{"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/genebreaker-jailbreak-attacks-against-dna","title":"GeneBreaker: Jailbreak Attacks against DNA Language Models with Pathogenicity Guidance","arxiv_id":"2505.23839","date":"2025-05-28","proceeding":null,"authors":["Zaixi Zhang","Zhenghong Zhou","Ruofan Jin","Le Cong","Mengdi Wang"],"abstract":"DNA, encoding genetic instructions for almost all living organisms, fuels groundbreaking advances in genomics and synthetic biology. Recently, DNA Foundation Models have achieved success in designing synthetic functional DNA sequences, even whole genomes, but their susceptibility to jailbreaking remains underexplored, leading to potential concern of generating harmful sequences such as pathogens or toxin-producing genes. In this paper, we introduce GeneBreaker, the first framework to systematically evaluate jailbreak vulnerabilities of DNA foundation models. GeneBreaker employs (1) an LLM agent with customized bioinformatic tools to design high-homology, non-pathogenic jailbreaking prompts, (2) beam search guided by PathoLM and log-probability heuristics to steer generation toward pathogen-like sequences, and (3) a BLAST-based evaluation pipeline against a curated Human Pathogen Database (JailbreakDNABench) to detect successful jailbreaks. Evaluated on our JailbreakDNABench, GeneBreaker successfully jailbreaks the latest Evo series models across 6 viral categories consistently (up to 60\\% Attack Success Rate for Evo2-40B). Further case studies on SARS-CoV-2 spike protein and HIV-1 envelope protein demonstrate the sequence and structural fidelity of jailbreak output, while evolutionary modeling of SARS-CoV-2 underscores biosecurity risks. Our findings also reveal that scaling DNA foundation models amplifies dual-use risks, motivating enhanced safety alignment and tracing mechanisms. Our code is at https://github.com/zaixizhang/GeneBreaker.","url_abs":"https://arxiv.org/abs/2505.23839v1","url_pdf":"https://arxiv.org/pdf/2505.23839v1.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":"links_only","authors_date_abstract":"arXiv metadata, CC0 1.0 (https://info.arxiv.org/help/license), from the Kaggle arXiv metadata snapshot of 2026-09-12"},"code_links":[{"paper_slug":"genebreaker-jailbreak-attacks-against-dna","repo_url":"https://github.com/zaixizhang/genebreaker","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":null}],"tasks":[],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=2505.23839","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2505.23839"}},"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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