PRAXIS-VirtualCell: A Programmable and Trustworthy Framework for Agentic Virtual Cell Experiments
Abstract
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.
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BibTeX
@misc{ma2026praxisvirtualcell,
title = {{PRAXIS-VirtualCell: A Programmable and Trustworthy Framework for Agentic Virtual Cell Experiments}},
author = {Zhenyu Ma and Xukai Jiang},
howpublished = {arXiv},
year = {2026},
month = sep,
doi = {10.48550/arxiv.2609.29221},
eprint = {2609.29221},
archivePrefix = {arXiv},
url = {https://arxiv.org/abs/2609.29221},
}
RIS
TY - UNPB
TI - PRAXIS-VirtualCell: A Programmable and Trustworthy Framework for Agentic Virtual Cell Experiments
AU - Zhenyu Ma
AU - Xukai Jiang
PY - 2026
DA - 2026/09/24
PB - arXiv
DO - 10.48550/arxiv.2609.29221
UR - https://arxiv.org/abs/2609.29221
AB - 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.
ER -