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

Translating C programs to safe Rust is challenging owing to significant differences in typing constraints, ownership, and borrowing rules. Interpreter programs are particularly important targets for such translation, as they often handle untrusted inputs and suffer from memory-related vulnerabilities. We present Reboot, a mostly-automatic technique that translates real-world interpreter programs from C to safe Rust. Using Reboot, we have translated six interpreters ranging from 6k to 23k lines of C code to safe Rust, with each translation requiring only 1 to 11 brief user interventions. All translations pass 100% of the provided test suites, and achieve 62%--92% pass rates on separately created validation tests that were never exposed to the system. A security case study on mujs shows that memory vulnerabilities such as heap buffer overflows and use-after-free present in C are eliminated in the safe Rust translation. Two ideas underpin Reboot. First, feature reduction decomposes the translation by program features, creating a sequence of milestones where each is a complete, testable program; the translation starts from the simplest version and incrementally restores features, with each milestone validated before proceeding. Second, a multi-agent architecture orchestrates inherently unreliable coding agents through automated validation and feedback, keeping long-running translation workflows on track with minimal human involvement. An ablation study confirms that feature reduction improves translation correctness compared to using multi-agent translation alone, with 6%--20% improvements in pass rates on validation test suites.

Large language model agents have shown promise in bioinformatics, but most existing systems focus primarily on producing final answers, treating planning, tool use, and code execution as transient interactions. This design is poorly suited to long-horizon bioinformatics tasks, where conclusions must remain connected to the data, computations, and intermediate evidence that support them. We introduce \textbf{Bioinfoysis}, a multi-agent harness that represents each request as a persistent, artifact-grounded analysis run. Bioinfoysis combines global planning with step-wise, evidence-driven replanning: the planner maintains an executable checklist and revises pending steps using structured handoffs returned after each worker execution. These handoffs bind intermediate results to their responsible agent, checklist step, and plan generation, preventing stale evidence from being silently reused after replanning. A controlled runtime validates generated scripts, tables, and figures before they are used in downstream analysis or reporting, while role-specific context, persistent memory, and governed bioinformatics skills support reliable execution over long analysis trajectories. We evaluate Bioinfoysis on BixBench and two question-answering tracks of LAB-Bench 2. On BixBench, Bioinfoysis achieves state-of-the-art accuracy of 82.4%. Across four underlying language models, Bioinfoysis increases average accuracy from 27.81% to 64.13% on SeqQA2 and from 3.13% to 31.25% on DbQA2. These results demonstrate that reliable bioinformatics automation depends not only on model capability, but also on the harness that governs planning, execution, memory, and evidence flow. We hope that the emergence of Bioinfoysis will play a driving and leading role in the development of the bioinformatics community. Our demo website can be seen in https://report.bioinfoysis.com/.

LLM agents are increasingly applied to vulnerability analysis, but existing benchmarks have not kept pace. They typically rely on small non-compilable snippets, focus on binary classification (vulnerable or not), and do not account for the risk that publicly-released datasets are part of model training corpora. We introduce RustMizan, a benchmarking framework for Rust vulnerability analysis that addresses these gaps. RustMizan contains compilable code variants at the crate, file, and function levels, with annotations for binary vulnerability detection, CWE classification, and function- and line-level localization. A paired mutation framework produces semantics-preserving code mutants for contamination testing and robustness probing. Across four frontier models in an agentic setup with command-line access, binary classification sits in the 56-65% range, but line localization F1 stays near 20%, and adversarial cues drop line F1 by about 27%.