{"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/space-your-genomic-profile-predictor-is-a","title":"SPACE: Your Genomic Profile Predictor is a Powerful DNA Foundation Model","arxiv_id":"2506.01833","date":"2025-06-02","proceeding":null,"authors":["Zhao Yang","Jiwei Zhu","Bing Su"],"abstract":"Inspired by the success of unsupervised pre-training paradigms, researchers have applied these approaches to DNA pre-training. However, we argue that these approaches alone yield suboptimal results because pure DNA sequences lack sufficient information, since their functions are regulated by genomic profiles like chromatin accessibility. Here, we demonstrate that supervised training for genomic profile prediction serves as a more effective alternative to pure sequence pre-training. Furthermore, considering the multi-species and multi-profile nature of genomic profile prediction, we introduce our $\\textbf{S}$pecies-$\\textbf{P}$rofile $\\textbf{A}$daptive $\\textbf{C}$ollaborative $\\textbf{E}$xperts (SPACE) that leverages Mixture of Experts (MoE) to better capture the relationships between DNA sequences across different species and genomic profiles, thereby learning more effective DNA representations. Through extensive experiments across various tasks, our model achieves state-of-the-art performance, establishing that DNA models trained with supervised genomic profiles serve as powerful DNA representation learners. The code is available at https://github.com/ZhuJiwei111/SPACE.","url_abs":"https://arxiv.org/abs/2506.01833v1","url_pdf":"https://arxiv.org/pdf/2506.01833v1.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":"space-your-genomic-profile-predictor-is-a","repo_url":"https://github.com/zhujiwei111/space","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":{"status":"ok","spdx":"MIT"}}],"tasks":[{"task_slug":"mixture-of-experts","task_name":"Mixture-of-Experts"},{"task_slug":"unsupervised-pre-training","task_name":"Unsupervised Pre-training"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=2506.01833","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2506.01833"}},"developers":"https://syntology.ai/developers","read_at":"2026-09-24T18:15:14+00:00","read_at_is":"when the build read Syntology's graph, not when any sample ran","claim":"Per-sample execution status on synthesized fixtures; not a correctness claim about the paper. 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