210RPLENCs\u3002<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li><strong>GWAS\u5206\u6790\uff1a<\/strong>\n<ul class=\"wp-block-list\">\n<li><strong>\u547c\u5438\u529f\u80fd\uff1a<\/strong> SPINCs\u548cRSPINCs\u5206\u522b\u68c0\u6d4b\u5230575\u548c659\u4e2a\u72ec\u7acb\u7684\u5168\u57fa\u56e0\u7ec4\u663e\u8457\u6027\uff08GWS\uff09\u4f4d\u70b9\uff0c\u5176\u4e2d\u8bb8\u591a\u662f\u4ee5\u524d\u672a\u68c0\u6d4b\u5230\u7684\u3002<\/li>\n\n\n\n<li><strong>\u5faa\u73af\u529f\u80fd\uff1a<\/strong> PLENCs\u548cRPLENCs\u5206\u522b\u68c0\u6d4b\u523090\u548c75\u4e2a\u72ec\u7acb\u7684GWS\u4f4d\u70b9\uff0c\u5176\u4e2d\u5927\u90e8\u5206\u4e3a\u65b0\u53d1\u73b0\u3002<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li><strong>PRS\u6784\u5efa\u4e0e\u8bc4\u4f30\uff1a<\/strong>\n<ul class=\"wp-block-list\">\n<li><strong>\u80ba\u529f\u80fd\u76f8\u5173\u75be\u75c5\uff08\u54ee\u5598\u548cCOPD\uff09\uff1a<\/strong> SPINCs\u548cEDFs+RSPINCs\u7684PRS\u5728UK Biobank\u4e2d\u663e\u8457\u6539\u5584\u4e86\u54ee\u5598\u548cCOPD\u7684\u9884\u6d4b\u3002<\/li>\n\n\n\n<li><strong>\u5fc3\u8840\u7ba1\u529f\u80fd\u76f8\u5173\u75be\u75c5\uff08\u9ad8\u8840\u538b\u548cSBP\uff09\uff1a<\/strong> PLENCs\u548cRPLENCs\u7684PRS\u5728\u591a\u4e2a\u72ec\u7acb\u6570\u636e\u96c6\uff08\u5982COPDGene\u3001eMERGE III\u548cEPIC-Norfolk\uff09\u4e2d\u6539\u5584\u4e86\u9ad8\u8840\u538b\u548cSBP\u7684\u9884\u6d4b\u3002<\/li>\n<\/ul>\n<\/li>\n<\/ol>\n\n\n\n<h4 class=\"wp-block-heading\">\u4e09\u3001\u8ba8\u8bba<\/h4>\n\n\n\n<ol class=\"wp-block-list\">\n<li><strong>\u6a21\u578b\u4f18\u52bf\uff1a<\/strong>\n<ul class=\"wp-block-list\">\n<li><strong>\u65e0\u76d1\u7763\u5b66\u4e60\uff1a<\/strong> REGLE\u65e0\u9700\u6807\u7b7e\uff0c\u80fd\u6709\u6548\u5229\u7528HDCD\u8fdb\u884c\u9057\u4f20\u53d1\u73b0\u3002<\/li>\n\n\n\n<li><strong>\u4f4e\u7ef4\u975e\u7ebf\u6027\u5d4c\u5165\uff1a<\/strong> VAE\u751f\u6210\u7684\u5d4c\u5165\u80fd\u66f4\u597d\u5730\u6355\u6349HDCD\u4e2d\u7684\u9057\u4f20\u4fe1\u53f7\u3002<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li><strong>\u6a21\u578b\u5c40\u9650\u6027\uff1a<\/strong>\n<ul class=\"wp-block-list\">\n<li><strong>GWAS\u4f18\u5316\uff1a<\/strong> 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\u5f15\u5165\u6700\u5927\u5316\u9057\u4f20\u529b\u7684\u76ee\u6807\u51fd\u6570\uff0c\u63d0\u5347\u5d4c\u5165\u7684\u9057\u4f20\u5206\u6790\u6027\u80fd\u3002<\/li>\n<\/ul>\n<\/li>\n<\/ol>\n\n\n\n<h4 class=\"wp-block-heading\">\u56db\u3001\u7ed3\u8bba<\/h4>\n\n\n\n<p>REGLE\u901a\u8fc7\u751f\u6210HDCD\u7684\u4f4e\u7ef4\u975e\u7ebf\u6027\u5d4c\u5165\uff0c\u663e\u8457\u6539\u5584\u4e86\u9057\u4f20\u53d1\u73b0\u548c\u75be\u75c5\u9884\u6d4b\uff0c\u4e3a\u9ad8\u7ef4\u4e34\u5e8a\u6570\u636e\u5728\u9057\u4f20\u5b66\u7814\u7a76\u4e2d\u7684\u5e94\u7528\u63d0\u4f9b\u4e86\u65b0\u65b9\u6cd5\u548c\u65b0\u89c6\u89d2\u3002<\/p>\n\n\n\n<h4 class=\"wp-block-heading\">\u4e94\u3001\u4e3b\u8981\u8d21\u732e<\/h4>\n\n\n\n<ol class=\"wp-block-list\">\n<li>\u63d0\u51fa\u4e86\u65e0\u76d1\u7763\u5b66\u4e60\u6a21\u578bREGLE\uff0c\u6709\u6548\u5229\u7528\u9ad8\u7ef4\u4e34\u5e8a\u6570\u636e\u8fdb\u884c\u9057\u4f20\u53d1\u73b0\u3002<\/li>\n\n\n\n<li>\u901a\u8fc7\u5b9e\u9a8c\u8bc1\u660eREGLE\u5728UK 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[&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"site-sidebar-layout":"default","site-content-layout":"","ast-site-content-layout":"default","site-content-style":"default","site-sidebar-style":"default","ast-global-header-display":"","ast-banner-title-visibility":"","ast-main-header-display":"","ast-hfb-above-header-display":"","ast-hfb-below-header-display":"","ast-hfb-mobile-header-display":"","site-post-title":"","ast-breadcrumbs-content":"","ast-featured-img":"","footer-sml-layout":"","ast-disable-related-posts":"","theme-transparent-header-meta":"","adv-header-id-meta":"","stick-header-meta":"","header-above-stick-meta":"","header-main-stick-meta":"","header-below-stick-meta":"","astra-migrate-meta-layouts":"set","ast-page-background-enabled":"default","ast-page-background-meta":{"desktop":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center 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