{"id":1016,"date":"2025-07-24T11:28:51","date_gmt":"2025-07-24T16:28:51","guid":{"rendered":"https:\/\/open.qtlmax.com\/guide\/?p=1016"},"modified":"2025-07-24T11:40:40","modified_gmt":"2025-07-24T16:40:40","slug":"deep-learning-algorithms-for-subpopulation-clustering","status":"publish","type":"post","link":"https:\/\/open.qtlmax.com\/guide\/index.php\/2025\/07\/24\/deep-learning-algorithms-for-subpopulation-clustering\/","title":{"rendered":"Clustering subpopulation using deep learning algorithm"},"content":{"rendered":"\n<p>This post explains how to predict <strong>subpopulation class<\/strong> for individuals given known genomic analytics, using <strong>deep learning algorithms<\/strong>.<\/p>\n\n\n\n<p>Figure 1 shows the &#8220;Deep-learning classification&#8221; tab selected in QTLmax Super.<\/p>\n\n\n\n<figure class=\"wp-block-image size-large\"><img decoding=\"async\" src=\"https:\/\/help.qtlmax.com\/kr\/data\/editor\/2401\/thumb-deep_learning6_1200x842.png\" alt=\"\"\/><\/figure>\n\n\n\n<p>(Figure 1)<\/p>\n\n\n\n<p>The data format for input into the &#8220;Deep-learning classification&#8221; calculation is as shown in Figure 2. As you can see, the input file has a &#8220;Subpopulation&#8221; column added to the right side of the PCA result file. You&#8217;ll notice that while subpopulation information is not present for the individuals at the top of the file, it is displayed for the individuals at the bottom.<\/p>\n\n\n\n<p>The deep learning algorithm will first perform training on the individuals for whom subpopulation information is available, and then proceed to predict subpopulation values for the individuals without that information.<\/p>\n\n\n\n<figure class=\"wp-block-image size-large\"><img decoding=\"async\" src=\"https:\/\/help.qtlmax.com\/kr\/data\/editor\/2401\/deep_learning.png\" alt=\"\"\/><\/figure>\n\n\n\n<p>(Figure 2)<\/p>\n\n\n\n<p>When you enter the project name and select the input file, the <strong>&#8220;Training set&#8221; tab<\/strong> will display individuals with subpopulation information, and the <strong>&#8220;Predictive set&#8221; tab<\/strong> will show individuals without subpopulation information (Figures 3, 4).<\/p>\n\n\n\n<figure class=\"wp-block-image size-large\"><img decoding=\"async\" src=\"https:\/\/help.qtlmax.com\/kr\/data\/editor\/2401\/thumb-deep_learning2_1200x842.png\" alt=\"\"\/><\/figure>\n\n\n\n<p>(Figure 3)<\/p>\n\n\n\n<figure class=\"wp-block-image size-large\"><img decoding=\"async\" src=\"https:\/\/help.qtlmax.com\/kr\/data\/editor\/2401\/thumb-deep_learining3_1200x842.png\" alt=\"\"\/><\/figure>\n\n\n\n<p>(Figure 4)<\/p>\n\n\n\n<p>When you click the <strong>[Execute] button<\/strong>, the deep learning task runs, and you&#8217;ll see the <strong>subpopulation information generated and displayed<\/strong> for the individuals in the &#8220;Predictive set&#8221; (Figure 5).<\/p>\n\n\n\n<p>The <strong>&#8220;Combined table&#8221; tab<\/strong> simply shows a table that merges the tables from the &#8220;Training set&#8221; tab and the &#8220;Predictive set&#8221; tab.<\/p>\n\n\n\n<figure class=\"wp-block-image size-large\"><img decoding=\"async\" src=\"https:\/\/help.qtlmax.com\/kr\/data\/editor\/2401\/thumb-deep_learning4_1200x842.png\" alt=\"\"\/><\/figure>\n\n\n\n<p>(Figure 5)<\/p>\n","protected":false},"excerpt":{"rendered":"<p>This post explains how to predict subpopulation class for individuals given known genomic analytics, using deep learning algorithms. Figure 1 shows the &#8220;Deep-learning classification&#8221; tab selected in QTLmax Super. (Figure 1) The data format for input into the &#8220;Deep-learning classification&#8221; calculation is as shown in Figure 2. As you can see, the input file has [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_bbp_topic_count":0,"_bbp_reply_count":0,"_bbp_total_topic_count":0,"_bbp_total_reply_count":0,"_bbp_voice_count":0,"_bbp_anonymous_reply_count":0,"_bbp_topic_count_hidden":0,"_bbp_reply_count_hidden":0,"_bbp_forum_subforum_count":0,"footnotes":""},"categories":[1],"tags":[],"class_list":["post-1016","post","type-post","status-publish","format-standard","hentry","category-guide"],"_links":{"self":[{"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/posts\/1016","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/comments?post=1016"}],"version-history":[{"count":7,"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/posts\/1016\/revisions"}],"predecessor-version":[{"id":1028,"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/posts\/1016\/revisions\/1028"}],"wp:attachment":[{"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/media?parent=1016"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/categories?post=1016"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/tags?post=1016"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}