PRAXIS-VirtualCell：面向智能体虚拟细胞实验的可编程且可信赖框架
PRAXIS-VirtualCell: A Programmable and Trustworthy Framework for Agentic Virtual Cell Experiments
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中文总结 AI 辅助
提出PRAXIS-VirtualCell模块化框架，统一组织生物数据、模型与验证证据，支持跨物种任务，通过生物契约和智能体编排实现可复现、可审计且可信赖的虚拟细胞实验。
中文摘要 AI 辅助
虚拟细胞正从单一任务的预测模型演变为可编程的生物模拟系统，然而异构数据、模型和验证证据仍缺乏统一组织框架。在此，我们提出PRAXIS-VirtualCell，一个模块化框架，用于组织生物数据、预测模型、扰动、适配器、执行环境和验证证据，以实现可复现且可审计的虚拟实验。该系统支持跨物种任务，涵盖大肠杆菌、酿酒酵母和人类K562细胞，同时利用生物契约和证据感知执行来区分受支持的预测与外推和弃权（不执行）。通过进一步集成智能体编排，PRAXIS-VirtualCell自动将自然语言问题转化为可追踪的虚拟实验，为可信赖且可扩展的虚拟细胞系统提供统一运行时基础。
英文摘要
Virtual cells are evolving from single-task predictive models toward programmable biological simulation systems, yet heterogeneous data, models, and validation evidence still lack a unified organizational framework. Here, we present PRAXIS-VirtualCell, a modular framework that organizes biological data, predictive models, perturbations, adapters, execution environments, and validation evidence to enable reproducible and auditable virtual experiments. The system supports cross-species tasks spanning Escherichia coli, Saccharomyces cerevisiae, and human K562 cells, while using biological contracts and evidence-aware execution to distinguish supported predictions from extrapolation and abstention. By further integrating agentic orchestration, PRAXIS-VirtualCell automatically translates natural-language questions into traceable virtual experiments, providing a unified runtime foundation for trustworthy and scalable Virtual Cell systems.
发表机构
- National Glycoengineering Research Center, Shandong University（国家糖工程研究中心，山东大学）
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