{"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/solving-the-tree-containment-problem-using","title":"Solving the Tree Containment Problem Using Graph Neural Networks","arxiv_id":"2404.09812","date":"2024-04-15","proceeding":null,"authors":["Arkadiy Dushatskiy","Esther Julien","Leen Stougie","Leo van Iersel"],"abstract":"Tree Containment is a fundamental problem in phylogenetics useful for verifying a proposed phylogenetic network, representing the evolutionary history of certain species. Tree Containment asks whether the given phylogenetic tree (for instance, constructed from a DNA fragment showing tree-like evolution) is contained in the given phylogenetic network. In the general case, this is an NP-complete problem. We propose to solve it approximately using Graph Neural Networks. In particular, we propose to combine the given network and the tree and apply a Graph Neural Network to this network-tree graph. This way, we achieve the capability of solving the tree containment instances representing a larger number of species than the instances contained in the training dataset (i.e., our algorithm has the inductive learning ability). Our algorithm demonstrates an accuracy of over $95\\%$ in solving the tree containment problem on instances with up to 100 leaves.","url_abs":"https://arxiv.org/abs/2404.09812v2","url_pdf":"https://arxiv.org/pdf/2404.09812v2.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":"solving-the-tree-containment-problem-using","repo_url":"https://github.com/arkadiyd/phylognn","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"pytorch","reach":null}],"tasks":[{"task_slug":"graph-neural-network","task_name":"Graph Neural Network"},{"task_slug":"inductive-learning","task_name":"Inductive Learning"}],"methods":[{"method_slug":"graph-neural-network","method_name":"Graph Neural Network"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}