CellAgent: An LLM-driven Multi-Agent Framework for Automated Single-cell Data Analysis

• URL: http://arxiv.org/abs/2407.09811v1
• Date: Sat, 13 Jul 2024 09:14:50 GMT
• Title: CellAgent: An LLM-driven Multi-Agent Framework for Automated Single-cell Data Analysis
• Authors: Yihang Xiao, Jinyi Liu, Yan Zheng, Xiaohan Xie, Jianye Hao, Mingzhi Li, Ruitao Wang, Fei Ni, Yuxiao Li, Jintian Luo, Shaoqing Jiao, Jiajie Peng,
• Abstract summary: Single-cell RNA sequencing (scRNA-seq) data analysis is crucial for biological research. However, manual manipulation of various tools to achieve desired outcomes can be labor-intensive for researchers. We introduce CellAgent, an LLM-driven multi-agent framework for the automatic processing and execution of scRNA-seq data analysis tasks.
• Score: 35.61361183175167
• License: http://arxiv.org/licenses/nonexclusive-distrib/1.0/
• Abstract: Single-cell RNA sequencing (scRNA-seq) data analysis is crucial for biological research, as it enables the precise characterization of cellular heterogeneity. However, manual manipulation of various tools to achieve desired outcomes can be labor-intensive for researchers. To address this, we introduce CellAgent (http://cell.agent4science.cn/), an LLM-driven multi-agent framework, specifically designed for the automatic processing and execution of scRNA-seq data analysis tasks, providing high-quality results with no human intervention. Firstly, to adapt general LLMs to the biological field, CellAgent constructs LLM-driven biological expert roles - planner, executor, and evaluator - each with specific responsibilities. Then, CellAgent introduces a hierarchical decision-making mechanism to coordinate these biological experts, effectively driving the planning and step-by-step execution of complex data analysis tasks. Furthermore, we propose a self-iterative optimization mechanism, enabling CellAgent to autonomously evaluate and optimize solutions, thereby guaranteeing output quality. We evaluate CellAgent on a comprehensive benchmark dataset encompassing dozens of tissues and hundreds of distinct cell types. Evaluation results consistently show that CellAgent effectively identifies the most suitable tools and hyperparameters for single-cell analysis tasks, achieving optimal performance. This automated framework dramatically reduces the workload for science data analyses, bringing us into the "Agent for Science" era.

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