CellAgent: An LLM-driven Multi-Agent Framework for Automated Single-cell Data Analysis
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arXiv
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| Autori principali: | , , , , , , , , , , , |
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| Natura: | Preprint |
| Pubblicazione: |
2024
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| _version_ | 1866914869533474816 |
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| author | Xiao, Yihang Liu, Jinyi Zheng, Yan Xie, Xiaohan Hao, Jianye Li, Mingzhi Wang, Ruitao Ni, Fei Li, Yuxiao Luo, Jintian Jiao, Shaoqing Peng, Jiajie |
| author_facet | Xiao, Yihang Liu, Jinyi Zheng, Yan Xie, Xiaohan Hao, Jianye Li, Mingzhi Wang, Ruitao Ni, Fei Li, Yuxiao Luo, Jintian Jiao, Shaoqing Peng, Jiajie |
| contents | 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. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2407_09811 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | CellAgent: An LLM-driven Multi-Agent Framework for Automated Single-cell Data Analysis Xiao, Yihang Liu, Jinyi Zheng, Yan Xie, Xiaohan Hao, Jianye Li, Mingzhi Wang, Ruitao Ni, Fei Li, Yuxiao Luo, Jintian Jiao, Shaoqing Peng, Jiajie Artificial Intelligence Human-Computer Interaction Genomics 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. |
| title | CellAgent: An LLM-driven Multi-Agent Framework for Automated Single-cell Data Analysis |
| topic | Artificial Intelligence Human-Computer Interaction Genomics |
| url | https://arxiv.org/abs/2407.09811 |