PerturbAgent: an agentic AI system for analysis and prediction of genetic perturbations

Conference item

We introduce PerturbAgent, a large language model (LLM)- based multi-agent system for single-cell genetic perturbation studies. In biomedical research, understanding cellular responses to perturbations is essential for interpreting gene function and regulatory pathways in single-cell data. Existing methods focus only on either single-cell analysis pipelines or perturbation prediction models, and often lack this necessary biological interpretation. PerturbAgent addresses these limitations, targeting both analysis and prediction tasks while also generating comprehensive biological interpretations with results grounded in mechanisms, pathways, and existing knowledge. We further propose MAST++, a general framework that evaluates agentic performance across profile, reasoning, perception, interaction, and memory, and complement it with biological validity assessments. On public single-cell Perturbseq and RNA-seq datasets, PerturbAgent reliably achieves high task completion and delivers citation-backed biological summaries, representing progress toward practical and interpretable agent workflows for scientific discovery.

Authors: Pei, K; Qu, S; Torr, PHS; Hedley, JG; Schroeder de Witt, C

• Publication status: Published
• Peer review status: Peer reviewed
• Publication date: 2026-01-27
• Acceptance date: 2025-11-07
• Event title: AAAI 2026 Workshop XAI4Science
• Event location: Singapore
• Event website: https://xai4science.github.io/
• Event start date: 2026-01-27
• Event end date: 2026-01-27
• Language: English
• Keywords: agentic system evaluation; LLM-based agents; genetic perturbation; interpretable AI; automated scientific discovery