Static analysis-guided agentic AI translation enables Rust as a full stack bioinformatics language

Engineering notes

Engineering notes will be added by the aipentium editorial team.

Chinese explanation / 中文解读

中文解读待补充：本站会优先为大语言模型、生成式AI、ChatGPT相关技术、计算机视觉、深度学习等高价值论文补充中文说明。

Original abstract

The field of bioinformatics struggles with legacy code - old code that is commonly used but may no longer have a maintainer, or may be written in an now-unfamiliar language (e.g. Perl, Fortran). This incurs maintenance cost (technical debt), but dynamically typed languages also negatively impacts the environment and fail to make use of modern hardware. Legacy code may also have security or safety problems that make it unsuited for use in clinical settings. Here we show that agentic AI, combined with static analysis, can be used to translate legacy code to the modern language Rust. We provide prompts and supporting software to aid systematic translation, and evaluate it on common software for NGS and imaging. We showcase the result on our software Bascet: Size was reduced by ~80x, build time decreased by ~10x, and performance of key steps improved >3x. Unix dependencies were also removed, making Bascet the only single-cell pipeline able to run on native Windows, without a container. Large-scale refactoring of bioinformatics software is thus now possible at a limited budget, enabling more complex tools to be developed.

Links and sources

• Official / arXiv page
• PDF from original source

Comments