{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/deep-motif-visualizing-genomic-sequence","title":"Deep Motif: Visualizing Genomic Sequence Classifications","arxiv_id":"1605.01133","date":"2016-05-04","proceeding":null,"authors":["Jack Lanchantin","Ritambhara Singh","Zeming Lin","Yanjun Qi"],"abstract":"This paper applies a deep convolutional/highway MLP framework to classify\ngenomic sequences on the transcription factor binding site task. To make the\nmodel understandable, we propose an optimization driven strategy to extract\n\"motifs\", or symbolic patterns which visualize the positive class learned by\nthe network. We show that our system, Deep Motif (DeMo), extracts motifs that\nare similar to, and in some cases outperform the current well known motifs. In\naddition, we find that a deeper model consisting of multiple convolutional and\nhighway layers can outperform a single convolutional and fully connected layer\nin the previous state-of-the-art.","url_abs":"http://arxiv.org/abs/1605.01133v2","url_pdf":"http://arxiv.org/pdf/1605.01133v2.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"deep-motif-visualizing-genomic-sequence","repo_url":"https://github.com/QData/DeepMotif","is_official":1,"mentioned_in_paper":0,"mentioned_in_github":0,"framework":"torch","reach":null},{"paper_slug":"deep-motif-visualizing-genomic-sequence","repo_url":"https://github.com/bakirillov/deepmotif4pytorch","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"pytorch","reach":null},{"paper_slug":"deep-motif-visualizing-genomic-sequence","repo_url":"https://github.com/xinshuaiqi/awesome-genome","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"none","reach":null}],"tasks":[],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}