{"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/a-brain-graph-foundation-model-pre-training","title":"A Brain Graph Foundation Model: Pre-Training and Prompt-Tuning for Any Atlas and Disorder","arxiv_id":"2506.02044","date":"2025-05-31","proceeding":null,"authors":["Xinxu Wei","Kanhao Zhao","Yong Jiao","Lifang He","Yu Zhang"],"abstract":"As large language models (LLMs) continue to revolutionize AI research, there is a growing interest in building large-scale brain foundation models to advance neuroscience. While most existing brain foundation models are pre-trained on time-series signals or region-of-interest (ROI) features, we propose a novel graph-based pre-training paradigm for constructing a brain graph foundation model. In this paper, we introduce the Brain Graph Foundation Model, termed BrainGFM, a unified framework that leverages graph contrastive learning and graph masked autoencoders for large-scale fMRI-based pre-training. BrainGFM is pre-trained on a diverse mixture of brain atlases with varying parcellations, significantly expanding the pre-training corpus and enhancing the model's ability to generalize across heterogeneous fMRI-derived brain representations. To support efficient and versatile downstream transfer, we integrate both graph prompts and language prompts into the model design, enabling BrainGFM to flexibly adapt to a wide range of atlases, neurological and psychiatric disorders, and task settings. Furthermore, we employ meta-learning to optimize the graph prompts, facilitating strong generalization to previously unseen disorders under both few-shot and zero-shot learning conditions via language-guided prompting. BrainGFM is pre-trained on 27 neuroimaging datasets spanning 25 common neurological and psychiatric disorders, encompassing 2 types of brain atlases (functional and anatomical) across 8 widely-used parcellations, and covering over 25,000 subjects, 60,000 fMRI scans, and a total of 400,000 graph samples aggregated across all atlases and parcellations. The code is available at: https://github.com/weixinxu666/BrainGFM","url_abs":"https://arxiv.org/abs/2506.02044v1","url_pdf":"https://arxiv.org/pdf/2506.02044v1.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":"a-brain-graph-foundation-model-pre-training","repo_url":"https://github.com/weixinxu666/braingfm","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[{"task_slug":"contrastive-learning","task_name":"Contrastive Learning"},{"task_slug":"meta-learning","task_name":"Meta-Learning"},{"task_slug":"zero-shot-learning","task_name":"Zero-Shot Learning"}],"methods":[{"method_slug":"contrastive-learning","method_name":"Contrastive Learning"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=2506.02044","mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}