{"id":505952,"date":"2022-11-03T00:05:40","date_gmt":"2022-11-02T21:05:40","guid":{"rendered":"https:\/\/en.buradabiliyorum.com\/machine-learning-generates-pictures-of-proteins-in-5d\/"},"modified":"2022-11-03T00:05:40","modified_gmt":"2022-11-02T21:05:40","slug":"machine-learning-generates-pictures-of-proteins-in-5d","status":"publish","type":"post","link":"https:\/\/buradabiliyorum.com\/en\/machine-learning-generates-pictures-of-proteins-in-5d\/","title":{"rendered":"#Machine learning generates pictures of proteins in 5D"},"content":{"rendered":"<div id=\"ez-toc-container\" class=\"ez-toc-v2_0_85 counter-hierarchy ez-toc-counter ez-toc-custom ez-toc-container-direction\">\n<p class=\"ez-toc-title\" style=\"cursor:inherit\">Table of Contents<\/p>\n<label for=\"ez-toc-cssicon-toggle-item-6a326cc955549\" class=\"ez-toc-cssicon-toggle-label\"><span class=\"\"><span class=\"eztoc-hide\" style=\"display:none;\">Toggle<\/span><span class=\"ez-toc-icon-toggle-span\"><svg style=\"fill: #dd3333;color:#dd3333\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" class=\"list-377408\" width=\"20px\" height=\"20px\" viewBox=\"0 0 24 24\" fill=\"none\"><path d=\"M6 6H4v2h2V6zm14 0H8v2h12V6zM4 11h2v2H4v-2zm16 0H8v2h12v-2zM4 16h2v2H4v-2zm16 0H8v2h12v-2z\" fill=\"currentColor\"><\/path><\/svg><svg style=\"fill: #dd3333;color:#dd3333\" class=\"arrow-unsorted-368013\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" width=\"10px\" height=\"10px\" viewBox=\"0 0 24 24\" version=\"1.2\" baseProfile=\"tiny\"><path d=\"M18.2 9.3l-6.2-6.3-6.2 6.3c-.2.2-.3.4-.3.7s.1.5.3.7c.2.2.4.3.7.3h11c.3 0 .5-.1.7-.3.2-.2.3-.5.3-.7s-.1-.5-.3-.7zM5.8 14.7l6.2 6.3 6.2-6.3c.2-.2.3-.5.3-.7s-.1-.5-.3-.7c-.2-.2-.4-.3-.7-.3h-11c-.3 0-.5.1-.7.3-.2.2-.3.5-.3.7s.1.5.3.7z\"\/><\/svg><\/span><\/span><\/label><input type=\"checkbox\"  id=\"ez-toc-cssicon-toggle-item-6a326cc955549\" checked aria-label=\"Toggle\" \/><nav><ul class='ez-toc-list ez-toc-list-level-1 ' ><li class='ez-toc-page-1 ez-toc-heading-level-1'><a class=\"ez-toc-link ez-toc-heading-1\" href=\"https:\/\/buradabiliyorum.com\/en\/machine-learning-generates-pictures-of-proteins-in-5d\/#%E2%80%9CMachine_learning_generates_pictures_of_proteins_in_5D%E2%80%9D\" >&#8220;Machine learning generates pictures of proteins in 5D&#8221;<\/a><\/li><\/ul><\/nav><\/div>\n<h1><span class=\"ez-toc-section\" id=\"%E2%80%9CMachine_learning_generates_pictures_of_proteins_in_5D%E2%80%9D\"><\/span>&#8220;Machine learning generates pictures of proteins in 5D&#8221;<span class=\"ez-toc-section-end\"><\/span><\/h1>\n<div>\n<div class=\"article-gallery lightGallery\">\n<div data-thumb=\"https:\/\/scx1.b-cdn.net\/csz\/news\/tmb\/2022\/machine-learning-gener-1.jpg\" data-src=\"https:\/\/scx2.b-cdn.net\/gfx\/news\/hires\/2022\/machine-learning-gener-1.jpg\" data-sub-html=\"Estimating 3D orientations and 2D positions of single molecules (SMs) using Deep-SMOLM. Credit: &lt;i&gt;Optics Express&lt;\/i&gt; (2022). DOI: 10.1364\/OE.470146\">\n<figure class=\"article-img\">\n            <img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/scx1.b-cdn.net\/csz\/news\/800a\/2022\/machine-learning-gener-1.jpg\" alt=\"Machine learning generates pictures of proteins in 5D\" title=\"Estimating 3D orientations and 2D positions of single molecules (SMs) using Deep-SMOLM. Credit: &lt;i&gt;Optics Express&lt;\/i&gt; (2022). DOI: 10.1364\/OE.470146\" width=\"800\" height=\"530\"\/><figcaption class=\"text-darken text-low-up text-truncate-js text-truncate mt-3\">\n                Estimating 3D orientations and 2D positions of single molecules (SMs) using Deep-SMOLM. Credit: <i>Optics Express<\/i> (2022). DOI: 10.1364\/OE.470146<br \/>\n            <\/figcaption><\/figure>\n<\/p><\/div>\n<\/div>\n<p>By combining machine learning with the laws of physics, researchers in the lab of Matthew Lew, associate professor of electrical and systems engineering at Washington University in St. Louis, have been able to sort out the orientation and position of overl<a href=\"https:\/\/buradabiliyorum.com\/en\/category\/download-scripts-themes-apps\/\" data-internallinksmanager029f6b8e52c=\"9\" title=\"Download Scripts &amp; Themes &amp; Apps\" target=\"_blank\" rel=\"noopener\">app<\/a>ing single molecules in 5D from a single image.<\/p>\n<p>                                                                                Their research was published Sept. 26 in the journal <i>Optics Express<\/i>.<\/p>\n<p>The five dimensions in question aren&#8217;t new or hidden spatial dimensions. Instead, a team headed by Tingting Wu, a Ph.D. student in the McKelvey School of Engineering&#8217;s imaging <a href=\"https:\/\/buradabiliyorum.com\/en\/category\/sciencee\/\" data-internallinksmanager029f6b8e52c=\"5\" title=\"Science\" target=\"_blank\" rel=\"noopener\">science<\/a>s program, was able to design a system that could tell the orientation of a molecule in 3D space as well as its position in 2D: five parameters from a single, noisy, pixelated image.<\/p>\n<figure class=\"mb-4\" itemscope=\"\" itemtype=\"http:\/\/schema.org\/VideoObject\">\n    <meta itemprop=\"name\" content=\"Machine learning generates pictures of proteins in 5D\"\/><br \/>\n    <meta itemprop=\"url\" content=\"https:\/\/www.youtube.com\/watch\/?v=t-WrqjCezt4\"\/><br \/>\n    <meta itemprop=\"description\" content=\"Using a machine learning algorithm coupled with post-processing allows the Lew lab to uncover the structureon the right from the noisy, pixelated image on the left. The image on the right is color coded with estimated 3D orientation. Credit: Lew lab\"\/><br \/>\n    <meta itemprop=\"uploadDate\" content=\"2022-11-02T16:42:02-04:00\"\/><br \/>\n        <meta itemprop=\"embedUrl\" content=\"https:\/\/www.youtube.com\/embed\/t-WrqjCezt4\"\/><br \/>\n    <meta itemprop=\"thumbnailUrl\" content=\"https:\/\/img.youtube.com\/vi\/t-WrqjCezt4\/maxresdefault.jpg\"\/><\/p>\n<p>             <iframe loading=\"lazy\" title=\"Lew lab \u2013 machine learning generates pictures of proteins in 5D\" width=\"640\" height=\"480\" src=\"https:\/\/www.youtube.com\/embed\/t-WrqjCezt4?feature=oembed\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share\" referrerpolicy=\"strict-origin-when-cross-origin\" allowfullscreen><\/iframe><figcaption class=\"text-darken text-low-up mt-4\" itemprop=\"caption\">Using a machine learning algorithm coupled with post-processing allows the Lew lab to uncover the structureon the right from the noisy, pixelated image on the left. The image on the right is color coded with estimated 3D orientation. Credit: Lew lab<\/figcaption><\/figure>\n<p>To wrest this additional complex information from a seemingly simple spot of light, the team did design a machine learning algorithm, but added an extra step.<\/p>\n<p>&#8220;A lot of people use AI end-to-end,&#8221; Wu said. &#8220;Just put in the thing you have and ask the neural network to give you the thing you want.&#8221; She decided to break the problem into two steps to lighten the load on the algorithm, making it more robust.<\/p>\n<p>The kind of imaging carried out in the Lew lab\u2014of single molecules\u2014tends to be very &#8220;noisy,&#8221; containing &#8220;specks&#8221; or fluctuations that can obscure an image. For most machine learning neural networks, Lew said, &#8220;robustly dealing with that kind of noise can be very complicated to learn.&#8221;<\/p>\n<div class=\"article-gallery lightGallery\">\n<div data-thumb=\"https:\/\/scx1.b-cdn.net\/csz\/news\/tmb\/2022\/machine-learning-gener-2.jpg\" data-src=\"https:\/\/scx2.b-cdn.net\/gfx\/news\/2022\/machine-learning-gener-2.jpg\" data-sub-html=\"Amyloid proteins. Their lengths and directions indicate the magnitude of their in-plane orientations and their orientations, respectively. Credit: Lew Lab\">\n<figure class=\"article-img text-center\">\n            <img decoding=\"async\" src=\"https:\/\/scx1.b-cdn.net\/csz\/news\/800a\/2022\/machine-learning-gener-2.jpg\" alt=\"Machine learning generates pictures of proteins in 5D\"\/><figcaption class=\"text-left text-darken text-truncate text-low-up mt-3\">\n                Amyloid proteins. Their lengths and directions indicate the magnitude of their in-plane orientations and their orientations, respectively. Credit: Lew Lab<br \/>\n            <\/figcaption><\/figure>\n<\/p><\/div>\n<\/div>\n<p>Humans, however, have already learned how signals from the molecules of interest and this noise are combined together within microscope images. Instead of asking the algorithm to re-learn the laws of physics, the team added a second &#8220;post-processing&#8221; algorithm\u2013a straightforward computation that applied these physical laws to the results from the first algorithm.<\/p>\n<p>&#8220;It&#8217;s like I&#8217;ve separated two problems into two algorithms,&#8221; Wu said.<\/p>\n<p>After processing thousands of snapshots, the result, Wu said, is a &#8220;beautiful image&#8221; that uses color, curvature and direction to indicate how thousands of molecules are connected to each other.<\/p>\n<p>Ultimately, this system will be able to help researchers better understand biological processes at tiny scales\u2014like the way in which amyloid proteins assemble to form the tangled structures associated with Alzheimer&#8217;s disease.\n                                                                                                                            <\/p>\n<div class=\"article-main__more p-4\">\n                                                                                                <strong>More information:<\/strong><br \/>\n                                                Tingting Wu et al, Deep-SMOLM: deep learning resolves the 3D orientations and 2D positions of overlapping single molecules with optimal nanoscale resolution, <i>Optics Express<\/i> (2022).  <a rel=\"nofollow noopener\" target=\"_blank\" data-doi=\"1\" href=\"https:\/\/dx.doi.org\/10.1364\/OE.470146\">DOI: 10.1364\/OE.470146<\/a><\/p><\/div>\n<div class=\"d-inline-block text-medium my-4\">\n                                                Provided by<br \/>\n                                                                                                    Washington University in St. Louis<br \/>\n                                                                                                        <a rel=\"nofollow noopener\" target=\"_blank\" class=\"icon_open\" href=\"http:\/\/www.wustl.edu\/\"><br \/>\n                                                        <svg>\n                                                            <use href=\"https:\/\/techx.b-cdn.net\/tmpl\/v2\/img\/svg\/sprite.svg#icon_open\" x=\"0\" y=\"0\"\/>\n                                                        <\/svg><br \/>\n                                                    <\/a><\/p><\/div>\n<p>                                        <!-- print only --><\/p>\n<div class=\"d-none d-print-block\">\n<p>                                                 <strong>Citation<\/strong>:<br \/>\n                                                 Machine learning generates pictures of proteins in 5D (2022, November  2)<br \/>\n                                                 retrieved  3 November 2022<br \/>\n                                                 from https:\/\/techxplore.com\/<a href=\"https:\/\/buradabiliyorum.com\/en\/category\/news\/\" data-internallinksmanager029f6b8e52c=\"2\" title=\"News\" target=\"_blank\" rel=\"noopener\">news<\/a>\/2022-11-machine-pictures-proteins-5d.html<\/p>\n<p>                                            This document is subject to copyright. 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Credit: Optics Express (2022). DOI: 10.1364\/OE.470146 By combining machine learning with the laws of physics, researchers in the lab of Matthew Lew, associate professor of electrical and systems engineering at Washington University in St. Louis,&#8230;<\/p>\n","protected":false},"author":1,"featured_media":505953,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"fifu_image_url":"https:\/\/scx2.b-cdn.net\/gfx\/news\/hires\/2022\/machine-learning-gener-1.jpg","fifu_image_alt":"","footnotes":""},"categories":[16],"tags":[],"class_list":["post-505952","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-sciencee"],"_links":{"self":[{"href":"https:\/\/buradabiliyorum.com\/en\/wp-json\/wp\/v2\/posts\/505952","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/buradabiliyorum.com\/en\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/buradabiliyorum.com\/en\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/buradabiliyorum.com\/en\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/buradabiliyorum.com\/en\/wp-json\/wp\/v2\/comments?post=505952"}],"version-history":[{"count":0,"href":"https:\/\/buradabiliyorum.com\/en\/wp-json\/wp\/v2\/posts\/505952\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/buradabiliyorum.com\/en\/wp-json\/wp\/v2\/media\/505953"}],"wp:attachment":[{"href":"https:\/\/buradabiliyorum.com\/en\/wp-json\/wp\/v2\/media?parent=505952"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/buradabiliyorum.com\/en\/wp-json\/wp\/v2\/categories?post=505952"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/buradabiliyorum.com\/en\/wp-json\/wp\/v2\/tags?post=505952"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}