{"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/evovgm-a-deep-variational-generative-model","title":"EvoVGM: a Deep Variational Generative Model for Evolutionary Parameter Estimation","arxiv_id":"2205.13034","date":"2022-05-25","proceeding":null,"authors":["Amine M. Remita","Abdoulaye Baniré Diallo"],"abstract":"Most evolutionary-oriented deep generative models do not explicitly consider the underlying evolutionary dynamics of biological sequences as it is performed within the Bayesian phylogenetic inference framework. In this study, we propose a method for a deep variational Bayesian generative model (EvoVGM) that jointly approximates the true posterior of local evolutionary parameters and generates sequence alignments. Moreover, it is instantiated and tuned for continuous-time Markov chain substitution models such as JC69, K80 and GTR. We train the model via a low-variance stochastic estimator and a gradient ascent algorithm. Here, we analyze the consistency and effectiveness of EvoVGM on synthetic sequence alignments simulated with several evolutionary scenarios and different sizes. Finally, we highlight the robustness of a fine-tuned EvoVGM model using a sequence alignment of gene S of coronaviruses.","url_abs":"https://arxiv.org/abs/2205.13034v2","url_pdf":"https://arxiv.org/pdf/2205.13034v2.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":"evovgm-a-deep-variational-generative-model","repo_url":"https://github.com/maremita/evovgm","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"pytorch","reach":null}],"tasks":[{"task_slug":"parameter-estimation","task_name":"parameter estimation"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}