{"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/gne-a-deep-learning-framework-for-gene","title":"GNE: a deep learning framework for gene network inference by aggregating biological information","arxiv_id":null,"date":"2019-04-05","proceeding":"BMC Systems Biology 2019 4","authors":["Kishan KC","Rui Li","Feng Cui","Qi Yu","Anne R. Haake"],"abstract":"The topological landscape of gene interaction networks provides a rich source of information for inferring functional patterns of genes or proteins. However, it is still a challenging task to aggregate heterogeneous biological information such as gene expression and gene interactions to achieve more accurate inference for prediction and discovery of new gene interactions. In particular, how to generate a unified vector representation to integrate diverse input data is a key challenge addressed here. We propose a scalable and robust deep learning framework to learn embedded representations to unify known gene interactions and gene expression for gene interaction predictions. These low- dimensional embeddings derive deeper insights into the structure of rapidly accumulating and diverse gene interaction networks and greatly simplify downstream modeling. We compare the predictive power of our deep embeddings to the strong baselines. The results suggest that our deep embeddings achieve significantly more accurate predictions. Moreover, a set of novel gene interaction predictions are validated by up-to-date literature-based database entries. The proposed model demonstrates the importance of integrating heterogeneous information about genes for gene network inference. GNE is freely available under the GNU General Public License and can be downloaded from GitHub (https://github.com/kckishan/GNE).","url_abs":"https://bmcsystbiol.biomedcentral.com/articles/10.1186/s12918-019-0694-y","url_pdf":"https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/s12918-019-0694-y","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":"gne-a-deep-learning-framework-for-gene","repo_url":"https://github.com/kckishan/GNE","is_official":0,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"tf","reach":null}],"tasks":[{"task_slug":"gene-interaction-prediction","task_name":"Gene Interaction Prediction"},{"task_slug":"link-prediction","task_name":"Link Prediction"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[{"leaderboard":"/sota/gene-interaction-prediction-on-biogrid-human","task":"Gene Interaction Prediction","dataset":"BioGRID (human)","model":"GNE","rank_in_archive_order":1,"of":1,"metrics":{"Average Precision":"0.939"},"uses_additional_data":true},{"leaderboard":"/sota/gene-interaction-prediction-on-biogridyeast","task":"Gene Interaction Prediction","dataset":"BioGRID(yeast)","model":"GNE","rank_in_archive_order":1,"of":1,"metrics":{"Average Precision":"0.821"},"uses_additional_data":true}],"syntology":{"syntology_url":null,"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}