{"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/dna-gcn-graph-convolutional-networks-for","title":"DNA-GCN: Graph convolutional networks for predicting DNA-protein binding","arxiv_id":"2106.01836","date":"2021-06-02","proceeding":null,"authors":["Yuhang Guo","Xiao Luo","Liang Chen","Minghua Deng"],"abstract":"Predicting DNA-protein binding is an important and classic problem in bioinformatics. Convolutional neural networks have outperformed conventional methods in modeling the sequence specificity of DNA-protein binding. However, none of the studies has utilized graph convolutional networks for motif inference. In this work, we propose to use graph convolutional networks for motif inference. We build a sequence k-mer graph for the whole dataset based on k-mer co-occurrence and k-mer sequence relationship and then learn DNA Graph Convolutional Network (DNA-GCN) for the whole dataset. Our DNA-GCN is initialized with a one-hot representation for all nodes, and it then jointly learns the embeddings for both k-mers and sequences, as supervised by the known labels of sequences. We evaluate our model on 50 datasets from ENCODE. DNA-GCN shows its competitive performance compared with the baseline model. Besides, we analyze our model and design several different architectures to help fit different datasets.","url_abs":"https://arxiv.org/abs/2106.01836v1","url_pdf":"https://arxiv.org/pdf/2106.01836v1.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":"dna-gcn-graph-convolutional-networks-for","repo_url":"https://github.com/Tinard/dnagcn","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[{"task_slug":"specificity","task_name":"Specificity"}],"methods":[{"method_slug":"graph-convolutional-networks","method_name":"Graph Convolutional Networks"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}