{"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/bayesian-neural-network-with-pretrained","title":"Bayesian neural network with pretrained protein embedding enhances prediction accuracy of drug-protein interaction","arxiv_id":"2012.08194","date":"2020-12-15","proceeding":null,"authors":["QHwan Kim","Joon-Hyuk Ko","Sunghoon Kim","Nojun Park","Wonho Jhe"],"abstract":"The characterization of drug-protein interactions is crucial in the high-throughput screening for drug discovery. The deep learning-based approaches have attracted attention because they can predict drug-protein interactions without trial-and-error by humans. However, because data labeling requires significant resources, the available protein data size is relatively small, which consequently decreases model performance. Here we propose two methods to construct a deep learning framework that exhibits superior performance with a small labeled dataset. At first, we use transfer learning in encoding protein sequences with a pretrained model, which trains general sequence representations in an unsupervised manner. Second, we use a Bayesian neural network to make a robust model by estimating the data uncertainty. As a result, our model performs better than the previous baselines for predicting drug-protein interactions. We also show that the quantified uncertainty from the Bayesian inference is related to the confidence and can be used for screening DPI data points.","url_abs":"https://arxiv.org/abs/2012.08194v2","url_pdf":"https://arxiv.org/pdf/2012.08194v2.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":"bayesian-neural-network-with-pretrained","repo_url":"https://github.com/QHwan/PretrainDPI","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"pytorch","reach":null}],"tasks":[{"task_slug":"bayesian-inference","task_name":"Bayesian Inference"},{"task_slug":"deep-learning","task_name":"Deep Learning"},{"task_slug":"drug-discovery","task_name":"Drug Discovery"},{"task_slug":"transfer-learning","task_name":"Transfer Learning"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}