{"id":1264,"date":"2018-10-08T15:10:18","date_gmt":"2018-10-08T19:10:18","guid":{"rendered":"http:\/\/mlmed.org\/w\/?p=1168"},"modified":"2019-06-19T01:11:27","modified_gmt":"2019-06-19T05:11:27","slug":"the-latent-transcriptome","status":"publish","type":"post","link":"https:\/\/josephpcohen.com\/w\/the-latent-transcriptome\/","title":{"rendered":"The Latent Transcriptome"},"content":{"rendered":"

\"\"<\/p>\n

In this work we propose a method to compute continuous embeddings for kmers from raw RNA-seq data of the transcriptome, without the need for alignment to a reference genome. The approach uses an RNN to transforms kmers of the RNA-seq reads into a 2 dimensional representation that is used to predict abundance of each kmer. In this latent transcriptome we observe the grouping of kmers that corresponds to the genes that they are expect to belong to. More info:
\nPaper<\/a> Slides<\/a><\/p>\n

Assya Trofimov, Francis Dutil, Claude Perreault, Sebastien Lemieux, Yoshua Bengio, Joseph Paul Cohen. Towards the Latent Transcriptome<\/i>. 2018, http:\/\/arxiv.org\/abs\/1810.03442.<\/p>\n","protected":false},"excerpt":{"rendered":"

In this work we propose a method to compute continuous embeddings for kmers from raw RNA-seq data of the transcriptome, without the need for alignment […]<\/a><\/p>\n<\/div>","protected":false},"author":1,"featured_media":1294,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":[],"categories":[17,23,18,22],"tags":[],"yoast_head":"\nThe Latent Transcriptome - Joseph Paul Cohen PhD<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/josephpcohen.com\/w\/the-latent-transcriptome\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"The Latent Transcriptome - Joseph Paul Cohen PhD\" \/>\n<meta property=\"og:description\" content=\"In this work we propose a method to compute continuous embeddings for kmers from raw RNA-seq data of the transcriptome, without the need for alignment [...]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/josephpcohen.com\/w\/the-latent-transcriptome\/\" \/>\n<meta property=\"og:site_name\" content=\"Joseph Paul Cohen PhD\" \/>\n<meta property=\"article:published_time\" content=\"2018-10-08T19:10:18+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2019-06-19T05:11:27+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/josephpcohen.com\/w\/wp-content\/uploads\/TLT.png\" \/>\n\t<meta property=\"og:image:width\" content=\"1800\" \/>\n\t<meta property=\"og:image:height\" content=\"1200\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/png\" \/>\n<meta name=\"author\" content=\"Joseph Paul Cohen\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"Joseph Paul Cohen\" \/>\n\t<meta name=\"twitter:label2\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"1 minute\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"Article\",\"@id\":\"https:\/\/josephpcohen.com\/w\/the-latent-transcriptome\/#article\",\"isPartOf\":{\"@id\":\"https:\/\/josephpcohen.com\/w\/the-latent-transcriptome\/\"},\"author\":{\"name\":\"Joseph Paul Cohen\",\"@id\":\"https:\/\/josephpcohen.com\/w\/#\/schema\/person\/e25d0d5746952220f35d182ca7aa8684\"},\"headline\":\"The Latent Transcriptome\",\"datePublished\":\"2018-10-08T19:10:18+00:00\",\"dateModified\":\"2019-06-19T05:11:27+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\/\/josephpcohen.com\/w\/the-latent-transcriptome\/\"},\"wordCount\":104,\"publisher\":{\"@id\":\"https:\/\/josephpcohen.com\/w\/#\/schema\/person\/e25d0d5746952220f35d182ca7aa8684\"},\"articleSection\":[\"Genomics\",\"Medical\",\"Projects\",\"Research\"],\"inLanguage\":\"en-US\"},{\"@type\":\"WebPage\",\"@id\":\"https:\/\/josephpcohen.com\/w\/the-latent-transcriptome\/\",\"url\":\"https:\/\/josephpcohen.com\/w\/the-latent-transcriptome\/\",\"name\":\"The Latent Transcriptome - 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