Abstract RNA velocity enables inference of cell state transitions from single-cell transcriptomics by modeling transcriptional dynamics from spliced and unspliced mRNA. However, existing methods overlook spatial context and struggle to scale to large datasets, limiting insights into tissue organization and dynamic processes. We introduce veloAgent, a deep generative and agent-based framework that estimates gene- and cell-specific transcriptional kinetics while integrating spatial information through agent-based simulations of local microenvironments. By leveraging both molecular and spatial cues, veloAgent improves velocity accuracy and achieves sublinear memory scaling, enabling efficient analysis of large and multi-batch spatial datasets. A distinctive feature of veloAgent is its in silico perturbation module, which allows targeted manipulation of spatial velocity vectors to simulate regulatory interventions and predict their impact on cell fate dynamics. These capabilities position veloAgent as a scalable and versatile framework for dissecting spatially resolved cellular dynamics and guiding cell fate manipulation across diverse biological processes.
Raghavan et al. (2026) studied this question.