{"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/the-role-of-graph-topology-in-the-performance","title":"The Role of Graph Topology in the Performance of Biomedical Knowledge Graph Completion Models","arxiv_id":"2409.04103","date":"2024-09-06","proceeding":null,"authors":["Alberto Cattaneo","Stephen Bonner","Thomas Martynec","Carlo Luschi","Ian P Barrett","Daniel Justus"],"abstract":"Knowledge Graph Completion has been increasingly adopted as a useful method for several tasks in biomedical research, like drug repurposing or drug-target identification. To that end, a variety of datasets and Knowledge Graph Embedding models has been proposed over the years. However, little is known about the properties that render a dataset useful for a given task and, even though theoretical properties of Knowledge Graph Embedding models are well understood, their practical utility in this field remains controversial. We conduct a comprehensive investigation into the topological properties of publicly available biomedical Knowledge Graphs and establish links to the accuracy observed in real-world applications. By releasing all model predictions and a new suite of analysis tools we invite the community to build upon our work and continue improving the understanding of these crucial applications.","url_abs":"https://arxiv.org/abs/2409.04103v1","url_pdf":"https://arxiv.org/pdf/2409.04103v1.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":"the-role-of-graph-topology-in-the-performance","repo_url":"https://github.com/graphcore-research/kg-topology-toolbox","is_official":1,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"none","reach":null}],"tasks":[{"task_slug":"graph-embedding","task_name":"Graph Embedding"},{"task_slug":"knowledge-graph-completion","task_name":"Knowledge Graph Completion"},{"task_slug":"knowledge-graph-embedding","task_name":"Knowledge Graph Embedding"},{"task_slug":"knowledge-graphs","task_name":"Knowledge Graphs"}],"methods":[],"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}