BioMaster: Multi-agent system for automated bioinformatics analysis workflow.
other · Level V
Where this comes from
- Record sourced from PubMed, PMID 42630761.
- Also identified by DOI 10.1016/j.patter.2026.101611 and PMC identifier 13494596.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
The growing volume and complexity of biological data have made bioinformatics workflows increasingly labor-intensive, error-prone, and difficult to scale. Large language model-based agents offer potential for automation but often fail in complex, multi-step analyses because of limited robustness. We present BioMaster, a multi-agent framework that integrates workflow planning, execution, error recovery, and output validation. BioMaster incorporates a dual retrieval-augmented design to leverage domain knowledge for tool selection, parameterization, and adaptation across tasks. A dedicated debug agent supports real-time error detection and correction, while memory optimization enables long, multi-stage workflows. In benchmarking across 49 bioinformatics tasks spanning 102 tools, BioMaster completed substantially more workflows than did existing automated systems, particularly in complex, interdependent pipelines. BioMaster supports both proprietary and open-source language models, enabling flexible deployment across different computational settings.