MATRIX: Multi-Layer Code Watermarking via Dual-Channel Constrained Parity-Check Encoding

Computer Science > Cryptography and Security [Submitted on 17 Apr 2026] MATRIX: Multi-Layer Code Watermarking via Dual-Channel Constrained Parity-Check Encoding Yuqing Nie, Chong Wang, Guosheng Xu, Guoai Xu, Chenyu Wang, Haoyu Wang, Kailong Wang Code Large Language Models (Code LLMs) have revolutionized software development but raised critical concerns regarding code provenance, copyright protection, and security. Existing code watermarking approaches suffer from two fundamental limitations: black-box methods either exhibit detectable syntactic patterns vulnerable to statistical analysis or rely on implicit neural embedding behaviors that weaken interpretability, auditability, and precise control, while white-box methods lack code-aware capabilities that may compromise functionality. Moreover, current single-layer watermarking schemes fail to address increasingly complex provenance requirements such as multi-level attribution and version tracking. We present MATRIX, a novel code watermarking framework that formulates watermark encoding as solving constrained parity-check matrix equations. MATRIX employs dual-channel watermarking through variable naming and semantic-preserving transformations, enhancing watermark coverage across a wider range of code while ensuring mutual backup for robustness. By integrating BCH error-correction codes with solution space diversity, our approach achieves robustness against statistical analysis. Extensive evaluation on Python code generated by multiple Code LLMs demonstrates that MATRIX achieves an average watermark detection accuracy of 99.20% with minimal functionality loss (0-0.14%), improves robustness by 7.70-26.67% against various attacks, and increases watermarking applicability by 2-6x compared with existing methods. These results establish MATRIX as an effective solution for complex code provenance scenarios while balancing among detectability, fidelity, and robustness. Comments: 14 pages, 6 figures Subjects: Cryptography and Security (cs.CR) Cite as: arXiv:2604.16001 [cs.CR]   (or arXiv:2604.16001v1 [cs.CR] for this version)   https://doi.org/10.48550/arXiv.2604.16001 Focus to learn more Submission history From: YuQing Nie [view email] [v1] Fri, 17 Apr 2026 12:25:41 UTC (1,069 KB) Access Paper: HTML (experimental) view license Current browse context: cs.CR < prev   |   next > new | recent | 2026-04 Change to browse by: cs References & Citations NASA ADS Google Scholar Semantic Scholar Export BibTeX Citation Bookmark Bibliographic Tools Bibliographic and Citation Tools Bibliographic Explorer Toggle Bibliographic Explorer (What is the Explorer?) Connected Papers Toggle Connected Papers (What is Connected Papers?) Litmaps Toggle Litmaps (What is Litmaps?) scite.ai Toggle scite Smart Citations (What are Smart Citations?) Code, Data, Media Demos Related Papers About arXivLabs Which authors of this paper are endorsers? | Disable MathJax (What is MathJax?)