{"id":175,"date":"2014-10-13T15:55:14","date_gmt":"2014-10-13T15:55:14","guid":{"rendered":"http:\/\/blogs.discovery.wisc.edu\/sysbiojournalclub\/?p=175"},"modified":"2014-10-13T16:01:19","modified_gmt":"2014-10-13T16:01:19","slug":"10-15-14","status":"publish","type":"post","link":"https:\/\/blogs.discovery.wisc.edu\/sysbiojournalclub\/2014\/10\/13\/10-15-14\/","title":{"rendered":"10.15.14"},"content":{"rendered":"<h1>Automatic Parameter Learning for Multiple Network Alignment<\/h1>\n<div class=\"textLayer\">\n<div><\/div>\n<div>Jason Flannick1, Antal Novak1, Chuong B. Do1, Balaji S. Srinivasan2, and Serafim Batzoglou1<\/div>\n<div>1Department of Computer Science, Stanford University, Stanford, CA 94305, USA<\/div>\n<div>2Department of Statistics, Stanford University, Stanford, CA 94305, USA<\/div>\n<h4>Abstract<\/h4>\n<div>We developed Gr\u00e6mlin 2.0, a new multiple network aligner with (1) a novel scoring func-<\/div>\n<div>tion; (2) an algorithm that automatically learns the scoring function\u2019s parameters; and (3) an<\/div>\n<div>algorithm that uses the scoring function to globally align multiple networks. Existing alignment<\/div>\n<div>tools use heuristic scoring functions, which must be hand-tuned to a given set of networks and<\/div>\n<div>do not apply to multiple network alignment.<\/div>\n<div>Our scoring function can use arbitrary features of a multiple network alignment, such as<\/div>\n<div>protein deletions, protein duplications, protein mutations, and interaction losses. Our parameter<\/div>\n<div>learning algorithm uses a training set of known network alignments to learn parameters for<\/div>\n<div>our scoring function and thereby automatically adapts it to any set of networks. Our global<\/div>\n<div>alignment algorithm finds approximate multiple network alignments in linear time.<\/div>\n<div>We tested Gr\u00e6mlin 2.0\u2019s accuracy on protein interaction networks from IntAct, DIP, and<\/div>\n<div>the Stanford Network Database. We show that, on each of these datasets, Gr\u00e6mlin 2.0 has<\/div>\n<div>higher sensitivity and specificity than existing network aligners. Gr\u00e6mlin 2.0 is available under<\/div>\n<div>the GNU public license at http:\/\/graemlin.stanford.edu.<\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>Automatic Parameter Learning for Multiple Network Alignment Jason Flannick1, Antal Novak1, Chuong B. Do1, Balaji S. Srinivasan2, and Serafim Batzoglou1 1Department of Computer Science, Stanford University, Stanford, CA 94305, USA 2Department of Statistics, Stanford University, Stanford, CA 94305, USA Abstract We developed Gr\u00e6mlin 2.0, a new multiple network aligner with (1) a novel scoring func- [&hellip;]<\/p>\n","protected":false},"author":88,"featured_media":0,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":[],"categories":[3,13],"tags":[5,63,61,62,4],"_links":{"self":[{"href":"https:\/\/blogs.discovery.wisc.edu\/sysbiojournalclub\/wp-json\/wp\/v2\/posts\/175"}],"collection":[{"href":"https:\/\/blogs.discovery.wisc.edu\/sysbiojournalclub\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/blogs.discovery.wisc.edu\/sysbiojournalclub\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/blogs.discovery.wisc.edu\/sysbiojournalclub\/wp-json\/wp\/v2\/users\/88"}],"replies":[{"embeddable":true,"href":"https:\/\/blogs.discovery.wisc.edu\/sysbiojournalclub\/wp-json\/wp\/v2\/comments?post=175"}],"version-history":[{"count":1,"href":"https:\/\/blogs.discovery.wisc.edu\/sysbiojournalclub\/wp-json\/wp\/v2\/posts\/175\/revisions"}],"predecessor-version":[{"id":176,"href":"https:\/\/blogs.discovery.wisc.edu\/sysbiojournalclub\/wp-json\/wp\/v2\/posts\/175\/revisions\/176"}],"wp:attachment":[{"href":"https:\/\/blogs.discovery.wisc.edu\/sysbiojournalclub\/wp-json\/wp\/v2\/media?parent=175"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/blogs.discovery.wisc.edu\/sysbiojournalclub\/wp-json\/wp\/v2\/categories?post=175"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/blogs.discovery.wisc.edu\/sysbiojournalclub\/wp-json\/wp\/v2\/tags?post=175"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}