{"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/conditional-diffusion-based-on-discrete-graph","title":"Conditional Diffusion Based on Discrete Graph Structures for Molecular Graph Generation","arxiv_id":"2301.00427","date":"2023-01-01","proceeding":null,"authors":["Han Huang","Leilei Sun","Bowen Du","Weifeng Lv"],"abstract":"Learning the underlying distribution of molecular graphs and generating high-fidelity samples is a fundamental research problem in drug discovery and material science. However, accurately modeling distribution and rapidly generating novel molecular graphs remain crucial and challenging goals. To accomplish these goals, we propose a novel Conditional Diffusion model based on discrete Graph Structures (CDGS) for molecular graph generation. Specifically, we construct a forward graph diffusion process on both graph structures and inherent features through stochastic differential equations (SDE) and derive discrete graph structures as the condition for reverse generative processes. We present a specialized hybrid graph noise prediction model that extracts the global context and the local node-edge dependency from intermediate graph states. We further utilize ordinary differential equation (ODE) solvers for efficient graph sampling, based on the semi-linear structure of the probability flow ODE. Experiments on diverse datasets validate the effectiveness of our framework. Particularly, the proposed method still generates high-quality molecular graphs in a limited number of steps. Our code is provided in https://github.com/GRAPH-0/CDGS.","url_abs":"https://arxiv.org/abs/2301.00427v2","url_pdf":"https://arxiv.org/pdf/2301.00427v2.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":"conditional-diffusion-based-on-discrete-graph","repo_url":"https://github.com/graph-0/cdgs","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":null}],"tasks":[{"task_slug":"drug-discovery","task_name":"Drug Discovery"},{"task_slug":"graph-generation","task_name":"Graph Generation"},{"task_slug":"graph-sampling","task_name":"Graph Sampling"},{"task_slug":"molecular-graph-generation","task_name":"Molecular Graph Generation"}],"methods":[{"method_slug":"diffusion","method_name":"Diffusion"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=2301.00427","mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}