论文标题
朝向细胞迁移的学习模拟器
Towards Learned Simulators for Cell Migration
论文作者
论文摘要
由深度学习驱动的模拟器已成为有效模拟准确但昂贵的数值模拟器的工具。这种神经模拟器的成功应用可以在物理,化学和结构生物学领域中找到。同样,用于细胞动力学的神经模拟器可以增强实验室实验和传统的计算方法,以增强我们对细胞与物理环境相互作用的理解。在这项工作中,我们提出了一种自回归概率模型,该模型可以再现单细胞迁移的时空动力学,传统上使用细胞Potts模型模拟。我们观察到,标准的单步训练方法不仅会导致不一致的推出稳定性,而且无法准确捕获动态的随机方面,并且我们提出了减轻这些问题的培训策略。我们对两个概念验证实验方案的评估表明,与细胞Potts模型的最新实现相比,神经方法可能会忠实地模拟随机细胞动力学的速度至少更快。
Simulators driven by deep learning are gaining popularity as a tool for efficiently emulating accurate but expensive numerical simulators. Successful applications of such neural simulators can be found in the domains of physics, chemistry, and structural biology, amongst others. Likewise, a neural simulator for cellular dynamics can augment lab experiments and traditional computational methods to enhance our understanding of a cell's interaction with its physical environment. In this work, we propose an autoregressive probabilistic model that can reproduce spatiotemporal dynamics of single cell migration, traditionally simulated with the Cellular Potts model. We observe that standard single-step training methods do not only lead to inconsistent rollout stability, but also fail to accurately capture the stochastic aspects of the dynamics, and we propose training strategies to mitigate these issues. Our evaluation on two proof-of-concept experimental scenarios shows that neural methods have the potential to faithfully simulate stochastic cellular dynamics at least an order of magnitude faster than a state-of-the-art implementation of the Cellular Potts model.