{"id":96,"date":"2026-08-23T08:45:27","date_gmt":"2026-08-23T08:45:27","guid":{"rendered":"https:\/\/genetec.io\/?page_id=96"},"modified":"2026-08-23T09:38:24","modified_gmt":"2026-08-23T09:38:24","slug":"training-the-heads","status":"publish","type":"page","link":"https:\/\/genetec.io\/?page_id=96","title":{"rendered":"Training the Heads"},"content":{"rendered":"\r\n<p>The heads sit between two kinds of measurement: the regulatory <a href=\"https:\/\/genetec.io\/?page_id=94\">databases<\/a> (what the genome says) and the spatial <a href=\"https:\/\/genetec.io\/?page_id=94\">atlases<\/a> (what the embryo does). Training is the loop that reconciles them, run per developmental stage.<\/p>\r\n\r\n\r\n\r\n<p><strong>Forward.<\/strong> Derive each head&#8217;s parameters from the genome: enhancer-to-gene maps give conductances and setpoints, super-enhancer clusters give the identity heads, accessibility gives the timing thresholds. Nothing is fitted to the atlas at this step &mdash; the parameters are read.<\/p>\r\n\r\n\r\n\r\n<p><strong>Reverse.<\/strong> Ask whether the atlas implements what was derived: does the predicted fate order match the measured one, does the derived axis match the embryo&#8217;s, does the forward-grown organ beat an uninformed baseline against the reconstructed 3D anatomy? Where a check passes, the head is confirmed genome-derived.<\/p>\r\n\r\n\r\n\r\n<p><strong>Adjust.<\/strong> Where it fails, the failure is kept, not hidden. The ledger is explicit: the anterior&ndash;posterior organ addresses are genome-derived (single-cell Hox boundary, Spearman 0.81); the dorso-ventral address is partial; the resting-potential magnitude is anchored to one measured value because a resting potential is a gating quantity, not a transcript quantity &mdash; the atlas cannot supply it. A handful of honest anchors, and every one is documented.<\/p>\r\n\r\n\r\n\r\n<p>A head, concretely, is a master-transcription-factor super-enhancer cluster: the mouse atlas annotates 35 of them, and the sequence front-end resolves roughly 85 &mdash; the discovery frontier. The loop&#8217;s product is the trained <a href=\"https:\/\/genetec.io\/?page_id=97\">NCA+LGM model<\/a>.<\/p>\r\n\r\n","protected":false},"excerpt":{"rendered":"<p>The heads sit between two kinds of measurement: the regulatory databases (what the genome says) and the spatial atlases (what the embryo does). Training is the loop that reconciles them, run per developmental stage. Forward. Derive each head&#8217;s parameters from the genome: enhancer-to-gene maps give conductances and setpoints, super-enhancer clusters give the identity heads, accessibility [&hellip;]<\/p>\n","protected":false},"author":0,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-96","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/genetec.io\/index.php?rest_route=\/wp\/v2\/pages\/96","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/genetec.io\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/genetec.io\/index.php?rest_route=\/wp\/v2\/types\/page"}],"replies":[{"embeddable":true,"href":"https:\/\/genetec.io\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=96"}],"version-history":[{"count":3,"href":"https:\/\/genetec.io\/index.php?rest_route=\/wp\/v2\/pages\/96\/revisions"}],"predecessor-version":[{"id":133,"href":"https:\/\/genetec.io\/index.php?rest_route=\/wp\/v2\/pages\/96\/revisions\/133"}],"wp:attachment":[{"href":"https:\/\/genetec.io\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=96"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}